[med-svn] [pysam] 09/13: Imported Upstream version 0.7.5
Charles Plessy
plessy at alioth.debian.org
Fri Aug 9 09:47:31 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository pysam.
commit fabbcdc720f13bfdd948bff8ec3fdd6381f5a940
Author: Charles Plessy <plessy at debian.org>
Date: Fri Aug 9 18:34:40 2013 +0900
Imported Upstream version 0.7.5
---
MANIFEST.in | 6 +
PKG-INFO | 2 +-
doc/Makefile | 96 +
doc/api.rst | 122 +
doc/conf.py | 204 +
doc/contents.rst | 73 +
doc/developer.rst | 75 +
doc/faq.rst | 40 +
doc/glossary.rst | 73 +
doc/make.bat | 112 +
doc/release.rst | 85 +
doc/usage.rst | 285 +
pysam.egg-info/PKG-INFO | 2 +-
pysam.egg-info/SOURCES.txt | 21 +-
pysam.py | 1 +
pysam/TabProxies.c | 3888 ++---
pysam/__init__.py | 4 +
pysam/csamtools.c |27233 +++++++++++++++++++---------------
pysam/csamtools.pyx | 48 +-
pysam/ctabix.c | 1970 ++-
pysam/ctabix.pxd | 6 +-
pysam/ctabix.pyx | 2 +-
pysam/cvcf.c |13214 +++++++++--------
pysam/cvcf.pyx | 19 +-
pysam/pysam_util.c | 19 +-
pysam/tabix_util.h | 6 +
pysam/version.py | 4 +-
samtools/bam.c.pysam.c | 136 +-
samtools/bam.h | 46 +-
samtools/bam2bcf.c.pysam.c | 298 +-
samtools/bam2bcf.h | 26 +-
samtools/bam2bcf_indel.c.pysam.c | 47 +-
samtools/bam2depth.c.pysam.c | 45 +-
samtools/bam_aux.c.pysam.c | 4 +
samtools/bam_cat.c.pysam.c | 9 +-
samtools/bam_color.c.pysam.c | 24 +-
samtools/bam_import.c.pysam.c | 16 +-
samtools/bam_index.c.pysam.c | 9 +-
samtools/bam_mate.c.pysam.c | 82 +-
samtools/bam_md.c.pysam.c | 7 +-
samtools/bam_plcmd.c.pysam.c | 154 +-
samtools/bam_reheader.c.pysam.c | 7 +-
samtools/bam_sort.c.pysam.c | 291 +-
samtools/bam_tview.c.pysam.c | 460 +-
samtools/bam_tview.h | 75 +
samtools/bam_tview_curses.c.pysam.c | 299 +
samtools/bam_tview_html.c.pysam.c | 351 +
samtools/bamshuf.c.pysam.c | 148 +
samtools/bcftools/bcf.c.pysam.c | 102 +-
samtools/bcftools/bcf.h | 9 +-
samtools/bcftools/bcfutils.c.pysam.c | 120 +-
samtools/bcftools/call1.c.pysam.c | 101 +-
samtools/bcftools/index.c.pysam.c | 1 +
samtools/bcftools/prob1.c.pysam.c | 470 +-
samtools/bcftools/prob1.h | 7 +
samtools/bcftools/vcf.c.pysam.c | 11 +-
samtools/bedcov.c.pysam.c | 129 +
samtools/bgzf.c.pysam.c | 1072 +-
samtools/bgzf.h | 272 +-
samtools/faidx.c.pysam.c | 5 +
samtools/kprobaln.c.pysam.c | 4 +-
samtools/kseq.h | 55 +-
samtools/ksort.h | 6 +-
samtools/kstring.c.pysam.c | 4 +-
samtools/kstring.h | 56 +-
samtools/misc/ace2sam.c.pysam.c | 251 +
samtools/misc/seqtk.c.pysam.c | 785 -
samtools/padding.c.pysam.c | 481 +
samtools/sam.c.pysam.c | 9 +-
samtools/sam.h | 1 +
samtools/sam_header.c.pysam.c | 78 +-
samtools/sam_header.h | 24 +
samtools/sam_view.c.pysam.c | 83 +-
setup.py | 18 +-
tests/Makefile | 12 +-
tests/pysam_test.py | 139 +-
tests/tabix_test.py | 114 +-
tests/test_unaligned.bam | Bin 0 -> 514 bytes
78 files changed, 31105 insertions(+), 23458 deletions(-)
diff --git a/MANIFEST.in b/MANIFEST.in
index a0c9889..e1b78c0 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -24,10 +24,12 @@ include pysam/cvcf.c
include pysam/*.c
include pysam/*.h
include pysam/pysam_util.h
+include pysam/tabix_util.h
include samtools/*.h
include samtools/*/*.h
include tabix/*.c
include tabix/*.h
+include pysam.py
# pysam tests
include tests/00README.txt
@@ -51,6 +53,7 @@ include tests/example_btag.bam
include tests/tag_bug.bam
include tests/example.vcf40
include tests/example_empty_header.bam
+include tests/test_unaligned.bam
include tests/issue100.bam
# tabix tests
@@ -60,3 +63,6 @@ include tests/example.gtf.gz.tbi
include tests/example.bed.gz
include tests/example.bed.gz.tbi
include tests/vcf-examples/*.vcf
+
+# documentation
+include doc/*
diff --git a/PKG-INFO b/PKG-INFO
index c527383..8d8f7c5 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.4
+Version: 0.7.5
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/doc/Makefile b/doc/Makefile
new file mode 100644
index 0000000..69e4e3a
--- /dev/null
+++ b/doc/Makefile
@@ -0,0 +1,96 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS =
+SPHINXBUILD = sphinx-build
+PAPER =
+
+# Internal variables.
+PAPEROPT_a4 = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS = -d _build/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+DIR_PUBLISH=/ifs/home/andreas/public_html/documentation/pysam
+
+.PHONY: help clean html dirhtml pickle json htmlhelp qthelp latex changes linkcheck doctest
+
+help:
+ @echo "Please use \`make <target>' where <target> is one of"
+ @echo " html to make standalone HTML files"
+ @echo " dirhtml to make HTML files named index.html in directories"
+ @echo " pickle to make pickle files"
+ @echo " json to make JSON files"
+ @echo " htmlhelp to make HTML files and a HTML help project"
+ @echo " qthelp to make HTML files and a qthelp project"
+ @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+ @echo " changes to make an overview of all changed/added/deprecated items"
+ @echo " linkcheck to check all external links for integrity"
+ @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+ @echo " publish to copy the HTML documentation to the server."
+
+clean:
+ -rm -rf _build/*
+
+html:
+ $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) _build/html
+ @echo
+ @echo "Build finished. The HTML pages are in _build/html."
+
+dirhtml:
+ $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) _build/dirhtml
+ @echo
+ @echo "Build finished. The HTML pages are in _build/dirhtml."
+
+pickle:
+ $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) _build/pickle
+ @echo
+ @echo "Build finished; now you can process the pickle files."
+
+json:
+ $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) _build/json
+ @echo
+ @echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+ $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) _build/htmlhelp
+ @echo
+ @echo "Build finished; now you can run HTML Help Workshop with the" \
+ ".hhp project file in _build/htmlhelp."
+
+qthelp:
+ $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) _build/qthelp
+ @echo
+ @echo "Build finished; now you can run "qcollectiongenerator" with the" \
+ ".qhcp project file in _build/qthelp, like this:"
+ @echo "# qcollectiongenerator _build/qthelp/samtools.qhcp"
+ @echo "To view the help file:"
+ @echo "# assistant -collectionFile _build/qthelp/samtools.qhc"
+
+latex:
+ $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) _build/latex
+ @echo
+ @echo "Build finished; the LaTeX files are in _build/latex."
+ @echo "Run \`make all-pdf' or \`make all-ps' in that directory to" \
+ "run these through (pdf)latex."
+
+changes:
+ $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) _build/changes
+ @echo
+ @echo "The overview file is in _build/changes."
+
+linkcheck:
+ $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) _build/linkcheck
+ @echo
+ @echo "Link check complete; look for any errors in the above output " \
+ "or in _build/linkcheck/output.txt."
+
+doctest:
+ $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) _build/doctest
+ @echo "Testing of doctests in the sources finished, look at the " \
+ "results in _build/doctest/output.txt."
+
+publish:
+ rm -rf $(DIR_PUBLISH)
+ mkdir -p $(DIR_PUBLISH)
+ cp -r _build/html/* $(DIR_PUBLISH)
diff --git a/doc/api.rst b/doc/api.rst
new file mode 100644
index 0000000..1333cf8
--- /dev/null
+++ b/doc/api.rst
@@ -0,0 +1,122 @@
+pysam - An interface for reading and writing SAM files
+======================================================
+
+Pysam is a python module that makes it easy to read and manipulate mapped short read sequence data stored in SAM/BAM files.
+It is a lightweight wrapper of the samtools_ C-API.
+
+This page provides a quick introduction in using pysam followed by the API.
+See :ref:`usage` for more detailed usage instructions.
+
+To use the module to read a file in BAM format, create a :class:`~pysam.Samfile` object::
+
+ import pysam
+ samfile = pysam.Samfile( "ex1.bam", "rb" )
+
+
+Once a file is opened you can iterate over all of the read mapping to a specified region using :meth:`~pysam.Samfile.fetch`.
+Each iteration returns a :class:`~pysam.AlignedRead` object which represents a single read along with its fields and optional tags::
+
+ for alignedread in samfile.fetch('chr1', 100, 120):
+ print alignedread
+
+ samfile.close()
+
+To give::
+
+ EAS56_57:6:190:289:82 0 99 <<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<; 69 CTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA 0 192 1
+ EAS56_57:6:190:289:82 0 99 <<<<<<;<<<<<<<<<<;<<;<<<<;8<6;9;;2; 137 AGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCAC 73 64 1
+ EAS51_64:3:190:727:308 0 102 <<<<<<<<<<<<<<<<<<<<<<<<<<<::<<<844 99 GGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGG 99 18 1
+ ...
+
+You can also write to a :class:`~pysam.Samfile`::
+
+ import pysam
+ samfile = pysam.Samfile("ex1.bam", "rb")
+ pairedreads = pysam.Samfile("allpaired.bam", "wb", template=samfile)
+ for read in samfile.fetch():
+ if read.is_paired:
+ pairedreads.write(read)
+
+ pairedreads.close()
+ samfile.close()
+
+An alternative way of accessing the data in a SAM file is by iterating
+over each base of a specified region using the :meth:`~pysam.Samfile.pileup`
+method. Each iteration returns a :class:`~pysam.PileupColumn` which
+represents all the reads in the SAM file that map to a single base in the
+reference sequence. The list of reads are represented as :class:`~pysam.PileupRead`
+objects in the :attr:`PileupColumn.pileups <pysam.PileupColumn.pileups>` property::
+
+ import pysam
+ samfile = pysam.Samfile("ex1.bam", "rb" )
+ for pileupcolumn in samfile.pileup( 'chr1', 100, 120):
+ print
+ print 'coverage at base %s = %s' % (pileupcolumn.pos , pileupcolumn.n)
+ for pileupread in pileupcolumn.pileups:
+ print '\tbase in read %s = %s' % (pileupread.alignment.qname, pileupread.alignment.seq[pileupread.qpos])
+
+ samfile.close()
+
+The above code outputs::
+
+ coverage at base 99 = 1
+ base in read EAS56_57:6:190:289:82 = A
+
+ coverage at base 100 = 1
+ base in read EAS56_57:6:190:289:82 = G
+
+ coverage at base 101 = 1
+ base in read EAS56_57:6:190:289:82 = G
+
+ coverage at base 102 = 2
+ base in read EAS56_57:6:190:289:82 = G
+ base in read EAS51_64:3:190:727:308 = G
+ ...
+
+Commands available in :term:`csamtools` are available as simple function calls. For example::
+
+ pysam.sort( "ex1.bam", "output" )
+
+corresponds to the command line::
+
+ samtools sort ex1.bam output
+
+Analogous to :class:`~pysam.Samfile`, a :class:`~pysam.Tabixfile` allows fast random access to compressed
+and tabix indexed tab-separated file formats with genomic data::
+
+ import pysam
+ tabixfile = pysam.Tabixfile( "example.gtf.gz" )
+
+ for gtf in tabixfile.fetch('chr1', 1000, 2000):
+ print gtf.contig, gtf.start, gtf.end, gtf.gene_id
+
+:class:`~pysam.Tabixfile` implements lazy parsing in order to iterate over large tables efficiently.
+
+More detailed usage instructions is at :ref:`usage`.
+
+.. note::
+ Coordinates in pysam are always 0-based (following the python convention). SAM text files use 1-based coordinates.
+
+.. note::
+ The above examples can be run in the :file:`tests` directory of the installation directory. Type 'make' before
+ running them.
+
+.. seealso::
+
+ http://code.google.com/p/pysam/
+ The pysam Google code page, containing source code and download instructions
+
+ http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/contents.html
+ The pysam website containing documentation
+
+.. _samtools: http://samtools.sourceforge.net/
+
+
+API
+*****
+
+.. automodule:: pysam
+ :members:
+ :undoc-members:
+
+
diff --git a/doc/conf.py b/doc/conf.py
new file mode 100644
index 0000000..24abc47
--- /dev/null
+++ b/doc/conf.py
@@ -0,0 +1,204 @@
+# -*- coding: utf-8 -*-
+#
+# samtools documentation build configuration file, created by
+# sphinx-quickstart on Wed Aug 12 14:43:42 2009.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os, glob
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+_libdir = "../build/lib.%s-%s-%s.%s" % (os.uname()[0].lower(), os.uname()[4],sys.version_info[0], sys.version_info[1] )
+if os.path.exists( _libdir ):
+ sys.path.append( os.path.abspath( _libdir ) )
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo',
+ 'sphinx.ext.ifconfig',
+ 'sphinx.ext.intersphinx']
+
+intersphinx_mapping = {'python': ('http://docs.python.org/3.2', None)}
+
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8'
+
+# The master toctree document.
+master_doc = 'contents'
+
+# General information about the project.
+project = u'pysam'
+copyright = u'2009, Andreas Heger, Tildon Grant Belgrad, Martin Goodson, Kevin Jacobs'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+sys.path.insert( 0, "../pysam")
+import version
+
+# The short X.Y version.
+version = version.__version__
+# The full version, including alpha/beta/rc tags.
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further. For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents. If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar. Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_use_modindex = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it. The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'samtoolsdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+ ('contents', 'samtools.tex', ur'samtools Documentation',
+ ur'Andreas Heger, Tildon Grant Belgrad, Martin Goodson', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True
diff --git a/doc/contents.rst b/doc/contents.rst
new file mode 100644
index 0000000..3fcfdbc
--- /dev/null
+++ b/doc/contents.rst
@@ -0,0 +1,73 @@
+.. samtools documentation master file, created by
+ sphinx-quickstart on Wed Aug 12 14:43:42 2009.
+ You can adapt this file completely to your liking, but it should at least
+ contain the root `toctree` directive.
+
+pysam: samtools interface for python
+====================================
+
+:Author: Andreas Heger, Tildon Grant Belgrad, Martin Goodson, Leo Goodstad, Kevin Jacobs
+:Date: |today|
+:Version: |version|
+
+The *SAM/BAM* format is a way to store efficiently large numbers of alignments
+[Li2009]_, such as those routinely are created by next-generation sequencing
+methods.
+
+This module provides a low-level wrapper around the samtools_ C-API using `cython`_
+and a high-level API for convenient access to the data in *SAM/BAM* formatted files.
+Also included is an interface to the tabix_ C-API for reading compressed and
+indexed tabular data.
+
+The current version wraps *samtools-0.1.18* and *tabix-0.2.6*.
+
+Contents
+--------
+
+.. toctree::
+ :maxdepth: 2
+
+ api.rst
+ usage.rst
+ tabix.rst
+ faq.rst
+ glossary.rst
+ developer.rst
+ release.rst
+
+Indices and tables
+------------------
+
+Contents:
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+References
+----------
+
+.. [Li2009] The Sequence Alignment/Map format and SAMtools. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup.
+ Bioinformatics. 2009 Aug 15;25(16):2078-9. Epub 2009 Jun 8.
+ `PMID: 19505943 <http://www.ncbi.nlm.nih.gov/pubmed/19505943?dopt=Abstract>`_
+
+.. seealso::
+
+ The samtools homepage
+ http://samtools.sourceforge.net
+
+ The cython C-extensions for python
+ http://cython.org/
+
+ The python language
+ http://www.python.org
+
+.. _samtools: http://samtools.sourceforge.net
+
+.. _tabix: http://samtools.sourceforge.net/tabix.shtml
+
+.. _cython: http://cython.org/
+
+.. _python: http://www.python.org
+
+
diff --git a/doc/developer.rst b/doc/developer.rst
new file mode 100644
index 0000000..42e042a
--- /dev/null
+++ b/doc/developer.rst
@@ -0,0 +1,75 @@
+*****************
+Developer's guide
+*****************
+
+Code organization
+*****************
+
+The top level directory is organized in the following
+directories:
+
+pysam
+ Code specific to pysam
+
+samtools
+ Original and unmodified source code from :term:`csamtools`. Use
+ :file:`setup.py` to obtain the latest code.
+
+tests
+ Examples and data for testing
+
+Importing :term:`csamtools`
+***************************
+
+Running :file:`setup.py` will import the csamtools source code.
+The command::
+
+ python setup.py import PATH
+
+where ``PATH`` points to a :term:`csamtools` source directory. For example::
+
+ python setup.py import ~/samtools-0.1.6
+
+Note that files will not be overwritten. To import all anew,
+delete all :file:`*.c` and :file:`*.h` files in the :file:`samtools`
+directory first.
+
+Unit testing
+************
+
+Unit tests are currently in the script :file:`pysam_test.py`.
+
+Unit tests for the python methods
+---------------------------------
+
+Few implemented yet. This will require also writing functionality,
+hence postponed
+
+Unit tests for the command line interface
+-----------------------------------------
+
+The current suite of tests compare the binary files of selected
+samtools commands against running the same commands from within
+the pysam module. The general expectation is that the files
+are binary identical given that most of the code is
+from :term:`csamtools` anyway. However, differences might be
+found if the installed :term:`csamtools` version is different
+from the one wrapped with pysam.
+
+The tests create files in the current test directory. They
+are modeled on the example given within the :term:`csamtools`
+distribution. Two files are required in the working directory
+of the test script:
+
+1. :file:`ex1.fa`: a fasta file
+2. :file:`ex1.sam.gz`: a sam file
+
+
+
+
+
+
+
+
+
+
diff --git a/doc/faq.rst b/doc/faq.rst
new file mode 100644
index 0000000..cd4b4c5
--- /dev/null
+++ b/doc/faq.rst
@@ -0,0 +1,40 @@
+pysam coordinates are wrong
+===========================
+
+pysam uses 0-based coordinates and the half-open notation for ranges
+as does python. Coordinates and intervals reported from pysam always
+follow that convention.
+
+Confusion might arise as different file formats might have different
+conventions. For example, the SAM format is 1-based while the BAM
+format is 0-based. It is important to remember that pysam will always
+conform to the python convention and translate to/from the file format
+automatically.
+
+The only exception is the :term:`region string` in the :meth:`Samfile.fetch`
+and :meth:`Samfile.pileup` methods. This string follows the convention
+of the samtools command line utilities. The same is true for any
+coordinates passed to the samtools command utilities directly, such
+as :meth:`pysam.mpileup`.
+
+BAM files with a large number of reference sequences is slow
+============================================================
+
+If you have many reference sequences in a bam file, the following
+might be slow::
+
+ track = pysam.Samfile(fname, "rb")
+ for aln in track.fetch():
+ pass
+
+The reason is that track.fetch() will iterate through the bam file
+for each reference sequence in the order as it is defined in the
+header. This might require a lot of jumping around in the file. To
+avoid this, use::
+
+ track = pysam.Samfile(fname, "rb")
+ for aln in track.fetch( until_eof = True ):
+ pass
+
+This will iterate through reads as they appear in the file.
+
diff --git a/doc/glossary.rst b/doc/glossary.rst
new file mode 100644
index 0000000..d10fd30
--- /dev/null
+++ b/doc/glossary.rst
@@ -0,0 +1,73 @@
+*********
+Glossary
+*********
+
+.. glossary::
+ :sorted:
+
+ cigar
+ An alignment format string. In the python API, the cigar alignment is
+ presented as a list of tuples ``(operation,length)``. For example, the tuple
+ ``[ (0,3), (1,5), (0,2) ]`` refers to an alignment with 3 matches, 5 insertions
+ and another 2 matches.
+
+ region
+ A genomic region, stated relative to a reference sequence. A region consists of
+ reference name ('chr1'), start (100000), and end (200000).
+ 0-based coordinates. Can be expressed as a string ('chr1:10000:20000')
+
+ column
+ Reads that are aligned to a base in the :term:`reference` sequence.
+
+ tid
+ The :term:`target` id. The target id is 0 or a positive integer mapping to
+ entries within the sequence dictionary in the header section of
+ a :term:`TAM` file or :term:`BAM` file.
+
+ Reference
+ The sequence that a :term:`tid` refers to. For example ``chr1``, ``contig123``.
+
+ SAM
+ A textual format for storing genomic alignment information.
+
+ BAM
+ Binary SAM format. BAM files are binary formatted, indexed and
+ allow random access.
+
+ TAM
+ Text SAM file. TAM files are human readable files of
+ tab-separated fields. TAM files do not allow random access.
+
+ sam file
+ A file containing aligned reads. The :term:`sam file` can either
+ be a :term:`BAM` file or a :term:`TAM` file.
+
+ pileup
+ Pileup
+
+ samtools
+ The samtools_ package.
+
+ csamtools
+ The samtools_ C-API.
+
+ fetching
+ Retrieving all mapped reads mapped to a :term:`region`.
+
+ target
+ The sequence that a read has been aligned to. Target
+ sequences have bot a numerical identifier (:term:`tid`)
+ and an alphanumeric name (:term:`Reference`).
+
+ tabix file
+ A sorted, compressed and indexed tab-separated file created
+ by the command line tool :file:`tabix` or the commands
+ :meth:`tabix_compress` and :meth:`tabix_index`. The file
+ is indexed by chromosomal coordinates.
+
+ tabix row
+ A row in a :term:`tabix file`. Fields within a row are
+ tab-separated.
+
+
+.. _samtools: http://samtools.sourceforge.net
diff --git a/doc/make.bat b/doc/make.bat
new file mode 100644
index 0000000..caca799
--- /dev/null
+++ b/doc/make.bat
@@ -0,0 +1,112 @@
+ at ECHO OFF
+
+REM Command file for Sphinx documentation
+
+set SPHINXBUILD=sphinx-build
+set ALLSPHINXOPTS=-d _build/doctrees %SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+ set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+ :help
+ echo.Please use `make ^<target^>` where ^<target^> is one of
+ echo. html to make standalone HTML files
+ echo. dirhtml to make HTML files named index.html in directories
+ echo. pickle to make pickle files
+ echo. json to make JSON files
+ echo. htmlhelp to make HTML files and a HTML help project
+ echo. qthelp to make HTML files and a qthelp project
+ echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+ echo. changes to make an overview over all changed/added/deprecated items
+ echo. linkcheck to check all external links for integrity
+ echo. doctest to run all doctests embedded in the documentation if enabled
+ goto end
+)
+
+if "%1" == "clean" (
+ for /d %%i in (_build\*) do rmdir /q /s %%i
+ del /q /s _build\*
+ goto end
+)
+
+if "%1" == "html" (
+ %SPHINXBUILD% -b html %ALLSPHINXOPTS% _build/html
+ echo.
+ echo.Build finished. The HTML pages are in _build/html.
+ goto end
+)
+
+if "%1" == "dirhtml" (
+ %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% _build/dirhtml
+ echo.
+ echo.Build finished. The HTML pages are in _build/dirhtml.
+ goto end
+)
+
+if "%1" == "pickle" (
+ %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% _build/pickle
+ echo.
+ echo.Build finished; now you can process the pickle files.
+ goto end
+)
+
+if "%1" == "json" (
+ %SPHINXBUILD% -b json %ALLSPHINXOPTS% _build/json
+ echo.
+ echo.Build finished; now you can process the JSON files.
+ goto end
+)
+
+if "%1" == "htmlhelp" (
+ %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% _build/htmlhelp
+ echo.
+ echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in _build/htmlhelp.
+ goto end
+)
+
+if "%1" == "qthelp" (
+ %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% _build/qthelp
+ echo.
+ echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in _build/qthelp, like this:
+ echo.^> qcollectiongenerator _build\qthelp\samtools.qhcp
+ echo.To view the help file:
+ echo.^> assistant -collectionFile _build\qthelp\samtools.ghc
+ goto end
+)
+
+if "%1" == "latex" (
+ %SPHINXBUILD% -b latex %ALLSPHINXOPTS% _build/latex
+ echo.
+ echo.Build finished; the LaTeX files are in _build/latex.
+ goto end
+)
+
+if "%1" == "changes" (
+ %SPHINXBUILD% -b changes %ALLSPHINXOPTS% _build/changes
+ echo.
+ echo.The overview file is in _build/changes.
+ goto end
+)
+
+if "%1" == "linkcheck" (
+ %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% _build/linkcheck
+ echo.
+ echo.Link check complete; look for any errors in the above output ^
+or in _build/linkcheck/output.txt.
+ goto end
+)
+
+if "%1" == "doctest" (
+ %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% _build/doctest
+ echo.
+ echo.Testing of doctests in the sources finished, look at the ^
+results in _build/doctest/output.txt.
+ goto end
+)
+
+:end
diff --git a/doc/release.rst b/doc/release.rst
new file mode 100644
index 0000000..58a58aa
--- /dev/null
+++ b/doc/release.rst
@@ -0,0 +1,85 @@
+=============
+Release notes
+=============
+
+Release 0.7.5
+=============
+
+ * switch to samtools 0.1.19
+ * issue 122: MACOSX getline missing
+ * issue 130: clean up tempfiles
+ * various other bugfixes
+
+Release 0.7.4
+=============
+
+ * further bugfixes to setup.py and package layout
+
+Release 0.7.3
+=============
+
+ * further bugfixes to setup.py
+ * upgraded distribute_setup.py to 0.6.34
+
+Release 0.7.2
+=============
+
+ * bugfix in installer - failed when cython not present
+ * changed installation locations of shared libraries
+
+Release 0.7.1
+=============
+
+ * bugfix: missing PP tag PG records in header
+ * added pre-built .c files to distribution
+
+Release 0.7
+===========
+
+ * switch to tabix 0.2.6
+ * added cigarstring field
+ * python3 compatibility
+ * added B tag handling
+ * added check_sq and check_header options to Samfile.__init__
+ * added lazy GTF parsing to tabix
+ * reworked support for VCF format parsing
+ * bugfixes
+
+Release 0.6
+===========
+
+ * switch to samtools 0.1.18
+ * various bugfixes
+ * removed references to deprecated 'samtools pileup' functionality
+ * AlignedRead.tags now returns an empty list if there are no tags.
+ * added pnext, rnext and tlen
+
+Release 0.5
+===========
+
+ * switch to samtools 0.1.16 and tabix 0.2.5
+ * improved tabix parsing, added vcf support
+ * re-organized code to permit linking againts pysam
+ * various bugfixes
+ * added Samfile.positions and Samfile.overlap
+
+Release 0.4
+===========
+
+ * switch to samtools 0.1.12a and tabix 0.2.3
+ * added snp and indel calling.
+ * switch from pyrex to cython
+ * changed handling of samtools stderr
+ * various bugfixes
+ * added Samfile.count and Samfile.mate
+ * deprecated AlignedRead.rname, added AlignedRead.tid
+
+Release 0.3
+===========
+
+ * switch to samtools 0.1.8
+ * added support for tabix files
+ * numerous bugfixes including
+ * permit simultaneous iterators on the same file
+ * working access to remote files
+
diff --git a/doc/usage.rst b/doc/usage.rst
new file mode 100644
index 0000000..e438015
--- /dev/null
+++ b/doc/usage.rst
@@ -0,0 +1,285 @@
+.. _Usage:
+
+*************************************
+Working with BAM/SAM-formatted files
+*************************************
+
+In order to follow the examples below, execute
+
+ make
+
+in the :file:`test` directory.
+
+Opening a sampfile
+------------------
+
+The first operation is to import the pysam module and open a
+:class:`pysam.Samfile`::
+
+ import pysam
+ samfile = pysam.Samfile( "ex1.bam", "rb" )
+
+The above command opens the file :file:`ex1.bam` for reading.
+The ``b`` qualifier indicates that this is a :term:`BAM` file.
+To open a :term:`SAM` file, type::
+
+ import pysam
+ samfile = pysam.Samfile( "ex1.bam", "r" )
+
+Fetching reads mapped to a :term:`region`
+-----------------------------------------
+
+There are two ways to obtain the reads mapped to a genomic region. The
+first method follows the :term:`csamtools` API and works
+via a callback function. The callback will be executed for each
+alignment in a :term:`region`::
+
+ def my_fetch_callback( alignment ):
+ print str(alignment)
+
+ samfile.fetch( 'seq1', 10, 20, callback = my_fetch_callback )
+
+Using a function object, work can be done on the alignments. The
+code below simply counts aligned reads::
+
+ class Counter:
+ cCounts = 0
+ def __call__(self, alignment):
+ self.counts += 1
+
+ c = Counter()
+ samfile.fetch( 'seq1', 10, 20, callback = c )
+ print "counts=", c.counts
+
+The second method uses python iterators. If you call :meth:`pysam.Samfile.fetch`
+without a callback, an iterator of the type :class:`pysam.IteratorRow` is returned.
+It will iterate through mapped reads
+and return a :class:`pysam.AlignedRead` object for each::
+
+ iter = samfile.fetch( 'seq1', 10, 20)
+ for x in iter: print str(x)
+
+Note that both methods iterate through a :term:`BAM` file
+on a read-by-read basis.
+
+:meth:`pysam.Samfile.fetch` returns all reads overlapping a region sorted
+by the first aligned base in the :term:`reference` sequence.
+Note that it will also return reads that are only partially
+overlapping with the :term:`region`. Thus the reads returned
+might span a region that is larger than the one queried.
+
+Using the pileup-engine
+-----------------------
+
+The :term:`pileup` engine of :term:`csamtools` iterates
+over all reads that are aligned to a :term:`region`. In
+contrast to :term:`fetching`, the :term:`pileup` engine
+returns for each base in the :term:`reference` sequence the reads that
+map to that particular position.
+
+Again, there are two principal methods to iterate.
+The first works via a callback function::
+
+ def my_pileup_callback( pileups ):
+ print str(pileups)
+ samfile.pileup( 'seq1', 10, 20, callback = my_pileup_callback )
+
+The second method uses python iterators. The iterator
+:class:`pysam.IteratorColumn` will iterate through each :term:`column`
+(reference bases) and return a list of aligned reads::
+
+ iter = samfile.pileup( 'seq1', 10, 20 )
+ for x in iter: print str(x)
+
+Aligned reads are returned as a :class:`pysam.PileupColumn`.
+
+Using samtools commands within python
+-------------------------------------
+
+Commands available in :term:`csamtools` are available
+as simple function calls. For example::
+
+ pysam.sort( "ex1.bam", "output" )
+
+corresponds to the command line::
+
+ samtools sort ex1.bam output
+
+Command line options can be provided as arguments::
+
+ pysam.sort( "-n", "ex1.bam", "output" )
+
+or::
+
+ pysam.sort( "-m", "1000000", "ex1.bam", "output" )
+
+In order to get usage information, try::
+
+ print pysam.sort.usage()
+
+Argument errors raise a :class:`pysam.SamtoolsError`::
+
+ pysam.sort()
+
+ Traceback (most recent call last):
+ File "x.py", line 12, in <module>
+ pysam.sort()
+ File "/home/andreas/pysam/build/lib.linux-x86_64-2.6/pysam/__init__.py", line 37, in __call__
+ if retval: raise SamtoolsError( "\n".join( stderr ) )
+ pysam.SamtoolsError: 'Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix>\n'
+
+Messages from :term:`csamtools` on stderr are captured and are
+available using the :meth:`getMessages` method::
+
+ pysam.sort.getMessage()
+
+Note that only the output from the last invocation of a command
+is stored.
+
+Creating SAM/BAM files from scratch
+-----------------------------------
+
+The following example shows how a new BAM file is constructed from scratch.
+The important part here is that the :class:`pysam.Samfile` class needs to receive
+the sequence identifiers. These can be given either as a dictionary in a
+header structure, as lists of names and sizes, or from a template file.
+Here, we use a header dictionary::
+
+ header = { 'HD': {'VN': '1.0'},
+ 'SQ': [{'LN': 1575, 'SN': 'chr1'},
+ {'LN': 1584, 'SN': 'chr2'}] }
+
+ outfile = pysam.Samfile( tmpfilename, "wh", header = header )
+ a = pysam.AlignedRead()
+ a.qname = "read_28833_29006_6945"
+ a.seq="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG"
+ a.flag = 99
+ a.rname = 0
+ a.pos = 32
+ a.mapq = 20
+ a.cigar = ( (0,10), (2,1), (0,25) )
+ a.mrnm = 0
+ a.mpos=199
+ a.isize=167
+ a.qual="<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<"
+ a.tags = ( ("NM", 1),
+ ("RG", "L1") )
+ outfile.write(a)
+ outfile.close()
+
+Using streams
+-------------
+
+Pysam does not support reading and writing from true python file objects, but
+it does support reading and writing from stdin and stdout. The following example reads
+from stdin and writes to stdout::
+
+ infile = pysam.Samfile( "-", "r" )
+ outfile = pysam.Samfile( "-", "w", template = infile )
+ for s in infile: outfile.write(s)
+
+It will also work with :term:`BAM` files. The following script converts a :term:`BAM` formatted file
+on stdin to a :term:`SAM` formatted file on stdout::
+
+ infile = pysam.Samfile( "-", "rb" )
+ outfile = pysam.Samfile( "-", "w", template = infile )
+ for s in infile: outfile.write(s)
+
+Note, only the file open mode needs to changed from ``r`` to ``rb``.
+
+.. Currently inactivated as pileup deprecated
+.. Using the samtools SNP caller
+.. -----------------------------
+
+.. There are two ways to access the samtools SNP caller. The :class:`pysam.IteratorSNPCalls`
+.. is appropriate when calling many consecutive SNPs, while :class:`pysam.SNPCaller` is
+.. best when calling SNPs at non-consecutive genomic positions. Each snp caller returns objects of
+.. type :class:`pysam.SNPCall`.
+
+.. To use :class:`pysam.IteratorSNPCalls`, associate it with a :class:`pysam.IteratorColumn`::
+
+.. samfile = pysam.Samfile( "ex1.bam", "rb")
+.. fastafile = pysam.Fastafile( "ex1.fa" )
+.. pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+.. sncpall_iter = pysam.IteratorSNPCalls(pileup_iter)
+.. for call in snpcall_iter:
+.. print str(call)
+
+.. Usage of :class:`pysam.SNPCaller` is similar::
+
+.. samfile = pysam.Samfile( "ex1.bam", "rb")
+.. fastafile = pysam.Fastafile( "ex1.fa" )
+.. pileup_iter = samfile.pileup( stepper = "samtools", fastafile = fastafile )
+.. snpcaller = pysam.SNPCaller.call(pileup_iter)
+.. print snpcaller( "chr1", 100 )
+
+.. Note the use of the option *stepper* to control which reads are included in the
+.. in the :term:`pileup`. The ``samtools`` stepper implements the same read selection
+.. and processing as in the samtools pileup command.
+
+.. Calling indels works along the same lines, using the :class:`pysam.IteratorIndelCalls`
+.. and :class:`pysam.IteratorIndelCaller`.
+
+Extending pysam
+---------------
+
+Using pyximport_, it is (relatively) straight-forward to access pysam
+internals and the underlying samtools library. An example is provided
+in the :file:`test` directory. The example emulates the samtools flagstat command
+and consists of three files:
+
+1. The main script :file:`pysam_flagstat.py`. The important lines in this script
+ are::
+
+ import pyximport
+ pyximport.install()
+ import _pysam_flagstat
+
+ ...
+
+ flag_counts = _pysam_flagstat.count( pysam_in )
+
+ The first part imports, sets up pyximport_ and imports the cython module :file:`_pysam_flagstat`.
+ The second part calls the ``count`` method in :file:`_pysam_flagstat`.
+
+2. The cython implementation :file:`_pysam_flagstat.pyx`. This script imports the pysam API via::
+
+ from csamtools cimport *
+
+ This statement imports, amongst others, :class:`AlignedRead` into the namespace. Speed can be
+ gained from declaring variables. For example, to efficiently iterate
+ over a file, an :class:`AlignedRead` object is declared::
+
+ # loop over samfile
+ cdef AlignedRead read
+ for read in samfile:
+ ...
+
+3. A :file:`pyxbld` providing pyximport_ with build information.
+ Required are the locations of the samtools and pysam header libraries
+ of a source installation of pysam plus the :file:`csamtools.so`
+ shared library. For example::
+
+ def make_ext(modname, pyxfilename):
+ from distutils.extension import Extension
+ import pysam, os
+ dirname = os.path.dirname( pysam.__file__ )[:-len("pysam")]
+ return Extension(name = modname,
+ sources=[pyxfilename],
+ extra_link_args=[ os.path.join( dirname, "csamtools.so")],
+ include_dirs = ['../samtools',
+ '../pysam',
+ ] )
+
+
+
+If the script :file:`pysam_flagstat.py` is called the first time, pyximport_ will
+compile the cython_ extension :file:`_pysam_flagstat.pyx` and make it available
+to the script. Compilation requires a working compiler and cython_ installation.
+Each time :file:`_pysam_flagstat.pyx` is modified, a new compilation will take place.
+
+pyximport_ comes with cython_.
+
+.. _cython: http://cython.org/
+
+.. _pyximport: http://www.prescod.net/pyximport/
diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO
index c527383..8d8f7c5 100644
--- a/pysam.egg-info/PKG-INFO
+++ b/pysam.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.4
+Version: 0.7.5
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/pysam.egg-info/SOURCES.txt b/pysam.egg-info/SOURCES.txt
index 718c4d2..dcf1ced 100644
--- a/pysam.egg-info/SOURCES.txt
+++ b/pysam.egg-info/SOURCES.txt
@@ -4,8 +4,19 @@ KNOWN_BUGS
MANIFEST.in
THANKS
distribute_setup.py
+pysam.py
setup.cfg
setup.py
+doc/Makefile
+doc/api.rst
+doc/conf.py
+doc/contents.rst
+doc/developer.rst
+doc/faq.rst
+doc/glossary.rst
+doc/make.bat
+doc/release.rst
+doc/usage.rst
pysam/Pileup.py
pysam/TabProxies.c
pysam/TabProxies.pxd
@@ -24,6 +35,7 @@ pysam/namedtuple.py
pysam/pysam_util.c
pysam/pysam_util.h
pysam/tabix_util.c
+pysam/tabix_util.h
pysam/version.py
pysam.egg-info/PKG-INFO
pysam.egg-info/SOURCES.txt
@@ -56,6 +68,11 @@ samtools/bam_rmdupse.c.pysam.c
samtools/bam_sort.c.pysam.c
samtools/bam_stat.c.pysam.c
samtools/bam_tview.c.pysam.c
+samtools/bam_tview.h
+samtools/bam_tview_curses.c.pysam.c
+samtools/bam_tview_html.c.pysam.c
+samtools/bamshuf.c.pysam.c
+samtools/bedcov.c.pysam.c
samtools/bedidx.c.pysam.c
samtools/bgzf.c.pysam.c
samtools/bgzf.h
@@ -76,6 +93,7 @@ samtools/kseq.h
samtools/ksort.h
samtools/kstring.c.pysam.c
samtools/kstring.h
+samtools/padding.c.pysam.c
samtools/phase.c.pysam.c
samtools/pysam.h
samtools/razf.c.pysam.c
@@ -103,9 +121,9 @@ samtools/bcftools/mut.c.pysam.c
samtools/bcftools/prob1.c.pysam.c
samtools/bcftools/prob1.h
samtools/bcftools/vcf.c.pysam.c
+samtools/misc/ace2sam.c.pysam.c
samtools/misc/md5.c.pysam.c
samtools/misc/md5.h
-samtools/misc/seqtk.c.pysam.c
samtools/win32/__init__.py
samtools/win32/xcurses.h
samtools/win32/zconf.h
@@ -161,6 +179,7 @@ tests/pysam_test.py
tests/segfault_tests.py
tests/tabix_test.py
tests/tag_bug.bam
+tests/test_unaligned.bam
tests/vcf-examples/10.vcf
tests/vcf-examples/11.vcf
tests/vcf-examples/12.vcf
diff --git a/pysam.py b/pysam.py
new file mode 100644
index 0000000..a3d9f6f
--- /dev/null
+++ b/pysam.py
@@ -0,0 +1 @@
+raise ImportError( '''calling "import pysam" from the source directory is not supported - please import pysam from somewhere else.''')
diff --git a/pysam/TabProxies.c b/pysam/TabProxies.c
index df3c35e..7c87ba2 100644
--- a/pysam/TabProxies.c
+++ b/pysam/TabProxies.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Tue Nov 20 15:06:33 2012 */
+/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,7 +11,6 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -23,22 +22,18 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
-
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,28 +41,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
-#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -75,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -89,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -101,11 +94,9 @@
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -115,31 +106,30 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
-
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
-
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -147,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -166,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -174,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -193,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -206,7 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -225,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -239,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -248,6 +228,7 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
@@ -268,8 +249,8 @@
#define _USE_MATH_DEFINES
#endif
#include <math.h>
-#define __PYX_HAVE__TabProxies
-#define __PYX_HAVE_API__TabProxies
+#define __PYX_HAVE__pysam__TabProxies
+#define __PYX_HAVE_API__pysam__TabProxies
#include "stdlib.h"
#include "string.h"
#include "stdint.h"
@@ -283,8 +264,6 @@
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-
-/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#define CYTHON_INLINE __inline__
@@ -296,8 +275,6 @@
#define CYTHON_INLINE
#endif
#endif
-
-/* unused attribute */
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -311,27 +288,25 @@
# define CYTHON_UNUSED
# endif
#endif
-
typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-/* Type Conversion Predeclarations */
-
#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
@@ -358,27 +333,28 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"TabProxies.pyx",
+ "type.pxd",
"bool.pxd",
"complex.pxd",
};
/*--- Type declarations ---*/
-struct __pyx_obj_10TabProxies_TupleProxy;
-struct __pyx_obj_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_10TabProxies_VCFProxy;
-struct __pyx_obj_10TabProxies_GTFProxy;
-struct __pyx_obj_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-/* "TabProxies.pxd":41
+/* "pysam/TabProxies.pxd":41
* ctypedef int uint64_t
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_TupleProxy {
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
PyObject_HEAD
- struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
char *data;
char **fields;
int nfields;
@@ -389,64 +365,64 @@ struct __pyx_obj_10TabProxies_TupleProxy {
};
-/* "TabProxies.pxd":69
+/* "pysam/TabProxies.pxd":69
* cdef char * getAttributes( self )
*
* cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
};
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
+/* "pysam/TabProxies.pxd":72
+ * pass
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_VCFProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
char *contig;
- uint32_t pos;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
};
-/* "TabProxies.pxd":60
+/* "pysam/TabProxies.pxd":83
* cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_GTFProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
};
-/* "TabProxies.pxd":72
- * pass
+/* "pysam/TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_BedProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
-/* "TabProxies.pyx":84
+/* "pysam/TabProxies.pyx":84
* return not (buffer <= p < buffer + nbytes )
*
* cdef class TupleProxy: # <<<<<<<<<<<<<<
@@ -454,17 +430,17 @@ struct __pyx_obj_10TabProxies_BedProxy {
*
*/
-struct __pyx_vtabstruct_10TabProxies_TupleProxy {
- int (*getMaxFields)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t);
- PyObject *(*take)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*present)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*copy)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*update)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
+struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy {
+ int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t);
+ PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
};
-static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
-/* "TabProxies.pyx":571
+/* "pysam/TabProxies.pyx":571
* self.fromDict( r )
*
* cdef class NamedTupleProxy( TupleProxy ): # <<<<<<<<<<<<<<
@@ -472,13 +448,13 @@ static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxi
* map_key2field = {}
*/
-struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pyx":656
+/* "pysam/TabProxies.pyx":656
* TupleProxy._setindex(self, idx, str(value) )
*
* cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
@@ -486,13 +462,13 @@ static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10Tab
*
*/
-struct __pyx_vtabstruct_10TabProxies_VCFProxy {
- struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-/* "TabProxies.pyx":590
+/* "pysam/TabProxies.pyx":590
* return f( self.fields[idx] )
*
* cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
@@ -500,13 +476,13 @@ static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies
*
*/
-struct __pyx_vtabstruct_10TabProxies_BedProxy {
- struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
-/* "TabProxies.pyx":326
+/* "pysam/TabProxies.pyx":326
* return str(v)
*
* cdef class GTFProxy( TupleProxy ): # <<<<<<<<<<<<<<
@@ -514,11 +490,11 @@ static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies
*
*/
-struct __pyx_vtabstruct_10TabProxies_GTFProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
- char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *);
+struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
-static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -575,6 +551,11 @@ static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -587,9 +568,11 @@ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
@@ -601,11 +584,10 @@ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (PyList_Append(L, x) < 0) return NULL;
+ if (unlikely(PyList_Append(L, x) < 0)) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- }
- else {
+ } else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -615,11 +597,9 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
}
}
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
- return unlikely(b < 0) ? b : !b;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
- return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+ int result = PySequence_Contains(seq, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
@@ -633,42 +613,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -684,35 +669,57 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_GetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
return m->sq_item(o, i);
}
}
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
+#if CYTHON_COMPILING_IN_PYPY
+#define __Pyx_PyObject_AsDouble(obj) \
+(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
+ likely(PyInt_CheckExact(obj)) ? \
+ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
+#else
#define __Pyx_PyObject_AsDouble(obj) \
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
+#endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len)) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
+ }
+ return PyList_Append(list, x);
+}
+#else
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#endif
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
@@ -765,10 +772,10 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
#endif
#endif
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
typedef struct {
int code_line;
PyCodeObject* code_object;
@@ -803,6 +810,8 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.list' */
+/* Module declarations from 'libc.string' */
+
/* Module declarations from 'libc.stdio' */
/* Module declarations from 'cpython.object' */
@@ -813,7 +822,10 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.iterator' */
+/* Module declarations from '__builtin__' */
+
/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
@@ -867,21 +879,21 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'cpython' */
-/* Module declarations from 'TabProxies' */
-static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
-static PyObject *__pyx_v_10TabProxies__FILENAME_ENCODING = 0;
-static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *); /*proto*/
-static PyObject *__pyx_f_10TabProxies__force_str(PyObject *); /*proto*/
-static char *__pyx_f_10TabProxies_StrOrEmpty(char *); /*proto*/
-static int __pyx_f_10TabProxies_isNew(char *, char *, size_t); /*proto*/
-#define __Pyx_MODULE_NAME "TabProxies"
-int __pyx_module_is_main_TabProxies = 0;
-
-/* Implementation of 'TabProxies' */
+/* Module declarations from 'pysam.TabProxies' */
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0;
+static PyObject *__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING = 0;
+static PyObject *__pyx_f_5pysam_10TabProxies__force_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_10TabProxies__force_str(PyObject *); /*proto*/
+static char *__pyx_f_5pysam_10TabProxies_StrOrEmpty(char *); /*proto*/
+static int __pyx_f_5pysam_10TabProxies_isNew(char *, char *, size_t); /*proto*/
+#define __Pyx_MODULE_NAME "pysam.TabProxies"
+int __pyx_module_is_main_pysam__TabProxies = 0;
+
+/* Implementation of 'pysam.TabProxies' */
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IndexError;
@@ -890,54 +902,54 @@ static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_xrange;
static PyObject *__pyx_builtin_AttributeError;
static PyObject *__pyx_builtin_KeyError;
-static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
-static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, int __pyx_v_index); /* proto */
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
-static Py_ssize_t __pyx_pf_10TabProxies_10TupleProxy_12__len__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */
-static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static void __pyx_pf_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6source___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_d); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, int __pyx_v_lcontig); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_item); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */
-static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __pyx_obj_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8BedProxy___str__(struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */
-static int __pyx_pf_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_pf_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, int __pyx_v_index); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
+static Py_ssize_t __pyx_pf_5pysam_10TabProxies_10TupleProxy_12__len__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6source___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_d); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, int __pyx_v_lcontig); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_item); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_15NamedTupleProxy_2__getattr__(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8BedProxy___str__(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self); /* proto */
+static Py_ssize_t __pyx_pf_5pysam_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */
static char __pyx_k_1[] = "Argument must be string or unicode.";
static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
static char __pyx_k_5[] = "malformatted entry at %s";
@@ -971,6 +983,7 @@ static char __pyx_k_55[] = "feature frame.";
static char __pyx_k_56[] = "feature attributes (as a string).";
static char __pyx_k_57[] = "getfilesystemencoding";
static char __pyx_k_60[] = "/home/andreas/devel/pysam/pysam/TabProxies.pyx";
+static char __pyx_k_61[] = "pysam.TabProxies";
static char __pyx_k__v[] = "v";
static char __pyx_k__id[] = "id";
static char __pyx_k__alt[] = "alt";
@@ -1017,7 +1030,6 @@ static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k___getindex[] = "_getindex";
static char __pyx_k___setindex[] = "_setindex";
static char __pyx_k__IndexError[] = "IndexError";
-static char __pyx_k__TabProxies[] = "TabProxies";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k__attributes[] = "attributes";
static char __pyx_k__blockCount[] = "blockCount";
@@ -1053,6 +1065,7 @@ static PyObject *__pyx_kp_s_5;
static PyObject *__pyx_n_s_57;
static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_kp_s_60;
+static PyObject *__pyx_n_s_61;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__AttributeError;
@@ -1060,7 +1073,6 @@ static PyObject *__pyx_n_s__IndexError;
static PyObject *__pyx_n_s__KeyError;
static PyObject *__pyx_n_s__StopIteration;
static PyObject *__pyx_n_s__StringTypes;
-static PyObject *__pyx_n_s__TabProxies;
static PyObject *__pyx_n_s__TypeError;
static PyObject *__pyx_n_s__ValueError;
static PyObject *__pyx_n_s____getattr__;
@@ -1153,11 +1165,11 @@ static PyObject *__pyx_k_tuple_42;
static PyObject *__pyx_k_tuple_43;
static PyObject *__pyx_k_tuple_47;
static PyObject *__pyx_k_tuple_58;
-static PyObject *__pyx_k_tuple_61;
+static PyObject *__pyx_k_tuple_62;
static PyObject *__pyx_k_codeobj_59;
-static PyObject *__pyx_k_codeobj_62;
+static PyObject *__pyx_k_codeobj_63;
-/* "TabProxies.pyx":7
+/* "pysam/TabProxies.pyx":7
* from cpython cimport PyErr_SetString, PyBytes_Check, PyUnicode_Check, PyBytes_FromStringAndSize
*
* cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<<
@@ -1165,7 +1177,7 @@ static PyObject *__pyx_k_codeobj_62;
* return s[:length]
*/
-static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
+static PyObject *__pyx_f_5pysam_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1175,7 +1187,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("from_string_and_size", 0);
- /* "TabProxies.pyx":8
+ /* "pysam/TabProxies.pyx":8
*
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -1185,7 +1197,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "TabProxies.pyx":9
+ /* "pysam/TabProxies.pyx":9
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3:
* return s[:length] # <<<<<<<<<<<<<<
@@ -1202,7 +1214,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
}
/*else*/ {
- /* "TabProxies.pyx":11
+ /* "pysam/TabProxies.pyx":11
* return s[:length]
* else:
* return s[:length].decode("ascii") # <<<<<<<<<<<<<<
@@ -1210,7 +1222,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
* # filename encoding (copied from lxml.etree.pyx)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1222,7 +1234,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1230,7 +1242,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
return __pyx_r;
}
-/* "TabProxies.pyx":21
+/* "pysam/TabProxies.pyx":21
* _FILENAME_ENCODING = 'ascii'
*
* cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<<
@@ -1238,7 +1250,7 @@ static PyObject *__pyx_f_10TabProxies_from_string_and_size(char *__pyx_v_s, size
* """
*/
-static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filename) {
+static PyObject *__pyx_f_5pysam_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1250,7 +1262,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_my_encodeFilename", 0);
- /* "TabProxies.pyx":24
+ /* "pysam/TabProxies.pyx":24
* u"""Make sure a filename is 8-bit encoded (or None).
* """
* if filename is None: # <<<<<<<<<<<<<<
@@ -1260,7 +1272,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
__pyx_t_1 = (__pyx_v_filename == Py_None);
if (__pyx_t_1) {
- /* "TabProxies.pyx":25
+ /* "pysam/TabProxies.pyx":25
* """
* if filename is None:
* return None # <<<<<<<<<<<<<<
@@ -1274,7 +1286,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
goto __pyx_L3;
}
- /* "TabProxies.pyx":26
+ /* "pysam/TabProxies.pyx":26
* if filename is None:
* return None
* elif PyBytes_Check(filename): # <<<<<<<<<<<<<<
@@ -1284,7 +1296,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
__pyx_t_1 = PyBytes_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "TabProxies.pyx":27
+ /* "pysam/TabProxies.pyx":27
* return None
* elif PyBytes_Check(filename):
* return filename # <<<<<<<<<<<<<<
@@ -1299,7 +1311,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
goto __pyx_L3;
}
- /* "TabProxies.pyx":28
+ /* "pysam/TabProxies.pyx":28
* elif PyBytes_Check(filename):
* return filename
* elif PyUnicode_Check(filename): # <<<<<<<<<<<<<<
@@ -1309,7 +1321,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
__pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "TabProxies.pyx":29
+ /* "pysam/TabProxies.pyx":29
* return filename
* elif PyUnicode_Check(filename):
* return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<<
@@ -1321,9 +1333,9 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
+ __Pyx_INCREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
__pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 29; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -1336,7 +1348,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
}
/*else*/ {
- /* "TabProxies.pyx":31
+ /* "pysam/TabProxies.pyx":31
* return filename.encode(_FILENAME_ENCODING)
* else:
* raise TypeError, u"Argument must be string or unicode." # <<<<<<<<<<<<<<
@@ -1354,7 +1366,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("TabProxies._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1362,7 +1374,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
return __pyx_r;
}
-/* "TabProxies.pyx":33
+/* "pysam/TabProxies.pyx":33
* raise TypeError, u"Argument must be string or unicode."
*
* cdef bytes _force_bytes(object s): # <<<<<<<<<<<<<<
@@ -1370,7 +1382,7 @@ static PyObject *__pyx_f_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filen
* """
*/
-static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1381,7 +1393,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_force_bytes", 0);
- /* "TabProxies.pyx":36
+ /* "pysam/TabProxies.pyx":36
* u"""convert string or unicode object to bytes, assuming ascii encoding.
* """
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -1391,7 +1403,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "TabProxies.pyx":37
+ /* "pysam/TabProxies.pyx":37
* """
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
@@ -1406,7 +1418,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
goto __pyx_L3;
}
- /* "TabProxies.pyx":38
+ /* "pysam/TabProxies.pyx":38
* if PY_MAJOR_VERSION < 3:
* return s
* elif s is None: # <<<<<<<<<<<<<<
@@ -1416,7 +1428,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = (__pyx_v_s == Py_None);
if (__pyx_t_1) {
- /* "TabProxies.pyx":39
+ /* "pysam/TabProxies.pyx":39
* return s
* elif s is None:
* return None # <<<<<<<<<<<<<<
@@ -1430,7 +1442,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
goto __pyx_L3;
}
- /* "TabProxies.pyx":40
+ /* "pysam/TabProxies.pyx":40
* elif s is None:
* return None
* elif PyBytes_Check(s): # <<<<<<<<<<<<<<
@@ -1440,7 +1452,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = PyBytes_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "TabProxies.pyx":41
+ /* "pysam/TabProxies.pyx":41
* return None
* elif PyBytes_Check(s):
* return s # <<<<<<<<<<<<<<
@@ -1455,7 +1467,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
goto __pyx_L3;
}
- /* "TabProxies.pyx":42
+ /* "pysam/TabProxies.pyx":42
* elif PyBytes_Check(s):
* return s
* elif PyUnicode_Check(s): # <<<<<<<<<<<<<<
@@ -1465,7 +1477,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = PyUnicode_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "TabProxies.pyx":43
+ /* "pysam/TabProxies.pyx":43
* return s
* elif PyUnicode_Check(s):
* return s.encode('ascii') # <<<<<<<<<<<<<<
@@ -1486,7 +1498,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
}
/*else*/ {
- /* "TabProxies.pyx":45
+ /* "pysam/TabProxies.pyx":45
* return s.encode('ascii')
* else:
* raise TypeError, u"Argument must be string, bytes or unicode." # <<<<<<<<<<<<<<
@@ -1503,7 +1515,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1511,7 +1523,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
return __pyx_r;
}
-/* "TabProxies.pyx":47
+/* "pysam/TabProxies.pyx":47
* raise TypeError, u"Argument must be string, bytes or unicode."
*
* cdef inline bytes _force_cmdline_bytes(object s): # <<<<<<<<<<<<<<
@@ -1519,7 +1531,7 @@ static PyObject *__pyx_f_10TabProxies__force_bytes(PyObject *__pyx_v_s) {
*
*/
-static CYTHON_INLINE PyObject *__pyx_f_10TabProxies__force_cmdline_bytes(PyObject *__pyx_v_s) {
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_10TabProxies__force_cmdline_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -1528,7 +1540,7 @@ static CYTHON_INLINE PyObject *__pyx_f_10TabProxies__force_cmdline_bytes(PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_force_cmdline_bytes", 0);
- /* "TabProxies.pyx":48
+ /* "pysam/TabProxies.pyx":48
*
* cdef inline bytes _force_cmdline_bytes(object s):
* return _force_bytes(s) # <<<<<<<<<<<<<<
@@ -1536,7 +1548,7 @@ static CYTHON_INLINE PyObject *__pyx_f_10TabProxies__force_cmdline_bytes(PyObjec
* cdef _charptr_to_str(char* s):
*/
__Pyx_XDECREF(((PyObject *)__pyx_r));
- __pyx_t_1 = ((PyObject *)__pyx_f_10TabProxies__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_10TabProxies__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
@@ -1546,7 +1558,7 @@ static CYTHON_INLINE PyObject *__pyx_f_10TabProxies__force_cmdline_bytes(PyObjec
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("TabProxies._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1554,7 +1566,7 @@ static CYTHON_INLINE PyObject *__pyx_f_10TabProxies__force_cmdline_bytes(PyObjec
return __pyx_r;
}
-/* "TabProxies.pyx":50
+/* "pysam/TabProxies.pyx":50
* return _force_bytes(s)
*
* cdef _charptr_to_str(char* s): # <<<<<<<<<<<<<<
@@ -1562,7 +1574,7 @@ static CYTHON_INLINE PyObject *__pyx_f_10TabProxies__force_cmdline_bytes(PyObjec
* return s
*/
-static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_10TabProxies__charptr_to_str(char *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1572,7 +1584,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_charptr_to_str", 0);
- /* "TabProxies.pyx":51
+ /* "pysam/TabProxies.pyx":51
*
* cdef _charptr_to_str(char* s):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -1582,7 +1594,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "TabProxies.pyx":52
+ /* "pysam/TabProxies.pyx":52
* cdef _charptr_to_str(char* s):
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
@@ -1599,7 +1611,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
}
/*else*/ {
- /* "TabProxies.pyx":54
+ /* "pysam/TabProxies.pyx":54
* return s
* else:
* return s.decode("ascii") # <<<<<<<<<<<<<<
@@ -1607,7 +1619,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
* cdef _force_str(object s):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, strlen(__pyx_v_s), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1619,7 +1631,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1627,7 +1639,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
return __pyx_r;
}
-/* "TabProxies.pyx":56
+/* "pysam/TabProxies.pyx":56
* return s.decode("ascii")
*
* cdef _force_str(object s): # <<<<<<<<<<<<<<
@@ -1635,7 +1647,7 @@ static PyObject *__pyx_f_10TabProxies__charptr_to_str(char *__pyx_v_s) {
* if s is None:
*/
-static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_10TabProxies__force_str(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1646,7 +1658,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_force_str", 0);
- /* "TabProxies.pyx":58
+ /* "pysam/TabProxies.pyx":58
* cdef _force_str(object s):
* """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
* if s is None: # <<<<<<<<<<<<<<
@@ -1656,7 +1668,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
__pyx_t_1 = (__pyx_v_s == Py_None);
if (__pyx_t_1) {
- /* "TabProxies.pyx":59
+ /* "pysam/TabProxies.pyx":59
* """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
* if s is None:
* return None # <<<<<<<<<<<<<<
@@ -1671,7 +1683,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
}
__pyx_L3:;
- /* "TabProxies.pyx":60
+ /* "pysam/TabProxies.pyx":60
* if s is None:
* return None
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -1681,7 +1693,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "TabProxies.pyx":61
+ /* "pysam/TabProxies.pyx":61
* return None
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
@@ -1695,7 +1707,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
goto __pyx_L4;
}
- /* "TabProxies.pyx":62
+ /* "pysam/TabProxies.pyx":62
* if PY_MAJOR_VERSION < 3:
* return s
* elif PyBytes_Check(s): # <<<<<<<<<<<<<<
@@ -1705,7 +1717,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
__pyx_t_1 = PyBytes_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "TabProxies.pyx":63
+ /* "pysam/TabProxies.pyx":63
* return s
* elif PyBytes_Check(s):
* return s.decode('ascii') # <<<<<<<<<<<<<<
@@ -1725,7 +1737,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
}
/*else*/ {
- /* "TabProxies.pyx":66
+ /* "pysam/TabProxies.pyx":66
* else:
* # assume unicode
* return s # <<<<<<<<<<<<<<
@@ -1744,7 +1756,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1752,7 +1764,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
return __pyx_r;
}
-/* "TabProxies.pyx":68
+/* "pysam/TabProxies.pyx":68
* return s
*
* cdef char * nextItem( char * buffer ): # <<<<<<<<<<<<<<
@@ -1760,7 +1772,7 @@ static PyObject *__pyx_f_10TabProxies__force_str(PyObject *__pyx_v_s) {
* pos = strchr( buffer, '\t' )
*/
-static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
+static char *__pyx_f_5pysam_10TabProxies_nextItem(char *__pyx_v_buffer) {
char *__pyx_v_pos;
char *__pyx_r;
__Pyx_RefNannyDeclarations
@@ -1772,7 +1784,7 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("nextItem", 0);
- /* "TabProxies.pyx":70
+ /* "pysam/TabProxies.pyx":70
* cdef char * nextItem( char * buffer ):
* cdef char * pos
* pos = strchr( buffer, '\t' ) # <<<<<<<<<<<<<<
@@ -1781,7 +1793,7 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
*/
__pyx_v_pos = strchr(__pyx_v_buffer, '\t');
- /* "TabProxies.pyx":71
+ /* "pysam/TabProxies.pyx":71
* cdef char * pos
* pos = strchr( buffer, '\t' )
* if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer ) # <<<<<<<<<<<<<<
@@ -1810,7 +1822,7 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
}
__pyx_L3:;
- /* "TabProxies.pyx":72
+ /* "pysam/TabProxies.pyx":72
* pos = strchr( buffer, '\t' )
* if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
* pos[0] = '\0' # <<<<<<<<<<<<<<
@@ -1819,7 +1831,7 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
*/
(__pyx_v_pos[0]) = '\x00';
- /* "TabProxies.pyx":73
+ /* "pysam/TabProxies.pyx":73
* if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
* pos[0] = '\0'
* pos += 1 # <<<<<<<<<<<<<<
@@ -1828,7 +1840,7 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
*/
__pyx_v_pos = (__pyx_v_pos + 1);
- /* "TabProxies.pyx":74
+ /* "pysam/TabProxies.pyx":74
* pos[0] = '\0'
* pos += 1
* return pos # <<<<<<<<<<<<<<
@@ -1843,14 +1855,14 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_WriteUnraisable("TabProxies.nextItem", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.TabProxies.nextItem", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":76
+/* "pysam/TabProxies.pyx":76
* return pos
*
* cdef char *StrOrEmpty( char * buffer ): # <<<<<<<<<<<<<<
@@ -1858,13 +1870,13 @@ static char *__pyx_f_10TabProxies_nextItem(char *__pyx_v_buffer) {
* else: return buffer
*/
-static char *__pyx_f_10TabProxies_StrOrEmpty(char *__pyx_v_buffer) {
+static char *__pyx_f_5pysam_10TabProxies_StrOrEmpty(char *__pyx_v_buffer) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_RefNannySetupContext("StrOrEmpty", 0);
- /* "TabProxies.pyx":77
+ /* "pysam/TabProxies.pyx":77
*
* cdef char *StrOrEmpty( char * buffer ):
* if buffer == NULL: return "" # <<<<<<<<<<<<<<
@@ -1879,7 +1891,7 @@ static char *__pyx_f_10TabProxies_StrOrEmpty(char *__pyx_v_buffer) {
}
/*else*/ {
- /* "TabProxies.pyx":78
+ /* "pysam/TabProxies.pyx":78
* cdef char *StrOrEmpty( char * buffer ):
* if buffer == NULL: return ""
* else: return buffer # <<<<<<<<<<<<<<
@@ -1897,7 +1909,7 @@ static char *__pyx_f_10TabProxies_StrOrEmpty(char *__pyx_v_buffer) {
return __pyx_r;
}
-/* "TabProxies.pyx":80
+/* "pysam/TabProxies.pyx":80
* else: return buffer
*
* cdef int isNew( char * p, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -1905,13 +1917,13 @@ static char *__pyx_f_10TabProxies_StrOrEmpty(char *__pyx_v_buffer) {
* return not (buffer <= p < buffer + nbytes )
*/
-static int __pyx_f_10TabProxies_isNew(char *__pyx_v_p, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static int __pyx_f_5pysam_10TabProxies_isNew(char *__pyx_v_p, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_RefNannySetupContext("isNew", 0);
- /* "TabProxies.pyx":81
+ /* "pysam/TabProxies.pyx":81
*
* cdef int isNew( char * p, char * buffer, size_t nbytes ):
* if p == NULL: return 0 # <<<<<<<<<<<<<<
@@ -1926,7 +1938,7 @@ static int __pyx_f_10TabProxies_isNew(char *__pyx_v_p, char *__pyx_v_buffer, siz
}
__pyx_L3:;
- /* "TabProxies.pyx":82
+ /* "pysam/TabProxies.pyx":82
* cdef int isNew( char * p, char * buffer, size_t nbytes ):
* if p == NULL: return 0
* return not (buffer <= p < buffer + nbytes ) # <<<<<<<<<<<<<<
@@ -1947,20 +1959,20 @@ static int __pyx_f_10TabProxies_isNew(char *__pyx_v_p, char *__pyx_v_buffer, siz
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_10TupleProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_10TabProxies_10TupleProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_5pysam_10TabProxies_10TupleProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_10TupleProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy___cinit__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy___cinit__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":95
+/* "pysam/TabProxies.pyx":95
* '''
*
* def __cinit__(self ): # <<<<<<<<<<<<<<
@@ -1968,12 +1980,12 @@ static int __pyx_pw_10TabProxies_10TupleProxy_1__cinit__(PyObject *__pyx_v_self,
* self.fields = NULL
*/
-static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self) {
+static int __pyx_pf_5pysam_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
- /* "TabProxies.pyx":96
+ /* "pysam/TabProxies.pyx":96
*
* def __cinit__(self ):
* self.data = NULL # <<<<<<<<<<<<<<
@@ -1982,7 +1994,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
*/
__pyx_v_self->data = NULL;
- /* "TabProxies.pyx":97
+ /* "pysam/TabProxies.pyx":97
* def __cinit__(self ):
* self.data = NULL
* self.fields = NULL # <<<<<<<<<<<<<<
@@ -1991,7 +2003,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
*/
__pyx_v_self->fields = NULL;
- /* "TabProxies.pyx":98
+ /* "pysam/TabProxies.pyx":98
* self.data = NULL
* self.fields = NULL
* self.index = 0 # <<<<<<<<<<<<<<
@@ -2000,7 +2012,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
*/
__pyx_v_self->index = 0;
- /* "TabProxies.pyx":99
+ /* "pysam/TabProxies.pyx":99
* self.fields = NULL
* self.index = 0
* self.nbytes = 0 # <<<<<<<<<<<<<<
@@ -2009,7 +2021,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
*/
__pyx_v_self->nbytes = 0;
- /* "TabProxies.pyx":100
+ /* "pysam/TabProxies.pyx":100
* self.index = 0
* self.nbytes = 0
* self.is_modified = 0 # <<<<<<<<<<<<<<
@@ -2018,7 +2030,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
*/
__pyx_v_self->is_modified = 0;
- /* "TabProxies.pyx":101
+ /* "pysam/TabProxies.pyx":101
* self.nbytes = 0
* self.is_modified = 0
* self.nfields = 0 # <<<<<<<<<<<<<<
@@ -2027,7 +2039,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
*/
__pyx_v_self->nfields = 0;
- /* "TabProxies.pyx":103
+ /* "pysam/TabProxies.pyx":103
* self.nfields = 0
* # start counting at field offset
* self.offset = 0 # <<<<<<<<<<<<<<
@@ -2042,15 +2054,15 @@ static int __pyx_pf_10TabProxies_10TupleProxy___cinit__(struct __pyx_obj_10TabPr
}
/* Python wrapper */
-static void __pyx_pw_10TabProxies_10TupleProxy_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_10TabProxies_10TupleProxy_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_5pysam_10TabProxies_10TupleProxy_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_10TabProxies_10TupleProxy_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self));
+ __pyx_pf_5pysam_10TabProxies_10TupleProxy_2__dealloc__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
}
-/* "TabProxies.pyx":105
+/* "pysam/TabProxies.pyx":105
* self.offset = 0
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -2058,7 +2070,7 @@ static void __pyx_pw_10TabProxies_10TupleProxy_3__dealloc__(PyObject *__pyx_v_se
* if self.is_modified:
*/
-static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self) {
+static void __pyx_pf_5pysam_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self) {
int __pyx_v_x;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -2066,7 +2078,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
int __pyx_t_3;
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "TabProxies.pyx":107
+ /* "pysam/TabProxies.pyx":107
* def __dealloc__(self):
* cdef int x
* if self.is_modified: # <<<<<<<<<<<<<<
@@ -2075,7 +2087,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
*/
if (__pyx_v_self->is_modified) {
- /* "TabProxies.pyx":108
+ /* "pysam/TabProxies.pyx":108
* cdef int x
* if self.is_modified:
* for x from 0 <= x < self.nfields: # <<<<<<<<<<<<<<
@@ -2085,17 +2097,17 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
__pyx_t_1 = __pyx_v_self->nfields;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_1; __pyx_v_x++) {
- /* "TabProxies.pyx":109
+ /* "pysam/TabProxies.pyx":109
* if self.is_modified:
* for x from 0 <= x < self.nfields:
* if isNew( self.fields[x], self.data, self.nbytes ): # <<<<<<<<<<<<<<
* free( self.fields[x] )
* self.fields[x] = NULL
*/
- __pyx_t_2 = __pyx_f_10TabProxies_isNew((__pyx_v_self->fields[__pyx_v_x]), __pyx_v_self->data, __pyx_v_self->nbytes);
+ __pyx_t_2 = __pyx_f_5pysam_10TabProxies_isNew((__pyx_v_self->fields[__pyx_v_x]), __pyx_v_self->data, __pyx_v_self->nbytes);
if (__pyx_t_2) {
- /* "TabProxies.pyx":110
+ /* "pysam/TabProxies.pyx":110
* for x from 0 <= x < self.nfields:
* if isNew( self.fields[x], self.data, self.nbytes ):
* free( self.fields[x] ) # <<<<<<<<<<<<<<
@@ -2104,7 +2116,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
*/
free((__pyx_v_self->fields[__pyx_v_x]));
- /* "TabProxies.pyx":111
+ /* "pysam/TabProxies.pyx":111
* if isNew( self.fields[x], self.data, self.nbytes ):
* free( self.fields[x] )
* self.fields[x] = NULL # <<<<<<<<<<<<<<
@@ -2120,7 +2132,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
}
__pyx_L3:;
- /* "TabProxies.pyx":113
+ /* "pysam/TabProxies.pyx":113
* self.fields[x] = NULL
*
* if self.data != NULL: free(self.data) # <<<<<<<<<<<<<<
@@ -2134,7 +2146,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
}
__pyx_L7:;
- /* "TabProxies.pyx":114
+ /* "pysam/TabProxies.pyx":114
*
* if self.data != NULL: free(self.data)
* if self.fields != NULL: free( self.fields ) # <<<<<<<<<<<<<<
@@ -2151,7 +2163,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
__Pyx_RefNannyFinishContext();
}
-/* "TabProxies.pyx":116
+/* "pysam/TabProxies.pyx":116
* if self.fields != NULL: free( self.fields )
*
* cdef take( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -2159,7 +2171,7 @@ static void __pyx_pf_10TabProxies_10TupleProxy_2__dealloc__(struct __pyx_obj_10T
*
*/
-static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static PyObject *__pyx_f_5pysam_10TabProxies_10TupleProxy_take(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -2168,7 +2180,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabPr
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("take", 0);
- /* "TabProxies.pyx":121
+ /* "pysam/TabProxies.pyx":121
* Take ownership of the pointer.
* '''
* self.data = buffer # <<<<<<<<<<<<<<
@@ -2177,7 +2189,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabPr
*/
__pyx_v_self->data = __pyx_v_buffer;
- /* "TabProxies.pyx":122
+ /* "pysam/TabProxies.pyx":122
* '''
* self.data = buffer
* self.nbytes = nbytes # <<<<<<<<<<<<<<
@@ -2186,14 +2198,14 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabPr
*/
__pyx_v_self->nbytes = __pyx_v_nbytes;
- /* "TabProxies.pyx":123
+ /* "pysam/TabProxies.pyx":123
* self.data = buffer
* self.nbytes = nbytes
* self.update( buffer, nbytes ) # <<<<<<<<<<<<<<
*
* cdef present( self, char * buffer, size_t nbytes ):
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->update(__pyx_v_self, __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->update(__pyx_v_self, __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -2201,7 +2213,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabPr
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("TabProxies.TupleProxy.take", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.take", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2209,7 +2221,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabPr
return __pyx_r;
}
-/* "TabProxies.pyx":125
+/* "pysam/TabProxies.pyx":125
* self.update( buffer, nbytes )
*
* cdef present( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -2217,7 +2229,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_take(struct __pyx_obj_10TabPr
*
*/
-static PyObject *__pyx_f_10TabProxies_10TupleProxy_present(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static PyObject *__pyx_f_5pysam_10TabProxies_10TupleProxy_present(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -2226,14 +2238,14 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_present(struct __pyx_obj_10Ta
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("present", 0);
- /* "TabProxies.pyx":130
+ /* "pysam/TabProxies.pyx":130
* Do not take ownership of the pointer.
* '''
* self.update( buffer, nbytes ) # <<<<<<<<<<<<<<
*
* cdef copy( self, char * buffer, size_t nbytes ):
*/
- __pyx_t_1 = ((struct __pyx_vtabstruct_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->update(__pyx_v_self, __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->update(__pyx_v_self, __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -2241,7 +2253,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_present(struct __pyx_obj_10Ta
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("TabProxies.TupleProxy.present", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.present", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2249,7 +2261,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_present(struct __pyx_obj_10Ta
return __pyx_r;
}
-/* "TabProxies.pyx":132
+/* "pysam/TabProxies.pyx":132
* self.update( buffer, nbytes )
*
* cdef copy( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -2257,7 +2269,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_present(struct __pyx_obj_10Ta
*
*/
-static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static PyObject *__pyx_f_5pysam_10TabProxies_10TupleProxy_copy(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
int __pyx_v_s;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -2268,7 +2280,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("copy", 0);
- /* "TabProxies.pyx":141
+ /* "pysam/TabProxies.pyx":141
* cdef int s
* # +1 for '\0'
* s = sizeof(char) * (nbytes + 1) # <<<<<<<<<<<<<<
@@ -2277,7 +2289,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
*/
__pyx_v_s = ((sizeof(char)) * (__pyx_v_nbytes + 1));
- /* "TabProxies.pyx":142
+ /* "pysam/TabProxies.pyx":142
* # +1 for '\0'
* s = sizeof(char) * (nbytes + 1)
* self.data = <char*>malloc( s ) # <<<<<<<<<<<<<<
@@ -2286,7 +2298,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
*/
__pyx_v_self->data = ((char *)malloc(__pyx_v_s));
- /* "TabProxies.pyx":143
+ /* "pysam/TabProxies.pyx":143
* s = sizeof(char) * (nbytes + 1)
* self.data = <char*>malloc( s )
* if self.data == NULL: # <<<<<<<<<<<<<<
@@ -2296,7 +2308,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
__pyx_t_1 = (__pyx_v_self->data == NULL);
if (__pyx_t_1) {
- /* "TabProxies.pyx":144
+ /* "pysam/TabProxies.pyx":144
* self.data = <char*>malloc( s )
* if self.data == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
@@ -2312,7 +2324,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
}
__pyx_L3:;
- /* "TabProxies.pyx":145
+ /* "pysam/TabProxies.pyx":145
* if self.data == NULL:
* raise ValueError("out of memory" )
* self.nbytes = nbytes # <<<<<<<<<<<<<<
@@ -2321,7 +2333,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
*/
__pyx_v_self->nbytes = __pyx_v_nbytes;
- /* "TabProxies.pyx":146
+ /* "pysam/TabProxies.pyx":146
* raise ValueError("out of memory" )
* self.nbytes = nbytes
* memcpy( <char*>self.data, buffer, s ) # <<<<<<<<<<<<<<
@@ -2330,14 +2342,14 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
*/
memcpy(((char *)__pyx_v_self->data), __pyx_v_buffer, __pyx_v_s);
- /* "TabProxies.pyx":147
+ /* "pysam/TabProxies.pyx":147
* self.nbytes = nbytes
* memcpy( <char*>self.data, buffer, s )
* self.update( self.data, nbytes ) # <<<<<<<<<<<<<<
*
* cdef int getMaxFields( self, size_t nbytes ):
*/
- __pyx_t_2 = ((struct __pyx_vtabstruct_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->update(__pyx_v_self, __pyx_v_self->data, __pyx_v_nbytes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->update(__pyx_v_self, __pyx_v_self->data, __pyx_v_nbytes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2345,7 +2357,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.TupleProxy.copy", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.copy", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2353,7 +2365,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
return __pyx_r;
}
-/* "TabProxies.pyx":149
+/* "pysam/TabProxies.pyx":149
* self.update( self.data, nbytes )
*
* cdef int getMaxFields( self, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -2361,12 +2373,12 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_copy(struct __pyx_obj_10TabPr
* return nbytes / 2
*/
-static int __pyx_f_10TabProxies_10TupleProxy_getMaxFields(CYTHON_UNUSED struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, size_t __pyx_v_nbytes) {
+static int __pyx_f_5pysam_10TabProxies_10TupleProxy_getMaxFields(CYTHON_UNUSED struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, size_t __pyx_v_nbytes) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getMaxFields", 0);
- /* "TabProxies.pyx":151
+ /* "pysam/TabProxies.pyx":151
* cdef int getMaxFields( self, size_t nbytes ):
* '''initialize fields.'''
* return nbytes / 2 # <<<<<<<<<<<<<<
@@ -2382,7 +2394,7 @@ static int __pyx_f_10TabProxies_10TupleProxy_getMaxFields(CYTHON_UNUSED struct _
return __pyx_r;
}
-/* "TabProxies.pyx":153
+/* "pysam/TabProxies.pyx":153
* return nbytes / 2
*
* cdef update( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -2390,7 +2402,7 @@ static int __pyx_f_10TabProxies_10TupleProxy_getMaxFields(CYTHON_UNUSED struct _
*
*/
-static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static PyObject *__pyx_f_5pysam_10TabProxies_10TupleProxy_update(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
char *__pyx_v_pos;
char *__pyx_v_old_pos;
int __pyx_v_field;
@@ -2411,7 +2423,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("update", 0);
- /* "TabProxies.pyx":173
+ /* "pysam/TabProxies.pyx":173
* cdef int max_fields, x
*
* assert strlen(buffer) == nbytes # <<<<<<<<<<<<<<
@@ -2425,7 +2437,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
#endif
- /* "TabProxies.pyx":175
+ /* "pysam/TabProxies.pyx":175
* assert strlen(buffer) == nbytes
*
* if buffer[nbytes] != 0: # <<<<<<<<<<<<<<
@@ -2435,7 +2447,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_t_1 = ((__pyx_v_buffer[__pyx_v_nbytes]) != 0);
if (__pyx_t_1) {
- /* "TabProxies.pyx":176
+ /* "pysam/TabProxies.pyx":176
*
* if buffer[nbytes] != 0:
* raise ValueError( "incomplete line at %s" % buffer ) # <<<<<<<<<<<<<<
@@ -2462,7 +2474,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L3:;
- /* "TabProxies.pyx":180
+ /* "pysam/TabProxies.pyx":180
* #################################
* # remove line breaks and feeds and update number of bytes
* x = nbytes - 1 # <<<<<<<<<<<<<<
@@ -2471,7 +2483,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_x = (__pyx_v_nbytes - 1);
- /* "TabProxies.pyx":181
+ /* "pysam/TabProxies.pyx":181
* # remove line breaks and feeds and update number of bytes
* x = nbytes - 1
* while x > 0 and (buffer[x] == '\n' or buffer[x] == '\r'): # <<<<<<<<<<<<<<
@@ -2494,7 +2506,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
if (!__pyx_t_4) break;
- /* "TabProxies.pyx":182
+ /* "pysam/TabProxies.pyx":182
* x = nbytes - 1
* while x > 0 and (buffer[x] == '\n' or buffer[x] == '\r'):
* buffer[x] = '\0' # <<<<<<<<<<<<<<
@@ -2503,7 +2515,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
(__pyx_v_buffer[__pyx_v_x]) = '\x00';
- /* "TabProxies.pyx":183
+ /* "pysam/TabProxies.pyx":183
* while x > 0 and (buffer[x] == '\n' or buffer[x] == '\r'):
* buffer[x] = '\0'
* x -= 1 # <<<<<<<<<<<<<<
@@ -2513,7 +2525,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_v_x = (__pyx_v_x - 1);
}
- /* "TabProxies.pyx":184
+ /* "pysam/TabProxies.pyx":184
* buffer[x] = '\0'
* x -= 1
* self.nbytes = x + 1 # <<<<<<<<<<<<<<
@@ -2522,7 +2534,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_self->nbytes = (__pyx_v_x + 1);
- /* "TabProxies.pyx":188
+ /* "pysam/TabProxies.pyx":188
* #################################
* # clear data
* if self.fields != NULL: free(self.fields) # <<<<<<<<<<<<<<
@@ -2536,7 +2548,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L6:;
- /* "TabProxies.pyx":190
+ /* "pysam/TabProxies.pyx":190
* if self.fields != NULL: free(self.fields)
*
* for field from 0 <= field < self.nfields: # <<<<<<<<<<<<<<
@@ -2546,17 +2558,17 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_t_7 = __pyx_v_self->nfields;
for (__pyx_v_field = 0; __pyx_v_field < __pyx_t_7; __pyx_v_field++) {
- /* "TabProxies.pyx":191
+ /* "pysam/TabProxies.pyx":191
*
* for field from 0 <= field < self.nfields:
* if isNew( self.fields[field], self.data, self.nbytes ): # <<<<<<<<<<<<<<
* free( self.fields[field] )
*
*/
- __pyx_t_8 = __pyx_f_10TabProxies_isNew((__pyx_v_self->fields[__pyx_v_field]), __pyx_v_self->data, __pyx_v_self->nbytes);
+ __pyx_t_8 = __pyx_f_5pysam_10TabProxies_isNew((__pyx_v_self->fields[__pyx_v_field]), __pyx_v_self->data, __pyx_v_self->nbytes);
if (__pyx_t_8) {
- /* "TabProxies.pyx":192
+ /* "pysam/TabProxies.pyx":192
* for field from 0 <= field < self.nfields:
* if isNew( self.fields[field], self.data, self.nbytes ):
* free( self.fields[field] ) # <<<<<<<<<<<<<<
@@ -2569,7 +2581,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_L9:;
}
- /* "TabProxies.pyx":194
+ /* "pysam/TabProxies.pyx":194
* free( self.fields[field] )
*
* self.is_modified = self.nfields = 0 # <<<<<<<<<<<<<<
@@ -2579,16 +2591,16 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_v_self->is_modified = 0;
__pyx_v_self->nfields = 0;
- /* "TabProxies.pyx":198
+ /* "pysam/TabProxies.pyx":198
* #################################
* # allocate new
* max_fields = self.getMaxFields( nbytes ) # <<<<<<<<<<<<<<
* self.fields = <char **>calloc( max_fields, sizeof(char *) )
* if self.fields == NULL:
*/
- __pyx_v_max_fields = ((struct __pyx_vtabstruct_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->getMaxFields(__pyx_v_self, __pyx_v_nbytes);
+ __pyx_v_max_fields = ((struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *)__pyx_v_self->__pyx_vtab)->getMaxFields(__pyx_v_self, __pyx_v_nbytes);
- /* "TabProxies.pyx":199
+ /* "pysam/TabProxies.pyx":199
* # allocate new
* max_fields = self.getMaxFields( nbytes )
* self.fields = <char **>calloc( max_fields, sizeof(char *) ) # <<<<<<<<<<<<<<
@@ -2597,7 +2609,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_self->fields = ((char **)calloc(__pyx_v_max_fields, (sizeof(char *))));
- /* "TabProxies.pyx":200
+ /* "pysam/TabProxies.pyx":200
* max_fields = self.getMaxFields( nbytes )
* self.fields = <char **>calloc( max_fields, sizeof(char *) )
* if self.fields == NULL: # <<<<<<<<<<<<<<
@@ -2607,7 +2619,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_t_4 = (__pyx_v_self->fields == NULL);
if (__pyx_t_4) {
- /* "TabProxies.pyx":201
+ /* "pysam/TabProxies.pyx":201
* self.fields = <char **>calloc( max_fields, sizeof(char *) )
* if self.fields == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
@@ -2623,7 +2635,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L10:;
- /* "TabProxies.pyx":205
+ /* "pysam/TabProxies.pyx":205
* #################################
* # start filling
* field = 0 # <<<<<<<<<<<<<<
@@ -2632,7 +2644,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_field = 0;
- /* "TabProxies.pyx":206
+ /* "pysam/TabProxies.pyx":206
* # start filling
* field = 0
* self.fields[field] = pos = buffer # <<<<<<<<<<<<<<
@@ -2642,7 +2654,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
(__pyx_v_self->fields[__pyx_v_field]) = __pyx_v_buffer;
__pyx_v_pos = __pyx_v_buffer;
- /* "TabProxies.pyx":207
+ /* "pysam/TabProxies.pyx":207
* field = 0
* self.fields[field] = pos = buffer
* field += 1 # <<<<<<<<<<<<<<
@@ -2651,7 +2663,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_field = (__pyx_v_field + 1);
- /* "TabProxies.pyx":208
+ /* "pysam/TabProxies.pyx":208
* self.fields[field] = pos = buffer
* field += 1
* old_pos = pos # <<<<<<<<<<<<<<
@@ -2660,7 +2672,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_old_pos = __pyx_v_pos;
- /* "TabProxies.pyx":210
+ /* "pysam/TabProxies.pyx":210
* old_pos = pos
*
* while 1: # <<<<<<<<<<<<<<
@@ -2670,7 +2682,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
while (1) {
if (!1) break;
- /* "TabProxies.pyx":212
+ /* "pysam/TabProxies.pyx":212
* while 1:
*
* pos = <char*>memchr( pos, '\t', nbytes ) # <<<<<<<<<<<<<<
@@ -2679,7 +2691,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_pos = ((char *)memchr(__pyx_v_pos, '\t', __pyx_v_nbytes));
- /* "TabProxies.pyx":213
+ /* "pysam/TabProxies.pyx":213
*
* pos = <char*>memchr( pos, '\t', nbytes )
* if pos == NULL: break # <<<<<<<<<<<<<<
@@ -2693,7 +2705,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L13:;
- /* "TabProxies.pyx":214
+ /* "pysam/TabProxies.pyx":214
* pos = <char*>memchr( pos, '\t', nbytes )
* if pos == NULL: break
* pos[0] = '\0' # <<<<<<<<<<<<<<
@@ -2702,7 +2714,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
(__pyx_v_pos[0]) = '\x00';
- /* "TabProxies.pyx":215
+ /* "pysam/TabProxies.pyx":215
* if pos == NULL: break
* pos[0] = '\0'
* pos += 1 # <<<<<<<<<<<<<<
@@ -2711,7 +2723,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_pos = (__pyx_v_pos + 1);
- /* "TabProxies.pyx":216
+ /* "pysam/TabProxies.pyx":216
* pos[0] = '\0'
* pos += 1
* self.fields[field] = pos # <<<<<<<<<<<<<<
@@ -2720,7 +2732,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
(__pyx_v_self->fields[__pyx_v_field]) = __pyx_v_pos;
- /* "TabProxies.pyx":217
+ /* "pysam/TabProxies.pyx":217
* pos += 1
* self.fields[field] = pos
* field += 1 # <<<<<<<<<<<<<<
@@ -2729,7 +2741,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_field = (__pyx_v_field + 1);
- /* "TabProxies.pyx":218
+ /* "pysam/TabProxies.pyx":218
* self.fields[field] = pos
* field += 1
* if field > max_fields: # <<<<<<<<<<<<<<
@@ -2739,7 +2751,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_t_4 = (__pyx_v_field > __pyx_v_max_fields);
if (__pyx_t_4) {
- /* "TabProxies.pyx":219
+ /* "pysam/TabProxies.pyx":219
* field += 1
* if field > max_fields:
* raise ValueError("row too large - more than %i fields" % max_fields ) # <<<<<<<<<<<<<<
@@ -2766,7 +2778,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L14:;
- /* "TabProxies.pyx":220
+ /* "pysam/TabProxies.pyx":220
* if field > max_fields:
* raise ValueError("row too large - more than %i fields" % max_fields )
* nbytes -= pos - old_pos # <<<<<<<<<<<<<<
@@ -2775,7 +2787,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
*/
__pyx_v_nbytes = (__pyx_v_nbytes - (__pyx_v_pos - __pyx_v_old_pos));
- /* "TabProxies.pyx":221
+ /* "pysam/TabProxies.pyx":221
* raise ValueError("row too large - more than %i fields" % max_fields )
* nbytes -= pos - old_pos
* if nbytes < 0: break # <<<<<<<<<<<<<<
@@ -2789,7 +2801,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L15:;
- /* "TabProxies.pyx":222
+ /* "pysam/TabProxies.pyx":222
* nbytes -= pos - old_pos
* if nbytes < 0: break
* old_pos = pos # <<<<<<<<<<<<<<
@@ -2800,7 +2812,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
__pyx_L12_break:;
- /* "TabProxies.pyx":224
+ /* "pysam/TabProxies.pyx":224
* old_pos = pos
*
* self.nfields = field # <<<<<<<<<<<<<<
@@ -2814,7 +2826,7 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.TupleProxy.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2823,9 +2835,9 @@ static PyObject *__pyx_f_10TabProxies_10TupleProxy_update(struct __pyx_obj_10Tab
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_5_getindex(PyObject *__pyx_v_self, PyObject *__pyx_arg_index); /*proto*/
-static char __pyx_doc_10TabProxies_10TupleProxy_4_getindex[] = "return item at idx index";
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_5_getindex(PyObject *__pyx_v_self, PyObject *__pyx_arg_index) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_5_getindex(PyObject *__pyx_v_self, PyObject *__pyx_arg_index); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_10TupleProxy_4_getindex[] = "return item at idx index";
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_5_getindex(PyObject *__pyx_v_self, PyObject *__pyx_arg_index) {
int __pyx_v_index;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
@@ -2835,16 +2847,16 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_5_getindex(PyObject *__pyx_v
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L3_error:;
- __Pyx_AddTraceback("TabProxies.TupleProxy._getindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy._getindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_4_getindex(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), ((int)__pyx_v_index));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_4_getindex(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), ((int)__pyx_v_index));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":226
+/* "pysam/TabProxies.pyx":226
* self.nfields = field
*
* def _getindex( self, int index ): # <<<<<<<<<<<<<<
@@ -2852,7 +2864,7 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_5_getindex(PyObject *__pyx_v
* cdef int i = index
*/
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, int __pyx_v_index) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, int __pyx_v_index) {
int __pyx_v_i;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -2865,7 +2877,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_getindex", 0);
- /* "TabProxies.pyx":228
+ /* "pysam/TabProxies.pyx":228
* def _getindex( self, int index ):
* '''return item at idx index'''
* cdef int i = index # <<<<<<<<<<<<<<
@@ -2874,7 +2886,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
*/
__pyx_v_i = __pyx_v_index;
- /* "TabProxies.pyx":229
+ /* "pysam/TabProxies.pyx":229
* '''return item at idx index'''
* cdef int i = index
* if i < 0: i += self.nfields # <<<<<<<<<<<<<<
@@ -2888,7 +2900,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
}
__pyx_L3:;
- /* "TabProxies.pyx":230
+ /* "pysam/TabProxies.pyx":230
* cdef int i = index
* if i < 0: i += self.nfields
* if i < 0: raise IndexError( "list index out of range" ) # <<<<<<<<<<<<<<
@@ -2906,7 +2918,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
}
__pyx_L4:;
- /* "TabProxies.pyx":231
+ /* "pysam/TabProxies.pyx":231
* if i < 0: i += self.nfields
* if i < 0: raise IndexError( "list index out of range" )
* i += self.offset # <<<<<<<<<<<<<<
@@ -2915,7 +2927,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
*/
__pyx_v_i = (__pyx_v_i + __pyx_v_self->offset);
- /* "TabProxies.pyx":232
+ /* "pysam/TabProxies.pyx":232
* if i < 0: raise IndexError( "list index out of range" )
* i += self.offset
* if i >= self.nfields: # <<<<<<<<<<<<<<
@@ -2925,7 +2937,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
__pyx_t_1 = (__pyx_v_i >= __pyx_v_self->nfields);
if (__pyx_t_1) {
- /* "TabProxies.pyx":233
+ /* "pysam/TabProxies.pyx":233
* i += self.offset
* if i >= self.nfields:
* raise IndexError( "list index out of range %i >= %i" % (i, self.nfields )) # <<<<<<<<<<<<<<
@@ -2962,7 +2974,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
}
__pyx_L5:;
- /* "TabProxies.pyx":234
+ /* "pysam/TabProxies.pyx":234
* if i >= self.nfields:
* raise IndexError( "list index out of range %i >= %i" % (i, self.nfields ))
* return self.fields[i] # <<<<<<<<<<<<<<
@@ -2982,7 +2994,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("TabProxies.TupleProxy._getindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy._getindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2991,17 +3003,17 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_4_getindex(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_7__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_7__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_6__getitem__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_6__getitem__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":236
+/* "pysam/TabProxies.pyx":236
* return self.fields[i]
*
* def __getitem__( self, key ): # <<<<<<<<<<<<<<
@@ -3009,7 +3021,7 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_7__getitem__(PyObject *__pyx
* # slice object
*/
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_key) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_key) {
PyObject *__pyx_v_start = NULL;
PyObject *__pyx_v_end = NULL;
PyObject *__pyx_v_step = NULL;
@@ -3032,15 +3044,14 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__getitem__", 0);
- /* "TabProxies.pyx":237
+ /* "pysam/TabProxies.pyx":237
*
* def __getitem__( self, key ):
* if type(key) == int: return self._getindex( key ) # <<<<<<<<<<<<<<
* # slice object
* start, end, step = key.indices( self.nfields )
*/
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_key)), ((PyObject *)((PyObject*)(&PyInt_Type))), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_key)), ((PyObject *)((PyObject*)(&PyInt_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
@@ -3063,7 +3074,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
}
__pyx_L3:;
- /* "TabProxies.pyx":239
+ /* "pysam/TabProxies.pyx":239
* if type(key) == int: return self._getindex( key )
* # slice object
* start, end, step = key.indices( self.nfields ) # <<<<<<<<<<<<<<
@@ -3085,21 +3096,22 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 3)) {
+ if (size > 3) __Pyx_RaiseTooManyValuesError(3);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
- if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_4 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_5 = PyTuple_GET_ITEM(sequence, 2);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
- if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_4 = PyList_GET_ITEM(sequence, 1);
__pyx_t_5 = PyList_GET_ITEM(sequence, 2);
@@ -3107,8 +3119,17 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_4);
__Pyx_INCREF(__pyx_t_5);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_5 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ #endif
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
__pyx_t_6 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
@@ -3121,12 +3142,13 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
index = 2; __pyx_t_5 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_5)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_5);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L5_unpacking_done;
__pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_7 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
}
@@ -3137,7 +3159,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
__pyx_v_step = __pyx_t_5;
__pyx_t_5 = 0;
- /* "TabProxies.pyx":240
+ /* "pysam/TabProxies.pyx":240
* # slice object
* start, end, step = key.indices( self.nfields )
* result = [] # <<<<<<<<<<<<<<
@@ -3146,10 +3168,10 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
*/
__pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_v_result = __pyx_t_3;
+ __pyx_v_result = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "TabProxies.pyx":241
+ /* "pysam/TabProxies.pyx":241
* start, end, step = key.indices( self.nfields )
* result = []
* for index in range( start, end, step ): # <<<<<<<<<<<<<<
@@ -3182,10 +3204,18 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
for (;;) {
if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_3)) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_5 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_5 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_3, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_3)) {
if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_8); __Pyx_INCREF(__pyx_t_5); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_3, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_5 = __pyx_t_9(__pyx_t_3);
if (unlikely(!__pyx_t_5)) {
@@ -3201,7 +3231,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
__pyx_v_index = __pyx_t_5;
__pyx_t_5 = 0;
- /* "TabProxies.pyx":242
+ /* "pysam/TabProxies.pyx":242
* result = []
* for index in range( start, end, step ):
* result.append( self._getindex( index ) ) # <<<<<<<<<<<<<<
@@ -3224,7 +3254,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "TabProxies.pyx":243
+ /* "pysam/TabProxies.pyx":243
* for index in range( start, end, step ):
* result.append( self._getindex( index ) )
* return result # <<<<<<<<<<<<<<
@@ -3244,7 +3274,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("TabProxies.TupleProxy.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_start);
@@ -3258,16 +3288,16 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_6__getitem__(struct __pyx_ob
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_10TabProxies_10TupleProxy_8_setindex[] = "set item at idx index.";
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_10TupleProxy_8_setindex[] = "set item at idx index.";
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_index = 0;
PyObject *__pyx_v_value = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__index,&__pyx_n_s__value,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_setindex (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__index,&__pyx_n_s__value,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -3281,12 +3311,10 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__index);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__index)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("_setindex", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -3307,16 +3335,16 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("_setindex", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("TabProxies.TupleProxy._setindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy._setindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_8_setindex(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_index, __pyx_v_value);
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_8_setindex(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_index, __pyx_v_value);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":245
+/* "pysam/TabProxies.pyx":245
* return result
*
* def _setindex( self, index, value ): # <<<<<<<<<<<<<<
@@ -3324,7 +3352,7 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_9_setindex(PyObject *__pyx_v
* cdef int idx = index
*/
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value) {
int __pyx_v_idx;
char *__pyx_v_tmp;
PyObject *__pyx_r = NULL;
@@ -3339,7 +3367,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
__Pyx_RefNannySetupContext("_setindex", 0);
__Pyx_INCREF(__pyx_v_value);
- /* "TabProxies.pyx":247
+ /* "pysam/TabProxies.pyx":247
* def _setindex( self, index, value ):
* '''set item at idx index.'''
* cdef int idx = index # <<<<<<<<<<<<<<
@@ -3349,7 +3377,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
__pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_index); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_idx = __pyx_t_1;
- /* "TabProxies.pyx":248
+ /* "pysam/TabProxies.pyx":248
* '''set item at idx index.'''
* cdef int idx = index
* if idx < 0: raise IndexError( "list index out of range" ) # <<<<<<<<<<<<<<
@@ -3367,7 +3395,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
}
__pyx_L3:;
- /* "TabProxies.pyx":249
+ /* "pysam/TabProxies.pyx":249
* cdef int idx = index
* if idx < 0: raise IndexError( "list index out of range" )
* if idx >= self.nfields: # <<<<<<<<<<<<<<
@@ -3377,7 +3405,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
__pyx_t_2 = (__pyx_v_idx >= __pyx_v_self->nfields);
if (__pyx_t_2) {
- /* "TabProxies.pyx":250
+ /* "pysam/TabProxies.pyx":250
* if idx < 0: raise IndexError( "list index out of range" )
* if idx >= self.nfields:
* raise IndexError( "list index out of range" ) # <<<<<<<<<<<<<<
@@ -3393,17 +3421,17 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
}
__pyx_L4:;
- /* "TabProxies.pyx":252
+ /* "pysam/TabProxies.pyx":252
* raise IndexError( "list index out of range" )
*
* if isNew( self.fields[idx], self.data, self.nbytes ): # <<<<<<<<<<<<<<
* free( self.fields[idx] )
*
*/
- __pyx_t_1 = __pyx_f_10TabProxies_isNew((__pyx_v_self->fields[__pyx_v_idx]), __pyx_v_self->data, __pyx_v_self->nbytes);
+ __pyx_t_1 = __pyx_f_5pysam_10TabProxies_isNew((__pyx_v_self->fields[__pyx_v_idx]), __pyx_v_self->data, __pyx_v_self->nbytes);
if (__pyx_t_1) {
- /* "TabProxies.pyx":253
+ /* "pysam/TabProxies.pyx":253
*
* if isNew( self.fields[idx], self.data, self.nbytes ):
* free( self.fields[idx] ) # <<<<<<<<<<<<<<
@@ -3415,7 +3443,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
}
__pyx_L5:;
- /* "TabProxies.pyx":255
+ /* "pysam/TabProxies.pyx":255
* free( self.fields[idx] )
*
* self.is_modified = 1 # <<<<<<<<<<<<<<
@@ -3424,20 +3452,19 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
*/
__pyx_v_self->is_modified = 1;
- /* "TabProxies.pyx":257
+ /* "pysam/TabProxies.pyx":257
* self.is_modified = 1
*
* if value == None: # <<<<<<<<<<<<<<
* self.fields[idx] = NULL
* return
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_value, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_value, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_2) {
- /* "TabProxies.pyx":258
+ /* "pysam/TabProxies.pyx":258
*
* if value == None:
* self.fields[idx] = NULL # <<<<<<<<<<<<<<
@@ -3446,7 +3473,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
*/
(__pyx_v_self->fields[__pyx_v_idx]) = NULL;
- /* "TabProxies.pyx":259
+ /* "pysam/TabProxies.pyx":259
* if value == None:
* self.fields[idx] = NULL
* return # <<<<<<<<<<<<<<
@@ -3460,20 +3487,20 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
}
__pyx_L6:;
- /* "TabProxies.pyx":262
+ /* "pysam/TabProxies.pyx":262
*
* # conversion with error checking
* value = _force_bytes(value) # <<<<<<<<<<<<<<
* cdef char * tmp = <char*>value
* self.fields[idx] = <char*>malloc( (strlen( tmp ) + 1) * sizeof(char) )
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_10TabProxies__force_bytes(__pyx_v_value)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_10TabProxies__force_bytes(__pyx_v_value)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
- /* "TabProxies.pyx":263
+ /* "pysam/TabProxies.pyx":263
* # conversion with error checking
* value = _force_bytes(value)
* cdef char * tmp = <char*>value # <<<<<<<<<<<<<<
@@ -3483,7 +3510,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
__pyx_t_4 = PyBytes_AsString(__pyx_v_value); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_tmp = ((char *)__pyx_t_4);
- /* "TabProxies.pyx":264
+ /* "pysam/TabProxies.pyx":264
* value = _force_bytes(value)
* cdef char * tmp = <char*>value
* self.fields[idx] = <char*>malloc( (strlen( tmp ) + 1) * sizeof(char) ) # <<<<<<<<<<<<<<
@@ -3492,7 +3519,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
*/
(__pyx_v_self->fields[__pyx_v_idx]) = ((char *)malloc(((strlen(__pyx_v_tmp) + 1) * (sizeof(char)))));
- /* "TabProxies.pyx":265
+ /* "pysam/TabProxies.pyx":265
* cdef char * tmp = <char*>value
* self.fields[idx] = <char*>malloc( (strlen( tmp ) + 1) * sizeof(char) )
* if self.fields[idx] == NULL: # <<<<<<<<<<<<<<
@@ -3502,7 +3529,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
__pyx_t_2 = ((__pyx_v_self->fields[__pyx_v_idx]) == NULL);
if (__pyx_t_2) {
- /* "TabProxies.pyx":266
+ /* "pysam/TabProxies.pyx":266
* self.fields[idx] = <char*>malloc( (strlen( tmp ) + 1) * sizeof(char) )
* if self.fields[idx] == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
@@ -3518,7 +3545,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
}
__pyx_L7:;
- /* "TabProxies.pyx":267
+ /* "pysam/TabProxies.pyx":267
* if self.fields[idx] == NULL:
* raise ValueError("out of memory" )
* strcpy( self.fields[idx], tmp ) # <<<<<<<<<<<<<<
@@ -3531,7 +3558,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.TupleProxy._setindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy._setindex", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_value);
@@ -3541,19 +3568,21 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_8_setindex(struct __pyx_obj_
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_10TupleProxy_11__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /*proto*/
-static char __pyx_doc_10TabProxies_10TupleProxy_10__setitem__[] = "set item at *index* to *value*";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_10TupleProxy_10__setitem__;
-static int __pyx_pw_10TabProxies_10TupleProxy_11__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_10TupleProxy_11__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_10TupleProxy_10__setitem__[] = "set item at *index* to *value*";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_10__setitem__;
+#endif
+static int __pyx_pw_5pysam_10TabProxies_10TupleProxy_11__setitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__setitem__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_index), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_10__setitem__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_index), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":269
+/* "pysam/TabProxies.pyx":269
* strcpy( self.fields[idx], tmp )
*
* def __setitem__(self, index, value ): # <<<<<<<<<<<<<<
@@ -3561,7 +3590,7 @@ static int __pyx_pw_10TabProxies_10TupleProxy_11__setitem__(PyObject *__pyx_v_se
* cdef int i = index
*/
-static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value) {
int __pyx_v_i;
int __pyx_r;
__Pyx_RefNannyDeclarations
@@ -3575,7 +3604,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10T
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__setitem__", 0);
- /* "TabProxies.pyx":271
+ /* "pysam/TabProxies.pyx":271
* def __setitem__(self, index, value ):
* '''set item at *index* to *value*'''
* cdef int i = index # <<<<<<<<<<<<<<
@@ -3585,7 +3614,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10T
__pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_index); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_i = __pyx_t_1;
- /* "TabProxies.pyx":272
+ /* "pysam/TabProxies.pyx":272
* '''set item at *index* to *value*'''
* cdef int i = index
* if i < 0: i += self.nfields # <<<<<<<<<<<<<<
@@ -3599,7 +3628,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10T
}
__pyx_L3:;
- /* "TabProxies.pyx":273
+ /* "pysam/TabProxies.pyx":273
* cdef int i = index
* if i < 0: i += self.nfields
* i += self.offset # <<<<<<<<<<<<<<
@@ -3608,7 +3637,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10T
*/
__pyx_v_i = (__pyx_v_i + __pyx_v_self->offset);
- /* "TabProxies.pyx":275
+ /* "pysam/TabProxies.pyx":275
* i += self.offset
*
* self._setindex( i, value ) # <<<<<<<<<<<<<<
@@ -3639,7 +3668,7 @@ static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10T
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("TabProxies.TupleProxy.__setitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.__setitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -3647,17 +3676,17 @@ static int __pyx_pf_10TabProxies_10TupleProxy_10__setitem__(struct __pyx_obj_10T
}
/* Python wrapper */
-static Py_ssize_t __pyx_pw_10TabProxies_10TupleProxy_13__len__(PyObject *__pyx_v_self); /*proto*/
-static Py_ssize_t __pyx_pw_10TabProxies_10TupleProxy_13__len__(PyObject *__pyx_v_self) {
+static Py_ssize_t __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__(PyObject *__pyx_v_self); /*proto*/
+static Py_ssize_t __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__(PyObject *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_12__len__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_12__len__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":277
+/* "pysam/TabProxies.pyx":277
* self._setindex( i, value )
*
* def __len__(self): # <<<<<<<<<<<<<<
@@ -3665,12 +3694,12 @@ static Py_ssize_t __pyx_pw_10TabProxies_10TupleProxy_13__len__(PyObject *__pyx_v
*
*/
-static Py_ssize_t __pyx_pf_10TabProxies_10TupleProxy_12__len__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self) {
+static Py_ssize_t __pyx_pf_5pysam_10TabProxies_10TupleProxy_12__len__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__len__", 0);
- /* "TabProxies.pyx":278
+ /* "pysam/TabProxies.pyx":278
*
* def __len__(self):
* return self.nfields # <<<<<<<<<<<<<<
@@ -3687,17 +3716,17 @@ static Py_ssize_t __pyx_pf_10TabProxies_10TupleProxy_12__len__(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_15__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_15__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_14__iter__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_14__iter__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":280
+/* "pysam/TabProxies.pyx":280
* return self.nfields
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -3705,12 +3734,12 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_15__iter__(PyObject *__pyx_v
* return self
*/
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__", 0);
- /* "TabProxies.pyx":281
+ /* "pysam/TabProxies.pyx":281
*
* def __iter__(self):
* self.index = 0 # <<<<<<<<<<<<<<
@@ -3719,7 +3748,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_
*/
__pyx_v_self->index = 0;
- /* "TabProxies.pyx":282
+ /* "pysam/TabProxies.pyx":282
* def __iter__(self):
* self.index = 0
* return self # <<<<<<<<<<<<<<
@@ -3739,19 +3768,21 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_17__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_10TabProxies_10TupleProxy_16__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_10TupleProxy_16__next__;
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_17__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_10TupleProxy_16__next__[] = "python version of next().\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_16__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_16__next__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_16__next__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":284
+/* "pysam/TabProxies.pyx":284
* return self
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -3759,7 +3790,7 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_17__next__(PyObject *__pyx_v
* """
*/
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self) {
char *__pyx_v_retval;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -3770,7 +3801,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__next__", 0);
- /* "TabProxies.pyx":287
+ /* "pysam/TabProxies.pyx":287
* """python version of next().
* """
* if self.index >= self.nfields: # <<<<<<<<<<<<<<
@@ -3780,7 +3811,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
__pyx_t_1 = (__pyx_v_self->index >= __pyx_v_self->nfields);
if (__pyx_t_1) {
- /* "TabProxies.pyx":288
+ /* "pysam/TabProxies.pyx":288
* """
* if self.index >= self.nfields:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -3793,7 +3824,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
}
__pyx_L3:;
- /* "TabProxies.pyx":289
+ /* "pysam/TabProxies.pyx":289
* if self.index >= self.nfields:
* raise StopIteration
* cdef char * retval = self.fields[self.index] # <<<<<<<<<<<<<<
@@ -3802,7 +3833,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
*/
__pyx_v_retval = (__pyx_v_self->fields[__pyx_v_self->index]);
- /* "TabProxies.pyx":290
+ /* "pysam/TabProxies.pyx":290
* raise StopIteration
* cdef char * retval = self.fields[self.index]
* self.index += 1 # <<<<<<<<<<<<<<
@@ -3811,7 +3842,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
*/
__pyx_v_self->index = (__pyx_v_self->index + 1);
- /* "TabProxies.pyx":291
+ /* "pysam/TabProxies.pyx":291
* cdef char * retval = self.fields[self.index]
* self.index += 1
* if retval == NULL: return None # <<<<<<<<<<<<<<
@@ -3828,7 +3859,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
}
/*else*/ {
- /* "TabProxies.pyx":292
+ /* "pysam/TabProxies.pyx":292
* self.index += 1
* if retval == NULL: return None
* else: return retval # <<<<<<<<<<<<<<
@@ -3848,7 +3879,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.TupleProxy.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -3857,19 +3888,21 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_16__next__(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_19__str__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_10TabProxies_10TupleProxy_18__str__[] = "return original data";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_10TupleProxy_18__str__;
-static PyObject *__pyx_pw_10TabProxies_10TupleProxy_19__str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_10TupleProxy_18__str__[] = "return original data";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_18__str__;
+#endif
+static PyObject *__pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_10TupleProxy_18__str__(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_10TupleProxy_18__str__(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":294
+/* "pysam/TabProxies.pyx":294
* else: return retval
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -3877,7 +3910,7 @@ static PyObject *__pyx_pw_10TabProxies_10TupleProxy_19__str__(PyObject *__pyx_v_
* # copy and replace \0 bytes with \t characters
*/
-static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_10TabProxies_TupleProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self) {
PyObject *__pyx_v_result = NULL;
long __pyx_v_x;
char *__pyx_v_cpy;
@@ -3895,7 +3928,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__str__", 0);
- /* "TabProxies.pyx":297
+ /* "pysam/TabProxies.pyx":297
* '''return original data'''
* # copy and replace \0 bytes with \t characters
* if self.is_modified: # <<<<<<<<<<<<<<
@@ -3904,7 +3937,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
*/
if (__pyx_v_self->is_modified) {
- /* "TabProxies.pyx":299
+ /* "pysam/TabProxies.pyx":299
* if self.is_modified:
* # todo: treat NULL values
* result = [] # <<<<<<<<<<<<<<
@@ -3916,7 +3949,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__pyx_v_result = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "TabProxies.pyx":300
+ /* "pysam/TabProxies.pyx":300
* # todo: treat NULL values
* result = []
* for x in xrange( 0, self.nfields ): # <<<<<<<<<<<<<<
@@ -3927,15 +3960,15 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
__pyx_v_x = __pyx_t_3;
- /* "TabProxies.pyx":301
+ /* "pysam/TabProxies.pyx":301
* result = []
* for x in xrange( 0, self.nfields ):
* result.append( StrOrEmpty( self.fields[x]).decode('ascii') ) # <<<<<<<<<<<<<<
* return "\t".join( result )
* else:
*/
- __pyx_t_4 = __pyx_f_10TabProxies_StrOrEmpty((__pyx_v_self->fields[__pyx_v_x]));
- __pyx_t_1 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_t_4, strlen(__pyx_t_4), NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_5pysam_10TabProxies_StrOrEmpty((__pyx_v_self->fields[__pyx_v_x]));
+ __pyx_t_1 = ((PyObject *)__Pyx_decode_c_string(__pyx_t_4, 0, strlen(__pyx_t_4), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_result, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
@@ -3943,7 +3976,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
- /* "TabProxies.pyx":302
+ /* "pysam/TabProxies.pyx":302
* for x in xrange( 0, self.nfields ):
* result.append( StrOrEmpty( self.fields[x]).decode('ascii') )
* return "\t".join( result ) # <<<<<<<<<<<<<<
@@ -3969,7 +4002,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
}
/*else*/ {
- /* "TabProxies.pyx":304
+ /* "pysam/TabProxies.pyx":304
* return "\t".join( result )
* else:
* cpy = <char*>calloc( sizeof(char), self.nbytes+1 ) # <<<<<<<<<<<<<<
@@ -3978,7 +4011,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
*/
__pyx_v_cpy = ((char *)calloc((sizeof(char)), (__pyx_v_self->nbytes + 1)));
- /* "TabProxies.pyx":305
+ /* "pysam/TabProxies.pyx":305
* else:
* cpy = <char*>calloc( sizeof(char), self.nbytes+1 )
* if cpy == NULL: # <<<<<<<<<<<<<<
@@ -3988,7 +4021,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__pyx_t_7 = (__pyx_v_cpy == NULL);
if (__pyx_t_7) {
- /* "TabProxies.pyx":306
+ /* "pysam/TabProxies.pyx":306
* cpy = <char*>calloc( sizeof(char), self.nbytes+1 )
* if cpy == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
@@ -4004,7 +4037,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
}
__pyx_L6:;
- /* "TabProxies.pyx":307
+ /* "pysam/TabProxies.pyx":307
* if cpy == NULL:
* raise ValueError("out of memory" )
* memcpy( cpy, self.data, self.nbytes+1) # <<<<<<<<<<<<<<
@@ -4013,7 +4046,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
*/
memcpy(__pyx_v_cpy, __pyx_v_self->data, (__pyx_v_self->nbytes + 1));
- /* "TabProxies.pyx":308
+ /* "pysam/TabProxies.pyx":308
* raise ValueError("out of memory" )
* memcpy( cpy, self.data, self.nbytes+1)
* for x from 0 <= x < self.nbytes: # <<<<<<<<<<<<<<
@@ -4023,7 +4056,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__pyx_t_2 = __pyx_v_self->nbytes;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_2; __pyx_v_x++) {
- /* "TabProxies.pyx":309
+ /* "pysam/TabProxies.pyx":309
* memcpy( cpy, self.data, self.nbytes+1)
* for x from 0 <= x < self.nbytes:
* if cpy[x] == '\0': cpy[x] = '\t' # <<<<<<<<<<<<<<
@@ -4038,7 +4071,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__pyx_L9:;
}
- /* "TabProxies.pyx":310
+ /* "pysam/TabProxies.pyx":310
* for x from 0 <= x < self.nbytes:
* if cpy[x] == '\0': cpy[x] = '\t'
* result = cpy[:self.nbytes] # <<<<<<<<<<<<<<
@@ -4050,7 +4083,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__pyx_v_result = ((PyObject *)__pyx_t_6);
__pyx_t_6 = 0;
- /* "TabProxies.pyx":311
+ /* "pysam/TabProxies.pyx":311
* if cpy[x] == '\0': cpy[x] = '\t'
* result = cpy[:self.nbytes]
* free(cpy) # <<<<<<<<<<<<<<
@@ -4059,7 +4092,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
*/
free(__pyx_v_cpy);
- /* "TabProxies.pyx":312
+ /* "pysam/TabProxies.pyx":312
* result = cpy[:self.nbytes]
* free(cpy)
* return result.decode('ascii') # <<<<<<<<<<<<<<
@@ -4084,7 +4117,7 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("TabProxies.TupleProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.TupleProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
@@ -4094,20 +4127,19 @@ static PyObject *__pyx_pf_10TabProxies_10TupleProxy_18__str__(struct __pyx_obj_1
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_1toDot(PyObject *__pyx_self, PyObject *__pyx_v_v); /*proto*/
-static char __pyx_doc_10TabProxies_toDot[] = "convert value to '.' if None";
-static PyMethodDef __pyx_mdef_10TabProxies_1toDot = {__Pyx_NAMESTR("toDot"), (PyCFunction)__pyx_pw_10TabProxies_1toDot, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_toDot)};
-static PyObject *__pyx_pw_10TabProxies_1toDot(PyObject *__pyx_self, PyObject *__pyx_v_v) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_1toDot(PyObject *__pyx_self, PyObject *__pyx_v_v); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_toDot[] = "convert value to '.' if None";
+static PyMethodDef __pyx_mdef_5pysam_10TabProxies_1toDot = {__Pyx_NAMESTR("toDot"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_1toDot, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_toDot)};
+static PyObject *__pyx_pw_5pysam_10TabProxies_1toDot(PyObject *__pyx_self, PyObject *__pyx_v_v) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("toDot (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_10TabProxies_toDot(__pyx_self, ((PyObject *)__pyx_v_v));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_toDot(__pyx_self, ((PyObject *)__pyx_v_v));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":314
+/* "pysam/TabProxies.pyx":314
* return result.decode('ascii')
*
* def toDot( v ): # <<<<<<<<<<<<<<
@@ -4115,7 +4147,7 @@ static PyObject *__pyx_pw_10TabProxies_1toDot(PyObject *__pyx_self, PyObject *__
* if v == None: return "."
*/
-static PyObject *__pyx_pf_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4126,15 +4158,14 @@ static PyObject *__pyx_pf_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self,
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("toDot", 0);
- /* "TabProxies.pyx":316
+ /* "pysam/TabProxies.pyx":316
* def toDot( v ):
* '''convert value to '.' if None'''
* if v == None: return "." # <<<<<<<<<<<<<<
* else: return str(v)
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
@@ -4146,7 +4177,7 @@ static PyObject *__pyx_pf_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self,
}
/*else*/ {
- /* "TabProxies.pyx":317
+ /* "pysam/TabProxies.pyx":317
* '''convert value to '.' if None'''
* if v == None: return "."
* else: return str(v) # <<<<<<<<<<<<<<
@@ -4173,7 +4204,7 @@ static PyObject *__pyx_pf_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self,
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.toDot", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.toDot", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4182,20 +4213,19 @@ static PyObject *__pyx_pf_10TabProxies_toDot(CYTHON_UNUSED PyObject *__pyx_self,
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_3quote(PyObject *__pyx_self, PyObject *__pyx_v_v); /*proto*/
-static char __pyx_doc_10TabProxies_2quote[] = "return a quoted attribute.";
-static PyMethodDef __pyx_mdef_10TabProxies_3quote = {__Pyx_NAMESTR("quote"), (PyCFunction)__pyx_pw_10TabProxies_3quote, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_2quote)};
-static PyObject *__pyx_pw_10TabProxies_3quote(PyObject *__pyx_self, PyObject *__pyx_v_v) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_3quote(PyObject *__pyx_self, PyObject *__pyx_v_v); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_2quote[] = "return a quoted attribute.";
+static PyMethodDef __pyx_mdef_5pysam_10TabProxies_3quote = {__Pyx_NAMESTR("quote"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_3quote, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_2quote)};
+static PyObject *__pyx_pw_5pysam_10TabProxies_3quote(PyObject *__pyx_self, PyObject *__pyx_v_v) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("quote (wrapper)", 0);
- __pyx_self = __pyx_self;
- __pyx_r = __pyx_pf_10TabProxies_2quote(__pyx_self, ((PyObject *)__pyx_v_v));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_2quote(__pyx_self, ((PyObject *)__pyx_v_v));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":319
+/* "pysam/TabProxies.pyx":319
* else: return str(v)
*
* def quote( v ): # <<<<<<<<<<<<<<
@@ -4203,7 +4233,7 @@ static PyObject *__pyx_pw_10TabProxies_3quote(PyObject *__pyx_self, PyObject *__
* if type(v) in types.StringTypes:
*/
-static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4214,7 +4244,7 @@ static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("quote", 0);
- /* "TabProxies.pyx":321
+ /* "pysam/TabProxies.pyx":321
* def quote( v ):
* '''return a quoted attribute.'''
* if type(v) in types.StringTypes: # <<<<<<<<<<<<<<
@@ -4226,11 +4256,11 @@ static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self
__pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__StringTypes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = ((PySequence_Contains(__pyx_t_2, ((PyObject *)Py_TYPE(__pyx_v_v))))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (__Pyx_PySequence_Contains(((PyObject *)Py_TYPE(__pyx_v_v)), __pyx_t_2, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "TabProxies.pyx":322
+ /* "pysam/TabProxies.pyx":322
* '''return a quoted attribute.'''
* if type(v) in types.StringTypes:
* return '"%s"' % v # <<<<<<<<<<<<<<
@@ -4247,7 +4277,7 @@ static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self
}
/*else*/ {
- /* "TabProxies.pyx":324
+ /* "pysam/TabProxies.pyx":324
* return '"%s"' % v
* else:
* return str(v) # <<<<<<<<<<<<<<
@@ -4274,7 +4304,7 @@ static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.quote", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.quote", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4283,20 +4313,20 @@ static PyObject *__pyx_pf_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy___cinit__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy___cinit__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":339
+/* "pysam/TabProxies.pyx":339
* '''
*
* def __cinit__(self ): # <<<<<<<<<<<<<<
@@ -4304,12 +4334,12 @@ static int __pyx_pw_10TabProxies_8GTFProxy_1__cinit__(PyObject *__pyx_v_self, Py
* self.hasOwnAttributes = False
*/
-static int __pyx_pf_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
- /* "TabProxies.pyx":341
+ /* "pysam/TabProxies.pyx":341
* def __cinit__(self ):
* # automatically calls TupleProxy.__cinit__
* self.hasOwnAttributes = False # <<<<<<<<<<<<<<
@@ -4318,7 +4348,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_10TabProxi
*/
__pyx_v_self->hasOwnAttributes = 0;
- /* "TabProxies.pyx":342
+ /* "pysam/TabProxies.pyx":342
* # automatically calls TupleProxy.__cinit__
* self.hasOwnAttributes = False
* self._attributes = NULL # <<<<<<<<<<<<<<
@@ -4333,15 +4363,15 @@ static int __pyx_pf_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_10TabProxi
}
/* Python wrapper */
-static void __pyx_pw_10TabProxies_8GTFProxy_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pw_10TabProxies_8GTFProxy_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_5pysam_10TabProxies_8GTFProxy_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_10TabProxies_8GTFProxy_3__dealloc__(PyObject *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
- __pyx_pf_10TabProxies_8GTFProxy_2__dealloc__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_pf_5pysam_10TabProxies_8GTFProxy_2__dealloc__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
}
-/* "TabProxies.pyx":344
+/* "pysam/TabProxies.pyx":344
* self._attributes = NULL
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -4349,11 +4379,11 @@ static void __pyx_pw_10TabProxies_8GTFProxy_3__dealloc__(PyObject *__pyx_v_self)
* if self.hasOwnAttributes:
*/
-static void __pyx_pf_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static void __pyx_pf_5pysam_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__dealloc__", 0);
- /* "TabProxies.pyx":346
+ /* "pysam/TabProxies.pyx":346
* def __dealloc__(self):
* # automatically calls TupleProxy.__dealloc__
* if self.hasOwnAttributes: # <<<<<<<<<<<<<<
@@ -4362,7 +4392,7 @@ static void __pyx_pf_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_10TabP
*/
if (__pyx_v_self->hasOwnAttributes) {
- /* "TabProxies.pyx":347
+ /* "pysam/TabProxies.pyx":347
* # automatically calls TupleProxy.__dealloc__
* if self.hasOwnAttributes:
* free(self._attributes) # <<<<<<<<<<<<<<
@@ -4377,7 +4407,7 @@ static void __pyx_pf_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_10TabP
__Pyx_RefNannyFinishContext();
}
-/* "TabProxies.pyx":349
+/* "pysam/TabProxies.pyx":349
* free(self._attributes)
*
* cdef int getMaxFields( self, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -4385,12 +4415,12 @@ static void __pyx_pf_10TabProxies_8GTFProxy_2__dealloc__(struct __pyx_obj_10TabP
* return 9
*/
-static int __pyx_f_10TabProxies_8GTFProxy_getMaxFields(CYTHON_UNUSED struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, CYTHON_UNUSED size_t __pyx_v_nbytes) {
+static int __pyx_f_5pysam_10TabProxies_8GTFProxy_getMaxFields(CYTHON_UNUSED struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, CYTHON_UNUSED size_t __pyx_v_nbytes) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getMaxFields", 0);
- /* "TabProxies.pyx":351
+ /* "pysam/TabProxies.pyx":351
* cdef int getMaxFields( self, size_t nbytes ):
* '''return max number of fields.'''
* return 9 # <<<<<<<<<<<<<<
@@ -4407,17 +4437,17 @@ static int __pyx_f_10TabProxies_8GTFProxy_getMaxFields(CYTHON_UNUSED struct __py
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6contig_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6contig_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6contig___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":355
+/* "pysam/TabProxies.pyx":355
* property contig:
* '''contig of feature.'''
* def __get__( self ): return self._getindex( 0 ) # <<<<<<<<<<<<<<
@@ -4425,7 +4455,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6contig_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4449,7 +4479,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_ob
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.contig.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.contig.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4458,17 +4488,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6contig___get__(struct __pyx_ob
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_6contig_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_6contig_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6contig_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":356
+/* "pysam/TabProxies.pyx":356
* '''contig of feature.'''
* def __get__( self ): return self._getindex( 0 )
* def __set__( self, value ): self._setindex( 0, value ) # <<<<<<<<<<<<<<
@@ -4476,7 +4506,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_6contig_3__set__(PyObject *__pyx_v_se
* property source:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4508,7 +4538,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_10T
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.contig.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.contig.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -4516,17 +4546,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_6contig_2__set__(struct __pyx_obj_10T
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6source_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6source_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6source___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6source___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":360
+/* "pysam/TabProxies.pyx":360
* property source:
* '''feature source.'''
* def __get__( self ): return self._getindex( 1 ) # <<<<<<<<<<<<<<
@@ -4534,7 +4564,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6source_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6source___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6source___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4558,7 +4588,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6source___get__(struct __pyx_ob
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.source.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.source.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4567,17 +4597,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6source___get__(struct __pyx_ob
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_6source_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_6source_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6source_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6source_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":361
+/* "pysam/TabProxies.pyx":361
* '''feature source.'''
* def __get__( self ): return self._getindex( 1 )
* def __set__( self, value ): self._setindex( 1, value ) # <<<<<<<<<<<<<<
@@ -4585,7 +4615,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_6source_3__set__(PyObject *__pyx_v_se
* property feature:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4617,7 +4647,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_10T
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.source.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.source.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -4625,17 +4655,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_6source_2__set__(struct __pyx_obj_10T
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_7feature_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_7feature_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_7feature___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":365
+/* "pysam/TabProxies.pyx":365
* property feature:
* '''feature name.'''
* def __get__( self ): return self._getindex( 2 ) # <<<<<<<<<<<<<<
@@ -4643,7 +4673,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_7feature_1__get__(PyObject *__p
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4667,7 +4697,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_o
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.feature.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.feature.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4676,17 +4706,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_7feature___get__(struct __pyx_o
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_7feature_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_7feature_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_7feature_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":366
+/* "pysam/TabProxies.pyx":366
* '''feature name.'''
* def __get__( self ): return self._getindex( 2 )
* def __set__( self, value ): self._setindex( 2, value ) # <<<<<<<<<<<<<<
@@ -4694,7 +4724,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_7feature_3__set__(PyObject *__pyx_v_s
* property start:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4726,7 +4756,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_10
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.feature.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.feature.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -4734,17 +4764,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_7feature_2__set__(struct __pyx_obj_10
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5start_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5start_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_5start___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_5start___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":370
+/* "pysam/TabProxies.pyx":370
* property start:
* '''feature start (in 0-based open/closed coordinates).'''
* def __get__( self ): return int( self._getindex( 3 )) - 1 # <<<<<<<<<<<<<<
@@ -4752,7 +4782,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5start_1__get__(PyObject *__pyx
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4787,7 +4817,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.start.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.start.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4796,17 +4826,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5start___get__(struct __pyx_obj
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_5start_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_5start_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_5start_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_5start_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":371
+/* "pysam/TabProxies.pyx":371
* '''feature start (in 0-based open/closed coordinates).'''
* def __get__( self ): return int( self._getindex( 3 )) - 1
* def __set__( self, value ): self._setindex( 3, str(value+1) ) # <<<<<<<<<<<<<<
@@ -4814,7 +4844,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_5start_3__set__(PyObject *__pyx_v_sel
* property end:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4856,7 +4886,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_10Ta
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.start.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.start.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -4864,17 +4894,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_5start_2__set__(struct __pyx_obj_10Ta
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_3end_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_3end_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_3end___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_3end___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":375
+/* "pysam/TabProxies.pyx":375
* property end:
* '''feature end (in 0-based open/closed coordinates).'''
* def __get__( self ): return int( self._getindex( 4 ) ) # <<<<<<<<<<<<<<
@@ -4882,7 +4912,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_3end_1__get__(PyObject *__pyx_v
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4914,7 +4944,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_1
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.end.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.end.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4923,17 +4953,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_3end___get__(struct __pyx_obj_1
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_3end_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_3end_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_3end_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_3end_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":376
+/* "pysam/TabProxies.pyx":376
* '''feature end (in 0-based open/closed coordinates).'''
* def __get__( self ): return int( self._getindex( 4 ) )
* def __set__( self, value ): self._setindex( 4, str(value) ) # <<<<<<<<<<<<<<
@@ -4941,7 +4971,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_3end_3__set__(PyObject *__pyx_v_self,
* property score:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4981,7 +5011,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_10TabP
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.end.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.end.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -4989,17 +5019,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_3end_2__set__(struct __pyx_obj_10TabP
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5score_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5score_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_5score___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_5score___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":380
+/* "pysam/TabProxies.pyx":380
* property score:
* '''feature score.'''
* def __get__( self ): # <<<<<<<<<<<<<<
@@ -5007,7 +5037,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5score_1__get__(PyObject *__pyx
* if v == "" or v[0] == '.':
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_v_v = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -5022,7 +5052,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "TabProxies.pyx":381
+ /* "pysam/TabProxies.pyx":381
* '''feature score.'''
* def __get__( self ):
* v = self._getindex(5) # <<<<<<<<<<<<<<
@@ -5037,26 +5067,30 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj
__pyx_v_v = __pyx_t_2;
__pyx_t_2 = 0;
- /* "TabProxies.pyx":382
+ /* "pysam/TabProxies.pyx":382
* def __get__( self ):
* v = self._getindex(5)
* if v == "" or v[0] == '.': # <<<<<<<<<<<<<<
* return None
* else:
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_6), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_6), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!__pyx_t_3) {
__pyx_t_2 = __Pyx_GetItemInt(__pyx_v_v, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_21), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_21), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_5 = __pyx_t_4;
} else {
__pyx_t_5 = __pyx_t_3;
}
if (__pyx_t_5) {
- /* "TabProxies.pyx":383
+ /* "pysam/TabProxies.pyx":383
* v = self._getindex(5)
* if v == "" or v[0] == '.':
* return None # <<<<<<<<<<<<<<
@@ -5071,7 +5105,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj
}
/*else*/ {
- /* "TabProxies.pyx":385
+ /* "pysam/TabProxies.pyx":385
* return None
* else:
* return float(v) # <<<<<<<<<<<<<<
@@ -5080,10 +5114,10 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_6 = __Pyx_PyObject_AsDouble(__pyx_v_v); if (unlikely(__pyx_t_6 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyFloat_FromDouble(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L0;
}
__pyx_L3:;
@@ -5093,7 +5127,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.score.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.score.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_v);
@@ -5103,17 +5137,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5score___get__(struct __pyx_obj
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_5score_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_5score_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_5score_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_5score_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":387
+/* "pysam/TabProxies.pyx":387
* return float(v)
*
* def __set__( self, value ): self._setindex( 5, value ) # <<<<<<<<<<<<<<
@@ -5121,7 +5155,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_5score_3__set__(PyObject *__pyx_v_sel
* property strand:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5153,7 +5187,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_10Ta
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.score.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.score.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -5161,17 +5195,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_5score_2__set__(struct __pyx_obj_10Ta
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6strand_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6strand_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6strand___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":391
+/* "pysam/TabProxies.pyx":391
* property strand:
* '''feature strand.'''
* def __get__( self ): return self._getindex( 6 ) # <<<<<<<<<<<<<<
@@ -5179,7 +5213,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_6strand_1__get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5203,7 +5237,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_ob
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.strand.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.strand.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -5212,17 +5246,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6strand___get__(struct __pyx_ob
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_6strand_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_6strand_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6strand_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":392
+/* "pysam/TabProxies.pyx":392
* '''feature strand.'''
* def __get__( self ): return self._getindex( 6 )
* def __set__( self, value ): self._setindex( 6, value ) # <<<<<<<<<<<<<<
@@ -5230,7 +5264,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_6strand_3__set__(PyObject *__pyx_v_se
* property frame:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5262,7 +5296,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_10T
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.strand.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.strand.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -5270,17 +5304,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_6strand_2__set__(struct __pyx_obj_10T
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5frame_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5frame_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_5frame___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":396
+/* "pysam/TabProxies.pyx":396
* property frame:
* '''feature frame.'''
* def __get__( self ): return self._getindex( 7 ) # <<<<<<<<<<<<<<
@@ -5288,7 +5322,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5frame_1__get__(PyObject *__pyx
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5312,7 +5346,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.frame.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.frame.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -5321,17 +5355,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_5frame___get__(struct __pyx_obj
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_5frame_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_5frame_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_5frame_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":397
+/* "pysam/TabProxies.pyx":397
* '''feature frame.'''
* def __get__( self ): return self._getindex( 7 )
* def __set__( self, value ): self._setindex( 7, value ) # <<<<<<<<<<<<<<
@@ -5339,7 +5373,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_5frame_3__set__(PyObject *__pyx_v_sel
* property attributes:
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5371,7 +5405,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_10Ta
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.frame.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.frame.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -5379,17 +5413,17 @@ static int __pyx_pf_10TabProxies_8GTFProxy_5frame_2__set__(struct __pyx_obj_10Ta
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_10attributes_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_10attributes_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes___get__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":401
+/* "pysam/TabProxies.pyx":401
* property attributes:
* '''feature attributes (as a string).'''
* def __get__( self ): # <<<<<<<<<<<<<<
@@ -5397,7 +5431,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_10attributes_1__get__(PyObject
* return self._attributes
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes___get__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5407,7 +5441,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __p
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "TabProxies.pyx":402
+ /* "pysam/TabProxies.pyx":402
* '''feature attributes (as a string).'''
* def __get__( self ):
* if self.hasOwnAttributes: # <<<<<<<<<<<<<<
@@ -5416,7 +5450,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __p
*/
if (__pyx_v_self->hasOwnAttributes) {
- /* "TabProxies.pyx":403
+ /* "pysam/TabProxies.pyx":403
* def __get__( self ):
* if self.hasOwnAttributes:
* return self._attributes # <<<<<<<<<<<<<<
@@ -5433,7 +5467,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __p
}
/*else*/ {
- /* "TabProxies.pyx":405
+ /* "pysam/TabProxies.pyx":405
* return self._attributes
* else:
* return self._getindex( 8 ) # <<<<<<<<<<<<<<
@@ -5457,7 +5491,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __p
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("TabProxies.GTFProxy.attributes.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.attributes.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -5466,17 +5500,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10attributes___get__(struct __p
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8GTFProxy_10attributes_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
-static int __pyx_pw_10TabProxies_8GTFProxy_10attributes_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes_2__set__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":406
+/* "pysam/TabProxies.pyx":406
* else:
* return self._getindex( 8 )
* def __set__( self, value ): # <<<<<<<<<<<<<<
@@ -5484,7 +5518,7 @@ static int __pyx_pw_10TabProxies_8GTFProxy_10attributes_3__set__(PyObject *__pyx
* free(self._attributes)
*/
-static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5495,7 +5529,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__set__", 0);
- /* "TabProxies.pyx":407
+ /* "pysam/TabProxies.pyx":407
* return self._getindex( 8 )
* def __set__( self, value ):
* if self.hasOwnAttributes: # <<<<<<<<<<<<<<
@@ -5504,7 +5538,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
*/
if (__pyx_v_self->hasOwnAttributes) {
- /* "TabProxies.pyx":408
+ /* "pysam/TabProxies.pyx":408
* def __set__( self, value ):
* if self.hasOwnAttributes:
* free(self._attributes) # <<<<<<<<<<<<<<
@@ -5513,7 +5547,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
*/
free(__pyx_v_self->_attributes);
- /* "TabProxies.pyx":409
+ /* "pysam/TabProxies.pyx":409
* if self.hasOwnAttributes:
* free(self._attributes)
* self._attributes = NULL # <<<<<<<<<<<<<<
@@ -5522,7 +5556,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
*/
__pyx_v_self->_attributes = NULL;
- /* "TabProxies.pyx":410
+ /* "pysam/TabProxies.pyx":410
* free(self._attributes)
* self._attributes = NULL
* self.hasOwnAttributes = False # <<<<<<<<<<<<<<
@@ -5534,7 +5568,7 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
}
__pyx_L3:;
- /* "TabProxies.pyx":411
+ /* "pysam/TabProxies.pyx":411
* self._attributes = NULL
* self.hasOwnAttributes = False
* self._setindex(8, value ) # <<<<<<<<<<<<<<
@@ -5563,14 +5597,14 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.attributes.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.attributes.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":413
+/* "pysam/TabProxies.pyx":413
* self._setindex(8, value )
*
* cdef char * getAttributes( self ): # <<<<<<<<<<<<<<
@@ -5578,12 +5612,12 @@ static int __pyx_pf_10TabProxies_8GTFProxy_10attributes_2__set__(struct __pyx_ob
* if self.hasOwnAttributes:
*/
-static char *__pyx_f_10TabProxies_8GTFProxy_getAttributes(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static char *__pyx_f_5pysam_10TabProxies_8GTFProxy_getAttributes(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getAttributes", 0);
- /* "TabProxies.pyx":415
+ /* "pysam/TabProxies.pyx":415
* cdef char * getAttributes( self ):
* '''return pointer to attributes.'''
* if self.hasOwnAttributes: # <<<<<<<<<<<<<<
@@ -5592,7 +5626,7 @@ static char *__pyx_f_10TabProxies_8GTFProxy_getAttributes(struct __pyx_obj_10Tab
*/
if (__pyx_v_self->hasOwnAttributes) {
- /* "TabProxies.pyx":416
+ /* "pysam/TabProxies.pyx":416
* '''return pointer to attributes.'''
* if self.hasOwnAttributes:
* return self._attributes # <<<<<<<<<<<<<<
@@ -5605,7 +5639,7 @@ static char *__pyx_f_10TabProxies_8GTFProxy_getAttributes(struct __pyx_obj_10Tab
}
/*else*/ {
- /* "TabProxies.pyx":418
+ /* "pysam/TabProxies.pyx":418
* return self._attributes
* else:
* return self.fields[ 8 ] # <<<<<<<<<<<<<<
@@ -5624,18 +5658,18 @@ static char *__pyx_f_10TabProxies_8GTFProxy_getAttributes(struct __pyx_obj_10Tab
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5asDict(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_10TabProxies_8GTFProxy_4asDict[] = "parse attributes - return as dict\n ";
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5asDict(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5asDict(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8GTFProxy_4asDict[] = "parse attributes - return as dict\n ";
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_5asDict(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("asDict (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_4asDict(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_4asDict(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":420
+/* "pysam/TabProxies.pyx":420
* return self.fields[ 8 ]
*
* def asDict( self ): # <<<<<<<<<<<<<<
@@ -5643,7 +5677,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_5asDict(PyObject *__pyx_v_self,
* """
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_v_attributes = NULL;
PyObject *__pyx_v_fields = NULL;
PyObject *__pyx_v_result = NULL;
@@ -5675,7 +5709,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("asDict", 0);
- /* "TabProxies.pyx":425
+ /* "pysam/TabProxies.pyx":425
*
* # remove comments
* attributes = self.attributes # <<<<<<<<<<<<<<
@@ -5687,7 +5721,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
__pyx_v_attributes = __pyx_t_1;
__pyx_t_1 = 0;
- /* "TabProxies.pyx":428
+ /* "pysam/TabProxies.pyx":428
*
* # separate into fields
* fields = [ x.strip() for x in attributes.split(";")[:-1]] # <<<<<<<<<<<<<<
@@ -5716,10 +5750,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_3)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_3)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_3);
if (unlikely(!__pyx_t_2)) {
@@ -5739,50 +5781,56 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
__pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_1));
- __pyx_v_fields = __pyx_t_1;
+ __pyx_t_3 = ((PyObject *)__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_v_fields = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "TabProxies.pyx":430
+ /* "pysam/TabProxies.pyx":430
* fields = [ x.strip() for x in attributes.split(";")[:-1]]
*
* result = {} # <<<<<<<<<<<<<<
*
* for f in fields:
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_result = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_v_result = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "TabProxies.pyx":432
+ /* "pysam/TabProxies.pyx":432
* result = {}
*
* for f in fields: # <<<<<<<<<<<<<<
*
* d = [ x.strip() for x in f.split(" ")]
*/
- __pyx_t_1 = ((PyObject *)__pyx_v_fields); __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
+ __pyx_t_3 = ((PyObject *)__pyx_v_fields); __Pyx_INCREF(__pyx_t_3); __pyx_t_4 = 0;
for (;;) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++;
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
__Pyx_XDECREF(__pyx_v_f);
- __pyx_v_f = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_f = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "TabProxies.pyx":434
+ /* "pysam/TabProxies.pyx":434
* for f in fields:
*
* d = [ x.strip() for x in f.split(" ")] # <<<<<<<<<<<<<<
*
* n,v = d[0], d[1]
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_k_tuple_35), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5800,10 +5848,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_6)) {
if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_6, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_6)) {
if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_6, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_6);
if (unlikely(!__pyx_t_2)) {
@@ -5823,91 +5879,97 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
__pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_8))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_8))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_3));
+ __pyx_t_6 = ((PyObject *)__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_XDECREF(((PyObject *)__pyx_v_d));
- __pyx_v_d = __pyx_t_3;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_v_d = ((PyObject*)__pyx_t_6);
+ __pyx_t_6 = 0;
- /* "TabProxies.pyx":436
+ /* "pysam/TabProxies.pyx":436
* d = [ x.strip() for x in f.split(" ")]
*
* n,v = d[0], d[1] # <<<<<<<<<<<<<<
* if len(d) > 2: v = d[1:]
*
*/
- __pyx_t_3 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_d), 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_d), 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_d), 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_d), 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_n);
- __pyx_v_n = __pyx_t_3;
- __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_6;
+ __pyx_v_n = __pyx_t_6;
__pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_v_v);
+ __pyx_v_v = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "TabProxies.pyx":437
+ /* "pysam/TabProxies.pyx":437
*
* n,v = d[0], d[1]
* if len(d) > 2: v = d[1:] # <<<<<<<<<<<<<<
*
* if v[0] == '"' and v[-1] == '"':
*/
- __pyx_t_7 = PyList_GET_SIZE(((PyObject *)__pyx_v_d));
+ __pyx_t_7 = PyList_GET_SIZE(((PyObject *)__pyx_v_d)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_9 = (__pyx_t_7 > 2);
if (__pyx_t_9) {
- __pyx_t_6 = __Pyx_PySequence_GetSlice(((PyObject *)__pyx_v_d), 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(((PyObject *)__pyx_v_d), 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(__pyx_v_v);
- __pyx_v_v = ((PyObject *)__pyx_t_6);
- __pyx_t_6 = 0;
+ __pyx_v_v = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
goto __pyx_L9;
}
__pyx_L9:;
- /* "TabProxies.pyx":439
+ /* "pysam/TabProxies.pyx":439
* if len(d) > 2: v = d[1:]
*
* if v[0] == '"' and v[-1] == '"': # <<<<<<<<<<<<<<
* v = v[1:-1]
* else:
*/
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_v, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_6, ((PyObject *)__pyx_kp_s_36), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_v, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_kp_s_36), Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_9) {
__pyx_t_6 = __Pyx_GetItemInt(__pyx_v_v, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_6, ((PyObject *)__pyx_kp_s_36), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, ((PyObject *)__pyx_kp_s_36), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_11 = __pyx_t_10;
} else {
__pyx_t_11 = __pyx_t_9;
}
if (__pyx_t_11) {
- /* "TabProxies.pyx":440
+ /* "pysam/TabProxies.pyx":440
*
* if v[0] == '"' and v[-1] == '"':
* v = v[1:-1] # <<<<<<<<<<<<<<
* else:
* ## try to convert to a value
*/
- __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_v, 1, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_v, 1, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_v = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L10;
}
/*else*/ {
- /* "TabProxies.pyx":443
+ /* "pysam/TabProxies.pyx":443
* else:
* ## try to convert to a value
* try: # <<<<<<<<<<<<<<
@@ -5921,7 +5983,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
__Pyx_XGOTREF(__pyx_t_14);
/*try:*/ {
- /* "TabProxies.pyx":444
+ /* "pysam/TabProxies.pyx":444
* ## try to convert to a value
* try:
* v = float( v ) # <<<<<<<<<<<<<<
@@ -5929,30 +5991,30 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
* except ValueError:
*/
__pyx_t_15 = __Pyx_PyObject_AsDouble(__pyx_v_v); if (unlikely(__pyx_t_15 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
- __pyx_t_6 = PyFloat_FromDouble(__pyx_t_15); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_t_15); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_v = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "TabProxies.pyx":445
+ /* "pysam/TabProxies.pyx":445
* try:
* v = float( v )
* v = int( v ) # <<<<<<<<<<<<<<
* except ValueError:
* pass
*/
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_v);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_v);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_v);
__Pyx_GIVEREF(__pyx_v_v);
- __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L11_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_v = __pyx_t_6;
+ __pyx_t_6 = 0;
}
__Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
__Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
@@ -5961,10 +6023,10 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
__pyx_L11_error:;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "TabProxies.pyx":446
+ /* "pysam/TabProxies.pyx":446
* v = float( v )
* v = int( v )
* except ValueError: # <<<<<<<<<<<<<<
@@ -5977,7 +6039,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
goto __pyx_L12_exception_handled;
}
- /* "TabProxies.pyx":448
+ /* "pysam/TabProxies.pyx":448
* except ValueError:
* pass
* except TypeError: # <<<<<<<<<<<<<<
@@ -6004,7 +6066,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
}
__pyx_L10:;
- /* "TabProxies.pyx":451
+ /* "pysam/TabProxies.pyx":451
* pass
*
* result[n] = v # <<<<<<<<<<<<<<
@@ -6013,9 +6075,9 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
*/
if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_n, __pyx_v_v) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "TabProxies.pyx":453
+ /* "pysam/TabProxies.pyx":453
* result[n] = v
*
* return result # <<<<<<<<<<<<<<
@@ -6035,7 +6097,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("TabProxies.GTFProxy.asDict", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.asDict", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_attributes);
@@ -6052,18 +6114,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_4asDict(struct __pyx_obj_10TabP
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_7fromDict(PyObject *__pyx_v_self, PyObject *__pyx_v_d); /*proto*/
-static char __pyx_doc_10TabProxies_8GTFProxy_6fromDict[] = "set attributes from a dictionary.";
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_7fromDict(PyObject *__pyx_v_self, PyObject *__pyx_v_d) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_7fromDict(PyObject *__pyx_v_self, PyObject *__pyx_v_d); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8GTFProxy_6fromDict[] = "set attributes from a dictionary.";
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_7fromDict(PyObject *__pyx_v_self, PyObject *__pyx_v_d) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("fromDict (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_6fromDict(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_d));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_6fromDict(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_d));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":455
+/* "pysam/TabProxies.pyx":455
* return result
*
* def fromDict( self, d ): # <<<<<<<<<<<<<<
@@ -6071,7 +6133,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_7fromDict(PyObject *__pyx_v_sel
* cdef char * p
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_d) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_d) {
char *__pyx_v_p;
int __pyx_v_l;
PyObject *__pyx_v_aa = NULL;
@@ -6096,7 +6158,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("fromDict", 0);
- /* "TabProxies.pyx":461
+ /* "pysam/TabProxies.pyx":461
*
* # clean up if this field is set twice
* if self.hasOwnAttributes: # <<<<<<<<<<<<<<
@@ -6105,7 +6167,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
*/
if (__pyx_v_self->hasOwnAttributes) {
- /* "TabProxies.pyx":462
+ /* "pysam/TabProxies.pyx":462
* # clean up if this field is set twice
* if self.hasOwnAttributes:
* free(self._attributes) # <<<<<<<<<<<<<<
@@ -6117,7 +6179,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
}
__pyx_L3:;
- /* "TabProxies.pyx":464
+ /* "pysam/TabProxies.pyx":464
* free(self._attributes)
*
* aa = [] # <<<<<<<<<<<<<<
@@ -6126,10 +6188,10 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_v_aa = __pyx_t_1;
+ __pyx_v_aa = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "TabProxies.pyx":465
+ /* "pysam/TabProxies.pyx":465
*
* aa = []
* for k,v in d.items(): # <<<<<<<<<<<<<<
@@ -6153,10 +6215,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
for (;;) {
if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_4(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
@@ -6170,27 +6240,35 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
}
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_5 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_5 = PyList_GET_ITEM(sequence, 0);
__pyx_t_6 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_5);
__Pyx_INCREF(__pyx_t_6);
+ #else
+ __pyx_t_5 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
__pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
@@ -6201,12 +6279,13 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
index = 1; __pyx_t_6 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_6)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_6);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L7_unpacking_done;
__pyx_L6_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_8 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L7_unpacking_done:;
}
@@ -6217,7 +6296,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__pyx_v_v = __pyx_t_6;
__pyx_t_6 = 0;
- /* "TabProxies.pyx":466
+ /* "pysam/TabProxies.pyx":466
* aa = []
* for k,v in d.items():
* if type(v) in types.StringTypes: # <<<<<<<<<<<<<<
@@ -6229,11 +6308,11 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__pyx_t_6 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__StringTypes); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_9 = ((PySequence_Contains(__pyx_t_6, ((PyObject *)Py_TYPE(__pyx_v_v))))); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = (__Pyx_PySequence_Contains(((PyObject *)Py_TYPE(__pyx_v_v)), __pyx_t_6, Py_EQ)); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_9) {
- /* "TabProxies.pyx":467
+ /* "pysam/TabProxies.pyx":467
* for k,v in d.items():
* if type(v) in types.StringTypes:
* aa.append( '%s "%s"' % (k,v) ) # <<<<<<<<<<<<<<
@@ -6257,7 +6336,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
}
/*else*/ {
- /* "TabProxies.pyx":469
+ /* "pysam/TabProxies.pyx":469
* aa.append( '%s "%s"' % (k,v) )
* else:
* aa.append( '%s %s' % (k,str(v)) ) # <<<<<<<<<<<<<<
@@ -6290,7 +6369,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "TabProxies.pyx":471
+ /* "pysam/TabProxies.pyx":471
* aa.append( '%s %s' % (k,str(v)) )
*
* a = "; ".join( aa ) + ";" # <<<<<<<<<<<<<<
@@ -6314,7 +6393,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__pyx_v_a = __pyx_t_6;
__pyx_t_6 = 0;
- /* "TabProxies.pyx":472
+ /* "pysam/TabProxies.pyx":472
*
* a = "; ".join( aa ) + ";"
* p = a # <<<<<<<<<<<<<<
@@ -6324,7 +6403,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__pyx_t_11 = PyBytes_AsString(__pyx_v_a); if (unlikely((!__pyx_t_11) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_p = __pyx_t_11;
- /* "TabProxies.pyx":473
+ /* "pysam/TabProxies.pyx":473
* a = "; ".join( aa ) + ";"
* p = a
* l = len(a) # <<<<<<<<<<<<<<
@@ -6334,7 +6413,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__pyx_t_3 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_l = __pyx_t_3;
- /* "TabProxies.pyx":474
+ /* "pysam/TabProxies.pyx":474
* p = a
* l = len(a)
* self._attributes = <char *>calloc( l + 1, sizeof(char) ) # <<<<<<<<<<<<<<
@@ -6343,7 +6422,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
*/
__pyx_v_self->_attributes = ((char *)calloc((__pyx_v_l + 1), (sizeof(char))));
- /* "TabProxies.pyx":475
+ /* "pysam/TabProxies.pyx":475
* l = len(a)
* self._attributes = <char *>calloc( l + 1, sizeof(char) )
* if self._attributes == NULL: # <<<<<<<<<<<<<<
@@ -6353,7 +6432,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__pyx_t_9 = (__pyx_v_self->_attributes == NULL);
if (__pyx_t_9) {
- /* "TabProxies.pyx":476
+ /* "pysam/TabProxies.pyx":476
* self._attributes = <char *>calloc( l + 1, sizeof(char) )
* if self._attributes == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
@@ -6369,7 +6448,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
}
__pyx_L9:;
- /* "TabProxies.pyx":477
+ /* "pysam/TabProxies.pyx":477
* if self._attributes == NULL:
* raise ValueError("out of memory" )
* memcpy( self._attributes, p, l ) # <<<<<<<<<<<<<<
@@ -6378,7 +6457,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
*/
memcpy(__pyx_v_self->_attributes, __pyx_v_p, __pyx_v_l);
- /* "TabProxies.pyx":479
+ /* "pysam/TabProxies.pyx":479
* memcpy( self._attributes, p, l )
*
* self.hasOwnAttributes = True # <<<<<<<<<<<<<<
@@ -6387,7 +6466,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
*/
__pyx_v_self->hasOwnAttributes = 1;
- /* "TabProxies.pyx":480
+ /* "pysam/TabProxies.pyx":480
*
* self.hasOwnAttributes = True
* self.is_modified = True # <<<<<<<<<<<<<<
@@ -6404,7 +6483,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_AddTraceback("TabProxies.GTFProxy.fromDict", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.fromDict", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_aa);
@@ -6417,17 +6496,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_6fromDict(struct __pyx_obj_10Ta
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_9__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_9__str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_9__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_9__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_8__str__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_8__str__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":482
+/* "pysam/TabProxies.pyx":482
* self.is_modified = True
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -6435,7 +6514,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_9__str__(PyObject *__pyx_v_self
* cdef int x
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -6454,7 +6533,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__str__", 0);
- /* "TabProxies.pyx":486
+ /* "pysam/TabProxies.pyx":486
* cdef int x
*
* if self.is_modified: # <<<<<<<<<<<<<<
@@ -6463,7 +6542,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
*/
if (__pyx_v_self->__pyx_base.is_modified) {
- /* "TabProxies.pyx":487
+ /* "pysam/TabProxies.pyx":487
*
* if self.is_modified:
* return "\t".join( # <<<<<<<<<<<<<<
@@ -6474,7 +6553,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_18), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "TabProxies.pyx":488
+ /* "pysam/TabProxies.pyx":488
* if self.is_modified:
* return "\t".join(
* (self.contig, # <<<<<<<<<<<<<<
@@ -6484,7 +6563,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__contig); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- /* "TabProxies.pyx":489
+ /* "pysam/TabProxies.pyx":489
* return "\t".join(
* (self.contig,
* self.source, # <<<<<<<<<<<<<<
@@ -6494,7 +6573,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__source); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- /* "TabProxies.pyx":490
+ /* "pysam/TabProxies.pyx":490
* (self.contig,
* self.source,
* self.feature, # <<<<<<<<<<<<<<
@@ -6504,7 +6583,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__feature); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- /* "TabProxies.pyx":491
+ /* "pysam/TabProxies.pyx":491
* self.source,
* self.feature,
* str(self.start+1), # <<<<<<<<<<<<<<
@@ -6525,7 +6604,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- /* "TabProxies.pyx":492
+ /* "pysam/TabProxies.pyx":492
* self.feature,
* str(self.start+1),
* str(self.end), # <<<<<<<<<<<<<<
@@ -6543,7 +6622,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- /* "TabProxies.pyx":493
+ /* "pysam/TabProxies.pyx":493
* str(self.start+1),
* str(self.end),
* toDot(self.score), # <<<<<<<<<<<<<<
@@ -6564,7 +6643,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- /* "TabProxies.pyx":494
+ /* "pysam/TabProxies.pyx":494
* str(self.end),
* toDot(self.score),
* self.strand, # <<<<<<<<<<<<<<
@@ -6574,7 +6653,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__strand); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- /* "TabProxies.pyx":495
+ /* "pysam/TabProxies.pyx":495
* toDot(self.score),
* self.strand,
* self.frame, # <<<<<<<<<<<<<<
@@ -6584,7 +6663,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__frame); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "TabProxies.pyx":496
+ /* "pysam/TabProxies.pyx":496
* self.strand,
* self.frame,
* self.attributes ) ) # <<<<<<<<<<<<<<
@@ -6638,7 +6717,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
}
/*else*/ {
- /* "TabProxies.pyx":498
+ /* "pysam/TabProxies.pyx":498
* self.attributes ) )
* else:
* return TupleProxy.__str__(self) # <<<<<<<<<<<<<<
@@ -6646,7 +6725,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
* def invert( self, int lcontig ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_11 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_TupleProxy)), __pyx_n_s____str__); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_TupleProxy)), __pyx_n_s____str__); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
@@ -6677,7 +6756,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("TabProxies.GTFProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -6686,9 +6765,9 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_8__str__(struct __pyx_obj_10Tab
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_11invert(PyObject *__pyx_v_self, PyObject *__pyx_arg_lcontig); /*proto*/
-static char __pyx_doc_10TabProxies_8GTFProxy_10invert[] = "invert coordinates to negative strand coordinates\n \n This method will only act if the feature is on the\n negative strand.";
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_11invert(PyObject *__pyx_v_self, PyObject *__pyx_arg_lcontig) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_11invert(PyObject *__pyx_v_self, PyObject *__pyx_arg_lcontig); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8GTFProxy_10invert[] = "invert coordinates to negative strand coordinates\n \n This method will only act if the feature is on the\n negative strand.";
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_11invert(PyObject *__pyx_v_self, PyObject *__pyx_arg_lcontig) {
int __pyx_v_lcontig;
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
@@ -6698,16 +6777,16 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_11invert(PyObject *__pyx_v_self
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L3_error:;
- __Pyx_AddTraceback("TabProxies.GTFProxy.invert", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.invert", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_10invert(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((int)__pyx_v_lcontig));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_10invert(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((int)__pyx_v_lcontig));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":500
+/* "pysam/TabProxies.pyx":500
* return TupleProxy.__str__(self)
*
* def invert( self, int lcontig ): # <<<<<<<<<<<<<<
@@ -6715,7 +6794,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_11invert(PyObject *__pyx_v_self
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, int __pyx_v_lcontig) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, int __pyx_v_lcontig) {
PyObject *__pyx_v_start = NULL;
PyObject *__pyx_v_end = NULL;
PyObject *__pyx_r = NULL;
@@ -6730,7 +6809,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10Tab
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("invert", 0);
- /* "TabProxies.pyx":506
+ /* "pysam/TabProxies.pyx":506
* negative strand.'''
*
* if self.strand[0] == '-': # <<<<<<<<<<<<<<
@@ -6742,67 +6821,71 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10Tab
__pyx_t_2 = __Pyx_GetItemInt(__pyx_t_1, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_41), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_41), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "TabProxies.pyx":507
+ /* "pysam/TabProxies.pyx":507
*
* if self.strand[0] == '-':
* start = min(self.start, self.end) # <<<<<<<<<<<<<<
* end = max(self.start, self.end)
* self.start, self.end = lcontig - end, lcontig - start
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__end); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_3) {
- __Pyx_INCREF(__pyx_t_2);
- __pyx_t_4 = __pyx_t_2;
- } else {
__Pyx_INCREF(__pyx_t_1);
__pyx_t_4 = __pyx_t_1;
+ } else {
+ __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_4 = __pyx_t_2;
}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_INCREF(__pyx_t_4);
- __pyx_v_start = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = __pyx_t_4;
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_start = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "TabProxies.pyx":508
+ /* "pysam/TabProxies.pyx":508
* if self.strand[0] == '-':
* start = min(self.start, self.end)
* end = max(self.start, self.end) # <<<<<<<<<<<<<<
* self.start, self.end = lcontig - end, lcontig - start
*
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_4, Py_GT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_3) {
- __Pyx_INCREF(__pyx_t_4);
- __pyx_t_1 = __pyx_t_4;
+ __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_2 = __pyx_t_1;
} else {
- __Pyx_INCREF(__pyx_t_2);
- __pyx_t_1 = __pyx_t_2;
+ __Pyx_INCREF(__pyx_t_4);
+ __pyx_t_2 = __pyx_t_4;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = __pyx_t_2;
__Pyx_INCREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_end = __pyx_t_1;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = 0;
- /* "TabProxies.pyx":509
+ /* "pysam/TabProxies.pyx":509
* start = min(self.start, self.end)
* end = max(self.start, self.end)
* self.start, self.end = lcontig - end, lcontig - start # <<<<<<<<<<<<<<
@@ -6811,18 +6894,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10Tab
*/
__pyx_t_1 = PyInt_FromLong(__pyx_v_lcontig); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyNumber_Subtract(__pyx_t_1, __pyx_v_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_2 = PyNumber_Subtract(__pyx_t_1, __pyx_v_end); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyInt_FromLong(__pyx_v_lcontig); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_Subtract(__pyx_t_1, __pyx_v_start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyNumber_Subtract(__pyx_t_1, __pyx_v_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__end, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__start, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__end, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L3;
}
__pyx_L3:;
@@ -6834,7 +6917,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10Tab
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("TabProxies.GTFProxy.invert", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.invert", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_start);
@@ -6845,18 +6928,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_10invert(struct __pyx_obj_10Tab
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_13keys(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_10TabProxies_8GTFProxy_12keys[] = "return a list of attributes defined in this entry.";
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_13keys(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_13keys(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8GTFProxy_12keys[] = "return a list of attributes defined in this entry.";
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_13keys(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("keys (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_12keys(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_12keys(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":511
+/* "pysam/TabProxies.pyx":511
* self.start, self.end = lcontig - end, lcontig - start
*
* def keys( self ): # <<<<<<<<<<<<<<
@@ -6864,7 +6947,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_13keys(PyObject *__pyx_v_self,
* r = self.attributes
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self) {
PyObject *__pyx_v_r = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_r = NULL;
@@ -6881,7 +6964,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabPr
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("keys", 0);
- /* "TabProxies.pyx":513
+ /* "pysam/TabProxies.pyx":513
* def keys( self ):
* '''return a list of attributes defined in this entry.'''
* r = self.attributes # <<<<<<<<<<<<<<
@@ -6893,7 +6976,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabPr
__pyx_v_r = __pyx_t_1;
__pyx_t_1 = 0;
- /* "TabProxies.pyx":514
+ /* "pysam/TabProxies.pyx":514
* '''return a list of attributes defined in this entry.'''
* r = self.attributes
* return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ] # <<<<<<<<<<<<<<
@@ -6920,10 +7003,18 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabPr
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_3 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_3 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_3); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_3 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_3 = __pyx_t_5(__pyx_t_2);
if (unlikely(!__pyx_t_3)) {
@@ -6943,25 +7034,27 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabPr
__pyx_t_6 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_7 = __Pyx_PyString_Equals(__pyx_t_6, ((PyObject *)__pyx_kp_s_6), Py_NE); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_6, ((PyObject *)__pyx_kp_s_6), Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_7) {
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_x, __pyx_n_s__strip); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_3 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_x, __pyx_n_s__strip); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_k_tuple_43), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__split); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_t_3, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_43), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_6))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_6, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_t_3))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
goto __pyx_L5;
}
__pyx_L5:;
@@ -6979,7 +7072,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabPr
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("TabProxies.GTFProxy.keys", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.keys", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_r);
@@ -6990,17 +7083,17 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_12keys(struct __pyx_obj_10TabPr
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_15__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_15__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_15__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_15__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_14__getitem__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_14__getitem__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":516
+/* "pysam/TabProxies.pyx":516
* return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ]
*
* def __getitem__(self, key): # <<<<<<<<<<<<<<
@@ -7008,7 +7101,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_15__getitem__(PyObject *__pyx_v
*
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_key) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_key) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -7019,7 +7112,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__getitem__", 0);
- /* "TabProxies.pyx":517
+ /* "pysam/TabProxies.pyx":517
*
* def __getitem__(self, key):
* return self.__getattr__( key ) # <<<<<<<<<<<<<<
@@ -7048,7 +7141,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.__getitem__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -7057,19 +7150,21 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_14__getitem__(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_17__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_item); /*proto*/
-static char __pyx_doc_10TabProxies_8GTFProxy_16__getattr__[] = "Generic lookup of attribute from GFF/GTF attributes \n Only called if there *isn't* an attribute with this name\n ";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_8GTFProxy_16__getattr__;
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_17__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_item) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_item); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8GTFProxy_16__getattr__[] = "Generic lookup of attribute from GFF/GTF attributes \n Only called if there *isn't* an attribute with this name\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_8GTFProxy_16__getattr__;
+#endif
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_item) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__getattr__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_16__getattr__(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_item));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_16__getattr__(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_item));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":519
+/* "pysam/TabProxies.pyx":519
* return self.__getattr__( key )
*
* def __getattr__(self, item ): # <<<<<<<<<<<<<<
@@ -7077,7 +7172,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_17__getattr__(PyObject *__pyx_v
* Only called if there *isn't* an attribute with this name
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_item) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_item) {
char *__pyx_v_start;
char *__pyx_v_query;
char *__pyx_v_end;
@@ -7098,28 +7193,28 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__getattr__", 0);
- /* "TabProxies.pyx":542
+ /* "pysam/TabProxies.pyx":542
* # disappeard after accessing the C data structures
* # directly and so did the bug.
* cdef char * attributes = self.getAttributes() # <<<<<<<<<<<<<<
*
* r = _force_bytes(item)
*/
- __pyx_v_attributes = ((struct __pyx_vtabstruct_10TabProxies_GTFProxy *)__pyx_v_self->__pyx_base.__pyx_vtab)->getAttributes(__pyx_v_self);
+ __pyx_v_attributes = ((struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *)__pyx_v_self->__pyx_base.__pyx_vtab)->getAttributes(__pyx_v_self);
- /* "TabProxies.pyx":544
+ /* "pysam/TabProxies.pyx":544
* cdef char * attributes = self.getAttributes()
*
* r = _force_bytes(item) # <<<<<<<<<<<<<<
* query = r
* start = strstr( attributes, query)
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_10TabProxies__force_bytes(__pyx_v_item)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_10TabProxies__force_bytes(__pyx_v_item)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_r = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "TabProxies.pyx":545
+ /* "pysam/TabProxies.pyx":545
*
* r = _force_bytes(item)
* query = r # <<<<<<<<<<<<<<
@@ -7129,7 +7224,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_r)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_query = __pyx_t_2;
- /* "TabProxies.pyx":546
+ /* "pysam/TabProxies.pyx":546
* r = _force_bytes(item)
* query = r
* start = strstr( attributes, query) # <<<<<<<<<<<<<<
@@ -7138,7 +7233,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
*/
__pyx_v_start = strstr(__pyx_v_attributes, __pyx_v_query);
- /* "TabProxies.pyx":548
+ /* "pysam/TabProxies.pyx":548
* start = strstr( attributes, query)
*
* if start == NULL: # <<<<<<<<<<<<<<
@@ -7148,7 +7243,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__pyx_t_3 = (__pyx_v_start == NULL);
if (__pyx_t_3) {
- /* "TabProxies.pyx":549
+ /* "pysam/TabProxies.pyx":549
*
* if start == NULL:
* raise AttributeError("'GTFProxy' has no attribute '%s'" % item ) # <<<<<<<<<<<<<<
@@ -7172,7 +7267,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
}
__pyx_L3:;
- /* "TabProxies.pyx":551
+ /* "pysam/TabProxies.pyx":551
* raise AttributeError("'GTFProxy' has no attribute '%s'" % item )
*
* start += strlen(query) + 1 # <<<<<<<<<<<<<<
@@ -7181,7 +7276,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
*/
__pyx_v_start = (__pyx_v_start + (strlen(__pyx_v_query) + 1));
- /* "TabProxies.pyx":553
+ /* "pysam/TabProxies.pyx":553
* start += strlen(query) + 1
* # skip gaps before
* while start[0] == ' ': start += 1 # <<<<<<<<<<<<<<
@@ -7194,7 +7289,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__pyx_v_start = (__pyx_v_start + 1);
}
- /* "TabProxies.pyx":555
+ /* "pysam/TabProxies.pyx":555
* while start[0] == ' ': start += 1
*
* if start[0] == '"': # <<<<<<<<<<<<<<
@@ -7204,7 +7299,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__pyx_t_3 = ((__pyx_v_start[0]) == '"');
if (__pyx_t_3) {
- /* "TabProxies.pyx":556
+ /* "pysam/TabProxies.pyx":556
*
* if start[0] == '"':
* start += 1 # <<<<<<<<<<<<<<
@@ -7213,7 +7308,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
*/
__pyx_v_start = (__pyx_v_start + 1);
- /* "TabProxies.pyx":557
+ /* "pysam/TabProxies.pyx":557
* if start[0] == '"':
* start += 1
* end = start # <<<<<<<<<<<<<<
@@ -7222,7 +7317,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
*/
__pyx_v_end = __pyx_v_start;
- /* "TabProxies.pyx":558
+ /* "pysam/TabProxies.pyx":558
* start += 1
* end = start
* while end[0] != '\0' and end[0] != '"': end += 1 # <<<<<<<<<<<<<<
@@ -7241,7 +7336,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__pyx_v_end = (__pyx_v_end + 1);
}
- /* "TabProxies.pyx":559
+ /* "pysam/TabProxies.pyx":559
* end = start
* while end[0] != '\0' and end[0] != '"': end += 1
* l = end - start # <<<<<<<<<<<<<<
@@ -7250,7 +7345,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
*/
__pyx_v_l = (__pyx_v_end - __pyx_v_start);
- /* "TabProxies.pyx":560
+ /* "pysam/TabProxies.pyx":560
* while end[0] != '\0' and end[0] != '"': end += 1
* l = end - start
* result = _force_str( PyBytes_FromStringAndSize( start, l ) ) # <<<<<<<<<<<<<<
@@ -7259,13 +7354,13 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
*/
__pyx_t_1 = ((PyObject *)PyBytes_FromStringAndSize(__pyx_v_start, __pyx_v_l)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __pyx_f_10TabProxies__force_str(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_5pysam_10TabProxies__force_str(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_result = __pyx_t_4;
__pyx_t_4 = 0;
- /* "TabProxies.pyx":561
+ /* "pysam/TabProxies.pyx":561
* l = end - start
* result = _force_str( PyBytes_FromStringAndSize( start, l ) )
* return result # <<<<<<<<<<<<<<
@@ -7280,7 +7375,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
}
/*else*/ {
- /* "TabProxies.pyx":563
+ /* "pysam/TabProxies.pyx":563
* return result
* else:
* return _force_str( start ) # <<<<<<<<<<<<<<
@@ -7290,7 +7385,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__Pyx_XDECREF(__pyx_r);
__pyx_t_4 = PyBytes_FromString(__pyx_v_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_1 = __pyx_f_10TabProxies__force_str(((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_10TabProxies__force_str(((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_r = __pyx_t_1;
@@ -7304,7 +7399,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("TabProxies.GTFProxy.__getattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.__getattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_r);
@@ -7315,16 +7410,16 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_16__getattr__(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_10TabProxies_8GTFProxy_18setAttribute[] = "convenience method to set an attribute.";
-static PyObject *__pyx_pw_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8GTFProxy_18setAttribute[] = "convenience method to set an attribute.";
+static PyObject *__pyx_pw_5pysam_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_name = 0;
PyObject *__pyx_v_value = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__name,&__pyx_n_s__value,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setAttribute (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__name,&__pyx_n_s__value,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -7338,12 +7433,10 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__name);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__name)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("setAttribute", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -7364,16 +7457,16 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("setAttribute", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("TabProxies.GTFProxy.setAttribute", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.setAttribute", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
- __pyx_r = __pyx_pf_10TabProxies_8GTFProxy_18setAttribute(((struct __pyx_obj_10TabProxies_GTFProxy *)__pyx_v_self), __pyx_v_name, __pyx_v_value);
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8GTFProxy_18setAttribute(((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)__pyx_v_self), __pyx_v_name, __pyx_v_value);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":565
+/* "pysam/TabProxies.pyx":565
* return _force_str( start )
*
* def setAttribute( self, name, value ): # <<<<<<<<<<<<<<
@@ -7381,7 +7474,7 @@ static PyObject *__pyx_pw_10TabProxies_8GTFProxy_19setAttribute(PyObject *__pyx_
* r = self.asDict()
*/
-static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self, PyObject *__pyx_v_name, PyObject *__pyx_v_value) {
PyObject *__pyx_v_r = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -7393,7 +7486,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setAttribute", 0);
- /* "TabProxies.pyx":567
+ /* "pysam/TabProxies.pyx":567
* def setAttribute( self, name, value ):
* '''convenience method to set an attribute.'''
* r = self.asDict() # <<<<<<<<<<<<<<
@@ -7408,7 +7501,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj
__pyx_v_r = __pyx_t_2;
__pyx_t_2 = 0;
- /* "TabProxies.pyx":568
+ /* "pysam/TabProxies.pyx":568
* '''convenience method to set an attribute.'''
* r = self.asDict()
* r[name] = value # <<<<<<<<<<<<<<
@@ -7417,7 +7510,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj
*/
if (PyObject_SetItem(__pyx_v_r, __pyx_v_name, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "TabProxies.pyx":569
+ /* "pysam/TabProxies.pyx":569
* r = self.asDict()
* r[name] = value
* self.fromDict( r ) # <<<<<<<<<<<<<<
@@ -7443,7 +7536,7 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.GTFProxy.setAttribute", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.GTFProxy.setAttribute", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_r);
@@ -7453,19 +7546,21 @@ static PyObject *__pyx_pf_10TabProxies_8GTFProxy_18setAttribute(struct __pyx_obj
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_15NamedTupleProxy_1__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/
-static char __pyx_doc_10TabProxies_15NamedTupleProxy___setattr__[] = "set attribute.";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__;
-static int __pyx_pw_10TabProxies_15NamedTupleProxy_1__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_1__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_15NamedTupleProxy___setattr__[] = "set attribute.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_15NamedTupleProxy___setattr__;
+#endif
+static int __pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_1__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__setattr__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(((struct __pyx_obj_10TabProxies_NamedTupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_15NamedTupleProxy___setattr__(((struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":575
+/* "pysam/TabProxies.pyx":575
* map_key2field = {}
*
* def __setattr__(self, key, value ): # <<<<<<<<<<<<<<
@@ -7473,7 +7568,7 @@ static int __pyx_pw_10TabProxies_15NamedTupleProxy_1__setattr__(PyObject *__pyx_
* cdef int idx
*/
-static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
int __pyx_v_idx;
CYTHON_UNUSED PyObject *__pyx_v_f = NULL;
int __pyx_r;
@@ -7490,7 +7585,7 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__setattr__", 0);
- /* "TabProxies.pyx":578
+ /* "pysam/TabProxies.pyx":578
* '''set attribute.'''
* cdef int idx
* idx, f = self.map_key2field[key] # <<<<<<<<<<<<<<
@@ -7504,27 +7599,35 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_3 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_3);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
__pyx_t_4 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
@@ -7535,12 +7638,13 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
index = 1; __pyx_t_3 = __pyx_t_5(__pyx_t_4); if (unlikely(!__pyx_t_3)) goto __pyx_L3_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_5(__pyx_t_4), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = NULL;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L4_unpacking_done;
__pyx_L3_unpacking_failed:;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_5 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L4_unpacking_done:;
}
@@ -7550,7 +7654,7 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
__pyx_v_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "TabProxies.pyx":579
+ /* "pysam/TabProxies.pyx":579
* cdef int idx
* idx, f = self.map_key2field[key]
* if self.nfields < idx: # <<<<<<<<<<<<<<
@@ -7560,7 +7664,7 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
__pyx_t_7 = (__pyx_v_self->__pyx_base.nfields < __pyx_v_idx);
if (__pyx_t_7) {
- /* "TabProxies.pyx":580
+ /* "pysam/TabProxies.pyx":580
* idx, f = self.map_key2field[key]
* if self.nfields < idx:
* raise KeyError( "field %s not set" % key ) # <<<<<<<<<<<<<<
@@ -7584,14 +7688,14 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
}
__pyx_L5:;
- /* "TabProxies.pyx":581
+ /* "pysam/TabProxies.pyx":581
* if self.nfields < idx:
* raise KeyError( "field %s not set" % key )
* TupleProxy.__setitem__(self, idx, str(value) ) # <<<<<<<<<<<<<<
*
* def __getattr__(self, key ):
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_TupleProxy)), __pyx_n_s____setitem__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_TupleProxy)), __pyx_n_s____setitem__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyInt_FromLong(__pyx_v_idx); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
@@ -7627,7 +7731,7 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("TabProxies.NamedTupleProxy.__setattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.NamedTupleProxy.__setattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_f);
@@ -7636,17 +7740,17 @@ static int __pyx_pf_10TabProxies_15NamedTupleProxy___setattr__(struct __pyx_obj_
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_15NamedTupleProxy_3__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_15NamedTupleProxy_3__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_3__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_3__getattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__getattr__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(((struct __pyx_obj_10TabProxies_NamedTupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_15NamedTupleProxy_2__getattr__(((struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":583
+/* "pysam/TabProxies.pyx":583
* TupleProxy.__setitem__(self, idx, str(value) )
*
* def __getattr__(self, key ): # <<<<<<<<<<<<<<
@@ -7654,7 +7758,7 @@ static PyObject *__pyx_pw_10TabProxies_15NamedTupleProxy_3__getattr__(PyObject *
* idx, f = self.map_key2field[key]
*/
-static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __pyx_obj_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_15NamedTupleProxy_2__getattr__(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *__pyx_v_self, PyObject *__pyx_v_key) {
int __pyx_v_idx;
PyObject *__pyx_v_f = NULL;
PyObject *__pyx_r = NULL;
@@ -7671,7 +7775,7 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__getattr__", 0);
- /* "TabProxies.pyx":585
+ /* "pysam/TabProxies.pyx":585
* def __getattr__(self, key ):
* cdef int idx
* idx, f = self.map_key2field[key] # <<<<<<<<<<<<<<
@@ -7685,27 +7789,35 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_3 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_3);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
__pyx_t_4 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
@@ -7716,12 +7828,13 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
index = 1; __pyx_t_3 = __pyx_t_5(__pyx_t_4); if (unlikely(!__pyx_t_3)) goto __pyx_L3_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_5(__pyx_t_4), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = NULL;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L4_unpacking_done;
__pyx_L3_unpacking_failed:;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_5 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L4_unpacking_done:;
}
@@ -7731,7 +7844,7 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
__pyx_v_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "TabProxies.pyx":586
+ /* "pysam/TabProxies.pyx":586
* cdef int idx
* idx, f = self.map_key2field[key]
* if self.nfields < idx: # <<<<<<<<<<<<<<
@@ -7741,7 +7854,7 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
__pyx_t_7 = (__pyx_v_self->__pyx_base.nfields < __pyx_v_idx);
if (__pyx_t_7) {
- /* "TabProxies.pyx":587
+ /* "pysam/TabProxies.pyx":587
* idx, f = self.map_key2field[key]
* if self.nfields < idx:
* raise KeyError( "field %s not set" % key ) # <<<<<<<<<<<<<<
@@ -7765,7 +7878,7 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
}
__pyx_L5:;
- /* "TabProxies.pyx":588
+ /* "pysam/TabProxies.pyx":588
* if self.nfields < idx:
* raise KeyError( "field %s not set" % key )
* return f( self.fields[idx] ) # <<<<<<<<<<<<<<
@@ -7794,7 +7907,7 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("TabProxies.NamedTupleProxy.__getattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.NamedTupleProxy.__getattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_f);
@@ -7803,7 +7916,7 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
return __pyx_r;
}
-/* "TabProxies.pyx":609
+/* "pysam/TabProxies.pyx":609
* 'blockStarts': (11, bytes), }
*
* cdef int getMaxFields( self, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -7811,12 +7924,12 @@ static PyObject *__pyx_pf_10TabProxies_15NamedTupleProxy_2__getattr__(struct __p
* return 12
*/
-static int __pyx_f_10TabProxies_8BedProxy_getMaxFields(CYTHON_UNUSED struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_self, CYTHON_UNUSED size_t __pyx_v_nbytes) {
+static int __pyx_f_5pysam_10TabProxies_8BedProxy_getMaxFields(CYTHON_UNUSED struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self, CYTHON_UNUSED size_t __pyx_v_nbytes) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getMaxFields", 0);
- /* "TabProxies.pyx":611
+ /* "pysam/TabProxies.pyx":611
* cdef int getMaxFields( self, size_t nbytes ):
* '''return max number of fields.'''
* return 12 # <<<<<<<<<<<<<<
@@ -7832,7 +7945,7 @@ static int __pyx_f_10TabProxies_8BedProxy_getMaxFields(CYTHON_UNUSED struct __py
return __pyx_r;
}
-/* "TabProxies.pyx":613
+/* "pysam/TabProxies.pyx":613
* return 12
*
* cdef update( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -7840,28 +7953,29 @@ static int __pyx_f_10TabProxies_8BedProxy_getMaxFields(CYTHON_UNUSED struct __py
*
*/
-static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static PyObject *__pyx_f_5pysam_10TabProxies_8BedProxy_update(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
int __pyx_t_2;
+ int __pyx_t_3;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("update", 0);
- /* "TabProxies.pyx":618
+ /* "pysam/TabProxies.pyx":618
* nbytes does not include the terminal '\0'.
* '''
* TupleProxy.update( self, buffer, nbytes ) # <<<<<<<<<<<<<<
*
* if self.nfields < 3:
*/
- __pyx_t_1 = __pyx_vtabptr_10TabProxies_TupleProxy->update(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5pysam_10TabProxies_TupleProxy->update(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "TabProxies.pyx":620
+ /* "pysam/TabProxies.pyx":620
* TupleProxy.update( self, buffer, nbytes )
*
* if self.nfields < 3: # <<<<<<<<<<<<<<
@@ -7871,7 +7985,7 @@ static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabPro
__pyx_t_2 = (__pyx_v_self->__pyx_base.__pyx_base.nfields < 3);
if (__pyx_t_2) {
- /* "TabProxies.pyx":621
+ /* "pysam/TabProxies.pyx":621
*
* if self.nfields < 3:
* raise ValueError( "bed format requires at least three columns" ) # <<<<<<<<<<<<<<
@@ -7887,16 +8001,17 @@ static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabPro
}
__pyx_L3:;
- /* "TabProxies.pyx":624
+ /* "pysam/TabProxies.pyx":624
*
* # determines bed format
* self.bedfields = self.nfields # <<<<<<<<<<<<<<
*
* # do automatic conversion
*/
- __pyx_v_self->bedfields = __pyx_v_self->__pyx_base.__pyx_base.nfields;
+ __pyx_t_3 = __pyx_v_self->__pyx_base.__pyx_base.nfields;
+ __pyx_v_self->bedfields = __pyx_t_3;
- /* "TabProxies.pyx":627
+ /* "pysam/TabProxies.pyx":627
*
* # do automatic conversion
* self.contig = self.fields[0] # <<<<<<<<<<<<<<
@@ -7905,7 +8020,7 @@ static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabPro
*/
__pyx_v_self->contig = (__pyx_v_self->__pyx_base.__pyx_base.fields[0]);
- /* "TabProxies.pyx":628
+ /* "pysam/TabProxies.pyx":628
* # do automatic conversion
* self.contig = self.fields[0]
* self.start = atoi( self.fields[1] ) # <<<<<<<<<<<<<<
@@ -7914,7 +8029,7 @@ static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabPro
*/
__pyx_v_self->start = atoi((__pyx_v_self->__pyx_base.__pyx_base.fields[1]));
- /* "TabProxies.pyx":629
+ /* "pysam/TabProxies.pyx":629
* self.contig = self.fields[0]
* self.start = atoi( self.fields[1] )
* self.end = atoi( self.fields[2] ) # <<<<<<<<<<<<<<
@@ -7927,7 +8042,7 @@ static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabPro
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("TabProxies.BedProxy.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.BedProxy.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -7936,17 +8051,17 @@ static PyObject *__pyx_f_10TabProxies_8BedProxy_update(struct __pyx_obj_10TabPro
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8BedProxy_1__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8BedProxy_1__str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8BedProxy_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8BedProxy_1__str__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8BedProxy___str__(((struct __pyx_obj_10TabProxies_BedProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8BedProxy___str__(((struct __pyx_obj_5pysam_10TabProxies_BedProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":638
+/* "pysam/TabProxies.pyx":638
* # def __get__( self ): return self.end
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -7954,59 +8069,62 @@ static PyObject *__pyx_pw_10TabProxies_8BedProxy_1__str__(PyObject *__pyx_v_self
* cdef int save_fields = self.nfields
*/
-static PyObject *__pyx_pf_10TabProxies_8BedProxy___str__(struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8BedProxy___str__(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self) {
int __pyx_v_save_fields;
PyObject *__pyx_v_retval = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__str__", 0);
- /* "TabProxies.pyx":640
+ /* "pysam/TabProxies.pyx":640
* def __str__(self):
*
* cdef int save_fields = self.nfields # <<<<<<<<<<<<<<
* # ensure fields to use correct format
* self.nfields = self.bedfields
*/
- __pyx_v_save_fields = __pyx_v_self->__pyx_base.__pyx_base.nfields;
+ __pyx_t_1 = __pyx_v_self->__pyx_base.__pyx_base.nfields;
+ __pyx_v_save_fields = __pyx_t_1;
- /* "TabProxies.pyx":642
+ /* "pysam/TabProxies.pyx":642
* cdef int save_fields = self.nfields
* # ensure fields to use correct format
* self.nfields = self.bedfields # <<<<<<<<<<<<<<
* retval = TupleProxy.__str__( self )
* self.nfields = save_fields
*/
- __pyx_v_self->__pyx_base.__pyx_base.nfields = __pyx_v_self->bedfields;
+ __pyx_t_1 = __pyx_v_self->bedfields;
+ __pyx_v_self->__pyx_base.__pyx_base.nfields = __pyx_t_1;
- /* "TabProxies.pyx":643
+ /* "pysam/TabProxies.pyx":643
* # ensure fields to use correct format
* self.nfields = self.bedfields
* retval = TupleProxy.__str__( self ) # <<<<<<<<<<<<<<
* self.nfields = save_fields
* return retval
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_TupleProxy)), __pyx_n_s____str__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_TupleProxy)), __pyx_n_s____str__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_v_retval = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_v_retval = __pyx_t_4;
+ __pyx_t_4 = 0;
- /* "TabProxies.pyx":644
+ /* "pysam/TabProxies.pyx":644
* self.nfields = self.bedfields
* retval = TupleProxy.__str__( self )
* self.nfields = save_fields # <<<<<<<<<<<<<<
@@ -8015,7 +8133,7 @@ static PyObject *__pyx_pf_10TabProxies_8BedProxy___str__(struct __pyx_obj_10TabP
*/
__pyx_v_self->__pyx_base.__pyx_base.nfields = __pyx_v_save_fields;
- /* "TabProxies.pyx":645
+ /* "pysam/TabProxies.pyx":645
* retval = TupleProxy.__str__( self )
* self.nfields = save_fields
* return retval # <<<<<<<<<<<<<<
@@ -8030,10 +8148,10 @@ static PyObject *__pyx_pf_10TabProxies_8BedProxy___str__(struct __pyx_obj_10TabP
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("TabProxies.BedProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.TabProxies.BedProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_retval);
@@ -8043,19 +8161,21 @@ static PyObject *__pyx_pf_10TabProxies_8BedProxy___str__(struct __pyx_obj_10TabP
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8BedProxy_3__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/
-static char __pyx_doc_10TabProxies_8BedProxy_2__setattr__[] = "set attribute.";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_8BedProxy_2__setattr__;
-static int __pyx_pw_10TabProxies_8BedProxy_3__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8BedProxy_3__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8BedProxy_2__setattr__[] = "set attribute.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_8BedProxy_2__setattr__;
+#endif
+static int __pyx_pw_5pysam_10TabProxies_8BedProxy_3__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__setattr__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8BedProxy_2__setattr__(((struct __pyx_obj_10TabProxies_BedProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8BedProxy_2__setattr__(((struct __pyx_obj_5pysam_10TabProxies_BedProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":647
+/* "pysam/TabProxies.pyx":647
* return retval
*
* def __setattr__(self, key, value ): # <<<<<<<<<<<<<<
@@ -8063,14 +8183,14 @@ static int __pyx_pw_10TabProxies_8BedProxy_3__setattr__(PyObject *__pyx_v_self,
* if key == "start": self.start = value
*/
-static int __pyx_pf_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_10TabProxies_BedProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_5pysam_10TabProxies_BedProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
int __pyx_v_idx;
CYTHON_UNUSED PyObject *__pyx_v_f = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- uint32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ uint32_t __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
PyObject *__pyx_t_6 = NULL;
@@ -8081,139 +8201,152 @@ static int __pyx_pf_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_10TabPr
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__setattr__", 0);
- /* "TabProxies.pyx":649
+ /* "pysam/TabProxies.pyx":649
* def __setattr__(self, key, value ):
* '''set attribute.'''
* if key == "start": self.start = value # <<<<<<<<<<<<<<
* elif key == "end": self.end = value
*
*/
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__start), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- __pyx_t_2 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_value); if (unlikely((__pyx_t_2 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->start = __pyx_t_2;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__start), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
+ __pyx_t_3 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_value); if (unlikely((__pyx_t_3 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->start = __pyx_t_3;
goto __pyx_L3;
}
- /* "TabProxies.pyx":650
+ /* "pysam/TabProxies.pyx":650
* '''set attribute.'''
* if key == "start": self.start = value
* elif key == "end": self.end = value # <<<<<<<<<<<<<<
*
* cdef int idx
*/
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__end), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- __pyx_t_2 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_value); if (unlikely((__pyx_t_2 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->end = __pyx_t_2;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__end), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
+ __pyx_t_3 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_value); if (unlikely((__pyx_t_3 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->end = __pyx_t_3;
goto __pyx_L3;
}
__pyx_L3:;
- /* "TabProxies.pyx":653
+ /* "pysam/TabProxies.pyx":653
*
* cdef int idx
* idx, f = self.map_key2field[key] # <<<<<<<<<<<<<<
* TupleProxy._setindex(self, idx, str(value) )
*
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__map_key2field); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetItem(__pyx_t_3, __pyx_v_key); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__map_key2field); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_5 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_5 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_5);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
__pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_3);
+ index = 0; __pyx_t_1 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
index = 1; __pyx_t_5 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_5)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_5);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L5_unpacking_done;
__pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_7 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
}
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = __pyx_t_8;
__pyx_v_f = __pyx_t_5;
__pyx_t_5 = 0;
- /* "TabProxies.pyx":654
+ /* "pysam/TabProxies.pyx":654
* cdef int idx
* idx, f = self.map_key2field[key]
* TupleProxy._setindex(self, idx, str(value) ) # <<<<<<<<<<<<<<
*
* cdef class VCFProxy( NamedTupleProxy ):
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_TupleProxy)), __pyx_n_s___setindex); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_TupleProxy)), __pyx_n_s___setindex); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyInt_FromLong(__pyx_v_idx); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("TabProxies.BedProxy.__setattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.BedProxy.__setattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_f);
@@ -8222,20 +8355,20 @@ static int __pyx_pf_10TabProxies_8BedProxy_2__setattr__(struct __pyx_obj_10TabPr
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8VCFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pw_10TabProxies_8VCFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pw_5pysam_10TabProxies_8VCFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_10TabProxies_8VCFProxy_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 0))) return -1;
- __pyx_r = __pyx_pf_10TabProxies_8VCFProxy___cinit__(((struct __pyx_obj_10TabProxies_VCFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8VCFProxy___cinit__(((struct __pyx_obj_5pysam_10TabProxies_VCFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":672
+/* "pysam/TabProxies.pyx":672
* 'format' : (8, bytes) }
*
* def __cinit__(self ): # <<<<<<<<<<<<<<
@@ -8243,12 +8376,12 @@ static int __pyx_pw_10TabProxies_8VCFProxy_1__cinit__(PyObject *__pyx_v_self, Py
* # start indexed access at genotypes
*/
-static int __pyx_pf_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self) {
+static int __pyx_pf_5pysam_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
- /* "TabProxies.pyx":675
+ /* "pysam/TabProxies.pyx":675
* # automatically calls TupleProxy.__cinit__
* # start indexed access at genotypes
* self.offset = 9 # <<<<<<<<<<<<<<
@@ -8262,7 +8395,7 @@ static int __pyx_pf_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_10TabProxi
return __pyx_r;
}
-/* "TabProxies.pyx":677
+/* "pysam/TabProxies.pyx":677
* self.offset = 9
*
* cdef update( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -8270,7 +8403,7 @@ static int __pyx_pf_10TabProxies_8VCFProxy___cinit__(struct __pyx_obj_10TabProxi
*
*/
-static PyObject *__pyx_f_10TabProxies_8VCFProxy_update(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
+static PyObject *__pyx_f_5pysam_10TabProxies_8VCFProxy_update(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self, char *__pyx_v_buffer, size_t __pyx_v_nbytes) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -8279,18 +8412,18 @@ static PyObject *__pyx_f_10TabProxies_8VCFProxy_update(struct __pyx_obj_10TabPro
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("update", 0);
- /* "TabProxies.pyx":682
+ /* "pysam/TabProxies.pyx":682
* nbytes does not include the terminal '\0'.
* '''
* TupleProxy.update( self, buffer, nbytes ) # <<<<<<<<<<<<<<
*
* self.contig = self.fields[0]
*/
- __pyx_t_1 = __pyx_vtabptr_10TabProxies_TupleProxy->update(((struct __pyx_obj_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5pysam_10TabProxies_TupleProxy->update(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "TabProxies.pyx":684
+ /* "pysam/TabProxies.pyx":684
* TupleProxy.update( self, buffer, nbytes )
*
* self.contig = self.fields[0] # <<<<<<<<<<<<<<
@@ -8299,7 +8432,7 @@ static PyObject *__pyx_f_10TabProxies_8VCFProxy_update(struct __pyx_obj_10TabPro
*/
__pyx_v_self->contig = (__pyx_v_self->__pyx_base.__pyx_base.fields[0]);
- /* "TabProxies.pyx":686
+ /* "pysam/TabProxies.pyx":686
* self.contig = self.fields[0]
* # vcf counts from 1 - correct here
* self.pos = atoi( self.fields[1] ) - 1 # <<<<<<<<<<<<<<
@@ -8312,7 +8445,7 @@ static PyObject *__pyx_f_10TabProxies_8VCFProxy_update(struct __pyx_obj_10TabPro
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("TabProxies.VCFProxy.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.VCFProxy.update", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -8321,19 +8454,21 @@ static PyObject *__pyx_f_10TabProxies_8VCFProxy_update(struct __pyx_obj_10TabPro
}
/* Python wrapper */
-static Py_ssize_t __pyx_pw_10TabProxies_8VCFProxy_3__len__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_10TabProxies_8VCFProxy_2__len__[] = "return number of genotype fields.";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_8VCFProxy_2__len__;
-static Py_ssize_t __pyx_pw_10TabProxies_8VCFProxy_3__len__(PyObject *__pyx_v_self) {
+static Py_ssize_t __pyx_pw_5pysam_10TabProxies_8VCFProxy_3__len__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8VCFProxy_2__len__[] = "return number of genotype fields.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_2__len__;
+#endif
+static Py_ssize_t __pyx_pw_5pysam_10TabProxies_8VCFProxy_3__len__(PyObject *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8VCFProxy_2__len__(((struct __pyx_obj_10TabProxies_VCFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8VCFProxy_2__len__(((struct __pyx_obj_5pysam_10TabProxies_VCFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":688
+/* "pysam/TabProxies.pyx":688
* self.pos = atoi( self.fields[1] ) - 1
*
* def __len__(self): # <<<<<<<<<<<<<<
@@ -8341,7 +8476,7 @@ static Py_ssize_t __pyx_pw_10TabProxies_8VCFProxy_3__len__(PyObject *__pyx_v_sel
* return max(0, self.nfields - 9)
*/
-static Py_ssize_t __pyx_pf_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self) {
+static Py_ssize_t __pyx_pf_5pysam_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
long __pyx_t_1;
@@ -8349,7 +8484,7 @@ static Py_ssize_t __pyx_pf_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_10Ta
long __pyx_t_3;
__Pyx_RefNannySetupContext("__len__", 0);
- /* "TabProxies.pyx":690
+ /* "pysam/TabProxies.pyx":690
* def __len__(self):
* '''return number of genotype fields.'''
* return max(0, self.nfields - 9) # <<<<<<<<<<<<<<
@@ -8373,17 +8508,17 @@ static Py_ssize_t __pyx_pf_10TabProxies_8VCFProxy_2__len__(struct __pyx_obj_10Ta
}
/* Python wrapper */
-static PyObject *__pyx_pw_10TabProxies_8VCFProxy_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pw_10TabProxies_8VCFProxy_3pos_1__get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pw_5pysam_10TabProxies_8VCFProxy_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_10TabProxies_8VCFProxy_3pos_1__get__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8VCFProxy_3pos___get__(((struct __pyx_obj_10TabProxies_VCFProxy *)__pyx_v_self));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8VCFProxy_3pos___get__(((struct __pyx_obj_5pysam_10TabProxies_VCFProxy *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":694
+/* "pysam/TabProxies.pyx":694
* property pos:
* '''feature end (in 0-based open/closed coordinates).'''
* def __get__( self ): # <<<<<<<<<<<<<<
@@ -8391,7 +8526,7 @@ static PyObject *__pyx_pw_10TabProxies_8VCFProxy_3pos_1__get__(PyObject *__pyx_v
*
*/
-static PyObject *__pyx_pf_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -8400,7 +8535,7 @@ static PyObject *__pyx_pf_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_1
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "TabProxies.pyx":695
+ /* "pysam/TabProxies.pyx":695
* '''feature end (in 0-based open/closed coordinates).'''
* def __get__( self ):
* return self.pos # <<<<<<<<<<<<<<
@@ -8418,7 +8553,7 @@ static PyObject *__pyx_pf_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_1
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("TabProxies.VCFProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.VCFProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -8427,19 +8562,21 @@ static PyObject *__pyx_pf_10TabProxies_8VCFProxy_3pos___get__(struct __pyx_obj_1
}
/* Python wrapper */
-static int __pyx_pw_10TabProxies_8VCFProxy_5__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/
-static char __pyx_doc_10TabProxies_8VCFProxy_4__setattr__[] = "set attribute.";
-struct wrapperbase __pyx_wrapperbase_10TabProxies_8VCFProxy_4__setattr__;
-static int __pyx_pw_10TabProxies_8VCFProxy_5__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
+static int __pyx_pw_5pysam_10TabProxies_8VCFProxy_5__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /*proto*/
+static char __pyx_doc_5pysam_10TabProxies_8VCFProxy_4__setattr__[] = "set attribute.";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_4__setattr__;
+#endif
+static int __pyx_pw_5pysam_10TabProxies_8VCFProxy_5__setattr__(PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__setattr__ (wrapper)", 0);
- __pyx_r = __pyx_pf_10TabProxies_8VCFProxy_4__setattr__(((struct __pyx_obj_10TabProxies_VCFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value));
+ __pyx_r = __pyx_pf_5pysam_10TabProxies_8VCFProxy_4__setattr__(((struct __pyx_obj_5pysam_10TabProxies_VCFProxy *)__pyx_v_self), ((PyObject *)__pyx_v_key), ((PyObject *)__pyx_v_value));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "TabProxies.pyx":697
+/* "pysam/TabProxies.pyx":697
* return self.pos
*
* def __setattr__(self, key, value ): # <<<<<<<<<<<<<<
@@ -8447,14 +8584,14 @@ static int __pyx_pw_10TabProxies_8VCFProxy_5__setattr__(PyObject *__pyx_v_self,
* if key == "pos":
*/
-static int __pyx_pf_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_10TabProxies_VCFProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
+static int __pyx_pf_5pysam_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_5pysam_10TabProxies_VCFProxy *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value) {
int __pyx_v_idx;
CYTHON_UNUSED PyObject *__pyx_v_f = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- uint32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ uint32_t __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
PyObject *__pyx_t_6 = NULL;
@@ -8466,145 +8603,156 @@ static int __pyx_pf_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_10TabPr
__Pyx_RefNannySetupContext("__setattr__", 0);
__Pyx_INCREF(__pyx_v_value);
- /* "TabProxies.pyx":699
+ /* "pysam/TabProxies.pyx":699
* def __setattr__(self, key, value ):
* '''set attribute.'''
* if key == "pos": # <<<<<<<<<<<<<<
* self.pos = value
* value += 1
*/
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__pos), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__pos), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
- /* "TabProxies.pyx":700
+ /* "pysam/TabProxies.pyx":700
* '''set attribute.'''
* if key == "pos":
* self.pos = value # <<<<<<<<<<<<<<
* value += 1
*
*/
- __pyx_t_2 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_value); if (unlikely((__pyx_t_2 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_self->pos = __pyx_t_2;
+ __pyx_t_3 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_value); if (unlikely((__pyx_t_3 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->pos = __pyx_t_3;
- /* "TabProxies.pyx":701
+ /* "pysam/TabProxies.pyx":701
* if key == "pos":
* self.pos = value
* value += 1 # <<<<<<<<<<<<<<
*
* cdef int idx
*/
- __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_value, __pyx_int_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_value, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_value = __pyx_t_1;
+ __pyx_t_1 = 0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "TabProxies.pyx":704
+ /* "pysam/TabProxies.pyx":704
*
* cdef int idx
* idx, f = self.map_key2field[key] # <<<<<<<<<<<<<<
* TupleProxy._setindex(self, idx, str(value) )
*
*/
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__map_key2field); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetItem(__pyx_t_3, __pyx_v_key); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__map_key2field); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_5 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_5 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_5);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_5 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
__pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_3);
+ index = 0; __pyx_t_1 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
index = 1; __pyx_t_5 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_5)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_5);
if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L5_unpacking_done;
__pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_7 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
}
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_idx = __pyx_t_8;
__pyx_v_f = __pyx_t_5;
__pyx_t_5 = 0;
- /* "TabProxies.pyx":705
+ /* "pysam/TabProxies.pyx":705
* cdef int idx
* idx, f = self.map_key2field[key]
* TupleProxy._setindex(self, idx, str(value) ) # <<<<<<<<<<<<<<
*
*/
- __pyx_t_4 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_10TabProxies_TupleProxy)), __pyx_n_s___setindex); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)((PyObject*)__pyx_ptype_5pysam_10TabProxies_TupleProxy)), __pyx_n_s___setindex); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyInt_FromLong(__pyx_v_idx); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_3, 2, __pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("TabProxies.VCFProxy.__setattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.TabProxies.VCFProxy.__setattr__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_f);
@@ -8612,33 +8760,33 @@ static int __pyx_pf_10TabProxies_8VCFProxy_4__setattr__(struct __pyx_obj_10TabPr
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-static struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_vtable_10TabProxies_TupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_vtable_5pysam_10TabProxies_TupleProxy;
-static PyObject *__pyx_tp_new_10TabProxies_TupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_10TabProxies_TupleProxy *p;
+static PyObject *__pyx_tp_new_5pysam_10TabProxies_TupleProxy(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_10TabProxies_TupleProxy *)o);
- p->__pyx_vtab = __pyx_vtabptr_10TabProxies_TupleProxy;
- if (__pyx_pw_10TabProxies_10TupleProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ p = ((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
+ if (__pyx_pw_5pysam_10TabProxies_10TupleProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_10TabProxies_TupleProxy(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_10TabProxies_10TupleProxy_3__dealloc__(o);
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_sq_item_10TabProxies_TupleProxy(PyObject *o, Py_ssize_t i) {
+static PyObject *__pyx_sq_item_5pysam_10TabProxies_TupleProxy(PyObject *o, Py_ssize_t i) {
PyObject *r;
PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
@@ -8646,9 +8794,9 @@ static PyObject *__pyx_sq_item_10TabProxies_TupleProxy(PyObject *o, Py_ssize_t i
return r;
}
-static int __pyx_mp_ass_subscript_10TabProxies_TupleProxy(PyObject *o, PyObject *i, PyObject *v) {
+static int __pyx_mp_ass_subscript_5pysam_10TabProxies_TupleProxy(PyObject *o, PyObject *i, PyObject *v) {
if (v) {
- return __pyx_pw_10TabProxies_10TupleProxy_11__setitem__(o, i, v);
+ return __pyx_pw_5pysam_10TabProxies_10TupleProxy_11__setitem__(o, i, v);
}
else {
PyErr_Format(PyExc_NotImplementedError,
@@ -8657,10 +8805,10 @@ static int __pyx_mp_ass_subscript_10TabProxies_TupleProxy(PyObject *o, PyObject
}
}
-static PyMethodDef __pyx_methods_10TabProxies_TupleProxy[] = {
- {__Pyx_NAMESTR("_getindex"), (PyCFunction)__pyx_pw_10TabProxies_10TupleProxy_5_getindex, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy_4_getindex)},
- {__Pyx_NAMESTR("_setindex"), (PyCFunction)__pyx_pw_10TabProxies_10TupleProxy_9_setindex, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy_8_setindex)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_10TabProxies_10TupleProxy_17__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_10TupleProxy_16__next__)},
+static PyMethodDef __pyx_methods_5pysam_10TabProxies_TupleProxy[] = {
+ {__Pyx_NAMESTR("_getindex"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_10TupleProxy_5_getindex, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_10TupleProxy_4_getindex)},
+ {__Pyx_NAMESTR("_setindex"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_10TupleProxy_9_setindex, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_10TupleProxy_8_setindex)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_10TupleProxy_16__next__)},
{0, 0, 0, 0}
};
@@ -8723,10 +8871,10 @@ static PyNumberMethods __pyx_tp_as_number_TupleProxy = {
};
static PySequenceMethods __pyx_tp_as_sequence_TupleProxy = {
- __pyx_pw_10TabProxies_10TupleProxy_13__len__, /*sq_length*/
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
- __pyx_sq_item_10TabProxies_TupleProxy, /*sq_item*/
+ __pyx_sq_item_5pysam_10TabProxies_TupleProxy, /*sq_item*/
0, /*sq_slice*/
0, /*sq_ass_item*/
0, /*sq_ass_slice*/
@@ -8736,9 +8884,9 @@ static PySequenceMethods __pyx_tp_as_sequence_TupleProxy = {
};
static PyMappingMethods __pyx_tp_as_mapping_TupleProxy = {
- __pyx_pw_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
- __pyx_pw_10TabProxies_10TupleProxy_7__getitem__, /*mp_subscript*/
- __pyx_mp_ass_subscript_10TabProxies_TupleProxy, /*mp_ass_subscript*/
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__, /*mp_subscript*/
+ __pyx_mp_ass_subscript_5pysam_10TabProxies_TupleProxy, /*mp_ass_subscript*/
};
static PyBufferProcs __pyx_tp_as_buffer_TupleProxy = {
@@ -8762,12 +8910,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TupleProxy = {
#endif
};
-static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
+static PyTypeObject __pyx_type_5pysam_10TabProxies_TupleProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("TabProxies.TupleProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_10TabProxies_TupleProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.TabProxies.TupleProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -8782,7 +8930,7 @@ static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
&__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_10TabProxies_10TupleProxy_19__str__, /*tp_str*/
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_TupleProxy, /*tp_as_buffer*/
@@ -8792,9 +8940,9 @@ static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
- __pyx_pw_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
- __pyx_methods_10TabProxies_TupleProxy, /*tp_methods*/
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_10TabProxies_TupleProxy, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -8804,7 +8952,7 @@ static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_10TabProxies_TupleProxy, /*tp_new*/
+ __pyx_tp_new_5pysam_10TabProxies_TupleProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -8817,33 +8965,33 @@ static PyTypeObject __pyx_type_10TabProxies_TupleProxy = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_10TabProxies_GTFProxy __pyx_vtable_10TabProxies_GTFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy __pyx_vtable_5pysam_10TabProxies_GTFProxy;
-static PyObject *__pyx_tp_new_10TabProxies_GTFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_10TabProxies_GTFProxy *p;
- PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_10TabProxies_GTFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_10TabProxies_GTFProxy *p;
+ PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_10TabProxies_GTFProxy *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_GTFProxy;
- if (__pyx_pw_10TabProxies_8GTFProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ p = ((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
+ if (__pyx_pw_5pysam_10TabProxies_8GTFProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_10TabProxies_GTFProxy(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_10TabProxies_GTFProxy(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_10TabProxies_8GTFProxy_3__dealloc__(o);
+ __pyx_pw_5pysam_10TabProxies_8GTFProxy_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- __pyx_tp_dealloc_10TabProxies_TupleProxy(o);
+ __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy(o);
}
-static PyObject *__pyx_sq_item_10TabProxies_GTFProxy(PyObject *o, Py_ssize_t i) {
+static PyObject *__pyx_sq_item_5pysam_10TabProxies_GTFProxy(PyObject *o, Py_ssize_t i) {
PyObject *r;
PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
@@ -8851,22 +8999,22 @@ static PyObject *__pyx_sq_item_10TabProxies_GTFProxy(PyObject *o, Py_ssize_t i)
return r;
}
-static PyObject *__pyx_tp_getattro_10TabProxies_GTFProxy(PyObject *o, PyObject *n) {
+static PyObject *__pyx_tp_getattro_5pysam_10TabProxies_GTFProxy(PyObject *o, PyObject *n) {
PyObject *v = PyObject_GenericGetAttr(o, n);
if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Clear();
- v = __pyx_pw_10TabProxies_8GTFProxy_17__getattr__(o, n);
+ v = __pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__(o, n);
}
return v;
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_contig(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_6contig_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_contig(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_6contig_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6contig_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8874,13 +9022,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_source(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_6source_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_source(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_6source_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8888,13 +9036,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_feature(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_7feature_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_feature(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_7feature_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8902,13 +9050,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_start(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_5start_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_start(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_5start_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5start_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8916,13 +9064,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_end(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_3end_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_end(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_3end_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_3end_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8930,13 +9078,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, vo
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_score(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_5score_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_score(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_5score_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5score_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8944,13 +9092,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_strand(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_6strand_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_strand(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_6strand_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6strand_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8958,13 +9106,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_frame(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_5frame_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_frame(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_5frame_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_5frame_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8972,13 +9120,13 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_10TabProxies_8GTFProxy_attributes(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8GTFProxy_10attributes_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_attributes(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_1__get__(o);
}
-static int __pyx_setprop_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pw_10TabProxies_8GTFProxy_10attributes_3__set__(o, v);
+ return __pyx_pw_5pysam_10TabProxies_8GTFProxy_10attributes_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -8986,26 +9134,26 @@ static int __pyx_setprop_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject
}
}
-static PyMethodDef __pyx_methods_10TabProxies_GTFProxy[] = {
- {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pw_10TabProxies_8GTFProxy_5asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_4asDict)},
- {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pw_10TabProxies_8GTFProxy_7fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_6fromDict)},
- {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pw_10TabProxies_8GTFProxy_11invert, METH_O, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_10invert)},
- {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pw_10TabProxies_8GTFProxy_13keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_12keys)},
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pw_10TabProxies_8GTFProxy_17__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_16__getattr__)},
- {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pw_10TabProxies_8GTFProxy_19setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_10TabProxies_8GTFProxy_18setAttribute)},
+static PyMethodDef __pyx_methods_5pysam_10TabProxies_GTFProxy[] = {
+ {__Pyx_NAMESTR("asDict"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_5asDict, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_4asDict)},
+ {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_7fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_6fromDict)},
+ {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_11invert, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_10invert)},
+ {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_13keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_12keys)},
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_16__getattr__)},
+ {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_19setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_18setAttribute)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_10TabProxies_GTFProxy[] = {
- {(char *)"contig", __pyx_getprop_10TabProxies_8GTFProxy_contig, __pyx_setprop_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_48), 0},
- {(char *)"source", __pyx_getprop_10TabProxies_8GTFProxy_source, __pyx_setprop_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_49), 0},
- {(char *)"feature", __pyx_getprop_10TabProxies_8GTFProxy_feature, __pyx_setprop_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_50), 0},
- {(char *)"start", __pyx_getprop_10TabProxies_8GTFProxy_start, __pyx_setprop_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_51), 0},
- {(char *)"end", __pyx_getprop_10TabProxies_8GTFProxy_end, __pyx_setprop_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_52), 0},
- {(char *)"score", __pyx_getprop_10TabProxies_8GTFProxy_score, __pyx_setprop_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_53), 0},
- {(char *)"strand", __pyx_getprop_10TabProxies_8GTFProxy_strand, __pyx_setprop_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_54), 0},
- {(char *)"frame", __pyx_getprop_10TabProxies_8GTFProxy_frame, __pyx_setprop_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_55), 0},
- {(char *)"attributes", __pyx_getprop_10TabProxies_8GTFProxy_attributes, __pyx_setprop_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_56), 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_10TabProxies_GTFProxy[] = {
+ {(char *)"contig", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_contig, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_contig, __Pyx_DOCSTR(__pyx_k_48), 0},
+ {(char *)"source", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_source, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_49), 0},
+ {(char *)"feature", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_feature, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_feature, __Pyx_DOCSTR(__pyx_k_50), 0},
+ {(char *)"start", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_start, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_51), 0},
+ {(char *)"end", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_end, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_52), 0},
+ {(char *)"score", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_score, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_53), 0},
+ {(char *)"strand", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_strand, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_54), 0},
+ {(char *)"frame", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_frame, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_55), 0},
+ {(char *)"attributes", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_attributes, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_56), 0},
{0, 0, 0, 0, 0}
};
@@ -9068,10 +9216,14 @@ static PyNumberMethods __pyx_tp_as_number_GTFProxy = {
};
static PySequenceMethods __pyx_tp_as_sequence_GTFProxy = {
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/
+ #else
0, /*sq_length*/
+ #endif
0, /*sq_concat*/
0, /*sq_repeat*/
- __pyx_sq_item_10TabProxies_GTFProxy, /*sq_item*/
+ __pyx_sq_item_5pysam_10TabProxies_GTFProxy, /*sq_item*/
0, /*sq_slice*/
0, /*sq_ass_item*/
0, /*sq_ass_slice*/
@@ -9081,8 +9233,12 @@ static PySequenceMethods __pyx_tp_as_sequence_GTFProxy = {
};
static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = {
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
+ #else
0, /*mp_length*/
- __pyx_pw_10TabProxies_8GTFProxy_15__getitem__, /*mp_subscript*/
+ #endif
+ __pyx_pw_5pysam_10TabProxies_8GTFProxy_15__getitem__, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
@@ -9107,12 +9263,12 @@ static PyBufferProcs __pyx_tp_as_buffer_GTFProxy = {
#endif
};
-static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
+static PyTypeObject __pyx_type_5pysam_10TabProxies_GTFProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("TabProxies.GTFProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_10TabProxies_GTFProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.TabProxies.GTFProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_10TabProxies_GTFProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_10TabProxies_GTFProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9127,8 +9283,8 @@ static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
&__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_10TabProxies_8GTFProxy_9__str__, /*tp_str*/
- __pyx_tp_getattro_10TabProxies_GTFProxy, /*tp_getattro*/
+ __pyx_pw_5pysam_10TabProxies_8GTFProxy_9__str__, /*tp_str*/
+ __pyx_tp_getattro_5pysam_10TabProxies_GTFProxy, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_GTFProxy, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
@@ -9137,11 +9293,19 @@ static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
+ #else
0, /*tp_iter*/
+ #endif
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
+ #else
0, /*tp_iternext*/
- __pyx_methods_10TabProxies_GTFProxy, /*tp_methods*/
+ #endif
+ __pyx_methods_5pysam_10TabProxies_GTFProxy, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_10TabProxies_GTFProxy, /*tp_getset*/
+ __pyx_getsets_5pysam_10TabProxies_GTFProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -9149,7 +9313,7 @@ static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_10TabProxies_GTFProxy, /*tp_new*/
+ __pyx_tp_new_5pysam_10TabProxies_GTFProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9162,39 +9326,39 @@ static PyTypeObject __pyx_type_10TabProxies_GTFProxy = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_vtable_10TabProxies_NamedTupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_vtable_5pysam_10TabProxies_NamedTupleProxy;
-static PyObject *__pyx_tp_new_10TabProxies_NamedTupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_10TabProxies_NamedTupleProxy *p;
- PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_10TabProxies_NamedTupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *p;
+ PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_10TabProxies_NamedTupleProxy *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+ p = ((struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
return o;
}
-static PyObject *__pyx_tp_getattro_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n) {
+static PyObject *__pyx_tp_getattro_5pysam_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n) {
PyObject *v = PyObject_GenericGetAttr(o, n);
if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
PyErr_Clear();
- v = __pyx_pw_10TabProxies_15NamedTupleProxy_3__getattr__(o, n);
+ v = __pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_3__getattr__(o, n);
}
return v;
}
-static int __pyx_tp_setattro_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n, PyObject *v) {
+static int __pyx_tp_setattro_5pysam_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pw_10TabProxies_15NamedTupleProxy_1__setattr__(o, n, v);
+ return __pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_1__setattr__(o, n, v);
}
else {
- if (__pyx_ptype_10TabProxies_TupleProxy->tp_setattro)
- return __pyx_ptype_10TabProxies_TupleProxy->tp_setattro(o, n, v);
+ if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_setattro)
+ return __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_setattro(o, n, v);
return PyObject_GenericSetAttr(o, n, 0);
}
}
-static PyMethodDef __pyx_methods_10TabProxies_NamedTupleProxy[] = {
- {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pw_10TabProxies_15NamedTupleProxy_3__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_5pysam_10TabProxies_NamedTupleProxy[] = {
+ {__Pyx_NAMESTR("__getattr__"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_15NamedTupleProxy_3__getattr__, METH_O|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
@@ -9257,7 +9421,11 @@ static PyNumberMethods __pyx_tp_as_number_NamedTupleProxy = {
};
static PySequenceMethods __pyx_tp_as_sequence_NamedTupleProxy = {
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/
+ #else
0, /*sq_length*/
+ #endif
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
@@ -9270,8 +9438,16 @@ static PySequenceMethods __pyx_tp_as_sequence_NamedTupleProxy = {
};
static PyMappingMethods __pyx_tp_as_mapping_NamedTupleProxy = {
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
+ #else
0, /*mp_length*/
+ #endif
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__, /*mp_subscript*/
+ #else
0, /*mp_subscript*/
+ #endif
0, /*mp_ass_subscript*/
};
@@ -9296,12 +9472,12 @@ static PyBufferProcs __pyx_tp_as_buffer_NamedTupleProxy = {
#endif
};
-static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
+static PyTypeObject __pyx_type_5pysam_10TabProxies_NamedTupleProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("TabProxies.NamedTupleProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.TabProxies.NamedTupleProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9316,9 +9492,13 @@ static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
&__pyx_tp_as_mapping_NamedTupleProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__, /*tp_str*/
+ #else
0, /*tp_str*/
- __pyx_tp_getattro_10TabProxies_NamedTupleProxy, /*tp_getattro*/
- __pyx_tp_setattro_10TabProxies_NamedTupleProxy, /*tp_setattro*/
+ #endif
+ __pyx_tp_getattro_5pysam_10TabProxies_NamedTupleProxy, /*tp_getattro*/
+ __pyx_tp_setattro_5pysam_10TabProxies_NamedTupleProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_NamedTupleProxy, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
0, /*tp_doc*/
@@ -9326,9 +9506,17 @@ static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
+ #else
0, /*tp_iter*/
+ #endif
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
+ #else
0, /*tp_iternext*/
- __pyx_methods_10TabProxies_NamedTupleProxy, /*tp_methods*/
+ #endif
+ __pyx_methods_5pysam_10TabProxies_NamedTupleProxy, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9338,7 +9526,7 @@ static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_10TabProxies_NamedTupleProxy, /*tp_new*/
+ __pyx_tp_new_5pysam_10TabProxies_NamedTupleProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9351,29 +9539,29 @@ static PyTypeObject __pyx_type_10TabProxies_NamedTupleProxy = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_10TabProxies_BedProxy __pyx_vtable_10TabProxies_BedProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy __pyx_vtable_5pysam_10TabProxies_BedProxy;
-static PyObject *__pyx_tp_new_10TabProxies_BedProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_10TabProxies_BedProxy *p;
- PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_10TabProxies_BedProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_10TabProxies_BedProxy *p;
+ PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_10TabProxies_BedProxy *)o);
- p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_BedProxy;
+ p = ((struct __pyx_obj_5pysam_10TabProxies_BedProxy *)o);
+ p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
return o;
}
-static int __pyx_tp_setattro_10TabProxies_BedProxy(PyObject *o, PyObject *n, PyObject *v) {
+static int __pyx_tp_setattro_5pysam_10TabProxies_BedProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pw_10TabProxies_8BedProxy_3__setattr__(o, n, v);
+ return __pyx_pw_5pysam_10TabProxies_8BedProxy_3__setattr__(o, n, v);
}
else {
- if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
- return __pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro(o, n, v);
+ if (__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_setattro)
+ return __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_setattro(o, n, v);
return PyObject_GenericSetAttr(o, n, 0);
}
}
-static PyMethodDef __pyx_methods_10TabProxies_BedProxy[] = {
+static PyMethodDef __pyx_methods_5pysam_10TabProxies_BedProxy[] = {
{0, 0, 0, 0}
};
@@ -9436,7 +9624,11 @@ static PyNumberMethods __pyx_tp_as_number_BedProxy = {
};
static PySequenceMethods __pyx_tp_as_sequence_BedProxy = {
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/
+ #else
0, /*sq_length*/
+ #endif
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
@@ -9449,8 +9641,16 @@ static PySequenceMethods __pyx_tp_as_sequence_BedProxy = {
};
static PyMappingMethods __pyx_tp_as_mapping_BedProxy = {
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
+ #else
0, /*mp_length*/
+ #endif
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__, /*mp_subscript*/
+ #else
0, /*mp_subscript*/
+ #endif
0, /*mp_ass_subscript*/
};
@@ -9475,12 +9675,12 @@ static PyBufferProcs __pyx_tp_as_buffer_BedProxy = {
#endif
};
-static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
+static PyTypeObject __pyx_type_5pysam_10TabProxies_BedProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("TabProxies.BedProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_10TabProxies_BedProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.TabProxies.BedProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_10TabProxies_BedProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9495,9 +9695,9 @@ static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
&__pyx_tp_as_mapping_BedProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pw_10TabProxies_8BedProxy_1__str__, /*tp_str*/
+ __pyx_pw_5pysam_10TabProxies_8BedProxy_1__str__, /*tp_str*/
0, /*tp_getattro*/
- __pyx_tp_setattro_10TabProxies_BedProxy, /*tp_setattro*/
+ __pyx_tp_setattro_5pysam_10TabProxies_BedProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_BedProxy, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to Bed fields.\n\n This class represents a GTF entry for fast read-access.\n "), /*tp_doc*/
@@ -9505,9 +9705,17 @@ static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
+ #else
0, /*tp_iter*/
+ #endif
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
+ #else
0, /*tp_iternext*/
- __pyx_methods_10TabProxies_BedProxy, /*tp_methods*/
+ #endif
+ __pyx_methods_5pysam_10TabProxies_BedProxy, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9517,7 +9725,7 @@ static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_10TabProxies_BedProxy, /*tp_new*/
+ __pyx_tp_new_5pysam_10TabProxies_BedProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9530,41 +9738,41 @@ static PyTypeObject __pyx_type_10TabProxies_BedProxy = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_10TabProxies_VCFProxy __pyx_vtable_10TabProxies_VCFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy __pyx_vtable_5pysam_10TabProxies_VCFProxy;
-static PyObject *__pyx_tp_new_10TabProxies_VCFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_10TabProxies_VCFProxy *p;
- PyObject *o = __pyx_tp_new_10TabProxies_TupleProxy(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_10TabProxies_VCFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_10TabProxies_VCFProxy *p;
+ PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_10TabProxies_VCFProxy *)o);
- p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__pyx_vtabptr_10TabProxies_VCFProxy;
- if (__pyx_pw_10TabProxies_8VCFProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
+ p = ((struct __pyx_obj_5pysam_10TabProxies_VCFProxy *)o);
+ p->__pyx_base.__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
+ if (__pyx_pw_5pysam_10TabProxies_8VCFProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static int __pyx_tp_setattro_10TabProxies_VCFProxy(PyObject *o, PyObject *n, PyObject *v) {
+static int __pyx_tp_setattro_5pysam_10TabProxies_VCFProxy(PyObject *o, PyObject *n, PyObject *v) {
if (v) {
- return __pyx_pw_10TabProxies_8VCFProxy_5__setattr__(o, n, v);
+ return __pyx_pw_5pysam_10TabProxies_8VCFProxy_5__setattr__(o, n, v);
}
else {
- if (__pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro)
- return __pyx_ptype_10TabProxies_NamedTupleProxy->tp_setattro(o, n, v);
+ if (__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_setattro)
+ return __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_setattro(o, n, v);
return PyObject_GenericSetAttr(o, n, 0);
}
}
-static PyObject *__pyx_getprop_10TabProxies_8VCFProxy_pos(PyObject *o, void *x) {
- return __pyx_pw_10TabProxies_8VCFProxy_3pos_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_10TabProxies_8VCFProxy_pos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_10TabProxies_8VCFProxy_3pos_1__get__(o);
}
-static PyMethodDef __pyx_methods_10TabProxies_VCFProxy[] = {
+static PyMethodDef __pyx_methods_5pysam_10TabProxies_VCFProxy[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_10TabProxies_VCFProxy[] = {
- {(char *)"pos", __pyx_getprop_10TabProxies_8VCFProxy_pos, 0, __Pyx_DOCSTR(__pyx_k_52), 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_10TabProxies_VCFProxy[] = {
+ {(char *)"pos", __pyx_getprop_5pysam_10TabProxies_8VCFProxy_pos, 0, __Pyx_DOCSTR(__pyx_k_52), 0},
{0, 0, 0, 0, 0}
};
@@ -9627,7 +9835,7 @@ static PyNumberMethods __pyx_tp_as_number_VCFProxy = {
};
static PySequenceMethods __pyx_tp_as_sequence_VCFProxy = {
- __pyx_pw_10TabProxies_8VCFProxy_3__len__, /*sq_length*/
+ __pyx_pw_5pysam_10TabProxies_8VCFProxy_3__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
@@ -9640,8 +9848,12 @@ static PySequenceMethods __pyx_tp_as_sequence_VCFProxy = {
};
static PyMappingMethods __pyx_tp_as_mapping_VCFProxy = {
- __pyx_pw_10TabProxies_8VCFProxy_3__len__, /*mp_length*/
+ __pyx_pw_5pysam_10TabProxies_8VCFProxy_3__len__, /*mp_length*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__, /*mp_subscript*/
+ #else
0, /*mp_subscript*/
+ #endif
0, /*mp_ass_subscript*/
};
@@ -9666,12 +9878,12 @@ static PyBufferProcs __pyx_tp_as_buffer_VCFProxy = {
#endif
};
-static PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
+static PyTypeObject __pyx_type_5pysam_10TabProxies_VCFProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("TabProxies.VCFProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_10TabProxies_VCFProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.TabProxies.VCFProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_10TabProxies_VCFProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_10TabProxies_TupleProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9686,9 +9898,13 @@ static PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
&__pyx_tp_as_mapping_VCFProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__, /*tp_str*/
+ #else
0, /*tp_str*/
+ #endif
0, /*tp_getattro*/
- __pyx_tp_setattro_10TabProxies_VCFProxy, /*tp_setattro*/
+ __pyx_tp_setattro_5pysam_10TabProxies_VCFProxy, /*tp_setattro*/
&__pyx_tp_as_buffer_VCFProxy, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
__Pyx_DOCSTR("Proxy class for access to VCF fields.\n\n The genotypes are accessed via index.\n "), /*tp_doc*/
@@ -9696,11 +9912,19 @@ static PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
+ #else
0, /*tp_iter*/
+ #endif
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
+ #else
0, /*tp_iternext*/
- __pyx_methods_10TabProxies_VCFProxy, /*tp_methods*/
+ #endif
+ __pyx_methods_5pysam_10TabProxies_VCFProxy, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_10TabProxies_VCFProxy, /*tp_getset*/
+ __pyx_getsets_5pysam_10TabProxies_VCFProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -9708,7 +9932,7 @@ static PyTypeObject __pyx_type_10TabProxies_VCFProxy = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_10TabProxies_VCFProxy, /*tp_new*/
+ __pyx_tp_new_5pysam_10TabProxies_VCFProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9728,7 +9952,11 @@ static PyMethodDef __pyx_methods[] = {
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
+ #if PY_VERSION_HEX < 0x03020000
+ { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
+ #else
PyModuleDef_HEAD_INIT,
+ #endif
__Pyx_NAMESTR("TabProxies"),
0, /* m_doc */
-1, /* m_size */
@@ -9763,6 +9991,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s_57, __pyx_k_57, sizeof(__pyx_k_57), 0, 0, 1, 1},
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
{&__pyx_kp_s_60, __pyx_k_60, sizeof(__pyx_k_60), 0, 0, 1, 0},
+ {&__pyx_n_s_61, __pyx_k_61, sizeof(__pyx_k_61), 0, 0, 1, 1},
{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_n_s__AttributeError, __pyx_k__AttributeError, sizeof(__pyx_k__AttributeError), 0, 0, 1, 1},
@@ -9770,7 +9999,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
{&__pyx_n_s__StopIteration, __pyx_k__StopIteration, sizeof(__pyx_k__StopIteration), 0, 0, 1, 1},
{&__pyx_n_s__StringTypes, __pyx_k__StringTypes, sizeof(__pyx_k__StringTypes), 0, 0, 1, 1},
- {&__pyx_n_s__TabProxies, __pyx_k__TabProxies, sizeof(__pyx_k__TabProxies), 0, 0, 1, 1},
{&__pyx_n_s__TypeError, __pyx_k__TypeError, sizeof(__pyx_k__TypeError), 0, 0, 1, 1},
{&__pyx_n_s__ValueError, __pyx_k__ValueError, sizeof(__pyx_k__ValueError), 0, 0, 1, 1},
{&__pyx_n_s____getattr__, __pyx_k____getattr__, sizeof(__pyx_k____getattr__), 0, 0, 1, 1},
@@ -9849,377 +10077,296 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "TabProxies.pyx":43
+ /* "pysam/TabProxies.pyx":43
* return s
* elif PyUnicode_Check(s):
* return s.encode('ascii') # <<<<<<<<<<<<<<
* else:
* raise TypeError, u"Argument must be string, bytes or unicode."
*/
- __pyx_k_tuple_2 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_2 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 43; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_2);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_2, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
- /* "TabProxies.pyx":63
+ /* "pysam/TabProxies.pyx":63
* return s
* elif PyBytes_Check(s):
* return s.decode('ascii') # <<<<<<<<<<<<<<
* else:
* # assume unicode
*/
- __pyx_k_tuple_4 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_4 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_4);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
- /* "TabProxies.pyx":144
+ /* "pysam/TabProxies.pyx":144
* self.data = <char*>malloc( s )
* if self.data == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
* self.nbytes = nbytes
* memcpy( <char*>self.data, buffer, s )
*/
- __pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_8 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_8);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_8));
- /* "TabProxies.pyx":201
+ /* "pysam/TabProxies.pyx":201
* self.fields = <char **>calloc( max_fields, sizeof(char *) )
* if self.fields == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
*
* #################################
*/
- __pyx_k_tuple_10 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_10 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_10);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_10, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
- /* "TabProxies.pyx":230
+ /* "pysam/TabProxies.pyx":230
* cdef int i = index
* if i < 0: i += self.nfields
* if i < 0: raise IndexError( "list index out of range" ) # <<<<<<<<<<<<<<
* i += self.offset
* if i >= self.nfields:
*/
- __pyx_k_tuple_13 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_13 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_12)); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_13);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_12));
- PyTuple_SET_ITEM(__pyx_k_tuple_13, 0, ((PyObject *)__pyx_kp_s_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_12));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
- /* "TabProxies.pyx":248
+ /* "pysam/TabProxies.pyx":248
* '''set item at idx index.'''
* cdef int idx = index
* if idx < 0: raise IndexError( "list index out of range" ) # <<<<<<<<<<<<<<
* if idx >= self.nfields:
* raise IndexError( "list index out of range" )
*/
- __pyx_k_tuple_15 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_15 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_12)); if (unlikely(!__pyx_k_tuple_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_15);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_12));
- PyTuple_SET_ITEM(__pyx_k_tuple_15, 0, ((PyObject *)__pyx_kp_s_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_12));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
- /* "TabProxies.pyx":250
+ /* "pysam/TabProxies.pyx":250
* if idx < 0: raise IndexError( "list index out of range" )
* if idx >= self.nfields:
* raise IndexError( "list index out of range" ) # <<<<<<<<<<<<<<
*
* if isNew( self.fields[idx], self.data, self.nbytes ):
*/
- __pyx_k_tuple_16 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_16 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_12)); if (unlikely(!__pyx_k_tuple_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_16);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_12));
- PyTuple_SET_ITEM(__pyx_k_tuple_16, 0, ((PyObject *)__pyx_kp_s_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_12));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_16));
- /* "TabProxies.pyx":266
+ /* "pysam/TabProxies.pyx":266
* self.fields[idx] = <char*>malloc( (strlen( tmp ) + 1) * sizeof(char) )
* if self.fields[idx] == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
* strcpy( self.fields[idx], tmp )
*
*/
- __pyx_k_tuple_17 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_17 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_17);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_17, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17));
- /* "TabProxies.pyx":306
+ /* "pysam/TabProxies.pyx":306
* cpy = <char*>calloc( sizeof(char), self.nbytes+1 )
* if cpy == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
* memcpy( cpy, self.data, self.nbytes+1)
* for x from 0 <= x < self.nbytes:
*/
- __pyx_k_tuple_19 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_19 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_19);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_19, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_19));
- /* "TabProxies.pyx":312
+ /* "pysam/TabProxies.pyx":312
* result = cpy[:self.nbytes]
* free(cpy)
* return result.decode('ascii') # <<<<<<<<<<<<<<
*
* def toDot( v ):
*/
- __pyx_k_tuple_20 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_20 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_20);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
- /* "TabProxies.pyx":355
+ /* "pysam/TabProxies.pyx":355
* property contig:
* '''contig of feature.'''
* def __get__( self ): return self._getindex( 0 ) # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 0, value )
*
*/
- __pyx_k_tuple_23 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_23 = PyTuple_Pack(1, __pyx_int_0); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_23);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_k_tuple_23, 0, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
- /* "TabProxies.pyx":360
+ /* "pysam/TabProxies.pyx":360
* property source:
* '''feature source.'''
* def __get__( self ): return self._getindex( 1 ) # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 1, value )
*
*/
- __pyx_k_tuple_24 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_24 = PyTuple_Pack(1, __pyx_int_1); if (unlikely(!__pyx_k_tuple_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_24);
- __Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_k_tuple_24, 0, __pyx_int_1);
- __Pyx_GIVEREF(__pyx_int_1);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_24));
- /* "TabProxies.pyx":365
+ /* "pysam/TabProxies.pyx":365
* property feature:
* '''feature name.'''
* def __get__( self ): return self._getindex( 2 ) # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 2, value )
*
*/
- __pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_25 = PyTuple_Pack(1, __pyx_int_2); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_25);
- __Pyx_INCREF(__pyx_int_2);
- PyTuple_SET_ITEM(__pyx_k_tuple_25, 0, __pyx_int_2);
- __Pyx_GIVEREF(__pyx_int_2);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_25));
- /* "TabProxies.pyx":370
+ /* "pysam/TabProxies.pyx":370
* property start:
* '''feature start (in 0-based open/closed coordinates).'''
* def __get__( self ): return int( self._getindex( 3 )) - 1 # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 3, str(value+1) )
*
*/
- __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_26 = PyTuple_Pack(1, __pyx_int_3); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_26);
- __Pyx_INCREF(__pyx_int_3);
- PyTuple_SET_ITEM(__pyx_k_tuple_26, 0, __pyx_int_3);
- __Pyx_GIVEREF(__pyx_int_3);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
- /* "TabProxies.pyx":375
+ /* "pysam/TabProxies.pyx":375
* property end:
* '''feature end (in 0-based open/closed coordinates).'''
* def __get__( self ): return int( self._getindex( 4 ) ) # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 4, str(value) )
*
*/
- __pyx_k_tuple_27 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_27 = PyTuple_Pack(1, __pyx_int_4); if (unlikely(!__pyx_k_tuple_27)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_27);
- __Pyx_INCREF(__pyx_int_4);
- PyTuple_SET_ITEM(__pyx_k_tuple_27, 0, __pyx_int_4);
- __Pyx_GIVEREF(__pyx_int_4);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_27));
- /* "TabProxies.pyx":381
+ /* "pysam/TabProxies.pyx":381
* '''feature score.'''
* def __get__( self ):
* v = self._getindex(5) # <<<<<<<<<<<<<<
* if v == "" or v[0] == '.':
* return None
*/
- __pyx_k_tuple_28 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_28 = PyTuple_Pack(1, __pyx_int_5); if (unlikely(!__pyx_k_tuple_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_28);
- __Pyx_INCREF(__pyx_int_5);
- PyTuple_SET_ITEM(__pyx_k_tuple_28, 0, __pyx_int_5);
- __Pyx_GIVEREF(__pyx_int_5);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_28));
- /* "TabProxies.pyx":391
+ /* "pysam/TabProxies.pyx":391
* property strand:
* '''feature strand.'''
* def __get__( self ): return self._getindex( 6 ) # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 6, value )
*
*/
- __pyx_k_tuple_29 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_29 = PyTuple_Pack(1, __pyx_int_6); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_29);
- __Pyx_INCREF(__pyx_int_6);
- PyTuple_SET_ITEM(__pyx_k_tuple_29, 0, __pyx_int_6);
- __Pyx_GIVEREF(__pyx_int_6);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29));
- /* "TabProxies.pyx":396
+ /* "pysam/TabProxies.pyx":396
* property frame:
* '''feature frame.'''
* def __get__( self ): return self._getindex( 7 ) # <<<<<<<<<<<<<<
* def __set__( self, value ): self._setindex( 7, value )
*
*/
- __pyx_k_tuple_30 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_30 = PyTuple_Pack(1, __pyx_int_7); if (unlikely(!__pyx_k_tuple_30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_30);
- __Pyx_INCREF(__pyx_int_7);
- PyTuple_SET_ITEM(__pyx_k_tuple_30, 0, __pyx_int_7);
- __Pyx_GIVEREF(__pyx_int_7);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_30));
- /* "TabProxies.pyx":405
+ /* "pysam/TabProxies.pyx":405
* return self._attributes
* else:
* return self._getindex( 8 ) # <<<<<<<<<<<<<<
* def __set__( self, value ):
* if self.hasOwnAttributes:
*/
- __pyx_k_tuple_31 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_31 = PyTuple_Pack(1, __pyx_int_8); if (unlikely(!__pyx_k_tuple_31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_31);
- __Pyx_INCREF(__pyx_int_8);
- PyTuple_SET_ITEM(__pyx_k_tuple_31, 0, __pyx_int_8);
- __Pyx_GIVEREF(__pyx_int_8);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_31));
- /* "TabProxies.pyx":428
+ /* "pysam/TabProxies.pyx":428
*
* # separate into fields
* fields = [ x.strip() for x in attributes.split(";")[:-1]] # <<<<<<<<<<<<<<
*
* result = {}
*/
- __pyx_k_tuple_33 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_33 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_33);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_k_tuple_33, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33));
- /* "TabProxies.pyx":434
+ /* "pysam/TabProxies.pyx":434
* for f in fields:
*
* d = [ x.strip() for x in f.split(" ")] # <<<<<<<<<<<<<<
*
* n,v = d[0], d[1]
*/
- __pyx_k_tuple_35 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_35 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_34)); if (unlikely(!__pyx_k_tuple_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_35);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_34));
- PyTuple_SET_ITEM(__pyx_k_tuple_35, 0, ((PyObject *)__pyx_kp_s_34));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_34));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35));
- /* "TabProxies.pyx":476
+ /* "pysam/TabProxies.pyx":476
* self._attributes = <char *>calloc( l + 1, sizeof(char) )
* if self._attributes == NULL:
* raise ValueError("out of memory" ) # <<<<<<<<<<<<<<
* memcpy( self._attributes, p, l )
*
*/
- __pyx_k_tuple_40 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_40 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_40);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_40, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
- /* "TabProxies.pyx":514
+ /* "pysam/TabProxies.pyx":514
* '''return a list of attributes defined in this entry.'''
* r = self.attributes
* return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ] # <<<<<<<<<<<<<<
*
* def __getitem__(self, key):
*/
- __pyx_k_tuple_42 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_42 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_42);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_k_tuple_42, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
- __pyx_k_tuple_43 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_43 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_34)); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_43);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_34));
- PyTuple_SET_ITEM(__pyx_k_tuple_43, 0, ((PyObject *)__pyx_kp_s_34));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_34));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43));
- /* "TabProxies.pyx":621
+ /* "pysam/TabProxies.pyx":621
*
* if self.nfields < 3:
* raise ValueError( "bed format requires at least three columns" ) # <<<<<<<<<<<<<<
*
* # determines bed format
*/
- __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_47 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_46)); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_47);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_46));
- PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_46));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_46));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
- /* "TabProxies.pyx":314
+ /* "pysam/TabProxies.pyx":314
* return result.decode('ascii')
*
* def toDot( v ): # <<<<<<<<<<<<<<
* '''convert value to '.' if None'''
* if v == None: return "."
*/
- __pyx_k_tuple_58 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_58 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__v)); if (unlikely(!__pyx_k_tuple_58)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_58);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__v));
- PyTuple_SET_ITEM(__pyx_k_tuple_58, 0, ((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_58));
__pyx_k_codeobj_59 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_58, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_60, __pyx_n_s__toDot, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "TabProxies.pyx":319
+ /* "pysam/TabProxies.pyx":319
* else: return str(v)
*
* def quote( v ): # <<<<<<<<<<<<<<
* '''return a quoted attribute.'''
* if type(v) in types.StringTypes:
*/
- __pyx_k_tuple_61 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_61);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__v));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 0, ((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
- __pyx_k_codeobj_62 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_60, __pyx_n_s__quote, 319, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_62 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__v)); if (unlikely(!__pyx_k_tuple_62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_62);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_62));
+ __pyx_k_codeobj_63 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_62, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_60, __pyx_n_s__quote, 319, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -10289,20 +10436,27 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("TabProxies"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("TabProxies"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
+ if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION >= 3
+ {
+ PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!PyDict_GetItemString(modules, "pysam.TabProxies")) {
+ if (unlikely(PyDict_SetItemString(modules, "pysam.TabProxies", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ }
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_module_is_main_TabProxies) {
+ if (__pyx_module_is_main_pysam__TabProxies) {
if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
}
/*--- Builtin init code ---*/
@@ -10310,125 +10464,148 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
/*--- Constants init code ---*/
if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
- __pyx_v_10TabProxies__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ __pyx_v_5pysam_10TabProxies__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- __pyx_vtabptr_10TabProxies_TupleProxy = &__pyx_vtable_10TabProxies_TupleProxy;
- __pyx_vtable_10TabProxies_TupleProxy.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_10TupleProxy_getMaxFields;
- __pyx_vtable_10TabProxies_TupleProxy.take = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_take;
- __pyx_vtable_10TabProxies_TupleProxy.present = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_present;
- __pyx_vtable_10TabProxies_TupleProxy.copy = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_copy;
- __pyx_vtable_10TabProxies_TupleProxy.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_10TupleProxy_update;
- if (PyType_Ready(&__pyx_type_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_TupleProxy = &__pyx_vtable_5pysam_10TabProxies_TupleProxy;
+ __pyx_vtable_5pysam_10TabProxies_TupleProxy.getMaxFields = (int (*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t))__pyx_f_5pysam_10TabProxies_10TupleProxy_getMaxFields;
+ __pyx_vtable_5pysam_10TabProxies_TupleProxy.take = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_10TabProxies_10TupleProxy_take;
+ __pyx_vtable_5pysam_10TabProxies_TupleProxy.present = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_10TabProxies_10TupleProxy_present;
+ __pyx_vtable_5pysam_10TabProxies_TupleProxy.copy = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_10TabProxies_10TupleProxy_copy;
+ __pyx_vtable_5pysam_10TabProxies_TupleProxy.update = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_10TabProxies_10TupleProxy_update;
+ if (PyType_Ready(&__pyx_type_5pysam_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__setitem__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_TupleProxy, "__setitem__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy_10__setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy_10__setitem__.doc = __pyx_doc_10TabProxies_10TupleProxy_10__setitem__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_10__setitem__;
+ __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_10__setitem__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_10__setitem__.doc = __pyx_doc_5pysam_10TabProxies_10TupleProxy_10__setitem__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_10__setitem__;
}
}
+ #endif
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_TupleProxy, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy_16__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy_16__next__.doc = __pyx_doc_10TabProxies_10TupleProxy_16__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_16__next__;
+ __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_16__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_16__next__.doc = __pyx_doc_5pysam_10TabProxies_10TupleProxy_16__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_16__next__;
}
}
+ #endif
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_TupleProxy, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_TupleProxy, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_10TupleProxy_18__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_10TupleProxy_18__str__.doc = __pyx_doc_10TabProxies_10TupleProxy_18__str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_10TupleProxy_18__str__;
+ __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_18__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_18__str__.doc = __pyx_doc_5pysam_10TabProxies_10TupleProxy_18__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_10TupleProxy_18__str__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_TupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "TupleProxy", (PyObject *)&__pyx_type_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_TupleProxy = &__pyx_type_10TabProxies_TupleProxy;
- __pyx_vtabptr_10TabProxies_GTFProxy = &__pyx_vtable_10TabProxies_GTFProxy;
- __pyx_vtable_10TabProxies_GTFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
- __pyx_vtable_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8GTFProxy_getMaxFields;
- __pyx_vtable_10TabProxies_GTFProxy.getAttributes = (char *(*)(struct __pyx_obj_10TabProxies_GTFProxy *))__pyx_f_10TabProxies_8GTFProxy_getAttributes;
- __pyx_type_10TabProxies_GTFProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_10TabProxies_TupleProxy.tp_dict, __pyx_vtabptr_5pysam_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "TupleProxy", (PyObject *)&__pyx_type_5pysam_10TabProxies_TupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy = &__pyx_type_5pysam_10TabProxies_TupleProxy;
+ __pyx_vtabptr_5pysam_10TabProxies_GTFProxy = &__pyx_vtable_5pysam_10TabProxies_GTFProxy;
+ __pyx_vtable_5pysam_10TabProxies_GTFProxy.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
+ __pyx_vtable_5pysam_10TabProxies_GTFProxy.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t))__pyx_f_5pysam_10TabProxies_8GTFProxy_getMaxFields;
+ __pyx_vtable_5pysam_10TabProxies_GTFProxy.getAttributes = (char *(*)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *))__pyx_f_5pysam_10TabProxies_8GTFProxy_getAttributes;
+ __pyx_type_5pysam_10TabProxies_GTFProxy.tp_base = __pyx_ptype_5pysam_10TabProxies_TupleProxy;
+ if (PyType_Ready(&__pyx_type_5pysam_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_GTFProxy, "__getattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8GTFProxy_16__getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8GTFProxy_16__getattr__.doc = __pyx_doc_10TabProxies_8GTFProxy_16__getattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8GTFProxy_16__getattr__;
+ __pyx_wrapperbase_5pysam_10TabProxies_8GTFProxy_16__getattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_8GTFProxy_16__getattr__.doc = __pyx_doc_5pysam_10TabProxies_8GTFProxy_16__getattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_8GTFProxy_16__getattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_GTFProxy = &__pyx_type_10TabProxies_GTFProxy;
- __pyx_vtabptr_10TabProxies_NamedTupleProxy = &__pyx_vtable_10TabProxies_NamedTupleProxy;
- __pyx_vtable_10TabProxies_NamedTupleProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
- __pyx_type_10TabProxies_NamedTupleProxy.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_10TabProxies_GTFProxy.tp_dict, __pyx_vtabptr_5pysam_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "GTFProxy", (PyObject *)&__pyx_type_5pysam_10TabProxies_GTFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_GTFProxy = &__pyx_type_5pysam_10TabProxies_GTFProxy;
+ __pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy = &__pyx_vtable_5pysam_10TabProxies_NamedTupleProxy;
+ __pyx_vtable_5pysam_10TabProxies_NamedTupleProxy.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
+ __pyx_type_5pysam_10TabProxies_NamedTupleProxy.tp_base = __pyx_ptype_5pysam_10TabProxies_TupleProxy;
+ if (PyType_Ready(&__pyx_type_5pysam_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_NamedTupleProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__.doc = __pyx_doc_10TabProxies_15NamedTupleProxy___setattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_15NamedTupleProxy___setattr__;
+ __pyx_wrapperbase_5pysam_10TabProxies_15NamedTupleProxy___setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_15NamedTupleProxy___setattr__.doc = __pyx_doc_5pysam_10TabProxies_15NamedTupleProxy___setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_15NamedTupleProxy___setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_NamedTupleProxy = &__pyx_type_10TabProxies_NamedTupleProxy;
- __pyx_vtabptr_10TabProxies_BedProxy = &__pyx_vtable_10TabProxies_BedProxy;
- __pyx_vtable_10TabProxies_BedProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
- __pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t))__pyx_f_10TabProxies_8BedProxy_getMaxFields;
- __pyx_vtable_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8BedProxy_update;
- __pyx_type_10TabProxies_BedProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_10TabProxies_NamedTupleProxy.tp_dict, __pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "NamedTupleProxy", (PyObject *)&__pyx_type_5pysam_10TabProxies_NamedTupleProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = &__pyx_type_5pysam_10TabProxies_NamedTupleProxy;
+ __pyx_vtabptr_5pysam_10TabProxies_BedProxy = &__pyx_vtable_5pysam_10TabProxies_BedProxy;
+ __pyx_vtable_5pysam_10TabProxies_BedProxy.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
+ __pyx_vtable_5pysam_10TabProxies_BedProxy.__pyx_base.__pyx_base.getMaxFields = (int (*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t))__pyx_f_5pysam_10TabProxies_8BedProxy_getMaxFields;
+ __pyx_vtable_5pysam_10TabProxies_BedProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_10TabProxies_8BedProxy_update;
+ __pyx_type_5pysam_10TabProxies_BedProxy.tp_base = __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy;
+ if (PyType_Ready(&__pyx_type_5pysam_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_BedProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_BedProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8BedProxy_2__setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8BedProxy_2__setattr__.doc = __pyx_doc_10TabProxies_8BedProxy_2__setattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8BedProxy_2__setattr__;
+ __pyx_wrapperbase_5pysam_10TabProxies_8BedProxy_2__setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_8BedProxy_2__setattr__.doc = __pyx_doc_5pysam_10TabProxies_8BedProxy_2__setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_8BedProxy_2__setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_BedProxy = &__pyx_type_10TabProxies_BedProxy;
- __pyx_vtabptr_10TabProxies_VCFProxy = &__pyx_vtable_10TabProxies_VCFProxy;
- __pyx_vtable_10TabProxies_VCFProxy.__pyx_base = *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
- __pyx_vtable_10TabProxies_VCFProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_10TabProxies_8VCFProxy_update;
- __pyx_type_10TabProxies_VCFProxy.tp_base = __pyx_ptype_10TabProxies_NamedTupleProxy;
- if (PyType_Ready(&__pyx_type_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_10TabProxies_BedProxy.tp_dict, __pyx_vtabptr_5pysam_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "BedProxy", (PyObject *)&__pyx_type_5pysam_10TabProxies_BedProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_BedProxy = &__pyx_type_5pysam_10TabProxies_BedProxy;
+ __pyx_vtabptr_5pysam_10TabProxies_VCFProxy = &__pyx_vtable_5pysam_10TabProxies_VCFProxy;
+ __pyx_vtable_5pysam_10TabProxies_VCFProxy.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
+ __pyx_vtable_5pysam_10TabProxies_VCFProxy.__pyx_base.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_10TabProxies_8VCFProxy_update;
+ __pyx_type_5pysam_10TabProxies_VCFProxy.tp_base = __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy;
+ if (PyType_Ready(&__pyx_type_5pysam_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_VCFProxy, "__len__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_VCFProxy, "__len__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8VCFProxy_2__len__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8VCFProxy_2__len__.doc = __pyx_doc_10TabProxies_8VCFProxy_2__len__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8VCFProxy_2__len__;
+ __pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_2__len__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_2__len__.doc = __pyx_doc_5pysam_10TabProxies_8VCFProxy_2__len__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_2__len__;
}
}
+ #endif
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_10TabProxies_VCFProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_10TabProxies_VCFProxy, "__setattr__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_10TabProxies_8VCFProxy_4__setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_10TabProxies_8VCFProxy_4__setattr__.doc = __pyx_doc_10TabProxies_8VCFProxy_4__setattr__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_10TabProxies_8VCFProxy_4__setattr__;
+ __pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_4__setattr__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_4__setattr__.doc = __pyx_doc_5pysam_10TabProxies_8VCFProxy_4__setattr__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_10TabProxies_8VCFProxy_4__setattr__;
}
}
- if (__Pyx_SetVtable(__pyx_type_10TabProxies_VCFProxy.tp_dict, __pyx_vtabptr_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "VCFProxy", (PyObject *)&__pyx_type_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_VCFProxy = &__pyx_type_10TabProxies_VCFProxy;
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_10TabProxies_VCFProxy.tp_dict, __pyx_vtabptr_5pysam_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "VCFProxy", (PyObject *)&__pyx_type_5pysam_10TabProxies_VCFProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_VCFProxy = &__pyx_type_5pysam_10TabProxies_VCFProxy;
/*--- Type import code ---*/
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
+ #if CYTHON_COMPILING_IN_PYPY
+ sizeof(PyTypeObject),
+ #else
+ sizeof(PyHeapTypeObject),
+ #endif
+ 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "TabProxies.pyx":1
+ /* "pysam/TabProxies.pyx":1
* import types, sys # <<<<<<<<<<<<<<
*
* from cpython.version cimport PY_MAJOR_VERSION
@@ -10442,7 +10619,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sys, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "TabProxies.pyx":15
+ /* "pysam/TabProxies.pyx":15
* # filename encoding (copied from lxml.etree.pyx)
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding() # <<<<<<<<<<<<<<
@@ -10458,23 +10635,23 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_XGOTREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
- __pyx_v_10TabProxies__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_v_5pysam_10TabProxies__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "TabProxies.pyx":16
+ /* "pysam/TabProxies.pyx":16
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding()
* if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None:
*/
- __pyx_t_3 = (__pyx_v_10TabProxies__FILENAME_ENCODING == ((PyObject*)Py_None));
+ __pyx_t_3 = (__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "TabProxies.pyx":17
+ /* "pysam/TabProxies.pyx":17
* _FILENAME_ENCODING = sys.getfilesystemencoding()
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = sys.getdefaultencoding() # <<<<<<<<<<<<<<
@@ -10490,26 +10667,26 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_XGOTREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
- __pyx_v_10TabProxies__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_v_5pysam_10TabProxies__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L2;
}
__pyx_L2:;
- /* "TabProxies.pyx":18
+ /* "pysam/TabProxies.pyx":18
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
* _FILENAME_ENCODING = 'ascii'
*
*/
- __pyx_t_3 = (__pyx_v_10TabProxies__FILENAME_ENCODING == ((PyObject*)Py_None));
+ __pyx_t_3 = (__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "TabProxies.pyx":19
+ /* "pysam/TabProxies.pyx":19
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = 'ascii' # <<<<<<<<<<<<<<
@@ -10517,39 +10694,39 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
* cdef bytes _my_encodeFilename(object filename):
*/
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_XGOTREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_10TabProxies__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_10TabProxies__FILENAME_ENCODING));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __pyx_v_10TabProxies__FILENAME_ENCODING = __pyx_n_s__ascii;
+ __pyx_v_5pysam_10TabProxies__FILENAME_ENCODING = __pyx_n_s__ascii;
goto __pyx_L3;
}
__pyx_L3:;
- /* "TabProxies.pyx":314
+ /* "pysam/TabProxies.pyx":314
* return result.decode('ascii')
*
* def toDot( v ): # <<<<<<<<<<<<<<
* '''convert value to '.' if None'''
* if v == None: return "."
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_10TabProxies_1toDot, NULL, __pyx_n_s__TabProxies); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_10TabProxies_1toDot, NULL, __pyx_n_s_61); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__toDot, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "TabProxies.pyx":319
+ /* "pysam/TabProxies.pyx":319
* else: return str(v)
*
* def quote( v ): # <<<<<<<<<<<<<<
* '''return a quoted attribute.'''
* if type(v) in types.StringTypes:
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_10TabProxies_3quote, NULL, __pyx_n_s__TabProxies); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_10TabProxies_3quote, NULL, __pyx_n_s_61); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__quote, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "TabProxies.pyx":573
+ /* "pysam/TabProxies.pyx":573
* cdef class NamedTupleProxy( TupleProxy ):
*
* map_key2field = {} # <<<<<<<<<<<<<<
@@ -10558,11 +10735,11 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
*/
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem((PyObject *)__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem((PyObject *)__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- PyType_Modified(__pyx_ptype_10TabProxies_NamedTupleProxy);
+ PyType_Modified(__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy);
- /* "TabProxies.pyx":595
+ /* "pysam/TabProxies.pyx":595
* This class represents a GTF entry for fast read-access.
* '''
* map_key2field = { # <<<<<<<<<<<<<<
@@ -10572,7 +10749,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "TabProxies.pyx":596
+ /* "pysam/TabProxies.pyx":596
* '''
* map_key2field = {
* 'contig' : (0, bytes), # <<<<<<<<<<<<<<
@@ -10590,7 +10767,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__contig), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":597
+ /* "pysam/TabProxies.pyx":597
* map_key2field = {
* 'contig' : (0, bytes),
* 'start' : (1, int), # <<<<<<<<<<<<<<
@@ -10608,7 +10785,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__start), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":598
+ /* "pysam/TabProxies.pyx":598
* 'contig' : (0, bytes),
* 'start' : (1, int),
* 'end' : (2, int), # <<<<<<<<<<<<<<
@@ -10626,7 +10803,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__end), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":599
+ /* "pysam/TabProxies.pyx":599
* 'start' : (1, int),
* 'end' : (2, int),
* 'name' : (3, bytes), # <<<<<<<<<<<<<<
@@ -10644,7 +10821,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__name), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":600
+ /* "pysam/TabProxies.pyx":600
* 'end' : (2, int),
* 'name' : (3, bytes),
* 'score' : (4, float), # <<<<<<<<<<<<<<
@@ -10662,7 +10839,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__score), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":601
+ /* "pysam/TabProxies.pyx":601
* 'name' : (3, bytes),
* 'score' : (4, float),
* 'strand' : (5, bytes), # <<<<<<<<<<<<<<
@@ -10680,7 +10857,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__strand), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":602
+ /* "pysam/TabProxies.pyx":602
* 'score' : (4, float),
* 'strand' : (5, bytes),
* 'thickStart' : (6, int ), # <<<<<<<<<<<<<<
@@ -10698,7 +10875,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__thickStart), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":603
+ /* "pysam/TabProxies.pyx":603
* 'strand' : (5, bytes),
* 'thickStart' : (6, int ),
* 'thickEnd' : (7, int), # <<<<<<<<<<<<<<
@@ -10716,7 +10893,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__thickEnd), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":604
+ /* "pysam/TabProxies.pyx":604
* 'thickStart' : (6, int ),
* 'thickEnd' : (7, int),
* 'itemRGB' : (8, bytes), # <<<<<<<<<<<<<<
@@ -10734,7 +10911,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__itemRGB), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":605
+ /* "pysam/TabProxies.pyx":605
* 'thickEnd' : (7, int),
* 'itemRGB' : (8, bytes),
* 'blockCount': (9, int), # <<<<<<<<<<<<<<
@@ -10752,7 +10929,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__blockCount), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":606
+ /* "pysam/TabProxies.pyx":606
* 'itemRGB' : (8, bytes),
* 'blockCount': (9, int),
* 'blockSizes': (10, bytes), # <<<<<<<<<<<<<<
@@ -10770,7 +10947,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__blockSizes), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":607
+ /* "pysam/TabProxies.pyx":607
* 'blockCount': (9, int),
* 'blockSizes': (10, bytes),
* 'blockStarts': (11, bytes), } # <<<<<<<<<<<<<<
@@ -10787,11 +10964,11 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyBytes_Type))));
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__blockStarts), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyDict_SetItem((PyObject *)__pyx_ptype_10TabProxies_BedProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem((PyObject *)__pyx_ptype_5pysam_10TabProxies_BedProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- PyType_Modified(__pyx_ptype_10TabProxies_BedProxy);
+ PyType_Modified(__pyx_ptype_5pysam_10TabProxies_BedProxy);
- /* "TabProxies.pyx":661
+ /* "pysam/TabProxies.pyx":661
* The genotypes are accessed via index.
* '''
* map_key2field = { # <<<<<<<<<<<<<<
@@ -10801,7 +10978,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "TabProxies.pyx":662
+ /* "pysam/TabProxies.pyx":662
* '''
* map_key2field = {
* 'contig' : (0, bytes), # <<<<<<<<<<<<<<
@@ -10819,7 +10996,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__contig), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":663
+ /* "pysam/TabProxies.pyx":663
* map_key2field = {
* 'contig' : (0, bytes),
* 'pos' : (1, int), # <<<<<<<<<<<<<<
@@ -10837,7 +11014,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":664
+ /* "pysam/TabProxies.pyx":664
* 'contig' : (0, bytes),
* 'pos' : (1, int),
* 'id' : (2, bytes), # <<<<<<<<<<<<<<
@@ -10855,7 +11032,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__id), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":665
+ /* "pysam/TabProxies.pyx":665
* 'pos' : (1, int),
* 'id' : (2, bytes),
* 'ref' : (3, bytes), # <<<<<<<<<<<<<<
@@ -10873,7 +11050,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ref), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":666
+ /* "pysam/TabProxies.pyx":666
* 'id' : (2, bytes),
* 'ref' : (3, bytes),
* 'alt' : (4, bytes), # <<<<<<<<<<<<<<
@@ -10891,7 +11068,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__alt), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":667
+ /* "pysam/TabProxies.pyx":667
* 'ref' : (3, bytes),
* 'alt' : (4, bytes),
* 'qual' : (5, bytes), # <<<<<<<<<<<<<<
@@ -10909,7 +11086,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":668
+ /* "pysam/TabProxies.pyx":668
* 'alt' : (4, bytes),
* 'qual' : (5, bytes),
* 'filter' : (6, bytes), # <<<<<<<<<<<<<<
@@ -10927,7 +11104,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__filter), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":669
+ /* "pysam/TabProxies.pyx":669
* 'qual' : (5, bytes),
* 'filter' : (6, bytes),
* 'info' : (7, bytes), # <<<<<<<<<<<<<<
@@ -10945,7 +11122,7 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "TabProxies.pyx":670
+ /* "pysam/TabProxies.pyx":670
* 'filter' : (6, bytes),
* 'info' : (7, bytes),
* 'format' : (8, bytes) } # <<<<<<<<<<<<<<
@@ -10962,11 +11139,11 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyBytes_Type))));
if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__format), ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyDict_SetItem((PyObject *)__pyx_ptype_10TabProxies_VCFProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem((PyObject *)__pyx_ptype_5pysam_10TabProxies_VCFProxy->tp_dict, __pyx_n_s__map_key2field, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- PyType_Modified(__pyx_ptype_10TabProxies_VCFProxy);
+ PyType_Modified(__pyx_ptype_5pysam_10TabProxies_VCFProxy);
- /* "TabProxies.pyx":1
+ /* "pysam/TabProxies.pyx":1
* import types, sys # <<<<<<<<<<<<<<
*
* from cpython.version cimport PY_MAJOR_VERSION
@@ -10980,10 +11157,10 @@ PyMODINIT_FUNC PyInit_TabProxies(void)
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
- __Pyx_AddTraceback("init TabProxies", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init pysam.TabProxies", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init TabProxies");
+ PyErr_SetString(PyExc_ImportError, "init pysam.TabProxies");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -11026,6 +11203,32 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
return result;
}
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
+ Py_ssize_t length;
+ if (unlikely((start < 0) | (stop < 0))) {
+ length = strlen(cstring);
+ if (start < 0) {
+ start += length;
+ if (start < 0)
+ start = 0;
+ }
+ if (stop < 0)
+ stop += length;
+ }
+ length = stop - start;
+ if (unlikely(length <= 0))
+ return PyUnicode_FromUnicode(NULL, 0);
+ cstring += start;
+ if (decode_func) {
+ return decode_func(cstring, length, errors);
+ } else {
+ return PyUnicode_Decode(cstring, length, encoding, errors);
+ }
+}
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
@@ -11061,33 +11264,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -11120,6 +11328,7 @@ raise_error:
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -11137,12 +11346,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -11159,9 +11392,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -11175,6 +11405,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
@@ -11199,7 +11430,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -11211,13 +11442,17 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
{
PyObject* key = 0;
Py_ssize_t pos = 0;
+#if CPYTHON_COMPILING_IN_PYPY
+ if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
+ goto invalid_keyword;
+ return 1;
+#else
while (PyDict_Next(kwdict, &pos, &key, 0)) {
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
- #else
- if (unlikely(!PyUnicode_Check(key)))
#endif
- goto invalid_keyword_type;
+ if (unlikely(!PyUnicode_Check(key)))
+ goto invalid_keyword_type;
}
if ((!kw_allowed) && unlikely(key))
goto invalid_keyword;
@@ -11226,6 +11461,7 @@ invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
"%s() keywords must be strings", function_name);
return 0;
+#endif
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
@@ -11238,23 +11474,40 @@ invalid_keyword:
return 0;
}
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
- index, (index == 1) ? "" : "s");
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ index, (index == 1) ? "" : "s");
}
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else if (PyErr_Occurred()) {
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
PyErr_Clear();
return 0;
@@ -11263,6 +11516,18 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
}
}
return 0;
+#endif
+}
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ } else {
+ return __Pyx_IterFinish();
+ }
+ return 0;
}
static void __Pyx_RaiseDoubleKeywordsError(
@@ -11274,7 +11539,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -11295,48 +11560,72 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
}
}
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
+ }
+ }
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -11355,10 +11644,11 @@ bad:
return -1;
}
-
-
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
+#if CYTHON_COMPILING_IN_PYPY
+ float_value = PyNumber_Float(obj);
+#else
if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
return PyFloat_AsDouble(obj);
} else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
@@ -11375,6 +11665,7 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyTuple_SET_ITEM(args, 0, 0);
Py_DECREF(args);
}
+#endif
if (likely(float_value)) {
double value = PyFloat_AS_DOUBLE(float_value);
Py_DECREF(float_value);
@@ -11385,6 +11676,7 @@ bad:
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -11392,8 +11684,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -11405,18 +11701,23 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
- PyObject *py_import = 0;
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
PyObject *empty_dict = 0;
PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import = 0;
py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
if (!py_import)
goto bad;
+ #endif
if (from_list)
list = from_list;
else {
@@ -11436,13 +11737,17 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
#if PY_MAJOR_VERSION >= 3
if (level == -1) {
if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(1);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
if (!module) {
if (!PyErr_ExceptionMatches(PyExc_ImportError))
goto bad;
@@ -11453,12 +11758,17 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
}
#endif
if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(level);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
}
}
#else
@@ -11470,84 +11780,14 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
name, global_dict, empty_dict, list, NULL);
#endif
bad:
- Py_XDECREF(empty_list);
+ #if PY_VERSION_HEX < 0x03030000
Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
Py_XDECREF(empty_dict);
return module;
}
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyBytes_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
- else
- return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
- } else {
- int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -11577,6 +11817,10 @@ static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
else
return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
uint32_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -11596,6 +11840,7 @@ static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
if (likely(!ret))
return val;
}
+ #endif
return (uint32_t)-1;
}
}
@@ -12025,8 +12270,8 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
}
}
-static void __Pyx_WriteUnraisable(const char *name, int clineno,
- int lineno, const char *filename) {
+static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
+ CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
@@ -12080,6 +12325,23 @@ bad:
return -1;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -12089,6 +12351,10 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+ Py_ssize_t basicsize;
+#ifdef Py_LIMITED_API
+ PyObject *py_basicsize;
+#endif
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
@@ -12108,7 +12374,19 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+#ifndef Py_LIMITED_API
+ basicsize = ((PyTypeObject *)result)->tp_basicsize;
+#else
+ py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
+ if (!py_basicsize)
+ goto bad;
+ basicsize = PyLong_AsSsize_t(py_basicsize);
+ Py_DECREF(py_basicsize);
+ py_basicsize = 0;
+ if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
+ goto bad;
+#endif
+ if (!strict && (size_t)basicsize > size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -12118,7 +12396,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -12132,23 +12410,6 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
int start = 0, mid = 0, end = count - 1;
if (end >= 0 && code_line > entries[end].code_line) {
@@ -12341,15 +12602,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-
-/* Type Conversion Functions */
-
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
else return PyObject_IsTrue(x);
}
-
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
@@ -12395,7 +12652,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
return res;
}
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject* x = PyNumber_Index(b);
@@ -12404,7 +12660,6 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
-
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
if (ival <= LONG_MAX)
@@ -12418,7 +12673,6 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
return PyInt_FromSize_t(ival);
#endif
}
-
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
diff --git a/pysam/__init__.py b/pysam/__init__.py
index 7e36c08..a02f62b 100644
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -107,6 +107,10 @@ SAMTOOLS_DISPATCH = {
# others
"samimport": ( "import", None),
"bam2fq" : ("bam2fq", None),
+ "pad2unpad" : ("pad2unpad", None),
+ "depad" : ("pad2unpad", None),
+ "bedcov" : ("bedcov", None),
+ "bamshuf" : ("bamshuf", None),
# obsolete
# "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
diff --git a/pysam/csamtools.c b/pysam/csamtools.c
index 35b4522..99a0350 100644
--- a/pysam/csamtools.c
+++ b/pysam/csamtools.c
@@ -1,16 +1,16 @@
-/* Generated by Cython 0.15.1 on Mon Jan 14 23:52:53 2013 */
+/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
#ifndef Py_PYTHON_H
#error Python headers needed to compile C extensions, please install development version of Python.
+#elif PY_VERSION_HEX < 0x02040000
+ #error Cython requires Python 2.4+.
#else
-
#include <stddef.h> /* For offsetof */
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -22,36 +22,47 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
-#if PY_VERSION_HEX < 0x02040000
- #define METH_COEXIST 0
- #define PyDict_CheckExact(op) (Py_TYPE(op) == &PyDict_Type)
- #define PyDict_Contains(d,o) PySequence_Contains(d,o)
+#ifndef Py_HUGE_VAL
+ #define Py_HUGE_VAL HUGE_VAL
+#endif
+#ifdef PYPY_VERSION
+#define CYTHON_COMPILING_IN_PYPY 1
+#define CYTHON_COMPILING_IN_CPYTHON 0
+#else
+#define CYTHON_COMPILING_IN_PYPY 0
+#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
+ #define __PYX_BUILD_PY_SSIZE_T "i"
+#else
+ #define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -59,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -73,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -83,24 +92,44 @@
#define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
#define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
-
+ #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
+ #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
+ typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
+ typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#else
#define __Pyx_BUILTIN_MODULE_NAME "builtins"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+#endif
+#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
+ #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+#endif
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -108,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -127,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -135,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -154,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -167,16 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -195,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -209,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -218,6 +228,15 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
#ifndef __PYX_EXTERN_C
#ifdef __cplusplus
#define __PYX_EXTERN_C extern "C"
@@ -230,8 +249,8 @@
#define _USE_MATH_DEFINES
#endif
#include <math.h>
-#define __PYX_HAVE__csamtools
-#define __PYX_HAVE_API__csamtools
+#define __PYX_HAVE__pysam__csamtools
+#define __PYX_HAVE_API__pysam__csamtools
#include "string.h"
#include "stdlib.h"
#include "math.h"
@@ -253,8 +272,6 @@
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-
-/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#define CYTHON_INLINE __inline__
@@ -266,8 +283,6 @@
#define CYTHON_INLINE
#endif
#endif
-
-/* unused attribute */
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -275,31 +290,29 @@
# else
# define CYTHON_UNUSED
# endif
-# elif defined(__ICC) || defined(__INTEL_COMPILER)
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
# define CYTHON_UNUSED __attribute__ ((__unused__))
# else
# define CYTHON_UNUSED
# endif
#endif
-
typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-/* Type Conversion Predeclarations */
-
#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
+#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
@@ -328,50 +341,43 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"csamtools.pyx",
+ "type.pxd",
"bool.pxd",
"complex.pxd",
};
-static PyObject *__Pyx_Generator_Next(PyObject *self);
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
-static PyObject *__Pyx_Generator_Close(PyObject *self);
-static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args, CYTHON_UNUSED PyObject *kwds);
-
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-
/*--- Type declarations ---*/
-struct __pyx_Generator_object;
-struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr;
-struct __pyx_obj_9csamtools_IteratorRow;
-struct __pyx_obj_9csamtools_IteratorRowAllRefs;
-struct __pyx_obj_9csamtools_IteratorRowAll;
-struct __pyx_obj_9csamtools_PileupProxy;
-struct __pyx_obj_9csamtools_AlignedRead;
-struct __pyx_obj_9csamtools_Fastafile;
-struct __pyx_obj_9csamtools_IteratorRowSelection;
-struct __pyx_obj_9csamtools_IteratorColumn;
-struct __pyx_obj_9csamtools_IteratorColumnAllRefs;
-struct __pyx_obj_9csamtools_IteratorRowRegion;
-struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_9csamtools_Samfile;
-struct __pyx_obj_9csamtools_SNPCall;
-struct __pyx_obj_9csamtools_IndexedReads;
-struct __pyx_obj_9csamtools_IteratorColumnRegion;
-struct __pyx_obj_9csamtools_PileupRead;
-struct __pyx_t_9csamtools___iterdata;
-typedef struct __pyx_t_9csamtools___iterdata __pyx_t_9csamtools___iterdata;
-struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData;
-struct __pyx_t_9csamtools_MateData;
-typedef struct __pyx_t_9csamtools_MateData __pyx_t_9csamtools_MateData;
-
-/* "csamtools.pxd":394
+struct __pyx_obj_5pysam_9csamtools_PileupRead;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
+struct __pyx_obj_5pysam_9csamtools_IteratorRow;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_5pysam_9csamtools_Samfile;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumn;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs;
+struct __pyx_obj_5pysam_9csamtools_Fastafile;
+struct __pyx_obj_5pysam_9csamtools_PileupProxy;
+struct __pyx_obj_5pysam_9csamtools_IndexedReads;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs;
+struct __pyx_obj_5pysam_9csamtools_AlignedRead;
+struct __pyx_obj_5pysam_9csamtools_SNPCall;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
+struct __pyx_t_5pysam_9csamtools___iterdata;
+typedef struct __pyx_t_5pysam_9csamtools___iterdata __pyx_t_5pysam_9csamtools___iterdata;
+struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData;
+struct __pyx_t_5pysam_9csamtools_MateData;
+typedef struct __pyx_t_5pysam_9csamtools_MateData __pyx_t_5pysam_9csamtools_MateData;
+
+/* "pysam/csamtools.pxd":394
* # Utility types
*
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
* samfile_t * samfile
* bam_iter_t iter
*/
-struct __pyx_t_9csamtools___iterdata {
+struct __pyx_t_5pysam_9csamtools___iterdata {
samfile_t *samfile;
bam_iter_t iter;
faidx_t *fastafile;
@@ -380,50 +386,59 @@ struct __pyx_t_9csamtools___iterdata {
int seq_len;
};
-/* "csamtools.pxd":523
+/* "pysam/csamtools.pxd":523
* cdef char * getSequence( self )
* cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
* int tid,
* int start,
*/
-struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData {
+struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData {
int __pyx_n;
int reopen;
};
-/* "csamtools.pyx":518
+/* "pysam/csamtools.pyx":518
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
* char * name
* bam1_t * mate
*/
-struct __pyx_t_9csamtools_MateData {
+struct __pyx_t_5pysam_9csamtools_MateData {
char *name;
bam1_t *mate;
uint32_t flag;
};
-/* "csamtools.pyx":140
+/* "pysam/csamtools.pxd":455
+ * cdef int n_pu
+ *
+ * cdef class PileupRead: # <<<<<<<<<<<<<<
+ * cdef AlignedRead _alignment
+ * cdef int32_t _qpos
+ */
+struct __pyx_obj_5pysam_9csamtools_PileupRead {
+ PyObject_HEAD
+ struct __pyx_obj_5pysam_9csamtools_AlignedRead *_alignment;
+ int32_t _qpos;
+ int _indel;
+ int _level;
+ uint32_t _is_del;
+ uint32_t _is_head;
+ uint32_t _is_tail;
+};
+
+
+/* "pysam/csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-struct __pyx_Generator_object {
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
PyObject_HEAD
- __pyx_generator_body_t body;
- int is_running;
- int resume_label;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
-};
-
-struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
- struct __pyx_Generator_object __pyx_base;
PyObject *__pyx_v_x;
PyObject *__pyx_v_y;
PyObject *__pyx_t_0;
@@ -432,214 +447,227 @@ struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr {
};
-/* "csamtools.pxd":464
+/* "pysam/csamtools.pxd":464
* cdef uint32_t _is_tail
*
* cdef class IteratorRow: # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_9csamtools_IteratorRow {
+struct __pyx_obj_5pysam_9csamtools_IteratorRow {
PyObject_HEAD
};
-/* "csamtools.pxd":487
- * cdef int cnext(self)
- *
- * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
- * cdef Samfile samfile
- * cdef int tid
- */
-struct __pyx_obj_9csamtools_IteratorRowAllRefs {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_obj_9csamtools_Samfile *samfile;
- int tid;
- struct __pyx_obj_9csamtools_IteratorRowRegion *rowiter;
-};
-
-
-/* "csamtools.pxd":480
- * cdef int cnext(self)
+/* "pysam/csamtools.pxd":467
+ * pass
*
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef samfile_t * fp
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam_iter_t iter # iterator state object
+ * cdef bam1_t * b
*/
-struct __pyx_obj_9csamtools_IteratorRowAll {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtab;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
+ bam_iter_t iter;
bam1_t *b;
+ int retval;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
samfile_t *fp;
int owns_samfile;
};
-/* "csamtools.pxd":449
- * cdef char * _getrname( self, int tid )
+/* "pysam/csamtools.pyx":142
+ * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
+ * else:
+ * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" )
*
- * cdef class PileupProxy: # <<<<<<<<<<<<<<
- * cdef bam_pileup1_t ** plp
- * cdef int tid
*/
-struct __pyx_obj_9csamtools_PileupProxy {
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
PyObject_HEAD
- bam_pileup1_t **plp;
- int tid;
- int pos;
- int n_pu;
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
-/* "csamtools.pxd":415
- * cdef char * _fetch( self, char * reference, int start, int end, int * length )
- *
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+/* "pysam/csamtools.pxd":420
+ * cdef bam1_t * _delegate
*
- * # object that this AlignedRead represents
- */
-struct __pyx_obj_9csamtools_AlignedRead {
- PyObject_HEAD
- bam1_t *_delegate;
-};
-
-
-/* "csamtools.pxd":408
- * # Note: need to declare all C fields and methods here
- * #
- * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * cdef class Samfile: # <<<<<<<<<<<<<<
* cdef char * _filename
- * # pointer to fastafile
+ * # pointer to samfile
*/
-struct __pyx_obj_9csamtools_Fastafile {
+struct __pyx_obj_5pysam_9csamtools_Samfile {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtab;
char *_filename;
- faidx_t *fastafile;
-};
-
-
-/* "csamtools.pxd":492
- * cdef IteratorRowRegion rowiter
- *
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef int current_pos
- */
-struct __pyx_obj_9csamtools_IteratorRowSelection {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtab;
+ samfile_t *samfile;
+ bam_index_t *index;
+ int isbam;
+ int isstream;
+ int isremote;
bam1_t *b;
- int current_pos;
- samfile_t *fp;
- PyObject *positions;
- int owns_samfile;
+ char *mode;
+ int64_t start_offset;
};
-/* "csamtools.pxd":504
+/* "pysam/csamtools.pxd":504
* cdef int cnext(self)
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
*
* # result of the last plbuf_push
*/
-struct __pyx_obj_9csamtools_IteratorColumn {
+struct __pyx_obj_5pysam_9csamtools_IteratorColumn {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtab;
- struct __pyx_obj_9csamtools_IteratorRowRegion *iter;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtab;
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *iter;
int tid;
int pos;
int n_plp;
int mask;
const bam_pileup1_t * plp;
bam_plp_t pileup_iter;
- __pyx_t_9csamtools___iterdata iterdata;
- struct __pyx_obj_9csamtools_Samfile *samfile;
- struct __pyx_obj_9csamtools_Fastafile *fastafile;
+ __pyx_t_5pysam_9csamtools___iterdata iterdata;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ struct __pyx_obj_5pysam_9csamtools_Fastafile *fastafile;
PyObject *stepper;
int max_depth;
};
-/* "csamtools.pxd":536
+/* "pysam/csamtools.pxd":536
* cdef int truncate
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_9csamtools_IteratorColumnAllRefs {
- struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
+};
+
+
+/* "pysam/csamtools.pxd":408
+ * # Note: need to declare all C fields and methods here
+ * #
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to fastafile
+ */
+struct __pyx_obj_5pysam_9csamtools_Fastafile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtab;
+ char *_filename;
+ faidx_t *fastafile;
+};
+
+
+/* "pysam/csamtools.pxd":449
+ * cdef char * _getrname( self, int tid )
+ *
+ * cdef class PileupProxy: # <<<<<<<<<<<<<<
+ * cdef bam_pileup1_t ** plp
+ * cdef int tid
+ */
+struct __pyx_obj_5pysam_9csamtools_PileupProxy {
+ PyObject_HEAD
+ bam_pileup1_t **plp;
+ int tid;
+ int pos;
+ int n_pu;
};
-/* "csamtools.pxd":467
+/* "pysam/csamtools.pxd":539
* pass
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam_iter_t iter # iterator state object
- * cdef bam1_t * b
+ * cdef class IndexedReads: # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_9csamtools_IteratorRowRegion {
- struct __pyx_obj_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
+struct __pyx_obj_5pysam_9csamtools_IndexedReads {
+ PyObject_HEAD
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ samfile_t *fp;
+ PyObject *index;
+ int owns_samfile;
+};
+
+
+/* "pysam/csamtools.pxd":480
+ * cdef int cnext(self)
+ *
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
+ */
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAll {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtab;
bam1_t *b;
- int retval;
- struct __pyx_obj_9csamtools_Samfile *samfile;
samfile_t *fp;
int owns_samfile;
};
-/* "csamtools.pyx":142
- * CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
- * else:
- * CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+/* "pysam/csamtools.pxd":531
+ * cdef reset( self, tid, start, end )
+ *
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * cdef int start
+ * cdef int end
+ */
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumn __pyx_base;
+ int start;
+ int end;
+ int truncate;
+};
+
+
+/* "pysam/csamtools.pxd":487
+ * cdef int cnext(self)
*
+ * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef int tid
*/
-struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr {
- struct __pyx_Generator_object __pyx_base;
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ int tid;
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *rowiter;
};
-/* "csamtools.pxd":420
- * cdef bam1_t * _delegate
+/* "pysam/csamtools.pxd":415
+ * cdef char * _fetch( self, char * reference, int start, int end, int * length )
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ *
+ * # object that this AlignedRead represents
*/
-struct __pyx_obj_9csamtools_Samfile {
+struct __pyx_obj_5pysam_9csamtools_AlignedRead {
PyObject_HEAD
- struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isstream;
- int isremote;
- bam1_t *b;
- char *mode;
- int64_t start_offset;
+ bam1_t *_delegate;
};
-/* "csamtools.pyx":3222
+/* "pysam/csamtools.pyx":3250
* return retval, out_stderr, out_stdout
*
* cdef class SNPCall: # <<<<<<<<<<<<<<
* '''the results of a SNP call.'''
* cdef int _tid
*/
-struct __pyx_obj_9csamtools_SNPCall {
+struct __pyx_obj_5pysam_9csamtools_SNPCall {
PyObject_HEAD
int _tid;
int _pos;
@@ -652,120 +680,106 @@ struct __pyx_obj_9csamtools_SNPCall {
};
-/* "csamtools.pxd":539
- * pass
+/* "pysam/csamtools.pxd":492
+ * cdef IteratorRowRegion rowiter
*
- * cdef class IndexedReads: # <<<<<<<<<<<<<<
- * cdef Samfile samfile
- * cdef samfile_t * fp
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef int current_pos
*/
-struct __pyx_obj_9csamtools_IndexedReads {
- PyObject_HEAD
- struct __pyx_obj_9csamtools_Samfile *samfile;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtab;
+ bam1_t *b;
+ int current_pos;
samfile_t *fp;
- PyObject *index;
+ PyObject *positions;
int owns_samfile;
};
-/* "csamtools.pxd":531
- * cdef reset( self, tid, start, end )
- *
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * cdef int start
- * cdef int end
- */
-struct __pyx_obj_9csamtools_IteratorColumnRegion {
- struct __pyx_obj_9csamtools_IteratorColumn __pyx_base;
- int start;
- int end;
- int truncate;
-};
-
-/* "csamtools.pxd":455
- * cdef int n_pu
+/* "pysam/csamtools.pyx":545
*
- * cdef class PileupRead: # <<<<<<<<<<<<<<
- * cdef AlignedRead _alignment
- * cdef int32_t _qpos
+ *
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
+ * add_sq_text = False, check_header = True, check_sq = True )*
*/
-struct __pyx_obj_9csamtools_PileupRead {
- PyObject_HEAD
- struct __pyx_obj_9csamtools_AlignedRead *_alignment;
- int32_t _qpos;
- int _indel;
- int _level;
- uint32_t _is_del;
- uint32_t _is_head;
- uint32_t _is_tail;
-};
+struct __pyx_vtabstruct_5pysam_9csamtools_Samfile {
+ bam_header_t *(*_buildHeader)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *);
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_Samfile *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_Samfile *);
+ int (*write)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
+ char *(*_getrname)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int);
+};
+static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
-/* "csamtools.pyx":1766
- * return ret
+/* "pysam/csamtools.pyx":1545
+ * if self.owns_samfile: samclose( self.fp )
*
- * cdef class IteratorColumn: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over columns.
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int reopen = True)*
*
*/
-struct __pyx_vtabstruct_9csamtools_IteratorColumn {
- int (*cnext)(struct __pyx_obj_9csamtools_IteratorColumn *);
- char *(*getSequence)(struct __pyx_obj_9csamtools_IteratorColumn *);
- PyObject *(*setMask)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *);
- PyObject *(*setupIteratorData)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
- PyObject *(*reset)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll {
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumn *__pyx_vtabptr_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
-/* "csamtools.pyx":1931
- * self.iterdata.seq = NULL
+/* "pysam/csamtools.pyx":1466
+ *
+ *
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
*/
-struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion {
- struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion {
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *);
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *__pyx_vtabptr_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
-/* "csamtools.pyx":1461
- *
+/* "pysam/csamtools.pyx":1771
+ * return ret
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int tid, int beg, int end, int reopen = True )*
+ * cdef class IteratorColumn: # <<<<<<<<<<<<<<
+ * '''abstract base class for iterators over columns.
*
*/
-struct __pyx_vtabstruct_9csamtools_IteratorRowRegion {
- bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowRegion *);
- int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowRegion *);
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn {
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *);
+ char *(*getSequence)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *);
+ PyObject *(*setMask)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *);
+ PyObject *(*setupIteratorData)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args);
+ PyObject *(*reset)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *);
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *__pyx_vtabptr_9csamtools_IteratorRowRegion;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
-/* "csamtools.pyx":1641
- * raise StopIteration
- *
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile)*
+/* "pysam/csamtools.pyx":1936
+ * self.iterdata.seq = NULL
*
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * '''iterates over a region only.
+ * '''
*/
-struct __pyx_vtabstruct_9csamtools_IteratorRowSelection {
- bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
- int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowSelection *);
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion {
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
-/* "csamtools.pyx":1968
+/* "pysam/csamtools.pyx":1973
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
@@ -773,31 +787,28 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *__pyx_vtabptr_9c
* """
*/
-struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs {
- struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs {
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
-/* "csamtools.pyx":545
+/* "pysam/csamtools.pyx":1646
+ * raise StopIteration
*
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * '''*(filename, mode=None, template = None, referencenames = None, referencelengths = None, text = NULL, header = None,
- * add_sq_text = False, check_header = True, check_sq = True )*
*/
-struct __pyx_vtabstruct_9csamtools_Samfile {
- bam_header_t *(*_buildHeader)(struct __pyx_obj_9csamtools_Samfile *, PyObject *);
- bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_Samfile *);
- int (*cnext)(struct __pyx_obj_9csamtools_Samfile *);
- int (*write)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch);
- char *(*_getrname)(struct __pyx_obj_9csamtools_Samfile *, int);
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection {
+ bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
};
-static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samfile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
-/* "csamtools.pyx":375
+/* "pysam/csamtools.pyx":375
* ## Public methods
* ######################################################################
* cdef class Fastafile: # <<<<<<<<<<<<<<
@@ -805,30 +816,13 @@ static struct __pyx_vtabstruct_9csamtools_Samfile *__pyx_vtabptr_9csamtools_Samf
*
*/
-struct __pyx_vtabstruct_9csamtools_Fastafile {
- char *(*_fetch)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *);
+struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
+ char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
};
-static struct __pyx_vtabstruct_9csamtools_Fastafile *__pyx_vtabptr_9csamtools_Fastafile;
-
-
-/* "csamtools.pyx":1540
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
- *
- */
-
-struct __pyx_vtabstruct_9csamtools_IteratorRowAll {
- bam1_t *(*getCurrent)(struct __pyx_obj_9csamtools_IteratorRowAll *);
- int (*cnext)(struct __pyx_obj_9csamtools_IteratorRowAll *);
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtools_IteratorRowAll;
-
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
-
#if CYTHON_REFNANNY
typedef struct {
void (*INCREF)(void*, PyObject*, int);
@@ -841,8 +835,21 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo
static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL;
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/
#define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL;
- #define __Pyx_RefNannySetupContext(name) __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
- #define __Pyx_RefNannyFinishContext() __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
+#ifdef WITH_THREAD
+ #define __Pyx_RefNannySetupContext(name, acquire_gil) \
+ if (acquire_gil) { \
+ PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
+ PyGILState_Release(__pyx_gilstate_save); \
+ } else { \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
+ }
+#else
+ #define __Pyx_RefNannySetupContext(name, acquire_gil) \
+ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
+#endif
+ #define __Pyx_RefNannyFinishContext() \
+ __Pyx_RefNanny->FinishContext(&__pyx_refnanny)
#define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
#define __Pyx_GOTREF(r) __Pyx_RefNanny->GOTREF(__pyx_refnanny, (PyObject *)(r), __LINE__)
@@ -853,7 +860,7 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo
#define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
#else
#define __Pyx_RefNannyDeclarations
- #define __Pyx_RefNannySetupContext(name)
+ #define __Pyx_RefNannySetupContext(name, acquire_gil)
#define __Pyx_RefNannyFinishContext()
#define __Pyx_INCREF(r) Py_INCREF(r)
#define __Pyx_DECREF(r) Py_DECREF(r)
@@ -864,23 +871,21 @@ static struct __pyx_vtabstruct_9csamtools_IteratorRowAll *__pyx_vtabptr_9csamtoo
#define __Pyx_XGOTREF(r)
#define __Pyx_XGIVEREF(r)
#endif /* CYTHON_REFNANNY */
+#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
+#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#ifndef CYTHON_PROFILE
#define CYTHON_PROFILE 1
#endif
-
#ifndef CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_PROFILE_REUSE_FRAME 0
#endif
-
#if CYTHON_PROFILE
-
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-
#if CYTHON_PROFILE_REUSE_FRAME
#define CYTHON_FRAME_MODIFIER static
#define CYTHON_FRAME_DEL
@@ -888,17 +893,14 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
#define CYTHON_FRAME_MODIFIER
#define CYTHON_FRAME_DEL Py_DECREF(__pyx_frame)
#endif
-
#define __Pyx_TraceDeclarations \
static PyCodeObject *__pyx_frame_code = NULL; \
CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
int __Pyx_use_tracing = 0;
-
#define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
if (unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc)) { \
__Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \
}
-
#define __Pyx_TraceException() \
if (unlikely(__Pyx_use_tracing( && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyObject *exc_info = __Pyx_GetExceptionTuple(); \
@@ -908,26 +910,26 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
Py_DECREF(exc_info); \
} \
}
-
#define __Pyx_TraceReturn(result) \
if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_profilefunc) { \
PyThreadState_GET()->c_profilefunc( \
PyThreadState_GET()->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
CYTHON_FRAME_DEL; \
}
-
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/
-
#else
-
#define __Pyx_TraceDeclarations
#define __Pyx_TraceCall(funcname, srcfile, firstlineno)
#define __Pyx_TraceException()
#define __Pyx_TraceReturn(result)
-
#endif /* CYTHON_PROFILE */
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -942,13 +944,13 @@ static CYTHON_INLINE PyObject* __Pyx_tp_new(PyObject* type_obj) {
static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict,
- const char* function_name, int kw_allowed); /*proto*/
+static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name, PyObject* kw_name); /*proto*/
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, const char* function_name); /*proto*/
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name); /*proto*/
static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
@@ -958,7 +960,6 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
PyObject *r;
if (!j) return NULL;
@@ -966,79 +967,107 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
Py_DECREF(j);
return r;
}
-
-
#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
-
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
-
-
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
- PyObject *r;
- if (PyList_CheckExact(o) && ((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (PyList_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
}
- else if (PyTuple_CheckExact(o) && ((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else { /* inlined PySequence_GetItem() */
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
+ return m->sq_item(o, i);
+ }
}
- else if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_item && (likely(i >= 0))) {
- r = PySequence_GetItem(o, i);
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
}
- else {
- r = __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len)) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
}
- return r;
+ return PyList_Append(list, x);
}
+#else
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#endif
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (PyList_Append(L, x) < 0) return NULL;
+ if (unlikely(PyList_Append(L, x) < 0)) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- }
- else {
+ } else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -1048,28 +1077,27 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
}
}
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
- return unlikely(b < 0) ? b : !b;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
- return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+ int result = PySequence_Contains(seq, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
+static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
+ int result = PyDict_Contains(dict, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+}
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
- if (unlikely(d == Py_None)) {
- __Pyx_RaiseNoneIndexingError();
- return NULL;
- }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -1095,7 +1123,6 @@ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObjec
Py_INCREF(value);
#else
if (PyString_CheckExact(key) || PyUnicode_CheckExact(key) || PyInt_CheckExact(key)) {
- /* these presumably have safe hash functions */
value = PyDict_GetItem(d, key);
if (unlikely(!value)) {
value = default_value;
@@ -1106,7 +1133,7 @@ static PyObject* __Pyx_PyDict_GetItemDefault(PyObject* d, PyObject* key, PyObjec
m = __Pyx_GetAttrString(d, "get");
if (!m) return NULL;
value = PyObject_CallFunctionObjArgs(m, key,
- (default_value == Py_None) ? NULL : default_value, NULL);
+ (default_value == Py_None) ? NULL : default_value, NULL);
Py_DECREF(m);
}
#endif
@@ -1122,7 +1149,6 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
#define __Pyx_DelItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_DelItemInt_Fast(o, i) : \
__Pyx_DelItem_Generic(o, to_py_func(i)))
-
static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
int r;
if (!j) return -1;
@@ -1130,49 +1156,85 @@ static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
Py_DECREF(j);
return r;
}
-
static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i) {
- if (Py_TYPE(o)->tp_as_sequence && Py_TYPE(o)->tp_as_sequence->sq_ass_item && likely(i >= 0))
+#if CYTHON_COMPILING_IN_PYPY
+ if (PySequence_Check(o)) {
return PySequence_DelItem(o, i);
- else {
- PyObject *j = PyInt_FromSsize_t(i);
- return __Pyx_DelItem_Generic(o, j);
}
+#else
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_ass_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return -1;
+ i += l;
+ }
+ return m->sq_ass_item(o, i, (PyObject *)NULL);
+ }
+#endif
+ return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
}
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
+
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
- PyObject *modname); /*proto*/
-
-#define __pyx_binding_PyCFunctionType_USED 1
-
+ PyObject *qualname, PyObject *modname); /*proto*/
+
+#define __Pyx_CyFunction_USED 1
+#include <structmember.h>
+#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
+#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
+#define __Pyx_CYFUNCTION_CCLASS 0x04
+#define __Pyx_CyFunction_GetClosure(f) \
+ (((__pyx_CyFunctionObject *) (f))->func_closure)
+#define __Pyx_CyFunction_GetClassObj(f) \
+ (((__pyx_CyFunctionObject *) (f))->func_classobj)
+#define __Pyx_CyFunction_Defaults(type, f) \
+ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
+#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
+ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
typedef struct {
PyCFunctionObject func;
-} __pyx_binding_PyCFunctionType_object;
+ int flags;
+ PyObject *func_dict;
+ PyObject *func_weakreflist;
+ PyObject *func_name;
+ PyObject *func_qualname;
+ PyObject *func_doc;
+ PyObject *func_code;
+ PyObject *func_closure;
+ PyObject *func_classobj; /* No-args super() class cell */
+ void *defaults;
+ int defaults_pyobjects;
+ PyObject *defaults_tuple; /* Const defaults tuple */
+ PyObject *(*defaults_getter)(PyObject *);
+} __pyx_CyFunctionObject;
+static PyTypeObject *__pyx_CyFunctionType = 0;
+#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, code) \
+ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, code)
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
+ int flags, PyObject* qualname,
+ PyObject *self, PyObject *module,
+ PyObject* code);
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
+ size_t size,
+ int pyobjects);
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
+ PyObject *tuple);
+static int __Pyx_CyFunction_init(void);
-static PyTypeObject __pyx_binding_PyCFunctionType_type;
-static PyTypeObject *__pyx_binding_PyCFunctionType = NULL;
-
-static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module); /* proto */
-#define __pyx_binding_PyCFunctionType_New(ml, self) __pyx_binding_PyCFunctionType_NewEx(ml, self, NULL)
-
-static int __pyx_binding_PyCFunctionType_init(void); /* proto */
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int8_t(int8_t);
@@ -1186,12 +1248,8 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int32_t(int32_t);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject *);
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t);
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject *);
-
static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject *);
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
@@ -1232,6 +1290,33 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
+#define __Pyx_Generator_USED
+#include <structmember.h>
+#include <frameobject.h>
+typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
+typedef struct {
+ PyObject_HEAD
+ __pyx_generator_body_t body;
+ PyObject *closure;
+ PyObject *exc_type;
+ PyObject *exc_value;
+ PyObject *exc_traceback;
+ PyObject *gi_weakreflist;
+ PyObject *classobj;
+ PyObject *yieldfrom;
+ int resume_label;
+ char is_running; // using T_BOOL for property below requires char value
+} __pyx_GeneratorObject;
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure);
+static int __pyx_Generator_init(void);
+static int __Pyx_Generator_clear(PyObject* self);
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
+#else
+#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
+#endif
+
static void __Pyx_WriteUnraisable(const char *name, int clineno,
int lineno, const char *filename); /*proto*/
@@ -1239,15 +1324,38 @@ static int __Pyx_check_binary_version(void);
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
- int __pyx_lineno, const char *__pyx_filename); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename); /*proto*/
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
+
/* Module declarations from 'cpython.version' */
/* Module declarations from 'cpython.ref' */
@@ -1262,6 +1370,8 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.list' */
+/* Module declarations from 'libc.string' */
+
/* Module declarations from 'libc.stdio' */
/* Module declarations from 'cpython.object' */
@@ -1272,7 +1382,10 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
/* Module declarations from 'cpython.iterator' */
+/* Module declarations from '__builtin__' */
+
/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
@@ -1326,54 +1439,53 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'cpython' */
-/* Module declarations from 'csamtools' */
-static PyTypeObject *__pyx_ptype_9csamtools_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_AlignedRead = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_Samfile = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_PileupProxy = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_PileupRead = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRow = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowRegion = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAll = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowAllRefs = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorRowSelection = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumn = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnRegion = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IteratorColumnAllRefs = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_IndexedReads = 0;
-static PyTypeObject *__pyx_ptype_9csamtools_SNPCall = 0;
-static PyTypeObject *__pyx_ptype_9csamtools___pyx_Generator = 0;
-static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct__genexpr = 0;
-static PyTypeObject *__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = 0;
-static PyObject *__pyx_v_9csamtools__FILENAME_ENCODING = 0;
-static char *__pyx_v_9csamtools_CODE2CIGAR;
-static char *__pyx_v_9csamtools_bam_nt16_rev_table;
-static int __pyx_v_9csamtools_max_pos;
-static PyObject *__pyx_f_9csamtools_from_string_and_size(char *, size_t); /*proto*/
-static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *); /*proto*/
-static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
-static PyObject *__pyx_f_9csamtools__charptr_to_str(char *); /*proto*/
-static PyObject *__pyx_f_9csamtools__force_str(PyObject *); /*proto*/
-static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
-static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
-static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
-static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
-static int __pyx_f_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_count_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
-static int __pyx_f_9csamtools___advance_all(void *, bam1_t *); /*proto*/
-static int __pyx_f_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *); /*proto*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
-#define __Pyx_MODULE_NAME "csamtools"
-int __pyx_module_is_main_csamtools = 0;
-
-/* Implementation of 'csamtools' */
+/* Module declarations from 'pysam.csamtools' */
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastafile = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_AlignedRead = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Samfile = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_PileupRead = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRow = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowRegion = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAll = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorRowSelection = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumn = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_IndexedReads = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_SNPCall = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = 0;
+static PyObject *__pyx_v_5pysam_9csamtools__FILENAME_ENCODING = 0;
+static char *__pyx_v_5pysam_9csamtools_CODE2CIGAR;
+static char *__pyx_v_5pysam_9csamtools_bam_nt16_rev_table;
+static int __pyx_v_5pysam_9csamtools_max_pos;
+static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *, size_t); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools__force_str(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools_makeAlignedRead(bam1_t *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **, int, int, int); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *); /*proto*/
+static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *); /*proto*/
+static int __pyx_f_5pysam_9csamtools_fetch_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_5pysam_9csamtools_pileup_callback(uint32_t, uint32_t, int, bam_pileup1_t *, void *); /*proto*/
+static int __pyx_f_5pysam_9csamtools_pileup_fetch_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_5pysam_9csamtools_count_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_5pysam_9csamtools_mate_callback(bam1_t *, void *); /*proto*/
+static int __pyx_f_5pysam_9csamtools___advance_all(void *, bam1_t *); /*proto*/
+static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *, bam1_t *); /*proto*/
+static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *); /*proto*/
+static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *, uint32_t, uint32_t); /*proto*/
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *, uint32_t, uint32_t); /*proto*/
+#define __Pyx_MODULE_NAME "pysam.csamtools"
+int __pyx_module_is_main_pysam__csamtools = 0;
+
+/* Implementation of 'pysam.csamtools' */
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_enumerate;
@@ -1394,6 +1506,191 @@ static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_chr;
static PyObject *__pyx_builtin_open;
static PyObject *__pyx_builtin_UnicodeDecodeError;
+static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static int __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8gettid(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_14reset(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_16seek(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_18tell(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_28close(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_32write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_42__next__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_fastafile); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_other); /* proto */
+static Py_hash_t __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall___str__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_2build(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_4find(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname); /* proto */
+static void __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self); /* proto */
static char __pyx_k_1[] = "Argument must be string or unicode.";
static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
static char __pyx_k_5[] = "\t";
@@ -1441,7 +1738,8 @@ static char __pyx_k_79[] = "count for a region is not available for sam files";
static char __pyx_k_82[] = "no index available for pileup";
static char __pyx_k_85[] = "pileup of samfiles not implemented yet";
static char __pyx_k_92[] = "Samfile.mapped only available in bam files";
-static char __pyx_k_95[] = "Samfile.unmapped only available in bam files";
+static char __pyx_k_94[] = "mapping information not recorded in index or index not available";
+static char __pyx_k_97[] = "Samfile.unmapped only available in bam files";
static char __pyx_k__A[] = "A";
static char __pyx_k__B[] = "B";
static char __pyx_k__C[] = "C";
@@ -1451,6 +1749,7 @@ static char __pyx_k__H[] = "H";
static char __pyx_k__I[] = "I";
static char __pyx_k__S[] = "S";
static char __pyx_k__Z[] = "Z";
+static char __pyx_k__a[] = "a";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__d[] = "d";
@@ -1461,131 +1760,147 @@ static char __pyx_k__n[] = "n";
static char __pyx_k__r[] = "r";
static char __pyx_k__s[] = "s";
static char __pyx_k__w[] = "w";
-static char __pyx_k_100[] = "@";
-static char __pyx_k_102[] = "header line without '@': '%s'";
-static char __pyx_k_104[] = "header line with invalid type '%s': '%s'";
-static char __pyx_k_105[] = ":";
-static char __pyx_k_107[] = "unknown field code '%s' in record '%s'";
-static char __pyx_k_108[] = "multiple '%s' lines are not permitted";
-static char __pyx_k_109[] = "@%s";
-static char __pyx_k_110[] = "%s:%s";
-static char __pyx_k_111[] = "invalid type for record %s: %s, expected %s";
-static char __pyx_k_113[] = "incomplete sequence information in '%s'";
-static char __pyx_k_116[] = "can not iterate over samfile without header";
-static char __pyx_k_119[] = "no index available for iteration";
-static char __pyx_k_125[] = "can only use this iterator on bam files";
-static char __pyx_k_126[] = "reference sequence for '%s' (tid=%i) not found";
-static char __pyx_k_127[] = "unknown stepper option `%s` in IteratorColumn";
-static char __pyx_k_129[] = "error during iteration";
-static char __pyx_k_132[] = "Invalid clipping in CIGAR string";
-static char __pyx_k_135[] = "%c%i";
-static char __pyx_k_136[] = "quality and sequence mismatch: %i != %i";
-static char __pyx_k_137[] = "%c";
-static char __pyx_k_138[] = "<";
-static char __pyx_k_140[] = "integer %i out of range of BAM/SAM specification";
-static char __pyx_k_141[] = "2sccI%i%s";
-static char __pyx_k_145[] = "2sc%is";
-static char __pyx_k_147[] = "create_string_buffer";
-static char __pyx_k_148[] = "tag '%s' not present";
-static char __pyx_k_149[] = "unknown auxilliary type '%s'";
-static char __pyx_k_150[] = "Contig index";
-static char __pyx_k_151[] = "Mapped position on contig";
-static char __pyx_k_152[] = "Contig index for mate pair";
-static char __pyx_k_153[] = "Position of mate pair";
-static char __pyx_k_154[] = "Insert size";
-static char __pyx_k_155[] = "Binary flag";
-static char __pyx_k_156[] = "Count of cigar entries";
-static char __pyx_k_157[] = "Cigar entries";
-static char __pyx_k_158[] = "Mapping quality";
-static char __pyx_k_159[] = "Bam index bin number";
-static char __pyx_k_160[] = "Length of query name";
-static char __pyx_k_161[] = "Query name";
-static char __pyx_k_162[] = "Length of query sequence";
-static char __pyx_k_163[] = "Query sequence";
-static char __pyx_k_164[] = "Quality scores";
-static char __pyx_k_165[] = "Length of auxilary data";
-static char __pyx_k_166[] = "Maximum data length";
-static char __pyx_k_167[] = "Current data length";
-static char __pyx_k_168[] = "%-30s %-10s= %s";
-static char __pyx_k_169[] = "(";
-static char __pyx_k_170[] = ")";
-static char __pyx_k_171[] = "This class cannot be instantiated from Python";
-static char __pyx_k_173[] = "PileupProxy accessed after iterator finished";
-static char __pyx_k_177[] = "No such file or directory: '%s'";
-static char __pyx_k_178[] = "-o";
-static char __pyx_k_179[] = "option -o is forbidden in samtools view";
-static char __pyx_k_185[] = "can only IndexReads on bam files";
-static char __pyx_k_186[] = "read %s not found";
-static char __pyx_k_187[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_188[] = "the query name (None if not present)";
-static char __pyx_k_189[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of operations. The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 |\n +-----+---------- [...]
-static char __pyx_k_190[] = "the :term:`cigar` alignment as a string.\n \n Returns the empty string if not present.\n ";
-static char __pyx_k_191[] = "read sequence bases, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.";
-static char __pyx_k_192[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.";
-static char __pyx_k_193[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorit [...]
-static char __pyx_k_194[] = "aligned query sequence quality values (None if not present). This property is read-only.\n\n In Python 3, this property is of type bytes.";
-static char __pyx_k_195[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
-static char __pyx_k_196[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
-static char __pyx_k_197[] = "Length of the aligned query sequence";
-static char __pyx_k_198[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n ";
-static char __pyx_k_199[] = "properties flag";
-static char __pyx_k_200[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()` [...]
-static char __pyx_k_201[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
-static char __pyx_k_202[] = "0-based leftmost coordinate";
-static char __pyx_k_203[] = "properties bin";
-static char __pyx_k_204[] = "length of the read (read only). Returns 0 if not given.";
-static char __pyx_k_205[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available.";
-static char __pyx_k_206[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
-static char __pyx_k_207[] = "mapping quality";
-static char __pyx_k_208[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
-static char __pyx_k_209[] = "the :term:`reference` id of the mate ";
-static char __pyx_k_210[] = "the position of the mate\n deprecated, use PNEXT instead.";
-static char __pyx_k_211[] = "the position of the mate";
-static char __pyx_k_212[] = "the insert size\n deprecated: use tlen instead";
-static char __pyx_k_213[] = "the insert size";
-static char __pyx_k_214[] = "true if read is paired in sequencing";
-static char __pyx_k_215[] = "true if read is mapped in a proper pair";
-static char __pyx_k_216[] = "true if read itself is unmapped";
-static char __pyx_k_217[] = "true if the mate is unmapped";
-static char __pyx_k_218[] = "true if read is mapped to reverse strand";
-static char __pyx_k_219[] = "true is read is mapped to reverse strand";
-static char __pyx_k_220[] = "true if this is read1";
-static char __pyx_k_221[] = "true if this is read2";
-static char __pyx_k_222[] = "true if not primary alignment";
-static char __pyx_k_223[] = "true if QC failure";
-static char __pyx_k_224[] = "true if optical or PCR duplicate";
-static char __pyx_k_225[] = "a list of reference positions that this read aligns to.";
-static char __pyx_k_226[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
-static char __pyx_k_227[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_228[] = "tuple with the names of :term:`reference` sequences.";
-static char __pyx_k_229[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n ";
-static char __pyx_k_230[] = "total number of mapped reads in file.\n ";
-static char __pyx_k_231[] = "total number of unmapped reads in file.\n ";
-static char __pyx_k_232[] = "full contents of the :term:`sam file` header as a string.";
-static char __pyx_k_233[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n ";
-static char __pyx_k_234[] = "the chromosome ID as is defined in the header";
-static char __pyx_k_235[] = "number of reads mapping to this column.";
-static char __pyx_k_236[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
-static char __pyx_k_237[] = "a :class:`pysam.AlignedRead` object of the aligned read";
-static char __pyx_k_238[] = "position of the read base at the pileup site, 0-based";
-static char __pyx_k_239[] = "indel length; 0 for no indel, positive for ins and negative for del";
-static char __pyx_k_240[] = "1 iff the base on the padded read is a deletion";
-static char __pyx_k_241[] = "current sequence length.";
-static char __pyx_k_242[] = "nucleotide position of SNP.";
-static char __pyx_k_243[] = "reference base at pos. ``N`` if no reference sequence supplied.";
-static char __pyx_k_244[] = "the genotype called.";
-static char __pyx_k_245[] = "the genotype quality (Phred-scaled).";
-static char __pyx_k_246[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
-static char __pyx_k_247[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
-static char __pyx_k_248[] = "coverage or read depth - the number of reads involved in the call.";
-static char __pyx_k_249[] = "getfilesystemencoding";
-static char __pyx_k_250[] = "MIDNSHP=X";
-static char __pyx_k_251[] = "([MIDNSHP=X])(\\d+)";
-static char __pyx_k_253[] = "=ACMGRSVTWYHKDBN";
-static char __pyx_k_254[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
-static char __pyx_k_255[] = "\n stderr is captured.\n ";
-static char __pyx_k_256[] = "does nothing. stderr can't be redirected on windows";
-static char __pyx_k_262[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
+static char __pyx_k_102[] = "@";
+static char __pyx_k_104[] = "header line without '@': '%s'";
+static char __pyx_k_106[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_107[] = ":";
+static char __pyx_k_108[] = "malformatted header: no ':' in field";
+static char __pyx_k_111[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_112[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_113[] = "@%s";
+static char __pyx_k_114[] = "%s:%s";
+static char __pyx_k_115[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_117[] = "incomplete sequence information in '%s'";
+static char __pyx_k_120[] = "can not iterate over samfile without header";
+static char __pyx_k_123[] = "no index available for iteration";
+static char __pyx_k_129[] = "can only use this iterator on bam files";
+static char __pyx_k_130[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_131[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_133[] = "error during iteration";
+static char __pyx_k_136[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_139[] = "%i%c";
+static char __pyx_k_140[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_141[] = "%c";
+static char __pyx_k_142[] = "<";
+static char __pyx_k_144[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_145[] = "2sccI%i%s";
+static char __pyx_k_149[] = "2sc%is";
+static char __pyx_k_151[] = "create_string_buffer";
+static char __pyx_k_152[] = "tag '%s' not present";
+static char __pyx_k_153[] = "unknown auxilliary type '%s'";
+static char __pyx_k_154[] = "Contig index";
+static char __pyx_k_155[] = "Mapped position on contig";
+static char __pyx_k_156[] = "Contig index for mate pair";
+static char __pyx_k_157[] = "Position of mate pair";
+static char __pyx_k_158[] = "Insert size";
+static char __pyx_k_159[] = "Binary flag";
+static char __pyx_k_160[] = "Count of cigar entries";
+static char __pyx_k_161[] = "Cigar entries";
+static char __pyx_k_162[] = "Mapping quality";
+static char __pyx_k_163[] = "Bam index bin number";
+static char __pyx_k_164[] = "Length of query name";
+static char __pyx_k_165[] = "Query name";
+static char __pyx_k_166[] = "Length of query sequence";
+static char __pyx_k_167[] = "Query sequence";
+static char __pyx_k_168[] = "Quality scores";
+static char __pyx_k_169[] = "Length of auxilary data";
+static char __pyx_k_170[] = "Maximum data length";
+static char __pyx_k_171[] = "Current data length";
+static char __pyx_k_172[] = "%-30s %-10s= %s";
+static char __pyx_k_173[] = "(";
+static char __pyx_k_174[] = ")";
+static char __pyx_k_175[] = "This class cannot be instantiated from Python";
+static char __pyx_k_177[] = "PileupProxy accessed after iterator finished";
+static char __pyx_k_181[] = "No such file or directory: '%s'";
+static char __pyx_k_182[] = "-o";
+static char __pyx_k_183[] = "option -o is forbidden in samtools view";
+static char __pyx_k_189[] = "can only IndexReads on bam files";
+static char __pyx_k_190[] = "read %s not found";
+static char __pyx_k_191[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_192[] = "the query name (None if not present)";
+static char __pyx_k_193[] = "the :term:`cigar` alignment (None if not present). The alignment\n is returned as a list of tuples of (operation, length). \n The operations are:\n\n +-----+--------------+-----+\n |M |BAM_CMATCH |0 |\n +-----+--------------+-----+\n |I |BAM_CINS |1 |\n +-----+--------------+-----+\n |D |BAM_CDEL |2 |\n +-----+--------------+-----+\n |N |BAM_CREF_SKIP |3 [...]
+static char __pyx_k_194[] = "the :term:`cigar` alignment as a string.\n \n The cigar string is a string of alternating integers\n and characters denoting the length and the type of\n an operation.\n\n .. note::\n The order length,operation is specified in the\n SAM format. It is different from the order of\n the :meth:`cigar` property.\n\n Returns the empty string if not present.\n ";
+static char __pyx_k_195[] = "read sequence bases, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.";
+static char __pyx_k_196[] = "read sequence base qualities, including :term:`soft clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.";
+static char __pyx_k_197[] = "aligned portion of the read and excludes any flanking bases that were :term:`soft clipped` (None if not present).\n\n In Python 3, this property is of type bytes. Assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient.\n\n SAM/BAM files may included extra flanking bases sequences that were\n not part of the alignment. These bases may be the result of the\n Smith-Waterman or other algorit [...]
+static char __pyx_k_198[] = "aligned query sequence quality values (None if not present). This property is read-only.\n\n In Python 3, this property is of type bytes.";
+static char __pyx_k_199[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_200[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_201[] = "Length of the aligned query sequence";
+static char __pyx_k_202[] = "the tags in the AUX field.\n\n This property permits convenience access to\n the tags. Changes it the returned list will\n not update the tags automatically. Instead,\n the following is required for adding a\n new tag::\n\n read.tags = read.tags + [(\"RG\",0)]\n\n\n This method will happily write the same tag\n multiple times.\n ";
+static char __pyx_k_203[] = "properties flag";
+static char __pyx_k_204[] = "\n :term:`target` ID\n\n DEPRECATED from pysam-0.4 - use tid in the future.\n The rname field caused a lot of confusion as it returns\n the :term:`target` ID instead of the reference sequence\n name.\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()` [...]
+static char __pyx_k_205[] = "\n :term:`target` ID\n\n .. note::\n\n This field contains the index of the reference sequence\n in the sequence dictionary. To obtain the name\n of the reference sequence, use :meth:`pysam.Samfile.getrname()`\n\n ";
+static char __pyx_k_206[] = "0-based leftmost coordinate";
+static char __pyx_k_207[] = "properties bin";
+static char __pyx_k_208[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_209[] = "aligned reference position of the read on the reference genome. \n \n aend points to one past the last aligned residue.\n Returns None if not available.";
+static char __pyx_k_210[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
+static char __pyx_k_211[] = "mapping quality";
+static char __pyx_k_212[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
+static char __pyx_k_213[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_214[] = "the position of the mate\n deprecated, use PNEXT instead.";
+static char __pyx_k_215[] = "the position of the mate";
+static char __pyx_k_216[] = "the insert size\n deprecated: use tlen instead";
+static char __pyx_k_217[] = "the insert size";
+static char __pyx_k_218[] = "true if read is paired in sequencing";
+static char __pyx_k_219[] = "true if read is mapped in a proper pair";
+static char __pyx_k_220[] = "true if read itself is unmapped";
+static char __pyx_k_221[] = "true if the mate is unmapped";
+static char __pyx_k_222[] = "true if read is mapped to reverse strand";
+static char __pyx_k_223[] = "true is read is mapped to reverse strand";
+static char __pyx_k_224[] = "true if this is read1";
+static char __pyx_k_225[] = "true if this is read2";
+static char __pyx_k_226[] = "true if not primary alignment";
+static char __pyx_k_227[] = "true if QC failure";
+static char __pyx_k_228[] = "true if optical or PCR duplicate";
+static char __pyx_k_229[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_230[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
+static char __pyx_k_231[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_232[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_233[] = "tuple of the lengths of the :term:`reference` sequences. The lengths are in the same order as\n :attr:`pysam.Samfile.references`\n ";
+static char __pyx_k_234[] = "total number of mapped reads in file.\n ";
+static char __pyx_k_235[] = "total number of unmapped reads in file.\n ";
+static char __pyx_k_236[] = "full contents of the :term:`sam file` header as a string.";
+static char __pyx_k_237[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n ";
+static char __pyx_k_238[] = "the chromosome ID as is defined in the header";
+static char __pyx_k_239[] = "number of reads mapping to this column.";
+static char __pyx_k_240[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
+static char __pyx_k_241[] = "a :class:`pysam.AlignedRead` object of the aligned read";
+static char __pyx_k_242[] = "position of the read base at the pileup site, 0-based";
+static char __pyx_k_243[] = "indel length; 0 for no indel, positive for ins and negative for del";
+static char __pyx_k_244[] = "1 iff the base on the padded read is a deletion";
+static char __pyx_k_245[] = "current sequence length.";
+static char __pyx_k_246[] = "nucleotide position of SNP.";
+static char __pyx_k_247[] = "reference base at pos. ``N`` if no reference sequence supplied.";
+static char __pyx_k_248[] = "the genotype called.";
+static char __pyx_k_249[] = "the genotype quality (Phred-scaled).";
+static char __pyx_k_250[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
+static char __pyx_k_251[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
+static char __pyx_k_252[] = "coverage or read depth - the number of reads involved in the call.";
+static char __pyx_k_253[] = "getfilesystemencoding";
+static char __pyx_k_254[] = "MIDNSHP=X";
+static char __pyx_k_255[] = "(\\d+)([MIDNSHP=X])";
+static char __pyx_k_257[] = "=ACMGRSVTWYHKDBN";
+static char __pyx_k_260[] = "/home/andreas/devel/pysam/pysam/csamtools.pyx";
+static char __pyx_k_261[] = "PileupColumn.__str__";
+static char __pyx_k_262[] = "pysam.csamtools";
+static char __pyx_k_263[] = "A pileup column. A pileup column contains\n all the reads that map to a certain target base.\n\n tid\n chromosome ID as is defined in the header\n pos\n the target base coordinate (0-based)\n n\n number of reads mapping to this column\n pileups\n list of reads (:class:`pysam.PileupRead`) aligned to this column\n ";
+static char __pyx_k_266[] = "StderrStore.__init__";
+static char __pyx_k_269[] = "StderrStore.readAndRelease";
+static char __pyx_k_272[] = "StderrStore.release";
+static char __pyx_k_275[] = "StderrStore.__del__";
+static char __pyx_k_276[] = "\n stderr is captured.\n ";
+static char __pyx_k_279[] = "StderrStoreWindows.__init__";
+static char __pyx_k_282[] = "StderrStoreWindows.readAndRelease";
+static char __pyx_k_285[] = "StderrStoreWindows.release";
+static char __pyx_k_286[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_295[] = "Outs.__init__";
+static char __pyx_k_298[] = "Outs.setdevice";
+static char __pyx_k_301[] = "Outs.setfile";
+static char __pyx_k_304[] = "Outs.setfd";
+static char __pyx_k_307[] = "Outs.restore";
+static char __pyx_k_308[] = "http://mail.python.org/pipermail/python-list/2000-June/038406.html";
static char __pyx_k__AS[] = "AS";
static char __pyx_k__CL[] = "CL";
static char __pyx_k__CN[] = "CN";
@@ -1628,9 +1943,11 @@ static char __pyx_k__bin[] = "bin";
static char __pyx_k__chr[] = "chr";
static char __pyx_k__dup[] = "dup";
static char __pyx_k__end[] = "end";
+static char __pyx_k__inf[] = "inf";
static char __pyx_k__map[] = "map";
static char __pyx_k__max[] = "max";
static char __pyx_k__min[] = "min";
+static char __pyx_k__ofd[] = "ofd";
static char __pyx_k__ord[] = "ord";
static char __pyx_k__pos[] = "pos";
static char __pyx_k__raw[] = "raw";
@@ -1675,6 +1992,7 @@ static char __pyx_k__warn[] = "warn";
static char __pyx_k___open[] = "_open";
static char __pyx_k__ascii[] = "ascii";
static char __pyx_k__bqual[] = "bqual";
+static char __pyx_k__cargs[] = "cargs";
static char __pyx_k__cigar[] = "cigar";
static char __pyx_k__close[] = "close";
static char __pyx_k__flush[] = "flush";
@@ -1712,6 +2030,7 @@ static char __pyx_k__record[] = "record";
static char __pyx_k__region[] = "region";
static char __pyx_k__remove[] = "remove";
static char __pyx_k__reopen[] = "reopen";
+static char __pyx_k__retval[] = "retval";
static char __pyx_k__sorted[] = "sorted";
static char __pyx_k__stderr[] = "stderr";
static char __pyx_k__stdout[] = "stdout";
@@ -1761,6 +2080,10 @@ static char __pyx_k__genotype[] = "genotype";
static char __pyx_k__nextiter[] = "nextiter";
static char __pyx_k__platform[] = "platform";
static char __pyx_k__samtools[] = "samtools";
+static char __pyx_k__stderr_f[] = "stderr_f";
+static char __pyx_k__stderr_h[] = "stderr_h";
+static char __pyx_k__stdout_f[] = "stdout_f";
+static char __pyx_k__stdout_h[] = "stdout_h";
static char __pyx_k__tempfile[] = "tempfile";
static char __pyx_k__template[] = "template";
static char __pyx_k__truncate[] = "truncate";
@@ -1770,7 +2093,6 @@ static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k____enter__[] = "__enter__";
static char __pyx_k___hasIndex[] = "_hasIndex";
static char __pyx_k__alignment[] = "alignment";
-static char __pyx_k__csamtools[] = "csamtools";
static char __pyx_k__enumerate[] = "enumerate";
static char __pyx_k__exc_value[] = "exc_value";
static char __pyx_k__fastafile[] = "fastafile";
@@ -1788,6 +2110,8 @@ static char __pyx_k__IS_PYTHON3[] = "IS_PYTHON3";
static char __pyx_k__PileupRead[] = "PileupRead";
static char __pyx_k__ValueError[] = "ValueError";
static char __pyx_k___buildLine[] = "_buildLine";
+static char __pyx_k__out_stderr[] = "out_stderr";
+static char __pyx_k__out_stdout[] = "out_stdout";
static char __pyx_k__references[] = "references";
static char __pyx_k__startswith[] = "startswith";
static char __pyx_k__AlignedRead[] = "AlignedRead";
@@ -1800,6 +2124,7 @@ static char __pyx_k__collections[] = "collections";
static char __pyx_k__defaultdict[] = "defaultdict";
static char __pyx_k__nreferences[] = "nreferences";
static char __pyx_k__snp_quality[] = "snp_quality";
+static char __pyx_k__stdout_save[] = "stdout_save";
static char __pyx_k__IndexedReads[] = "IndexedReads";
static char __pyx_k__PileupColumn[] = "PileupColumn";
static char __pyx_k___parseRegion[] = "_parseRegion";
@@ -1828,36 +2153,33 @@ static char __pyx_k__NotImplementedError[] = "NotImplementedError";
static char __pyx_k__VALID_HEADER_FIELDS[] = "VALID_HEADER_FIELDS";
static PyObject *__pyx_kp_u_1;
static PyObject *__pyx_kp_s_10;
-static PyObject *__pyx_kp_s_100;
static PyObject *__pyx_kp_s_102;
static PyObject *__pyx_kp_s_104;
-static PyObject *__pyx_kp_s_105;
+static PyObject *__pyx_kp_s_106;
static PyObject *__pyx_kp_s_107;
static PyObject *__pyx_kp_s_108;
-static PyObject *__pyx_kp_s_109;
-static PyObject *__pyx_kp_s_110;
static PyObject *__pyx_kp_s_111;
+static PyObject *__pyx_kp_s_112;
static PyObject *__pyx_kp_s_113;
-static PyObject *__pyx_kp_s_116;
-static PyObject *__pyx_kp_s_119;
-static PyObject *__pyx_kp_s_125;
-static PyObject *__pyx_kp_s_126;
-static PyObject *__pyx_kp_s_127;
+static PyObject *__pyx_kp_s_114;
+static PyObject *__pyx_kp_s_115;
+static PyObject *__pyx_kp_s_117;
+static PyObject *__pyx_kp_s_120;
+static PyObject *__pyx_kp_s_123;
static PyObject *__pyx_kp_s_129;
static PyObject *__pyx_kp_s_13;
-static PyObject *__pyx_kp_s_135;
-static PyObject *__pyx_kp_s_136;
-static PyObject *__pyx_kp_s_137;
-static PyObject *__pyx_kp_s_138;
+static PyObject *__pyx_kp_s_130;
+static PyObject *__pyx_kp_s_131;
+static PyObject *__pyx_kp_s_133;
+static PyObject *__pyx_kp_s_139;
static PyObject *__pyx_kp_s_140;
static PyObject *__pyx_kp_s_141;
+static PyObject *__pyx_kp_s_142;
+static PyObject *__pyx_kp_s_144;
static PyObject *__pyx_kp_s_145;
-static PyObject *__pyx_n_s_147;
-static PyObject *__pyx_kp_s_148;
static PyObject *__pyx_kp_s_149;
static PyObject *__pyx_kp_s_15;
-static PyObject *__pyx_kp_s_150;
-static PyObject *__pyx_kp_s_151;
+static PyObject *__pyx_n_s_151;
static PyObject *__pyx_kp_s_152;
static PyObject *__pyx_kp_s_153;
static PyObject *__pyx_kp_s_154;
@@ -1881,24 +2203,43 @@ static PyObject *__pyx_kp_s_169;
static PyObject *__pyx_kp_s_17;
static PyObject *__pyx_kp_s_170;
static PyObject *__pyx_kp_s_171;
+static PyObject *__pyx_kp_s_172;
static PyObject *__pyx_kp_s_173;
+static PyObject *__pyx_kp_s_174;
+static PyObject *__pyx_kp_s_175;
static PyObject *__pyx_kp_s_177;
-static PyObject *__pyx_kp_s_178;
-static PyObject *__pyx_kp_s_179;
static PyObject *__pyx_kp_s_18;
-static PyObject *__pyx_kp_s_185;
-static PyObject *__pyx_kp_s_186;
+static PyObject *__pyx_kp_s_181;
+static PyObject *__pyx_kp_s_182;
+static PyObject *__pyx_kp_s_183;
+static PyObject *__pyx_kp_s_189;
static PyObject *__pyx_kp_s_19;
+static PyObject *__pyx_kp_s_190;
static PyObject *__pyx_kp_s_24;
-static PyObject *__pyx_n_s_249;
-static PyObject *__pyx_kp_s_251;
-static PyObject *__pyx_kp_s_254;
+static PyObject *__pyx_n_s_253;
static PyObject *__pyx_kp_s_255;
-static PyObject *__pyx_kp_s_256;
-static PyObject *__pyx_kp_s_262;
+static PyObject *__pyx_kp_s_260;
+static PyObject *__pyx_n_s_261;
+static PyObject *__pyx_n_s_262;
+static PyObject *__pyx_kp_s_263;
+static PyObject *__pyx_n_s_266;
+static PyObject *__pyx_n_s_269;
+static PyObject *__pyx_n_s_272;
+static PyObject *__pyx_n_s_275;
+static PyObject *__pyx_kp_s_276;
+static PyObject *__pyx_n_s_279;
+static PyObject *__pyx_n_s_282;
+static PyObject *__pyx_n_s_285;
+static PyObject *__pyx_kp_s_286;
static PyObject *__pyx_kp_s_29;
+static PyObject *__pyx_n_s_295;
+static PyObject *__pyx_n_s_298;
static PyObject *__pyx_kp_u_3;
static PyObject *__pyx_kp_s_30;
+static PyObject *__pyx_n_s_301;
+static PyObject *__pyx_n_s_304;
+static PyObject *__pyx_n_s_307;
+static PyObject *__pyx_kp_s_308;
static PyObject *__pyx_kp_s_31;
static PyObject *__pyx_kp_s_32;
static PyObject *__pyx_kp_s_33;
@@ -1931,7 +2272,8 @@ static PyObject *__pyx_kp_s_82;
static PyObject *__pyx_kp_s_85;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_kp_s_92;
-static PyObject *__pyx_kp_s_95;
+static PyObject *__pyx_kp_s_94;
+static PyObject *__pyx_kp_s_97;
static PyObject *__pyx_kp_s__2scB;
static PyObject *__pyx_kp_s__2scH;
static PyObject *__pyx_kp_s__2scI;
@@ -2025,6 +2367,7 @@ static PyObject *__pyx_n_s___isOpen;
static PyObject *__pyx_n_s___open;
static PyObject *__pyx_n_s___parseRegion;
static PyObject *__pyx_n_s___samtools_dispatch;
+static PyObject *__pyx_n_s__a;
static PyObject *__pyx_n_s__add_sq_text;
static PyObject *__pyx_n_s__alignment;
static PyObject *__pyx_n_s__all;
@@ -2037,6 +2380,7 @@ static PyObject *__pyx_n_s__bqual;
static PyObject *__pyx_n_s__c;
static PyObject *__pyx_n_s__calcsize;
static PyObject *__pyx_n_s__callback;
+static PyObject *__pyx_n_s__cargs;
static PyObject *__pyx_n_s__catch_stdout;
static PyObject *__pyx_n_s__check_header;
static PyObject *__pyx_n_s__check_sq;
@@ -2047,7 +2391,6 @@ static PyObject *__pyx_n_s__collections;
static PyObject *__pyx_n_s__compile;
static PyObject *__pyx_n_s__consensus_quality;
static PyObject *__pyx_n_s__coverage;
-static PyObject *__pyx_n_s__csamtools;
static PyObject *__pyx_n_s__ctypes;
static PyObject *__pyx_n_s__d;
static PyObject *__pyx_n_s__data_len;
@@ -2080,6 +2423,7 @@ static PyObject *__pyx_n_s__i;
static PyObject *__pyx_n_s__id;
static PyObject *__pyx_n_s__indel;
static PyObject *__pyx_n_s__index;
+static PyObject *__pyx_n_s__inf;
static PyObject *__pyx_n_s__is_del;
static PyObject *__pyx_n_s__is_head;
static PyObject *__pyx_n_s__is_tail;
@@ -2113,10 +2457,13 @@ static PyObject *__pyx_n_s__n_cigar;
static PyObject *__pyx_n_s__nextiter;
static PyObject *__pyx_n_s__nreferences;
static PyObject *__pyx_n_s__object;
+static PyObject *__pyx_n_s__ofd;
static PyObject *__pyx_n_s__offset;
static PyObject *__pyx_n_s__open;
static PyObject *__pyx_n_s__ord;
static PyObject *__pyx_n_s__os;
+static PyObject *__pyx_n_s__out_stderr;
+static PyObject *__pyx_n_s__out_stdout;
static PyObject *__pyx_n_s__pack_into;
static PyObject *__pyx_n_s__path;
static PyObject *__pyx_n_s__pileups;
@@ -2149,6 +2496,7 @@ static PyObject *__pyx_n_s__release;
static PyObject *__pyx_n_s__remove;
static PyObject *__pyx_n_s__reopen;
static PyObject *__pyx_n_s__restore;
+static PyObject *__pyx_n_s__retval;
static PyObject *__pyx_n_s__rlen;
static PyObject *__pyx_n_s__rname;
static PyObject *__pyx_n_s__s;
@@ -2166,7 +2514,12 @@ static PyObject *__pyx_n_s__split;
static PyObject *__pyx_n_s__start;
static PyObject *__pyx_n_s__startswith;
static PyObject *__pyx_n_s__stderr;
+static PyObject *__pyx_n_s__stderr_f;
+static PyObject *__pyx_n_s__stderr_h;
static PyObject *__pyx_n_s__stdout;
+static PyObject *__pyx_n_s__stdout_f;
+static PyObject *__pyx_n_s__stdout_h;
+static PyObject *__pyx_n_s__stdout_save;
static PyObject *__pyx_n_s__stepper;
static PyObject *__pyx_n_s__streams;
static PyObject *__pyx_n_s__strip;
@@ -2220,8 +2573,8 @@ static PyObject *__pyx_k_22;
static PyObject *__pyx_k_23;
static PyObject *__pyx_k_54;
static PyObject *__pyx_k_73;
-static int __pyx_k_128;
-static PyObject *__pyx_k_176;
+static int __pyx_k_132;
+static PyObject *__pyx_k_180;
static PyObject *__pyx_k_tuple_2;
static PyObject *__pyx_k_tuple_4;
static PyObject *__pyx_k_tuple_8;
@@ -2263,50 +2616,81 @@ static PyObject *__pyx_k_tuple_89;
static PyObject *__pyx_k_tuple_90;
static PyObject *__pyx_k_tuple_91;
static PyObject *__pyx_k_tuple_93;
-static PyObject *__pyx_k_tuple_94;
+static PyObject *__pyx_k_tuple_95;
static PyObject *__pyx_k_tuple_96;
-static PyObject *__pyx_k_tuple_97;
static PyObject *__pyx_k_tuple_98;
static PyObject *__pyx_k_tuple_99;
+static PyObject *__pyx_k_tuple_100;
static PyObject *__pyx_k_tuple_101;
static PyObject *__pyx_k_tuple_103;
-static PyObject *__pyx_k_tuple_106;
-static PyObject *__pyx_k_tuple_112;
-static PyObject *__pyx_k_tuple_114;
-static PyObject *__pyx_k_tuple_115;
-static PyObject *__pyx_k_tuple_117;
+static PyObject *__pyx_k_tuple_105;
+static PyObject *__pyx_k_tuple_109;
+static PyObject *__pyx_k_tuple_110;
+static PyObject *__pyx_k_tuple_116;
static PyObject *__pyx_k_tuple_118;
-static PyObject *__pyx_k_tuple_120;
+static PyObject *__pyx_k_tuple_119;
static PyObject *__pyx_k_tuple_121;
static PyObject *__pyx_k_tuple_122;
-static PyObject *__pyx_k_tuple_123;
static PyObject *__pyx_k_tuple_124;
-static PyObject *__pyx_k_tuple_130;
-static PyObject *__pyx_k_tuple_131;
-static PyObject *__pyx_k_tuple_133;
+static PyObject *__pyx_k_tuple_125;
+static PyObject *__pyx_k_tuple_126;
+static PyObject *__pyx_k_tuple_127;
+static PyObject *__pyx_k_tuple_128;
static PyObject *__pyx_k_tuple_134;
-static PyObject *__pyx_k_tuple_139;
-static PyObject *__pyx_k_tuple_142;
+static PyObject *__pyx_k_tuple_135;
+static PyObject *__pyx_k_tuple_137;
+static PyObject *__pyx_k_tuple_138;
static PyObject *__pyx_k_tuple_143;
-static PyObject *__pyx_k_tuple_144;
static PyObject *__pyx_k_tuple_146;
-static PyObject *__pyx_k_tuple_172;
-static PyObject *__pyx_k_tuple_174;
-static PyObject *__pyx_k_tuple_175;
-static PyObject *__pyx_k_tuple_180;
-static PyObject *__pyx_k_tuple_181;
-static PyObject *__pyx_k_tuple_182;
-static PyObject *__pyx_k_tuple_183;
+static PyObject *__pyx_k_tuple_147;
+static PyObject *__pyx_k_tuple_148;
+static PyObject *__pyx_k_tuple_150;
+static PyObject *__pyx_k_tuple_176;
+static PyObject *__pyx_k_tuple_178;
+static PyObject *__pyx_k_tuple_179;
static PyObject *__pyx_k_tuple_184;
-static PyObject *__pyx_k_tuple_252;
-static PyObject *__pyx_k_tuple_257;
+static PyObject *__pyx_k_tuple_185;
+static PyObject *__pyx_k_tuple_186;
+static PyObject *__pyx_k_tuple_187;
+static PyObject *__pyx_k_tuple_188;
+static PyObject *__pyx_k_tuple_256;
static PyObject *__pyx_k_tuple_258;
-static PyObject *__pyx_k_tuple_259;
-static PyObject *__pyx_k_tuple_260;
-static PyObject *__pyx_k_tuple_261;
-static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
-
-/* "csamtools.pyx":140
+static PyObject *__pyx_k_tuple_264;
+static PyObject *__pyx_k_tuple_267;
+static PyObject *__pyx_k_tuple_270;
+static PyObject *__pyx_k_tuple_273;
+static PyObject *__pyx_k_tuple_277;
+static PyObject *__pyx_k_tuple_280;
+static PyObject *__pyx_k_tuple_283;
+static PyObject *__pyx_k_tuple_287;
+static PyObject *__pyx_k_tuple_288;
+static PyObject *__pyx_k_tuple_289;
+static PyObject *__pyx_k_tuple_290;
+static PyObject *__pyx_k_tuple_291;
+static PyObject *__pyx_k_tuple_292;
+static PyObject *__pyx_k_tuple_294;
+static PyObject *__pyx_k_tuple_296;
+static PyObject *__pyx_k_tuple_299;
+static PyObject *__pyx_k_tuple_302;
+static PyObject *__pyx_k_tuple_305;
+static PyObject *__pyx_k_tuple_309;
+static PyObject *__pyx_k_codeobj_259;
+static PyObject *__pyx_k_codeobj_265;
+static PyObject *__pyx_k_codeobj_268;
+static PyObject *__pyx_k_codeobj_271;
+static PyObject *__pyx_k_codeobj_274;
+static PyObject *__pyx_k_codeobj_278;
+static PyObject *__pyx_k_codeobj_281;
+static PyObject *__pyx_k_codeobj_284;
+static PyObject *__pyx_k_codeobj_293;
+static PyObject *__pyx_k_codeobj_297;
+static PyObject *__pyx_k_codeobj_300;
+static PyObject *__pyx_k_codeobj_303;
+static PyObject *__pyx_k_codeobj_306;
+static PyObject *__pyx_k_codeobj_310;
+static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
+
+/* "pysam/csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
@@ -2314,29 +2698,35 @@ static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___py
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
-static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_1genexpr[] = "genexpr()";
-static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
- struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
+static PyObject *__pyx_pf_5pysam_9csamtools_2genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("genexpr");
- __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
+ __Pyx_RefNannySetupContext("genexpr", 0);
+ __pyx_cur_scope = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr->tp_new(__pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 140);
- __pyx_self = __pyx_self;
- __pyx_cur_scope->__pyx_base.resume_label = 0;
- __pyx_cur_scope->__pyx_base.body = (__pyx_generator_body_t) __pyx_gb_9csamtools_2generator;
- __Pyx_GIVEREF(__pyx_cur_scope);
- __Pyx_RefNannyFinishContext();
- return (PyObject *) __pyx_cur_scope;
+ {
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_4generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) gen;
+ }
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("pysam.csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
@@ -2344,16 +2734,17 @@ static PyObject *__pyx_pf_9csamtools_1genexpr(PyObject *__pyx_self, CYTHON_UNUSE
return __pyx_r;
}
-static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
{
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *__pyx_cur_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *(*__pyx_t_4)(PyObject *);
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("None");
- switch (__pyx_cur_scope->__pyx_base.resume_label) {
+ __Pyx_RefNannySetupContext("None", 0);
+ switch (__pyx_generator->resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
@@ -2364,7 +2755,7 @@ static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___py
if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_2 = PyBytes_FromString(__pyx_v_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
@@ -2398,7 +2789,7 @@ static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___py
__pyx_t_1 = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
@@ -2415,7 +2806,7 @@ static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___py
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_cur_scope->__pyx_base.resume_label = 1;
+ __pyx_generator->resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
@@ -2429,7 +2820,7 @@ static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___py
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetNone(PyExc_StopIteration);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
@@ -2438,43 +2829,50 @@ static PyObject *__pyx_gb_9csamtools_2generator(struct __pyx_obj_9csamtools___py
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_cur_scope->__pyx_base.resume_label = -1;
+ __pyx_generator->resume_label = -1;
+ __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
-static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value); /* proto */
+static PyObject *__pyx_gb_5pysam_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-/* "csamtools.pyx":142
+/* "pysam/csamtools.pyx":142
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+ * CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" )
*
*/
-static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_3genexpr[] = "genexpr()";
-static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSED PyObject *unused) {
- struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
+static PyObject *__pyx_pf_5pysam_9csamtools_5genexpr(CYTHON_UNUSED PyObject *__pyx_self) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("genexpr");
- __pyx_cur_scope = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
+ __Pyx_RefNannySetupContext("genexpr", 0);
+ __pyx_cur_scope = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr->tp_new(__pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr, __pyx_empty_tuple, NULL);
if (unlikely(!__pyx_cur_scope)) {
__Pyx_RefNannyFinishContext();
return NULL;
}
__Pyx_GOTREF(__pyx_cur_scope);
__Pyx_TraceCall("genexpr", __pyx_f[0], 142);
- __pyx_self = __pyx_self;
- __pyx_cur_scope->__pyx_base.resume_label = 0;
- __pyx_cur_scope->__pyx_base.body = (__pyx_generator_body_t) __pyx_gb_9csamtools_4generator1;
- __Pyx_GIVEREF(__pyx_cur_scope);
- __Pyx_RefNannyFinishContext();
- return (PyObject *) __pyx_cur_scope;
+ {
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_9csamtools_7generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_cur_scope);
+ __Pyx_RefNannyFinishContext();
+ return (PyObject *) gen;
+ }
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("pysam.csamtools.genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
__Pyx_DECREF(((PyObject *)__pyx_cur_scope));
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
@@ -2482,8 +2880,9 @@ static PyObject *__pyx_pf_9csamtools_3genexpr(PyObject *__pyx_self, CYTHON_UNUSE
return __pyx_r;
}
-static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope, PyObject *__pyx_sent_value) /* generator body */
+static PyObject *__pyx_gb_5pysam_9csamtools_7generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value) /* generator body */
{
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *__pyx_cur_scope = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)__pyx_generator->closure);
PyObject *__pyx_r = NULL;
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
@@ -2491,8 +2890,8 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
PyObject *(*__pyx_t_4)(PyObject *);
PyObject *__pyx_t_5 = NULL;
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("None");
- switch (__pyx_cur_scope->__pyx_base.resume_label) {
+ __Pyx_RefNannySetupContext("None", 0);
+ switch (__pyx_generator->resume_label) {
case 0: goto __pyx_L3_first_run;
case 1: goto __pyx_L6_resume_from_yield;
default: /* CPython raises the right error here */
@@ -2503,7 +2902,7 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_2 = PyBytes_FromString(__pyx_v_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_5pysam_9csamtools_CODE2CIGAR); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_t_3 = PyObject_GetIter(((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
@@ -2537,7 +2936,7 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
__pyx_t_1 = __pyx_t_2;
__pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_y);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_cur_scope->__pyx_v_y);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_y);
@@ -2545,7 +2944,7 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_x);
@@ -2562,7 +2961,7 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
__Pyx_XGIVEREF(__pyx_r);
__Pyx_RefNannyFinishContext();
/* return from generator, yielding value */
- __pyx_cur_scope->__pyx_base.resume_label = 1;
+ __pyx_generator->resume_label = 1;
return __pyx_r;
__pyx_L6_resume_from_yield:;
__pyx_t_1 = __pyx_cur_scope->__pyx_t_0;
@@ -2576,7 +2975,7 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- PyErr_SetNone(PyExc_StopIteration); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetNone(PyExc_StopIteration);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
@@ -2586,12 +2985,13 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
__Pyx_AddTraceback("genexpr", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
- __pyx_cur_scope->__pyx_base.resume_label = -1;
+ __pyx_generator->resume_label = -1;
+ __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
-/* "csamtools.pyx":24
+/* "pysam/csamtools.pyx":24
* ########################################################################
* IS_PYTHON3 = PY_MAJOR_VERSION >= 3
* cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<<
@@ -2599,7 +2999,7 @@ static PyObject *__pyx_gb_9csamtools_4generator1(struct __pyx_obj_9csamtools___p
* return s[:length]
*/
-static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
+static PyObject *__pyx_f_5pysam_9csamtools_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -2608,10 +3008,10 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("from_string_and_size");
+ __Pyx_RefNannySetupContext("from_string_and_size", 0);
__Pyx_TraceCall("from_string_and_size", __pyx_f[0], 24);
- /* "csamtools.pyx":25
+ /* "pysam/csamtools.pyx":25
* IS_PYTHON3 = PY_MAJOR_VERSION >= 3
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -2621,7 +3021,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "csamtools.pyx":26
+ /* "pysam/csamtools.pyx":26
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3:
* return s[:length] # <<<<<<<<<<<<<<
@@ -2638,7 +3038,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
}
/*else*/ {
- /* "csamtools.pyx":28
+ /* "pysam/csamtools.pyx":28
* return s[:length]
* else:
* return s[:length].decode("ascii") # <<<<<<<<<<<<<<
@@ -2646,7 +3046,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
* # filename encoding (copied from lxml.etree.pyx)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 28; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -2658,7 +3058,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2667,7 +3067,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
return __pyx_r;
}
-/* "csamtools.pyx":41
+/* "pysam/csamtools.pyx":41
* #_C_FILENAME_ENCODING = <char*>_FILENAME_ENCODING
*
* cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<<
@@ -2675,7 +3075,7 @@ static PyObject *__pyx_f_9csamtools_from_string_and_size(char *__pyx_v_s, size_t
* """
*/
-static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filename) {
+static PyObject *__pyx_f_5pysam_9csamtools__my_encodeFilename(PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -2686,10 +3086,10 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_my_encodeFilename");
+ __Pyx_RefNannySetupContext("_my_encodeFilename", 0);
__Pyx_TraceCall("_my_encodeFilename", __pyx_f[0], 41);
- /* "csamtools.pyx":44
+ /* "pysam/csamtools.pyx":44
* u"""Make sure a filename is 8-bit encoded (or None).
* """
* if filename is None: # <<<<<<<<<<<<<<
@@ -2699,7 +3099,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
__pyx_t_1 = (__pyx_v_filename == Py_None);
if (__pyx_t_1) {
- /* "csamtools.pyx":45
+ /* "pysam/csamtools.pyx":45
* """
* if filename is None:
* return None # <<<<<<<<<<<<<<
@@ -2713,7 +3113,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
goto __pyx_L3;
}
- /* "csamtools.pyx":46
+ /* "pysam/csamtools.pyx":46
* if filename is None:
* return None
* elif PyBytes_Check(filename): # <<<<<<<<<<<<<<
@@ -2723,7 +3123,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
__pyx_t_1 = PyBytes_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "csamtools.pyx":47
+ /* "pysam/csamtools.pyx":47
* return None
* elif PyBytes_Check(filename):
* return filename # <<<<<<<<<<<<<<
@@ -2738,7 +3138,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
goto __pyx_L3;
}
- /* "csamtools.pyx":48
+ /* "pysam/csamtools.pyx":48
* elif PyBytes_Check(filename):
* return filename
* elif PyUnicode_Check(filename): # <<<<<<<<<<<<<<
@@ -2748,7 +3148,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
__pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "csamtools.pyx":49
+ /* "pysam/csamtools.pyx":49
* return filename
* elif PyUnicode_Check(filename):
* return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<<
@@ -2759,10 +3159,10 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
__pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_INCREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
__pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -2775,7 +3175,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
}
/*else*/ {
- /* "csamtools.pyx":51
+ /* "pysam/csamtools.pyx":51
* return filename.encode(_FILENAME_ENCODING)
* else:
* raise TypeError, u"Argument must be string or unicode." # <<<<<<<<<<<<<<
@@ -2793,7 +3193,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._my_encodeFilename", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2802,7 +3202,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
return __pyx_r;
}
-/* "csamtools.pyx":54
+/* "pysam/csamtools.pyx":54
*
*
* cdef bytes _force_bytes(object s): # <<<<<<<<<<<<<<
@@ -2810,7 +3210,7 @@ static PyObject *__pyx_f_9csamtools__my_encodeFilename(PyObject *__pyx_v_filenam
* """
*/
-static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_9csamtools__force_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -2820,10 +3220,10 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_bytes");
+ __Pyx_RefNannySetupContext("_force_bytes", 0);
__Pyx_TraceCall("_force_bytes", __pyx_f[0], 54);
- /* "csamtools.pyx":57
+ /* "pysam/csamtools.pyx":57
* u"""convert string or unicode object to bytes, assuming ascii encoding.
* """
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -2833,7 +3233,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "csamtools.pyx":58
+ /* "pysam/csamtools.pyx":58
* """
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
@@ -2848,7 +3248,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":59
+ /* "pysam/csamtools.pyx":59
* if PY_MAJOR_VERSION < 3:
* return s
* elif s is None: # <<<<<<<<<<<<<<
@@ -2858,7 +3258,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = (__pyx_v_s == Py_None);
if (__pyx_t_1) {
- /* "csamtools.pyx":60
+ /* "pysam/csamtools.pyx":60
* return s
* elif s is None:
* return None # <<<<<<<<<<<<<<
@@ -2872,7 +3272,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":61
+ /* "pysam/csamtools.pyx":61
* elif s is None:
* return None
* elif PyBytes_Check(s): # <<<<<<<<<<<<<<
@@ -2882,7 +3282,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = PyBytes_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "csamtools.pyx":62
+ /* "pysam/csamtools.pyx":62
* return None
* elif PyBytes_Check(s):
* return s # <<<<<<<<<<<<<<
@@ -2897,7 +3297,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":63
+ /* "pysam/csamtools.pyx":63
* elif PyBytes_Check(s):
* return s
* elif PyUnicode_Check(s): # <<<<<<<<<<<<<<
@@ -2907,7 +3307,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
__pyx_t_1 = PyUnicode_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "csamtools.pyx":64
+ /* "pysam/csamtools.pyx":64
* return s
* elif PyUnicode_Check(s):
* return s.encode('ascii') # <<<<<<<<<<<<<<
@@ -2928,7 +3328,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
}
/*else*/ {
- /* "csamtools.pyx":66
+ /* "pysam/csamtools.pyx":66
* return s.encode('ascii')
* else:
* raise TypeError, u"Argument must be string, bytes or unicode." # <<<<<<<<<<<<<<
@@ -2945,7 +3345,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._force_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -2954,7 +3354,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
return __pyx_r;
}
-/* "csamtools.pyx":68
+/* "pysam/csamtools.pyx":68
* raise TypeError, u"Argument must be string, bytes or unicode."
*
* cdef inline bytes _force_cmdline_bytes(object s): # <<<<<<<<<<<<<<
@@ -2962,7 +3362,7 @@ static PyObject *__pyx_f_9csamtools__force_bytes(PyObject *__pyx_v_s) {
*
*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject *__pyx_v_s) {
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools__force_cmdline_bytes(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -2970,10 +3370,10 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_cmdline_bytes");
+ __Pyx_RefNannySetupContext("_force_cmdline_bytes", 0);
__Pyx_TraceCall("_force_cmdline_bytes", __pyx_f[0], 68);
- /* "csamtools.pyx":69
+ /* "pysam/csamtools.pyx":69
*
* cdef inline bytes _force_cmdline_bytes(object s):
* return _force_bytes(s) # <<<<<<<<<<<<<<
@@ -2981,7 +3381,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject
* cdef _charptr_to_str(char* s):
*/
__Pyx_XDECREF(((PyObject *)__pyx_r));
- __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_s)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
@@ -2991,7 +3391,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._force_cmdline_bytes", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -3000,7 +3400,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":71
+/* "pysam/csamtools.pyx":71
* return _force_bytes(s)
*
* cdef _charptr_to_str(char* s): # <<<<<<<<<<<<<<
@@ -3008,7 +3408,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools__force_cmdline_bytes(PyObject
* return s
*/
-static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_9csamtools__charptr_to_str(char *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -3017,10 +3417,10 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_charptr_to_str");
+ __Pyx_RefNannySetupContext("_charptr_to_str", 0);
__Pyx_TraceCall("_charptr_to_str", __pyx_f[0], 71);
- /* "csamtools.pyx":72
+ /* "pysam/csamtools.pyx":72
*
* cdef _charptr_to_str(char* s):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -3030,7 +3430,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "csamtools.pyx":73
+ /* "pysam/csamtools.pyx":73
* cdef _charptr_to_str(char* s):
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
@@ -3047,7 +3447,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
}
/*else*/ {
- /* "csamtools.pyx":75
+ /* "pysam/csamtools.pyx":75
* return s
* else:
* return s.decode("ascii") # <<<<<<<<<<<<<<
@@ -3055,7 +3455,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
* cdef _force_str(object s):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, strlen(__pyx_v_s), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -3067,7 +3467,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._charptr_to_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -3076,7 +3476,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
return __pyx_r;
}
-/* "csamtools.pyx":77
+/* "pysam/csamtools.pyx":77
* return s.decode("ascii")
*
* cdef _force_str(object s): # <<<<<<<<<<<<<<
@@ -3084,7 +3484,7 @@ static PyObject *__pyx_f_9csamtools__charptr_to_str(char *__pyx_v_s) {
* if s is None:
*/
-static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_9csamtools__force_str(PyObject *__pyx_v_s) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -3094,10 +3494,10 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_force_str");
+ __Pyx_RefNannySetupContext("_force_str", 0);
__Pyx_TraceCall("_force_str", __pyx_f[0], 77);
- /* "csamtools.pyx":79
+ /* "pysam/csamtools.pyx":79
* cdef _force_str(object s):
* """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
* if s is None: # <<<<<<<<<<<<<<
@@ -3107,7 +3507,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
__pyx_t_1 = (__pyx_v_s == Py_None);
if (__pyx_t_1) {
- /* "csamtools.pyx":80
+ /* "pysam/csamtools.pyx":80
* """Return s converted to str type of current Python (bytes in Py2, unicode in Py3)"""
* if s is None:
* return None # <<<<<<<<<<<<<<
@@ -3122,7 +3522,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
}
__pyx_L3:;
- /* "csamtools.pyx":81
+ /* "pysam/csamtools.pyx":81
* if s is None:
* return None
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -3132,7 +3532,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "csamtools.pyx":82
+ /* "pysam/csamtools.pyx":82
* return None
* if PY_MAJOR_VERSION < 3:
* return s # <<<<<<<<<<<<<<
@@ -3146,7 +3546,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
goto __pyx_L4;
}
- /* "csamtools.pyx":83
+ /* "pysam/csamtools.pyx":83
* if PY_MAJOR_VERSION < 3:
* return s
* elif PyBytes_Check(s): # <<<<<<<<<<<<<<
@@ -3156,7 +3556,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
__pyx_t_1 = PyBytes_Check(__pyx_v_s);
if (__pyx_t_1) {
- /* "csamtools.pyx":84
+ /* "pysam/csamtools.pyx":84
* return s
* elif PyBytes_Check(s):
* return s.decode('ascii') # <<<<<<<<<<<<<<
@@ -3176,7 +3576,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
}
/*else*/ {
- /* "csamtools.pyx":87
+ /* "pysam/csamtools.pyx":87
* else:
* # assume unicode
* return s # <<<<<<<<<<<<<<
@@ -3195,7 +3595,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._force_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -3204,7 +3604,7 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
return __pyx_r;
}
-/* "csamtools.pyx":160
+/* "pysam/csamtools.pyx":160
* #####################################################################
* cdef class AlignedRead
* cdef makeAlignedRead(bam1_t * src): # <<<<<<<<<<<<<<
@@ -3212,8 +3612,8 @@ static PyObject *__pyx_f_9csamtools__force_str(PyObject *__pyx_v_s) {
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
-static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
- struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
+static PyObject *__pyx_f_5pysam_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
+ struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -3221,23 +3621,23 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makeAlignedRead");
+ __Pyx_RefNannySetupContext("makeAlignedRead", 0);
__Pyx_TraceCall("makeAlignedRead", __pyx_f[0], 160);
- /* "csamtools.pyx":162
+ /* "pysam/csamtools.pyx":162
* cdef makeAlignedRead(bam1_t * src):
* '''enter src into AlignedRead.'''
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
* dest._delegate = bam_dup1(src)
* return dest
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":163
+ /* "pysam/csamtools.pyx":163
* '''enter src into AlignedRead.'''
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = bam_dup1(src) # <<<<<<<<<<<<<<
@@ -3246,7 +3646,7 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
*/
__pyx_v_dest->_delegate = bam_dup1(__pyx_v_src);
- /* "csamtools.pyx":164
+ /* "pysam/csamtools.pyx":164
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = bam_dup1(src)
* return dest # <<<<<<<<<<<<<<
@@ -3262,7 +3662,7 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.makeAlignedRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.makeAlignedRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
@@ -3272,7 +3672,7 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
return __pyx_r;
}
-/* "csamtools.pyx":167
+/* "pysam/csamtools.pyx":167
*
* cdef class PileupProxy
* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ): # <<<<<<<<<<<<<<
@@ -3280,8 +3680,8 @@ static PyObject *__pyx_f_9csamtools_makeAlignedRead(bam1_t *__pyx_v_src) {
* dest.plp = plp
*/
-static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
- struct __pyx_obj_9csamtools_PileupProxy *__pyx_v_dest = 0;
+static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) {
+ struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -3289,23 +3689,23 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupProxy");
+ __Pyx_RefNannySetupContext("makePileupProxy", 0);
__Pyx_TraceCall("makePileupProxy", __pyx_f[0], 167);
- /* "csamtools.pyx":168
+ /* "pysam/csamtools.pyx":168
* cdef class PileupProxy
* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
* cdef PileupProxy dest = PileupProxy.__new__(PileupProxy) # <<<<<<<<<<<<<<
* dest.plp = plp
* dest.tid = tid
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_PileupProxy)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_PileupProxy)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":169
+ /* "pysam/csamtools.pyx":169
* cdef makePileupProxy( bam_pileup1_t ** plp, int tid, int pos, int n ):
* cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
* dest.plp = plp # <<<<<<<<<<<<<<
@@ -3314,7 +3714,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
*/
__pyx_v_dest->plp = __pyx_v_plp;
- /* "csamtools.pyx":170
+ /* "pysam/csamtools.pyx":170
* cdef PileupProxy dest = PileupProxy.__new__(PileupProxy)
* dest.plp = plp
* dest.tid = tid # <<<<<<<<<<<<<<
@@ -3323,7 +3723,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
*/
__pyx_v_dest->tid = __pyx_v_tid;
- /* "csamtools.pyx":171
+ /* "pysam/csamtools.pyx":171
* dest.plp = plp
* dest.tid = tid
* dest.pos = pos # <<<<<<<<<<<<<<
@@ -3332,7 +3732,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
*/
__pyx_v_dest->pos = __pyx_v_pos;
- /* "csamtools.pyx":172
+ /* "pysam/csamtools.pyx":172
* dest.tid = tid
* dest.pos = pos
* dest.n = n # <<<<<<<<<<<<<<
@@ -3344,7 +3744,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
if (PyObject_SetAttr(((PyObject *)__pyx_v_dest), __pyx_n_s__n, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":173
+ /* "pysam/csamtools.pyx":173
* dest.pos = pos
* dest.n = n
* return dest # <<<<<<<<<<<<<<
@@ -3360,7 +3760,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.makePileupProxy", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.makePileupProxy", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
@@ -3370,7 +3770,7 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
return __pyx_r;
}
-/* "csamtools.pyx":176
+/* "pysam/csamtools.pyx":176
*
* cdef class PileupRead
* cdef makePileupRead( bam_pileup1_t * src ): # <<<<<<<<<<<<<<
@@ -3378,102 +3778,111 @@ static PyObject *__pyx_f_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp,
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
*/
-static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
- struct __pyx_obj_9csamtools_PileupRead *__pyx_v_dest = 0;
+static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
+ struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
+ int32_t __pyx_t_2;
+ int __pyx_t_3;
+ uint32_t __pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("makePileupRead");
+ __Pyx_RefNannySetupContext("makePileupRead", 0);
__Pyx_TraceCall("makePileupRead", __pyx_f[0], 176);
- /* "csamtools.pyx":178
+ /* "pysam/csamtools.pyx":178
* cdef makePileupRead( bam_pileup1_t * src ):
* '''fill a PileupRead object from a bam_pileup1_t * object.'''
* cdef PileupRead dest = PileupRead.__new__(PileupRead) # <<<<<<<<<<<<<<
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos
*/
- __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_PileupRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_PileupRead)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_PileupRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_PileupRead *)__pyx_t_1);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_PileupRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":179
+ /* "pysam/csamtools.pyx":179
* '''fill a PileupRead object from a bam_pileup1_t * object.'''
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
* dest._alignment = makeAlignedRead( src.b ) # <<<<<<<<<<<<<<
* dest._qpos = src.qpos
* dest._indel = src.indel
*/
- __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_src->b); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_src->b); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_9csamtools_AlignedRead))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5pysam_9csamtools_AlignedRead))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_v_dest->_alignment);
__Pyx_DECREF(((PyObject *)__pyx_v_dest->_alignment));
- __pyx_v_dest->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_1);
+ __pyx_v_dest->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":180
+ /* "pysam/csamtools.pyx":180
* cdef PileupRead dest = PileupRead.__new__(PileupRead)
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos # <<<<<<<<<<<<<<
* dest._indel = src.indel
* dest._level = src.level
*/
- __pyx_v_dest->_qpos = __pyx_v_src->qpos;
+ __pyx_t_2 = __pyx_v_src->qpos;
+ __pyx_v_dest->_qpos = __pyx_t_2;
- /* "csamtools.pyx":181
+ /* "pysam/csamtools.pyx":181
* dest._alignment = makeAlignedRead( src.b )
* dest._qpos = src.qpos
* dest._indel = src.indel # <<<<<<<<<<<<<<
* dest._level = src.level
* dest._is_del = src.is_del
*/
- __pyx_v_dest->_indel = __pyx_v_src->indel;
+ __pyx_t_3 = __pyx_v_src->indel;
+ __pyx_v_dest->_indel = __pyx_t_3;
- /* "csamtools.pyx":182
+ /* "pysam/csamtools.pyx":182
* dest._qpos = src.qpos
* dest._indel = src.indel
* dest._level = src.level # <<<<<<<<<<<<<<
* dest._is_del = src.is_del
* dest._is_head = src.is_head
*/
- __pyx_v_dest->_level = __pyx_v_src->level;
+ __pyx_t_3 = __pyx_v_src->level;
+ __pyx_v_dest->_level = __pyx_t_3;
- /* "csamtools.pyx":183
+ /* "pysam/csamtools.pyx":183
* dest._indel = src.indel
* dest._level = src.level
* dest._is_del = src.is_del # <<<<<<<<<<<<<<
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail
*/
- __pyx_v_dest->_is_del = __pyx_v_src->is_del;
+ __pyx_t_4 = __pyx_v_src->is_del;
+ __pyx_v_dest->_is_del = __pyx_t_4;
- /* "csamtools.pyx":184
+ /* "pysam/csamtools.pyx":184
* dest._level = src.level
* dest._is_del = src.is_del
* dest._is_head = src.is_head # <<<<<<<<<<<<<<
* dest._is_tail = src.is_tail
* return dest
*/
- __pyx_v_dest->_is_head = __pyx_v_src->is_head;
+ __pyx_t_4 = __pyx_v_src->is_head;
+ __pyx_v_dest->_is_head = __pyx_t_4;
- /* "csamtools.pyx":185
+ /* "pysam/csamtools.pyx":185
* dest._is_del = src.is_del
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail # <<<<<<<<<<<<<<
* return dest
*
*/
- __pyx_v_dest->_is_tail = __pyx_v_src->is_tail;
+ __pyx_t_4 = __pyx_v_src->is_tail;
+ __pyx_v_dest->_is_tail = __pyx_t_4;
- /* "csamtools.pyx":186
+ /* "pysam/csamtools.pyx":186
* dest._is_head = src.is_head
* dest._is_tail = src.is_tail
* return dest # <<<<<<<<<<<<<<
@@ -3489,7 +3898,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.makePileupRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.makePileupRead", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
@@ -3499,7 +3908,7 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
return __pyx_r;
}
-/* "csamtools.pyx":188
+/* "pysam/csamtools.pyx":188
* return dest
*
* cdef convertBinaryTagToList( uint8_t * s ): # <<<<<<<<<<<<<<
@@ -3507,12 +3916,12 @@ static PyObject *__pyx_f_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v_src) {
* cdef char auxtype
*/
-static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
+static PyObject *__pyx_f_5pysam_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
char __pyx_v_auxtype;
uint8_t __pyx_v_byte_size;
int32_t __pyx_v_nvalues;
PyObject *__pyx_v_values = NULL;
- long __pyx_v_x;
+ CYTHON_UNUSED long __pyx_v_x;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -3525,10 +3934,10 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("convertBinaryTagToList");
+ __Pyx_RefNannySetupContext("convertBinaryTagToList", 0);
__Pyx_TraceCall("convertBinaryTagToList", __pyx_f[0], 188);
- /* "csamtools.pyx":195
+ /* "pysam/csamtools.pyx":195
*
* # get byte size
* auxtype = s[0] # <<<<<<<<<<<<<<
@@ -3537,7 +3946,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
*/
__pyx_v_auxtype = (__pyx_v_s[0]);
- /* "csamtools.pyx":196
+ /* "pysam/csamtools.pyx":196
* # get byte size
* auxtype = s[0]
* byte_size = bam_aux_type2size( auxtype ) # <<<<<<<<<<<<<<
@@ -3546,7 +3955,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
*/
__pyx_v_byte_size = bam_aux_type2size(__pyx_v_auxtype);
- /* "csamtools.pyx":197
+ /* "pysam/csamtools.pyx":197
* auxtype = s[0]
* byte_size = bam_aux_type2size( auxtype )
* s += 1 # <<<<<<<<<<<<<<
@@ -3555,7 +3964,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "csamtools.pyx":199
+ /* "pysam/csamtools.pyx":199
* s += 1
* # get number of values in array
* nvalues = (<int32_t*>s)[0] # <<<<<<<<<<<<<<
@@ -3564,7 +3973,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
*/
__pyx_v_nvalues = (((int32_t *)__pyx_v_s)[0]);
- /* "csamtools.pyx":200
+ /* "pysam/csamtools.pyx":200
* # get number of values in array
* nvalues = (<int32_t*>s)[0]
* s += 4 # <<<<<<<<<<<<<<
@@ -3573,7 +3982,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
*/
__pyx_v_s = (__pyx_v_s + 4);
- /* "csamtools.pyx":202
+ /* "pysam/csamtools.pyx":202
* s += 4
* # get values
* values = [] # <<<<<<<<<<<<<<
@@ -3581,11 +3990,11 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
* for x from 0 <= x < nvalues:
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_values = __pyx_t_1;
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_values = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":203
+ /* "pysam/csamtools.pyx":203
* # get values
* values = []
* if auxtype == 'c': # <<<<<<<<<<<<<<
@@ -3595,7 +4004,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 'c');
if (__pyx_t_2) {
- /* "csamtools.pyx":204
+ /* "pysam/csamtools.pyx":204
* values = []
* if auxtype == 'c':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3605,22 +4014,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":205
+ /* "pysam/csamtools.pyx":205
* if auxtype == 'c':
* for x from 0 <= x < nvalues:
* values.append((<int8_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype == 'C':
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = __Pyx_PyInt_to_py_int8_t((((int8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":206
+ /* "pysam/csamtools.pyx":206
* for x from 0 <= x < nvalues:
* values.append((<int8_t*>s)[0])
* s += 1 # <<<<<<<<<<<<<<
@@ -3632,7 +4038,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":207
+ /* "pysam/csamtools.pyx":207
* values.append((<int8_t*>s)[0])
* s += 1
* elif auxtype == 'C': # <<<<<<<<<<<<<<
@@ -3642,7 +4048,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 'C');
if (__pyx_t_2) {
- /* "csamtools.pyx":208
+ /* "pysam/csamtools.pyx":208
* s += 1
* elif auxtype == 'C':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3652,22 +4058,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":209
+ /* "pysam/csamtools.pyx":209
* elif auxtype == 'C':
* for x from 0 <= x < nvalues:
* values.append((<uint8_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype == 's':
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((((uint8_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":210
+ /* "pysam/csamtools.pyx":210
* for x from 0 <= x < nvalues:
* values.append((<uint8_t*>s)[0])
* s += 1 # <<<<<<<<<<<<<<
@@ -3679,7 +4082,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":211
+ /* "pysam/csamtools.pyx":211
* values.append((<uint8_t*>s)[0])
* s += 1
* elif auxtype == 's': # <<<<<<<<<<<<<<
@@ -3689,7 +4092,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 's');
if (__pyx_t_2) {
- /* "csamtools.pyx":212
+ /* "pysam/csamtools.pyx":212
* s += 1
* elif auxtype == 's':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3699,22 +4102,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":213
+ /* "pysam/csamtools.pyx":213
* elif auxtype == 's':
* for x from 0 <= x < nvalues:
* values.append((<int16_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype == 'S':
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = __Pyx_PyInt_to_py_int16_t((((int16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":214
+ /* "pysam/csamtools.pyx":214
* for x from 0 <= x < nvalues:
* values.append((<int16_t*>s)[0])
* s += 2 # <<<<<<<<<<<<<<
@@ -3726,7 +4126,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":215
+ /* "pysam/csamtools.pyx":215
* values.append((<int16_t*>s)[0])
* s += 2
* elif auxtype == 'S': # <<<<<<<<<<<<<<
@@ -3736,7 +4136,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 'S');
if (__pyx_t_2) {
- /* "csamtools.pyx":216
+ /* "pysam/csamtools.pyx":216
* s += 2
* elif auxtype == 'S':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3746,22 +4146,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":217
+ /* "pysam/csamtools.pyx":217
* elif auxtype == 'S':
* for x from 0 <= x < nvalues:
* values.append((<uint16_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype == 'i':
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = __Pyx_PyInt_to_py_uint16_t((((uint16_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":218
+ /* "pysam/csamtools.pyx":218
* for x from 0 <= x < nvalues:
* values.append((<uint16_t*>s)[0])
* s += 2 # <<<<<<<<<<<<<<
@@ -3773,7 +4170,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":219
+ /* "pysam/csamtools.pyx":219
* values.append((<uint16_t*>s)[0])
* s += 2
* elif auxtype == 'i': # <<<<<<<<<<<<<<
@@ -3783,7 +4180,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 'i');
if (__pyx_t_2) {
- /* "csamtools.pyx":220
+ /* "pysam/csamtools.pyx":220
* s += 2
* elif auxtype == 'i':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3793,22 +4190,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":221
+ /* "pysam/csamtools.pyx":221
* elif auxtype == 'i':
* for x from 0 <= x < nvalues:
* values.append((<int32_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'I':
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = __Pyx_PyInt_to_py_int32_t((((int32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":222
+ /* "pysam/csamtools.pyx":222
* for x from 0 <= x < nvalues:
* values.append((<int32_t*>s)[0])
* s += 4 # <<<<<<<<<<<<<<
@@ -3820,7 +4214,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":223
+ /* "pysam/csamtools.pyx":223
* values.append((<int32_t*>s)[0])
* s += 4
* elif auxtype == 'I': # <<<<<<<<<<<<<<
@@ -3830,7 +4224,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 'I');
if (__pyx_t_2) {
- /* "csamtools.pyx":224
+ /* "pysam/csamtools.pyx":224
* s += 4
* elif auxtype == 'I':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3840,22 +4234,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":225
+ /* "pysam/csamtools.pyx":225
* elif auxtype == 'I':
* for x from 0 <= x < nvalues:
* values.append((<uint32_t*>s)[0]) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'f':
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = __Pyx_PyInt_to_py_uint32_t((((uint32_t *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":226
+ /* "pysam/csamtools.pyx":226
* for x from 0 <= x < nvalues:
* values.append((<uint32_t*>s)[0])
* s += 4 # <<<<<<<<<<<<<<
@@ -3867,7 +4258,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
goto __pyx_L3;
}
- /* "csamtools.pyx":227
+ /* "pysam/csamtools.pyx":227
* values.append((<uint32_t*>s)[0])
* s += 4
* elif auxtype == 'f': # <<<<<<<<<<<<<<
@@ -3877,7 +4268,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_2 = (__pyx_v_auxtype == 'f');
if (__pyx_t_2) {
- /* "csamtools.pyx":228
+ /* "pysam/csamtools.pyx":228
* s += 4
* elif auxtype == 'f':
* for x from 0 <= x < nvalues: # <<<<<<<<<<<<<<
@@ -3887,22 +4278,19 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_3 = __pyx_v_nvalues;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":229
+ /* "pysam/csamtools.pyx":229
* elif auxtype == 'f':
* for x from 0 <= x < nvalues:
* values.append((<float*>s)[0]) # <<<<<<<<<<<<<<
* s += 4
*
*/
- if (unlikely(((PyObject *)__pyx_v_values) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyFloat_FromDouble((((float *)__pyx_v_s)[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = PyList_Append(__pyx_v_values, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":230
+ /* "pysam/csamtools.pyx":230
* for x from 0 <= x < nvalues:
* values.append((<float*>s)[0])
* s += 4 # <<<<<<<<<<<<<<
@@ -3915,7 +4303,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
}
__pyx_L3:;
- /* "csamtools.pyx":232
+ /* "pysam/csamtools.pyx":232
* s += 4
*
* return byte_size, nvalues, values # <<<<<<<<<<<<<<
@@ -3928,7 +4316,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__pyx_t_5 = __Pyx_PyInt_to_py_int32_t(__pyx_v_nvalues); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
@@ -3948,7 +4336,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("csamtools.convertBinaryTagToList", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.convertBinaryTagToList", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_values);
@@ -3958,7 +4346,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
return __pyx_r;
}
-/* "csamtools.pyx":239
+/* "pysam/csamtools.pyx":239
* ## Generic callbacks for inserting python callbacks.
* #####################################################################
* cdef int fetch_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
@@ -3966,7 +4354,7 @@ static PyObject *__pyx_f_9csamtools_convertBinaryTagToList(uint8_t *__pyx_v_s) {
*
*/
-static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+static int __pyx_f_5pysam_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
PyObject *__pyx_v_a = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
@@ -3976,22 +4364,22 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch_callback");
+ __Pyx_RefNannySetupContext("fetch_callback", 0);
__Pyx_TraceCall("fetch_callback", __pyx_f[0], 239);
- /* "csamtools.pyx":244
+ /* "pysam/csamtools.pyx":244
* calls function in *f* with a new :class:`AlignedRead` object as parameter.
* '''
* a = makeAlignedRead( alignment ) # <<<<<<<<<<<<<<
* (<object>f)(a)
*
*/
- __pyx_t_1 = __pyx_f_9csamtools_makeAlignedRead(__pyx_v_alignment); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_alignment); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_a = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":245
+ /* "pysam/csamtools.pyx":245
* '''
* a = makeAlignedRead( alignment )
* (<object>f)(a) # <<<<<<<<<<<<<<
@@ -3999,7 +4387,7 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
* class PileupColumn(object):
*/
__pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_a);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_a);
__Pyx_GIVEREF(__pyx_v_a);
@@ -4013,7 +4401,7 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_WriteUnraisable("csamtools.fetch_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.csamtools.fetch_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_a);
@@ -4022,7 +4410,20 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
return __pyx_r;
}
-/* "csamtools.pyx":260
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_12PileupColumn_1__str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12PileupColumn_1__str__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12PileupColumn___str__)};
+static PyObject *__pyx_pw_5pysam_9csamtools_12PileupColumn_1__str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_12PileupColumn___str__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":260
* list of reads (:class:`pysam.PileupRead`) aligned to this column
* '''
* def __str__(self): # <<<<<<<<<<<<<<
@@ -4030,10 +4431,7 @@ static int __pyx_f_9csamtools_fetch_callback(bam1_t *__pyx_v_alignment, void *__
* "\n" + "\n".join( map(str, self.pileups) )
*/
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_12PileupColumn___str__[] = "PileupColumn.__str__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_12PileupColumn___str__ = {__Pyx_NAMESTR("__str__"), (PyCFunction)__pyx_pf_9csamtools_12PileupColumn___str__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12PileupColumn___str__)};
-static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_12PileupColumn___str__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4045,11 +4443,10 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
+ __Pyx_RefNannySetupContext("__str__", 0);
__Pyx_TraceCall("__str__", __pyx_f[0], 260);
- __pyx_self = __pyx_self;
- /* "csamtools.pyx":261
+ /* "pysam/csamtools.pyx":261
* '''
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
@@ -4058,7 +4455,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
*/
__Pyx_XDECREF(__pyx_r);
- /* "csamtools.pyx":262
+ /* "pysam/csamtools.pyx":262
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
@@ -4068,7 +4465,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":261
+ /* "pysam/csamtools.pyx":261
* '''
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
@@ -4082,7 +4479,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
@@ -4093,7 +4490,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__pyx_t_3 = 0;
__pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -4104,7 +4501,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
@@ -4116,7 +4513,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "csamtools.pyx":262
+ /* "pysam/csamtools.pyx":262
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
@@ -4128,7 +4525,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
@@ -4139,7 +4536,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -4163,7 +4560,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.PileupColumn.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupColumn.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4172,7 +4569,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
return __pyx_r;
}
-/* "csamtools.pyx":264
+/* "pysam/csamtools.pyx":264
* "\n" + "\n".join( map(str, self.pileups) )
*
* cdef int pileup_callback( uint32_t tid, uint32_t pos, int n, bam_pileup1_t *pl, void *f): # <<<<<<<<<<<<<<
@@ -4180,7 +4577,7 @@ static PyObject *__pyx_pf_9csamtools_12PileupColumn___str__(PyObject *__pyx_self
*
*/
-static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __pyx_v_pos, int __pyx_v_n, bam_pileup1_t *__pyx_v_pl, void *__pyx_v_f) {
+static int __pyx_f_5pysam_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __pyx_v_pos, int __pyx_v_n, bam_pileup1_t *__pyx_v_pl, void *__pyx_v_f) {
PyObject *__pyx_v_p = NULL;
PyObject *__pyx_v_pileups = NULL;
int __pyx_v_x;
@@ -4194,10 +4591,10 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_callback");
+ __Pyx_RefNannySetupContext("pileup_callback", 0);
__Pyx_TraceCall("pileup_callback", __pyx_f[0], 264);
- /* "csamtools.pyx":281
+ /* "pysam/csamtools.pyx":281
* '''
*
* p = PileupColumn() # <<<<<<<<<<<<<<
@@ -4212,7 +4609,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
__pyx_v_p = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":282
+ /* "pysam/csamtools.pyx":282
*
* p = PileupColumn()
* p.tid = tid # <<<<<<<<<<<<<<
@@ -4224,7 +4621,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__tid, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":283
+ /* "pysam/csamtools.pyx":283
* p = PileupColumn()
* p.tid = tid
* p.pos = pos # <<<<<<<<<<<<<<
@@ -4236,7 +4633,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pos, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":284
+ /* "pysam/csamtools.pyx":284
* p.tid = tid
* p.pos = pos
* p.n = n # <<<<<<<<<<<<<<
@@ -4248,7 +4645,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__n, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":285
+ /* "pysam/csamtools.pyx":285
* p.pos = pos
* p.n = n
* pileups = [] # <<<<<<<<<<<<<<
@@ -4256,11 +4653,11 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
* cdef int x
*/
__pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_pileups = __pyx_t_2;
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_pileups = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":288
+ /* "pysam/csamtools.pyx":288
*
* cdef int x
* for x from 0 <= x < n: # <<<<<<<<<<<<<<
@@ -4270,23 +4667,20 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
__pyx_t_3 = __pyx_v_n;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":289
+ /* "pysam/csamtools.pyx":289
* cdef int x
* for x from 0 <= x < n:
* pileups.append( makePileupRead( &(pl[x]) ) ) # <<<<<<<<<<<<<<
* p.pileups = pileups
*
*/
- if (unlikely(((PyObject *)__pyx_v_pileups) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __pyx_f_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupRead((&(__pyx_v_pl[__pyx_v_x]))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- /* "csamtools.pyx":290
+ /* "pysam/csamtools.pyx":290
* for x from 0 <= x < n:
* pileups.append( makePileupRead( &(pl[x]) ) )
* p.pileups = pileups # <<<<<<<<<<<<<<
@@ -4295,7 +4689,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
*/
if (PyObject_SetAttr(__pyx_v_p, __pyx_n_s__pileups, ((PyObject *)__pyx_v_pileups)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":292
+ /* "pysam/csamtools.pyx":292
* p.pileups = pileups
*
* (<object>f)(p) # <<<<<<<<<<<<<<
@@ -4303,7 +4697,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
* cdef int pileup_fetch_callback( bam1_t *b, void *data):
*/
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_p);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_p);
__Pyx_GIVEREF(__pyx_v_p);
@@ -4317,7 +4711,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_WriteUnraisable("csamtools.pileup_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.csamtools.pileup_callback", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_p);
@@ -4327,7 +4721,7 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
return __pyx_r;
}
-/* "csamtools.pyx":294
+/* "pysam/csamtools.pyx":294
* (<object>f)(p)
*
* cdef int pileup_fetch_callback( bam1_t *b, void *data): # <<<<<<<<<<<<<<
@@ -4335,15 +4729,15 @@ static int __pyx_f_9csamtools_pileup_callback(uint32_t __pyx_v_tid, uint32_t __p
*
*/
-static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__pyx_v_data) {
+static int __pyx_f_5pysam_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__pyx_v_data) {
bam_plbuf_t *__pyx_v_buf;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup_fetch_callback");
+ __Pyx_RefNannySetupContext("pileup_fetch_callback", 0);
__Pyx_TraceCall("pileup_fetch_callback", __pyx_f[0], 294);
- /* "csamtools.pyx":300
+ /* "pysam/csamtools.pyx":300
* '''
* cdef bam_plbuf_t * buf
* buf = <bam_plbuf_t*>data # <<<<<<<<<<<<<<
@@ -4352,7 +4746,7 @@ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__p
*/
__pyx_v_buf = ((bam_plbuf_t *)__pyx_v_data);
- /* "csamtools.pyx":301
+ /* "pysam/csamtools.pyx":301
* cdef bam_plbuf_t * buf
* buf = <bam_plbuf_t*>data
* bam_plbuf_push(b, buf) # <<<<<<<<<<<<<<
@@ -4361,7 +4755,7 @@ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__p
*/
bam_plbuf_push(__pyx_v_b, __pyx_v_buf);
- /* "csamtools.pyx":302
+ /* "pysam/csamtools.pyx":302
* buf = <bam_plbuf_t*>data
* bam_plbuf_push(b, buf)
* return 0 # <<<<<<<<<<<<<<
@@ -4378,7 +4772,20 @@ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__p
return __pyx_r;
}
-/* "csamtools.pyx":308
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore___init__)};
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore___init__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":308
* stderr is captured.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
@@ -4386,18 +4793,14 @@ static int __pyx_f_9csamtools_pileup_fetch_callback(bam1_t *__pyx_v_b, void *__p
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore___init__[] = "StderrStore.__init__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore___init__)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
+ __Pyx_RefNannySetupContext("__init__", 0);
__Pyx_TraceCall("__init__", __pyx_f[0], 308);
- __pyx_self = __pyx_self;
- /* "csamtools.pyx":309
+ /* "pysam/csamtools.pyx":309
* '''
* def __init__(self):
* return # <<<<<<<<<<<<<<
@@ -4416,7 +4819,20 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self
return __pyx_r;
}
-/* "csamtools.pyx":314
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11StderrStore_2readAndRelease[] = "StderrStore.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore_2readAndRelease)};
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":314
* self.stderr_save.setfd( self.stderr_h )
*
* def readAndRelease( self ): # <<<<<<<<<<<<<<
@@ -4424,10 +4840,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore___init__(PyObject *__pyx_self
* self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_1readAndRelease[] = "StderrStore.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_1readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_1readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_1readAndRelease)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4435,11 +4848,10 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease");
+ __Pyx_RefNannySetupContext("readAndRelease", 0);
__Pyx_TraceCall("readAndRelease", __pyx_f[0], 314);
- __pyx_self = __pyx_self;
- /* "csamtools.pyx":315
+ /* "pysam/csamtools.pyx":315
*
* def readAndRelease( self ):
* return [] # <<<<<<<<<<<<<<
@@ -4448,7 +4860,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p
*/
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
@@ -4457,7 +4869,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.StderrStore.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.StderrStore.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4466,7 +4878,20 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":323
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11StderrStore_4release[] = "StderrStore.release(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore_4release)};
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("release (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore_4release(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":323
* return lines
*
* def release(self): # <<<<<<<<<<<<<<
@@ -4474,18 +4899,14 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_1readAndRelease(PyObject *__p
* self.stderr_save.restore()
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_2release[] = "StderrStore.release(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_2release)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release");
+ __Pyx_RefNannySetupContext("release", 0);
__Pyx_TraceCall("release", __pyx_f[0], 323);
- __pyx_self = __pyx_self;
- /* "csamtools.pyx":324
+ /* "pysam/csamtools.pyx":324
*
* def release(self):
* return # <<<<<<<<<<<<<<
@@ -4504,7 +4925,20 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self
return __pyx_r;
}
-/* "csamtools.pyx":329
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11StderrStore_6__del__[] = "StderrStore.__del__(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_11StderrStore_7__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11StderrStore_7__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11StderrStore_6__del__)};
+static PyObject *__pyx_pw_5pysam_9csamtools_11StderrStore_7__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__del__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":329
* os.remove( self.stderr_f )
*
* def __del__(self): # <<<<<<<<<<<<<<
@@ -4512,10 +4946,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_2release(PyObject *__pyx_self
*
*/
-static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11StderrStore_3__del__[] = "StderrStore.__del__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_11StderrStore_3__del__ = {__Pyx_NAMESTR("__del__"), (PyCFunction)__pyx_pf_9csamtools_11StderrStore_3__del__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11StderrStore_3__del__)};
-static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11StderrStore_6__del__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4524,11 +4955,10 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__del__");
+ __Pyx_RefNannySetupContext("__del__", 0);
__Pyx_TraceCall("__del__", __pyx_f[0], 329);
- __pyx_self = __pyx_self;
- /* "csamtools.pyx":330
+ /* "pysam/csamtools.pyx":330
*
* def __del__(self):
* self.release() # <<<<<<<<<<<<<<
@@ -4547,7 +4977,7 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.StderrStore.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.StderrStore.__del__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4556,7 +4986,20 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self
return __pyx_r;
}
-/* "csamtools.pyx":334
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_1__init__, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18StderrStoreWindows___init__)};
+static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_1__init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":334
* class StderrStoreWindows():
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass # <<<<<<<<<<<<<<
@@ -4564,16 +5007,12 @@ static PyObject *__pyx_pf_9csamtools_11StderrStore_3__del__(PyObject *__pyx_self
* def release(self): pass
*/
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows___init__[] = "StderrStoreWindows.__init__(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows___init__, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows___init__)};
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows___init__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
+ __Pyx_RefNannySetupContext("__init__", 0);
__Pyx_TraceCall("__init__", __pyx_f[0], 334);
- __pyx_self = __pyx_self;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -4582,7 +5021,20 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":335
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease)};
+static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("readAndRelease (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":335
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
* def readAndRelease(self): return [] # <<<<<<<<<<<<<<
@@ -4590,10 +5042,7 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows___init__(PyObject *__p
*
*/
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows_1readAndRelease[] = "StderrStoreWindows.readAndRelease(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease = {__Pyx_NAMESTR("readAndRelease"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_1readAndRelease)};
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_2readAndRelease(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4601,12 +5050,11 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("readAndRelease");
+ __Pyx_RefNannySetupContext("readAndRelease", 0);
__Pyx_TraceCall("readAndRelease", __pyx_f[0], 335);
- __pyx_self = __pyx_self;
__Pyx_XDECREF(__pyx_r);
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __Pyx_GOTREF(__pyx_t_1);
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L0;
@@ -4615,7 +5063,7 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObje
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.StderrStoreWindows.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.StderrStoreWindows.readAndRelease", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4624,7 +5072,20 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObje
return __pyx_r;
}
-/* "csamtools.pyx":336
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_18StderrStoreWindows_4release[] = "StderrStoreWindows.release(self)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_5release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_5release, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18StderrStoreWindows_4release)};
+static PyObject *__pyx_pw_5pysam_9csamtools_18StderrStoreWindows_5release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("release (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":336
* def __init__(self): pass
* def readAndRelease(self): return []
* def release(self): pass # <<<<<<<<<<<<<<
@@ -4632,16 +5093,12 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_1readAndRelease(PyObje
* if platform.system()=='Windows':
*/
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18StderrStoreWindows_2release[] = "StderrStoreWindows.release(self)";
-static PyMethodDef __pyx_mdef_9csamtools_18StderrStoreWindows_2release = {__Pyx_NAMESTR("release"), (PyCFunction)__pyx_pf_9csamtools_18StderrStoreWindows_2release, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_18StderrStoreWindows_2release)};
-static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_18StderrStoreWindows_4release(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("release");
+ __Pyx_RefNannySetupContext("release", 0);
__Pyx_TraceCall("release", __pyx_f[0], 336);
- __pyx_self = __pyx_self;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -4650,7 +5107,28 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":387
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":387
* '''
*
* def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
@@ -4658,62 +5136,57 @@ static PyObject *__pyx_pf_9csamtools_18StderrStoreWindows_2release(PyObject *__p
* self._filename = NULL
*/
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
+static int __pyx_pf_5pysam_9csamtools_9Fastafile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_RefNannySetupContext("__cinit__", 0);
__Pyx_TraceCall("__cinit__", __pyx_f[0], 387);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
- /* "csamtools.pyx":388
+ /* "pysam/csamtools.pyx":388
*
* def __cinit__(self, *args, **kwargs ):
* self.fastafile = NULL # <<<<<<<<<<<<<<
* self._filename = NULL
* self._open( *args, **kwargs )
*/
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
+ __pyx_v_self->fastafile = NULL;
- /* "csamtools.pyx":389
+ /* "pysam/csamtools.pyx":389
* def __cinit__(self, *args, **kwargs ):
* self.fastafile = NULL
* self._filename = NULL # <<<<<<<<<<<<<<
* self._open( *args, **kwargs )
*
*/
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = NULL;
+ __pyx_v_self->_filename = NULL;
- /* "csamtools.pyx":390
+ /* "pysam/csamtools.pyx":390
* self.fastafile = NULL
* self._filename = NULL
* self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
*
* def _isOpen( self ):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_r = 0;
goto __pyx_L0;
@@ -4721,17 +5194,28 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Fastafile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_args);
- __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":392
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_9Fastafile_2_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":392
* self._open( *args, **kwargs )
*
* def _isOpen( self ): # <<<<<<<<<<<<<<
@@ -4739,9 +5223,7 @@ static int __pyx_pf_9csamtools_9Fastafile___cinit__(PyObject *__pyx_v_self, PyOb
* return self.fastafile != NULL
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_1_isOpen[] = "Fastafile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -4749,10 +5231,10 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen");
+ __Pyx_RefNannySetupContext("_isOpen", 0);
__Pyx_TraceCall("_isOpen", __pyx_f[0], 392);
- /* "csamtools.pyx":394
+ /* "pysam/csamtools.pyx":394
* def _isOpen( self ):
* '''return true if samfile has been opened.'''
* return self.fastafile != NULL # <<<<<<<<<<<<<<
@@ -4760,7 +5242,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self,
* def __len__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fastafile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -4770,7 +5252,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self,
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Fastafile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -4779,7 +5261,18 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "csamtools.pyx":396
+/* Python wrapper */
+static Py_ssize_t __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self); /*proto*/
+static Py_ssize_t __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__(PyObject *__pyx_v_self) {
+ Py_ssize_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__len__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":396
* return self.fastafile != NULL
*
* def __len__(self): # <<<<<<<<<<<<<<
@@ -4787,8 +5280,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_1_isOpen(PyObject *__pyx_v_self,
* raise ValueError( "calling len() on closed file" )
*/
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self); /*proto*/
-static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self) {
+static Py_ssize_t __pyx_pf_5pysam_9csamtools_9Fastafile_4__len__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
Py_ssize_t __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -4797,20 +5289,20 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__len__");
+ __Pyx_RefNannySetupContext("__len__", 0);
__Pyx_TraceCall("__len__", __pyx_f[0], 396);
- /* "csamtools.pyx":397
+ /* "pysam/csamtools.pyx":397
*
* def __len__(self):
* if self.fastafile == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "calling len() on closed file" )
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
+ __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":398
+ /* "pysam/csamtools.pyx":398
* def __len__(self):
* if self.fastafile == NULL:
* raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
@@ -4822,25 +5314,25 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":400
+ /* "pysam/csamtools.pyx":400
* raise ValueError( "calling len() on closed file" )
*
* return faidx_fetch_nseq(self.fastafile) # <<<<<<<<<<<<<<
*
* def _open( self,
*/
- __pyx_r = faidx_fetch_nseq(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
+ __pyx_r = faidx_fetch_nseq(__pyx_v_self->fastafile);
goto __pyx_L0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile.__len__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -4848,7 +5340,19 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self
return __pyx_r;
}
-/* "csamtools.pyx":402
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_9Fastafile_6_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_open (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_6_open(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self), ((PyObject *)__pyx_v_filename));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":402
* return faidx_fetch_nseq(self.fastafile)
*
* def _open( self, # <<<<<<<<<<<<<<
@@ -4856,9 +5360,7 @@ static Py_ssize_t __pyx_pf_9csamtools_9Fastafile_2__len__(PyObject *__pyx_v_self
* '''open an indexed fasta file.
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_3_open[] = "Fastafile._open(self, filename)\nopen an indexed fasta file.\n\n This method expects an indexed fasta file.\n ";
-static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_6_open(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -4869,57 +5371,57 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open");
+ __Pyx_RefNannySetupContext("_open", 0);
__Pyx_TraceCall("_open", __pyx_f[0], 402);
__Pyx_INCREF(__pyx_v_filename);
- /* "csamtools.pyx":410
+ /* "pysam/csamtools.pyx":410
*
* # close a previously opened file
* if self.fastafile != NULL: self.close() # <<<<<<<<<<<<<<
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename)
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
+ __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
if (__pyx_t_1) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":411
+ /* "pysam/csamtools.pyx":411
* # close a previously opened file
* if self.fastafile != NULL: self.close()
* if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename)
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
+ __pyx_t_1 = (__pyx_v_self->_filename != NULL);
if (__pyx_t_1) {
- free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
- goto __pyx_L6;
+ free(__pyx_v_self->_filename);
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":412
+ /* "pysam/csamtools.pyx":412
* if self.fastafile != NULL: self.close()
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<<
* self._filename = strdup(filename)
* self.fastafile = fai_load( filename )
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_v_filename);
__pyx_v_filename = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":413
+ /* "pysam/csamtools.pyx":413
* if self._filename != NULL: free(self._filename)
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename) # <<<<<<<<<<<<<<
@@ -4927,9 +5429,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
*
*/
__pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename = strdup(__pyx_t_4);
+ __pyx_v_self->_filename = strdup(__pyx_t_4);
- /* "csamtools.pyx":414
+ /* "pysam/csamtools.pyx":414
* filename = _my_encodeFilename(filename)
* self._filename = strdup(filename)
* self.fastafile = fai_load( filename ) # <<<<<<<<<<<<<<
@@ -4937,19 +5439,19 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
* if self.fastafile == NULL:
*/
__pyx_t_4 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_4) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = fai_load(__pyx_t_4);
+ __pyx_v_self->fastafile = fai_load(__pyx_t_4);
- /* "csamtools.pyx":416
+ /* "pysam/csamtools.pyx":416
* self.fastafile = fai_load( filename )
*
* if self.fastafile == NULL: # <<<<<<<<<<<<<<
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile == NULL);
+ __pyx_t_1 = (__pyx_v_self->fastafile == NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":417
+ /* "pysam/csamtools.pyx":417
*
* if self.fastafile == NULL:
* raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
@@ -4959,7 +5461,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
__pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_3));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
__pyx_t_3 = 0;
@@ -4969,16 +5471,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Fastafile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_filename);
@@ -4988,7 +5490,19 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
return __pyx_r;
}
-/* "csamtools.pyx":419
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_9Fastafile_8close[] = "Fastafile.close(self)";
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_9close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("close (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_8close(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":419
* raise IOError("could not open file `%s`" % filename )
*
* def close( self ): # <<<<<<<<<<<<<<
@@ -4996,46 +5510,44 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_3_open(PyObject *__pyx_v_self, P
* fai_destroy( self.fastafile )
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_4close[] = "Fastafile.close(self)";
-static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close");
+ __Pyx_RefNannySetupContext("close", 0);
__Pyx_TraceCall("close", __pyx_f[0], 419);
- /* "csamtools.pyx":420
+ /* "pysam/csamtools.pyx":420
*
* def close( self ):
* if self.fastafile != NULL: # <<<<<<<<<<<<<<
* fai_destroy( self.fastafile )
* self.fastafile = NULL
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile != NULL);
+ __pyx_t_1 = (__pyx_v_self->fastafile != NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":421
+ /* "pysam/csamtools.pyx":421
* def close( self ):
* if self.fastafile != NULL:
* fai_destroy( self.fastafile ) # <<<<<<<<<<<<<<
* self.fastafile = NULL
*
*/
- fai_destroy(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile);
+ fai_destroy(__pyx_v_self->fastafile);
- /* "csamtools.pyx":422
+ /* "pysam/csamtools.pyx":422
* if self.fastafile != NULL:
* fai_destroy( self.fastafile )
* self.fastafile = NULL # <<<<<<<<<<<<<<
*
* def __dealloc__(self):
*/
- ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile = NULL;
- goto __pyx_L5;
+ __pyx_v_self->fastafile = NULL;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -5044,7 +5556,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, C
return __pyx_r;
}
-/* "csamtools.pyx":424
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_9Fastafile_11__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":424
* self.fastafile = NULL
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -5052,8 +5573,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_4close(PyObject *__pyx_v_self, C
* if self._filename != NULL: free(self._filename)
*/
-static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_9Fastafile_10__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
@@ -5062,48 +5582,59 @@ static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self)
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
__Pyx_TraceCall("__dealloc__", __pyx_f[0], 424);
- /* "csamtools.pyx":425
+ /* "pysam/csamtools.pyx":425
*
* def __dealloc__(self):
* self.close() # <<<<<<<<<<<<<<
* if self._filename != NULL: free(self._filename)
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":426
+ /* "pysam/csamtools.pyx":426
* def __dealloc__(self):
* self.close()
* if self._filename != NULL: free(self._filename) # <<<<<<<<<<<<<<
*
* property filename:
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename != NULL);
+ __pyx_t_3 = (__pyx_v_self->_filename != NULL);
if (__pyx_t_3) {
- free(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename);
- goto __pyx_L5;
+ free(__pyx_v_self->_filename);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":430
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":430
* property filename:
* '''number of :term:`filename` associated with this object.'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -5111,8 +5642,7 @@ static void __pyx_pf_9csamtools_9Fastafile_5__dealloc__(PyObject *__pyx_v_self)
* return self._filename
*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -5123,17 +5653,17 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
+ __Pyx_RefNannySetupContext("__get__", 0);
__Pyx_TraceCall("__get__", __pyx_f[0], 430);
- /* "csamtools.pyx":431
+ /* "pysam/csamtools.pyx":431
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self._filename
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -5147,11 +5677,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":432
+ /* "pysam/csamtools.pyx":432
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return self._filename # <<<<<<<<<<<<<<
@@ -5159,7 +5689,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py
* def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -5170,7 +5700,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -5179,42 +5709,22 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_8filename___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":434
- * return self._filename
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_9Fastafile_6fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *reference* i [...]
-static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_9Fastafile_12fetch[] = "Fastafile.fetch(self, reference=None, start=None, end=None, region=None)\n*(reference = None, start = None, end = None, region = None)*\n\n fetch :meth:`AlignedRead` objects in a :term:`region` using 0-based indexing.\n\n The region is specified by :term:`reference`, *start* and *end*.\n\n fetch returns an empty string if the region is out of range or addresses an unknown *reference*.\n\n If *refe [...]
+static PyObject *__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- int __pyx_v_length;
- char *__pyx_v_seq;
- PyObject *__pyx_v_py_seq = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch");
- __Pyx_TraceCall("fetch", __pyx_f[0], 434);
+ __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[4] = {0,0,0,0};
- /* "csamtools.pyx":435
+ /* "pysam/csamtools.pyx":435
*
* def fetch( self,
* reference = None, # <<<<<<<<<<<<<<
@@ -5223,7 +5733,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*/
values[0] = ((PyObject *)Py_None);
- /* "csamtools.pyx":436
+ /* "pysam/csamtools.pyx":436
* def fetch( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
@@ -5232,7 +5742,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*/
values[1] = ((PyObject *)Py_None);
- /* "csamtools.pyx":437
+ /* "pysam/csamtools.pyx":437
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
@@ -5241,7 +5751,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*/
values[2] = ((PyObject *)Py_None);
- /* "csamtools.pyx":438
+ /* "pysam/csamtools.pyx":438
* start = None,
* end = None,
* region = None): # <<<<<<<<<<<<<<
@@ -5251,7 +5761,8 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
values[3] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -5260,7 +5771,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -5283,7 +5794,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -5304,22 +5815,52 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":434
+ * return self._filename
+ *
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_12fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
+ int __pyx_v_length;
+ char *__pyx_v_seq;
+ PyObject *__pyx_v_py_seq = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch", 0);
+ __Pyx_TraceCall("fetch", __pyx_f[0], 434);
__Pyx_INCREF(__pyx_v_start);
__Pyx_INCREF(__pyx_v_end);
__Pyx_INCREF(__pyx_v_region);
- /* "csamtools.pyx":455
+ /* "pysam/csamtools.pyx":455
* '''
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
@@ -5329,7 +5870,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":456
+ /* "pysam/csamtools.pyx":456
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
@@ -5341,11 +5882,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":461
+ /* "pysam/csamtools.pyx":461
* cdef char * seq
*
* if not region: # <<<<<<<<<<<<<<
@@ -5356,7 +5897,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "csamtools.pyx":462
+ /* "pysam/csamtools.pyx":462
*
* if not region:
* if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
@@ -5370,11 +5911,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ goto __pyx_L5;
}
- __pyx_L8:;
+ __pyx_L5:;
- /* "csamtools.pyx":463
+ /* "pysam/csamtools.pyx":463
* if not region:
* if reference is None: raise ValueError( 'no sequence/region supplied.' )
* if start is None: start = 0 # <<<<<<<<<<<<<<
@@ -5386,11 +5927,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_INCREF(__pyx_int_0);
__Pyx_DECREF(__pyx_v_start);
__pyx_v_start = __pyx_int_0;
- goto __pyx_L9;
+ goto __pyx_L6;
}
- __pyx_L9:;
+ __pyx_L6:;
- /* "csamtools.pyx":464
+ /* "pysam/csamtools.pyx":464
* if reference is None: raise ValueError( 'no sequence/region supplied.' )
* if start is None: start = 0
* if end is None: end = max_pos -1 # <<<<<<<<<<<<<<
@@ -5399,29 +5940,28 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*/
__pyx_t_3 = (__pyx_v_end == Py_None);
if (__pyx_t_3) {
- __pyx_t_2 = PyInt_FromLong((__pyx_v_9csamtools_max_pos - 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong((__pyx_v_5pysam_9csamtools_max_pos - 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_end);
__pyx_v_end = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L10;
+ goto __pyx_L7;
}
- __pyx_L10:;
+ __pyx_L7:;
- /* "csamtools.pyx":466
+ /* "pysam/csamtools.pyx":466
* if end is None: end = max_pos -1
*
* if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) ) # <<<<<<<<<<<<<<
* if start == end: return b""
* # valid ranges are from 0 to 2^29-1
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_start);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_start);
__Pyx_GIVEREF(__pyx_v_start);
@@ -5432,7 +5972,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -5442,19 +5982,18 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ goto __pyx_L8;
}
- __pyx_L11:;
+ __pyx_L8:;
- /* "csamtools.pyx":467
+ /* "pysam/csamtools.pyx":467
*
* if start > end: raise ValueError( 'invalid region: start (%i) > end (%i)' % (start, end) )
* if start == end: return b"" # <<<<<<<<<<<<<<
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_v_end, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
@@ -5462,25 +6001,23 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L12;
+ goto __pyx_L9;
}
- __pyx_L12:;
+ __pyx_L9:;
- /* "csamtools.pyx":469
+ /* "pysam/csamtools.pyx":469
* if start == end: return b""
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
* if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end )
* # note: faidx_fetch_seq has a bug such that out-of-range access
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_5pysam_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5490,7 +6027,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -5500,25 +6037,23 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L13;
+ goto __pyx_L10;
}
- __pyx_L13:;
+ __pyx_L10:;
- /* "csamtools.pyx":470
+ /* "pysam/csamtools.pyx":470
* # valid ranges are from 0 to 2^29-1
* if not 0 <= start < max_pos: raise ValueError( 'start out of range (%i)' % start )
* if not 0 <= end < max_pos: raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
* # note: faidx_fetch_seq has a bug such that out-of-range access
* # always returns the last residue. Hence do not use faidx_fetch_seq,
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_int_0, __pyx_v_end, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_5pysam_9csamtools_max_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -5528,7 +6063,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
@@ -5538,11 +6073,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ goto __pyx_L11;
}
- __pyx_L14:;
+ __pyx_L11:;
- /* "csamtools.pyx":479
+ /* "pysam/csamtools.pyx":479
* # end-1,
* # &length)
* region = "%s:%i-%i" % (reference, start+1, end) # <<<<<<<<<<<<<<
@@ -5552,7 +6087,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_1 = PyNumber_Add(__pyx_v_start, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -5569,7 +6104,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_v_region = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":480
+ /* "pysam/csamtools.pyx":480
* # &length)
* region = "%s:%i-%i" % (reference, start+1, end)
* if PY_MAJOR_VERSION >= 3: # <<<<<<<<<<<<<<
@@ -5579,7 +6114,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_3 = (PY_MAJOR_VERSION >= 3);
if (__pyx_t_3) {
- /* "csamtools.pyx":481
+ /* "pysam/csamtools.pyx":481
* region = "%s:%i-%i" % (reference, start+1, end)
* if PY_MAJOR_VERSION >= 3:
* region = region.encode('ascii') # <<<<<<<<<<<<<<
@@ -5594,11 +6129,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L15;
+ goto __pyx_L12;
}
- __pyx_L15:;
+ __pyx_L12:;
- /* "csamtools.pyx":483
+ /* "pysam/csamtools.pyx":483
* region = region.encode('ascii')
* seq = fai_fetch( self.fastafile,
* region, # <<<<<<<<<<<<<<
@@ -5607,19 +6142,19 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*/
__pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":484
+ /* "pysam/csamtools.pyx":484
* seq = fai_fetch( self.fastafile,
* region,
* &length ) # <<<<<<<<<<<<<<
* else:
* # samtools adds a '\0' at the end
*/
- __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
- goto __pyx_L7;
+ __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
+ goto __pyx_L4;
}
/*else*/ {
- /* "csamtools.pyx":487
+ /* "pysam/csamtools.pyx":487
* else:
* # samtools adds a '\0' at the end
* seq = fai_fetch( self.fastafile, region, &length ) # <<<<<<<<<<<<<<
@@ -5627,11 +6162,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
* # copy to python
*/
__pyx_t_5 = PyBytes_AsString(__pyx_v_region); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_seq = fai_fetch(((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_self)->fastafile, __pyx_t_5, (&__pyx_v_length));
+ __pyx_v_seq = fai_fetch(__pyx_v_self->fastafile, __pyx_t_5, (&__pyx_v_length));
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "csamtools.pyx":490
+ /* "pysam/csamtools.pyx":490
*
* # copy to python
* if seq == NULL: # <<<<<<<<<<<<<<
@@ -5641,7 +6176,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_t_3 = (__pyx_v_seq == NULL);
if (__pyx_t_3) {
- /* "csamtools.pyx":491
+ /* "pysam/csamtools.pyx":491
* # copy to python
* if seq == NULL:
* return b"" # <<<<<<<<<<<<<<
@@ -5652,11 +6187,11 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__Pyx_INCREF(((PyObject *)__pyx_kp_b_16));
__pyx_r = ((PyObject *)__pyx_kp_b_16);
goto __pyx_L0;
- goto __pyx_L16;
+ goto __pyx_L13;
}
/*else*/ {
- /* "csamtools.pyx":493
+ /* "pysam/csamtools.pyx":493
* return b""
* else:
* try: # <<<<<<<<<<<<<<
@@ -5665,20 +6200,20 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*/
/*try:*/ {
- /* "csamtools.pyx":494
+ /* "pysam/csamtools.pyx":494
* else:
* try:
* py_seq = seq[:length] # <<<<<<<<<<<<<<
* finally:
* free(seq)
*/
- __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L18;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_seq + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L15;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_py_seq = __pyx_t_2;
+ __pyx_v_py_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
}
- /* "csamtools.pyx":496
+ /* "pysam/csamtools.pyx":496
* py_seq = seq[:length]
* finally:
* free(seq) # <<<<<<<<<<<<<<
@@ -5690,16 +6225,16 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
PyObject *__pyx_exc_type, *__pyx_exc_value, *__pyx_exc_tb;
int __pyx_exc_lineno;
__pyx_exc_type = 0; __pyx_exc_value = 0; __pyx_exc_tb = 0; __pyx_exc_lineno = 0;
- __pyx_why = 0; goto __pyx_L19;
- __pyx_L18: {
+ __pyx_why = 0; goto __pyx_L16;
+ __pyx_L15: {
__pyx_why = 4;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_ErrFetch(&__pyx_exc_type, &__pyx_exc_value, &__pyx_exc_tb);
__pyx_exc_lineno = __pyx_lineno;
- goto __pyx_L19;
+ goto __pyx_L16;
}
- __pyx_L19:;
+ __pyx_L16:;
free(__pyx_v_seq);
switch (__pyx_why) {
case 4: {
@@ -5713,9 +6248,9 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
}
}
}
- __pyx_L16:;
+ __pyx_L13:;
- /* "csamtools.pyx":498
+ /* "pysam/csamtools.pyx":498
* free(seq)
*
* return py_seq # <<<<<<<<<<<<<<
@@ -5732,7 +6267,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Fastafile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_py_seq);
@@ -5745,7 +6280,7 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
return __pyx_r;
}
-/* "csamtools.pyx":500
+/* "pysam/csamtools.pyx":500
* return py_seq
*
* cdef char * _fetch( self, char * reference, int start, int end, int * length ): # <<<<<<<<<<<<<<
@@ -5753,14 +6288,14 @@ static PyObject *__pyx_pf_9csamtools_9Fastafile_6fetch(PyObject *__pyx_v_self, P
*
*/
-static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fastafile *__pyx_v_self, char *__pyx_v_reference, int __pyx_v_start, int __pyx_v_end, int *__pyx_v_length) {
+static char *__pyx_f_5pysam_9csamtools_9Fastafile__fetch(struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_self, char *__pyx_v_reference, int __pyx_v_start, int __pyx_v_end, int *__pyx_v_length) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_fetch");
+ __Pyx_RefNannySetupContext("_fetch", 0);
__Pyx_TraceCall("_fetch", __pyx_f[0], 500);
- /* "csamtools.pyx":507
+ /* "pysam/csamtools.pyx":507
* start,
* end-1,
* length ) # <<<<<<<<<<<<<<
@@ -5777,7 +6312,7 @@ static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fa
return __pyx_r;
}
-/* "csamtools.pyx":512
+/* "pysam/csamtools.pyx":512
* #------------------------------------------------------------------------
* #------------------------------------------------------------------------
* cdef int count_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
@@ -5785,16 +6320,16 @@ static char *__pyx_f_9csamtools_9Fastafile__fetch(struct __pyx_obj_9csamtools_Fa
* '''
*/
-static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+static int __pyx_f_5pysam_9csamtools_count_callback(CYTHON_UNUSED bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
int *__pyx_v_counter;
int __pyx_r;
__Pyx_RefNannyDeclarations
long __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count_callback");
+ __Pyx_RefNannySetupContext("count_callback", 0);
__Pyx_TraceCall("count_callback", __pyx_f[0], 512);
- /* "csamtools.pyx":515
+ /* "pysam/csamtools.pyx":515
* '''callback for bam_fetch - count number of reads.
* '''
* cdef int* counter = (<int*>f) # <<<<<<<<<<<<<<
@@ -5803,7 +6338,7 @@ static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__
*/
__pyx_v_counter = ((int *)__pyx_v_f);
- /* "csamtools.pyx":516
+ /* "pysam/csamtools.pyx":516
* '''
* cdef int* counter = (<int*>f)
* counter[0] += 1; # <<<<<<<<<<<<<<
@@ -5819,7 +6354,7 @@ static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__
return __pyx_r;
}
-/* "csamtools.pyx":526
+/* "pysam/csamtools.pyx":526
* #------------------------------------------------------------------------
* #------------------------------------------------------------------------
* cdef int mate_callback( bam1_t *alignment, void *f): # <<<<<<<<<<<<<<
@@ -5827,27 +6362,27 @@ static int __pyx_f_9csamtools_count_callback(bam1_t *__pyx_v_alignment, void *__
* '''
*/
-static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
- __pyx_t_9csamtools_MateData *__pyx_v_d;
+static int __pyx_f_5pysam_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__pyx_v_f) {
+ __pyx_t_5pysam_9csamtools_MateData *__pyx_v_d;
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate_callback");
+ __Pyx_RefNannySetupContext("mate_callback", 0);
__Pyx_TraceCall("mate_callback", __pyx_f[0], 526);
- /* "csamtools.pyx":529
+ /* "pysam/csamtools.pyx":529
* '''callback for bam_fetch = filter mate
* '''
* cdef MateData * d = (<MateData*>f) # <<<<<<<<<<<<<<
* # printf("mate = %p, name1 = %s, name2=%s\t%i\t%i\t%i\n",
* # d.mate, d.name, bam1_qname(alignment),
*/
- __pyx_v_d = ((__pyx_t_9csamtools_MateData *)__pyx_v_f);
+ __pyx_v_d = ((__pyx_t_5pysam_9csamtools_MateData *)__pyx_v_f);
- /* "csamtools.pyx":534
+ /* "pysam/csamtools.pyx":534
* # d.flag, alignment.core.flag, alignment.core.flag & d.flag)
*
* if d.mate == NULL: # <<<<<<<<<<<<<<
@@ -5857,7 +6392,7 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
__pyx_t_1 = (__pyx_v_d->mate == NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":540
+ /* "pysam/csamtools.pyx":540
* # also, make sure that we get the other read by comparing
* # the flags
* if alignment.core.flag & d.flag != 0 and \ # <<<<<<<<<<<<<<
@@ -5867,7 +6402,7 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
__pyx_t_1 = ((__pyx_v_alignment->core.flag & __pyx_v_d->flag) != 0);
if (__pyx_t_1) {
- /* "csamtools.pyx":541
+ /* "pysam/csamtools.pyx":541
* # the flags
* if alignment.core.flag & d.flag != 0 and \
* strcmp( bam1_qname( alignment ), d.name ) == 0: # <<<<<<<<<<<<<<
@@ -5881,7 +6416,7 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
}
if (__pyx_t_3) {
- /* "csamtools.pyx":542
+ /* "pysam/csamtools.pyx":542
* if alignment.core.flag & d.flag != 0 and \
* strcmp( bam1_qname( alignment ), d.name ) == 0:
* d.mate = bam_dup1( alignment ) # <<<<<<<<<<<<<<
@@ -5902,7 +6437,28 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
return __pyx_r;
}
-/* "csamtools.pyx":592
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ PyObject *__pyx_v_args = 0;
+ PyObject *__pyx_v_kwargs = 0;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
+ if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
+ __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
+ if (unlikely(!__pyx_v_kwargs)) return -1;
+ __Pyx_GOTREF(__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_args);
+ __pyx_v_args = __pyx_args;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_args, __pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_args);
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":592
* '''
*
* def __cinit__(self, *args, **kwargs ): # <<<<<<<<<<<<<<
@@ -5910,89 +6466,84 @@ static int __pyx_f_9csamtools_mate_callback(bam1_t *__pyx_v_alignment, void *__p
* self._filename = NULL
*/
-static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_args = 0;
- PyObject *__pyx_v_kwargs = 0;
+static int __pyx_pf_5pysam_9csamtools_7Samfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
+ __Pyx_RefNannySetupContext("__cinit__", 0);
__Pyx_TraceCall("__cinit__", __pyx_f[0], 592);
- if (unlikely(__pyx_kwds) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__cinit__", 1))) return -1;
- __pyx_v_kwargs = (__pyx_kwds) ? PyDict_Copy(__pyx_kwds) : PyDict_New();
- if (unlikely(!__pyx_v_kwargs)) return -1;
- __Pyx_GOTREF(__pyx_v_kwargs);
- __Pyx_INCREF(__pyx_args);
- __pyx_v_args = __pyx_args;
- /* "csamtools.pyx":593
+ /* "pysam/csamtools.pyx":593
*
* def __cinit__(self, *args, **kwargs ):
* self.samfile = NULL # <<<<<<<<<<<<<<
* self._filename = NULL
* self.isbam = False
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
+ __pyx_v_self->samfile = NULL;
- /* "csamtools.pyx":594
+ /* "pysam/csamtools.pyx":594
* def __cinit__(self, *args, **kwargs ):
* self.samfile = NULL
* self._filename = NULL # <<<<<<<<<<<<<<
* self.isbam = False
* self.isstream = False
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = NULL;
+ __pyx_v_self->_filename = NULL;
- /* "csamtools.pyx":595
+ /* "pysam/csamtools.pyx":595
* self.samfile = NULL
* self._filename = NULL
* self.isbam = False # <<<<<<<<<<<<<<
* self.isstream = False
* self._open( *args, **kwargs )
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = 0;
+ __pyx_v_self->isbam = 0;
- /* "csamtools.pyx":596
+ /* "pysam/csamtools.pyx":596
* self._filename = NULL
* self.isbam = False
* self.isstream = False # <<<<<<<<<<<<<<
* self._open( *args, **kwargs )
*
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = 0;
+ __pyx_v_self->isstream = 0;
- /* "csamtools.pyx":597
+ /* "pysam/csamtools.pyx":597
* self.isbam = False
* self.isstream = False
* self._open( *args, **kwargs ) # <<<<<<<<<<<<<<
*
* # allocate memory for iterator
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_3 = PyEval_CallObjectWithKeywords(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = ((PyObject *)__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":600
+ /* "pysam/csamtools.pyx":600
*
* # allocate memory for iterator
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
* def _isOpen( self ):
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
__pyx_r = 0;
goto __pyx_L0;
@@ -6000,17 +6551,28 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObje
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_args);
- __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":602
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_2_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_isOpen (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":602
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
* def _isOpen( self ): # <<<<<<<<<<<<<<
@@ -6018,9 +6580,7 @@ static int __pyx_pf_9csamtools_7Samfile___cinit__(PyObject *__pyx_v_self, PyObje
* return self.samfile != NULL
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_1_isOpen[] = "Samfile._isOpen(self)\nreturn true if samfile has been opened.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -6028,10 +6588,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, C
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_isOpen");
+ __Pyx_RefNannySetupContext("_isOpen", 0);
__Pyx_TraceCall("_isOpen", __pyx_f[0], 602);
- /* "csamtools.pyx":604
+ /* "pysam/csamtools.pyx":604
* def _isOpen( self ):
* '''return true if samfile has been opened.'''
* return self.samfile != NULL # <<<<<<<<<<<<<<
@@ -6039,7 +6599,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, C
* def _hasIndex( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->samfile != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -6049,7 +6609,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, C
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Samfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._isOpen", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -6058,7 +6618,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, C
return __pyx_r;
}
-/* "csamtools.pyx":606
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_4_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("_hasIndex (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":606
* return self.samfile != NULL
*
* def _hasIndex( self ): # <<<<<<<<<<<<<<
@@ -6066,9 +6638,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_1_isOpen(PyObject *__pyx_v_self, C
* return self.index != NULL
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_2_hasIndex[] = "Samfile._hasIndex(self)\nreturn true if samfile has an existing (and opened) index.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4_hasIndex(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -6076,10 +6646,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_hasIndex");
+ __Pyx_RefNannySetupContext("_hasIndex", 0);
__Pyx_TraceCall("_hasIndex", __pyx_f[0], 606);
- /* "csamtools.pyx":608
+ /* "pysam/csamtools.pyx":608
* def _hasIndex( self ):
* '''return true if samfile has an existing (and opened) index.'''
* return self.index != NULL # <<<<<<<<<<<<<<
@@ -6087,7 +6657,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self,
* def _open( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -6097,7 +6667,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self,
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Samfile._hasIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._hasIndex", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -6106,20 +6676,13 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_2_hasIndex(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "csamtools.pyx":610
- * return self.index != NULL
- *
- * def _open( self, # <<<<<<<<<<<<<<
- * filename,
- * mode = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_3_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_6_open[] = "Samfile._open(self, filename, mode=None, Samfile template=None, referencenames=None, referencelengths=None, text=None, header=None, port=None, add_sq_text=True, check_header=True, check_sq=True)\nopen a sam/bam file.\n\n If _open is called on an existing bamfile, the current file will be\n closed and a new file will be opened.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_filename = 0;
PyObject *__pyx_v_mode = 0;
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_template = 0;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template = 0;
PyObject *__pyx_v_referencenames = 0;
PyObject *__pyx_v_referencelengths = 0;
PyObject *__pyx_v_text = 0;
@@ -6128,49 +6691,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
PyObject *__pyx_v_add_sq_text = 0;
PyObject *__pyx_v_check_header = 0;
PyObject *__pyx_v_check_sq = 0;
- PyObject *__pyx_v_msg = NULL;
- bam_header_t *__pyx_v_header_to_write;
- PyObject *__pyx_v_bmode = 0;
- char *__pyx_v_ctext;
- PyObject *__pyx_v_n = NULL;
- PyObject *__pyx_v_x = NULL;
- PyObject *__pyx_v_name = NULL;
- PyObject *__pyx_v_store = NULL;
- PyObject *__pyx_v_ref = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
- int __pyx_t_10;
- int __pyx_t_11;
- char *__pyx_t_12;
- Py_ssize_t __pyx_t_13;
- Py_ssize_t __pyx_t_14;
- PyObject *(*__pyx_t_15)(PyObject *);
- size_t __pyx_t_16;
- int32_t __pyx_t_17;
- long __pyx_t_18;
- uint32_t __pyx_t_19;
- const char* __pyx_t_20;
- int __pyx_t_21;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_open");
- __Pyx_TraceCall("_open", __pyx_f[0], 610);
+ __Pyx_RefNannySetupContext("_open (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,&__pyx_n_s__template,&__pyx_n_s__referencenames,&__pyx_n_s__referencelengths,&__pyx_n_s__text,&__pyx_n_s__header,&__pyx_n_s__port,&__pyx_n_s__add_sq_text,&__pyx_n_s__check_header,&__pyx_n_s__check_sq,0};
PyObject* values[11] = {0,0,0,0,0,0,0,0,0,0,0};
- /* "csamtools.pyx":612
+ /* "pysam/csamtools.pyx":612
* def _open( self,
* filename,
* mode = None, # <<<<<<<<<<<<<<
@@ -6179,16 +6707,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
values[1] = ((PyObject *)Py_None);
- /* "csamtools.pyx":613
+ /* "pysam/csamtools.pyx":613
* filename,
* mode = None,
* Samfile template = None, # <<<<<<<<<<<<<<
* referencenames = None,
* referencelengths = None,
*/
- values[2] = (PyObject *)((struct __pyx_obj_9csamtools_Samfile *)Py_None);
+ values[2] = (PyObject *)((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None);
- /* "csamtools.pyx":614
+ /* "pysam/csamtools.pyx":614
* mode = None,
* Samfile template = None,
* referencenames = None, # <<<<<<<<<<<<<<
@@ -6197,7 +6725,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
values[3] = ((PyObject *)Py_None);
- /* "csamtools.pyx":615
+ /* "pysam/csamtools.pyx":615
* Samfile template = None,
* referencenames = None,
* referencelengths = None, # <<<<<<<<<<<<<<
@@ -6206,7 +6734,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
values[4] = ((PyObject *)Py_None);
- /* "csamtools.pyx":616
+ /* "pysam/csamtools.pyx":616
* referencenames = None,
* referencelengths = None,
* text = None, # <<<<<<<<<<<<<<
@@ -6215,7 +6743,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
values[5] = ((PyObject *)Py_None);
- /* "csamtools.pyx":617
+ /* "pysam/csamtools.pyx":617
* referencelengths = None,
* text = None,
* header = None, # <<<<<<<<<<<<<<
@@ -6224,7 +6752,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
values[6] = ((PyObject *)Py_None);
- /* "csamtools.pyx":618
+ /* "pysam/csamtools.pyx":618
* text = None,
* header = None,
* port = None, # <<<<<<<<<<<<<<
@@ -6237,7 +6765,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
values[10] = __pyx_k_23;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 11: values[10] = PyTuple_GET_ITEM(__pyx_args, 10);
case 10: values[9] = PyTuple_GET_ITEM(__pyx_args, 9);
case 9: values[8] = PyTuple_GET_ITEM(__pyx_args, 8);
@@ -6253,10 +6782,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -6310,7 +6838,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_open") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -6331,7 +6859,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
}
__pyx_v_filename = values[0];
__pyx_v_mode = values[1];
- __pyx_v_template = ((struct __pyx_obj_9csamtools_Samfile *)values[2]);
+ __pyx_v_template = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[2]);
__pyx_v_referencenames = values[3];
__pyx_v_referencelengths = values[4];
__pyx_v_text = values[5];
@@ -6345,16 +6873,73 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__pyx_L5_argtuple_error:;
__Pyx_RaiseArgtupleInvalid("_open", 0, 1, 11, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_6_open(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_filename, __pyx_v_mode, __pyx_v_template, __pyx_v_referencenames, __pyx_v_referencelengths, __pyx_v_text, __pyx_v_header, __pyx_v_port, __pyx_v_add_sq_text, __pyx_v_check_header, __pyx_v_check_sq);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":610
+ * return self.index != NULL
+ *
+ * def _open( self, # <<<<<<<<<<<<<<
+ * filename,
+ * mode = None,
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_template, PyObject *__pyx_v_referencenames, PyObject *__pyx_v_referencelengths, PyObject *__pyx_v_text, PyObject *__pyx_v_header, PyObject *__pyx_v_port, PyObject *__pyx_v_add_sq_text, PyObject *__pyx_v_check_header, PyObject *__pyx_v_check_sq) {
+ CYTHON_UNUSED PyObject *__pyx_v_msg = NULL;
+ bam_header_t *__pyx_v_header_to_write;
+ PyObject *__pyx_v_bmode = 0;
+ char *__pyx_v_ctext;
+ PyObject *__pyx_v_n = NULL;
+ PyObject *__pyx_v_x = NULL;
+ PyObject *__pyx_v_name = NULL;
+ PyObject *__pyx_v_store = NULL;
+ PyObject *__pyx_v_ref = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ int __pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_t_11;
+ char *__pyx_t_12;
+ Py_ssize_t __pyx_t_13;
+ bam_header_t *__pyx_t_14;
+ Py_ssize_t __pyx_t_15;
+ PyObject *(*__pyx_t_16)(PyObject *);
+ size_t __pyx_t_17;
+ int32_t __pyx_t_18;
+ long __pyx_t_19;
+ uint32_t __pyx_t_20;
+ const char* __pyx_t_21;
+ int __pyx_t_22;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_open", 0);
+ __Pyx_TraceCall("_open", __pyx_f[0], 610);
__Pyx_INCREF(__pyx_v_filename);
__Pyx_INCREF(__pyx_v_referencenames);
__Pyx_INCREF(__pyx_v_text);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_template), __pyx_ptype_9csamtools_Samfile, 1, "template", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":630
+ /* "pysam/csamtools.pyx":630
*
* # read mode autodetection
* if mode is None: # <<<<<<<<<<<<<<
@@ -6364,7 +6949,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__pyx_t_1 = (__pyx_v_mode == Py_None);
if (__pyx_t_1) {
- /* "csamtools.pyx":631
+ /* "pysam/csamtools.pyx":631
* # read mode autodetection
* if mode is None:
* try: # <<<<<<<<<<<<<<
@@ -6378,81 +6963,81 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_XGOTREF(__pyx_t_4);
/*try:*/ {
- /* "csamtools.pyx":632
+ /* "pysam/csamtools.pyx":632
* if mode is None:
* try:
* self._open(filename, 'rb', template=template, # <<<<<<<<<<<<<<
* referencenames=referencenames,
* referencelengths=referencelengths,
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "csamtools.pyx":633
+ /* "pysam/csamtools.pyx":633
* try:
* self._open(filename, 'rb', template=template,
* referencenames=referencenames, # <<<<<<<<<<<<<<
* referencelengths=referencelengths,
* text=text, header=header, port=port,
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "csamtools.pyx":634
+ /* "pysam/csamtools.pyx":634
* self._open(filename, 'rb', template=template,
* referencenames=referencenames,
* referencelengths=referencelengths, # <<<<<<<<<<<<<<
* text=text, header=header, port=port,
* check_header=check_header,
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "csamtools.pyx":635
+ /* "pysam/csamtools.pyx":635
* referencenames=referencenames,
* referencelengths=referencelengths,
* text=text, header=header, port=port, # <<<<<<<<<<<<<<
* check_header=check_header,
* check_sq=check_sq)
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__text), __pyx_v_text) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "csamtools.pyx":636
+ /* "pysam/csamtools.pyx":636
* referencelengths=referencelengths,
* text=text, header=header, port=port,
* check_header=check_header, # <<<<<<<<<<<<<<
* check_sq=check_sq)
* return
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- /* "csamtools.pyx":637
+ /* "pysam/csamtools.pyx":637
* text=text, header=header, port=port,
* check_header=check_header,
* check_sq=check_sq) # <<<<<<<<<<<<<<
* return
* except ValueError, msg:
*/
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
- __pyx_t_8 = PyEval_CallObjectWithKeywords(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":638
+ /* "pysam/csamtools.pyx":638
* check_header=check_header,
* check_sq=check_sq)
* return # <<<<<<<<<<<<<<
@@ -6461,25 +7046,25 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L11_try_return;
+ goto __pyx_L8_try_return;
}
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L14_try_end;
- __pyx_L11_try_return:;
+ goto __pyx_L11_try_end;
+ __pyx_L8_try_return:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
goto __pyx_L0;
- __pyx_L7_error:;
+ __pyx_L4_error:;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":639
+ /* "pysam/csamtools.pyx":639
* check_sq=check_sq)
* return
* except ValueError, msg: # <<<<<<<<<<<<<<
@@ -6488,8 +7073,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_t_9 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_9) {
- __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_8, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_6);
@@ -6498,33 +7083,33 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L8_exception_handled;
+ goto __pyx_L5_exception_handled;
}
- __pyx_L9_except_error:;
+ __pyx_L6_except_error:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
goto __pyx_L1_error;
- __pyx_L8_exception_handled:;
+ __pyx_L5_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_2);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_ExceptionReset(__pyx_t_2, __pyx_t_3, __pyx_t_4);
- __pyx_L14_try_end:;
+ __pyx_L11_try_end:;
}
- /* "csamtools.pyx":642
+ /* "pysam/csamtools.pyx":642
* pass
*
* self._open(filename, 'r', template=template, # <<<<<<<<<<<<<<
* referencenames=referencenames,
* referencelengths=referencelengths,
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___open); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
@@ -6535,7 +7120,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__template), ((PyObject *)__pyx_v_template)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":643
+ /* "pysam/csamtools.pyx":643
*
* self._open(filename, 'r', template=template,
* referencenames=referencenames, # <<<<<<<<<<<<<<
@@ -6544,7 +7129,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__referencenames), __pyx_v_referencenames) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":644
+ /* "pysam/csamtools.pyx":644
* self._open(filename, 'r', template=template,
* referencenames=referencenames,
* referencelengths=referencelengths, # <<<<<<<<<<<<<<
@@ -6553,7 +7138,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__referencelengths), __pyx_v_referencelengths) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":645
+ /* "pysam/csamtools.pyx":645
* referencenames=referencenames,
* referencelengths=referencelengths,
* text=text, header=header, port=port, # <<<<<<<<<<<<<<
@@ -6564,7 +7149,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__header), __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__port), __pyx_v_port) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":646
+ /* "pysam/csamtools.pyx":646
* referencelengths=referencelengths,
* text=text, header=header, port=port,
* check_header=check_header, # <<<<<<<<<<<<<<
@@ -6573,7 +7158,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_header), __pyx_v_check_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":647
+ /* "pysam/csamtools.pyx":647
* text=text, header=header, port=port,
* check_header=check_header,
* check_sq=check_sq) # <<<<<<<<<<<<<<
@@ -6581,14 +7166,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*
*/
if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__check_sq), __pyx_v_check_sq) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = PyEval_CallObjectWithKeywords(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "csamtools.pyx":648
+ /* "pysam/csamtools.pyx":648
* check_header=check_header,
* check_sq=check_sq)
* return # <<<<<<<<<<<<<<
@@ -6598,11 +7183,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":650
+ /* "pysam/csamtools.pyx":650
* return
*
* assert mode in ( "r","w","rb","wb", "wh", "wbu", "rU" ), "invalid file opening mode `%s`" % mode # <<<<<<<<<<<<<<
@@ -6612,39 +7197,53 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
#ifndef CYTHON_WITHOUT_ASSERTIONS
__Pyx_INCREF(__pyx_v_mode);
__pyx_t_5 = __pyx_v_mode;
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (!((int)__pyx_t_1)) {
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_11 = ((int)__pyx_t_10);
} else {
__pyx_t_11 = ((int)__pyx_t_1);
}
if (!__pyx_t_11) {
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__rb), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__rb), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_10 = ((int)__pyx_t_1);
} else {
__pyx_t_10 = __pyx_t_11;
}
if (!__pyx_t_10) {
- __pyx_t_11 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wb), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__wb), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_1 = ((int)__pyx_t_11);
} else {
__pyx_t_1 = __pyx_t_10;
}
if (!__pyx_t_1) {
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wh), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__wh), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_11 = ((int)__pyx_t_10);
} else {
__pyx_t_11 = __pyx_t_1;
}
if (!__pyx_t_11) {
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__wbu), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__wbu), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_10 = ((int)__pyx_t_1);
} else {
__pyx_t_10 = __pyx_t_11;
}
if (!__pyx_t_10) {
- __pyx_t_11 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__rU), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__rU), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_1 = ((int)__pyx_t_11);
} else {
__pyx_t_1 = __pyx_t_10;
@@ -6659,35 +7258,35 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
}
#endif
- /* "csamtools.pyx":655
+ /* "pysam/csamtools.pyx":655
*
* # close a previously opened file
* if self.samfile != NULL: self.close() # <<<<<<<<<<<<<<
* self.samfile = NULL
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
+ __pyx_t_1 = (__pyx_v_self->samfile != NULL);
if (__pyx_t_1) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L17;
+ goto __pyx_L14;
}
- __pyx_L17:;
+ __pyx_L14:;
- /* "csamtools.pyx":656
+ /* "pysam/csamtools.pyx":656
* # close a previously opened file
* if self.samfile != NULL: self.close()
* self.samfile = NULL # <<<<<<<<<<<<<<
*
* cdef bam_header_t * header_to_write
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
+ __pyx_v_self->samfile = NULL;
- /* "csamtools.pyx":659
+ /* "pysam/csamtools.pyx":659
*
* cdef bam_header_t * header_to_write
* header_to_write = NULL # <<<<<<<<<<<<<<
@@ -6696,34 +7295,34 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_header_to_write = NULL;
- /* "csamtools.pyx":661
+ /* "pysam/csamtools.pyx":661
* header_to_write = NULL
*
* if self._filename != NULL: free(self._filename ) # <<<<<<<<<<<<<<
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii')
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
+ __pyx_t_1 = (__pyx_v_self->_filename != NULL);
if (__pyx_t_1) {
- free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
- goto __pyx_L18;
+ free(__pyx_v_self->_filename);
+ goto __pyx_L15;
}
- __pyx_L18:;
+ __pyx_L15:;
- /* "csamtools.pyx":662
+ /* "pysam/csamtools.pyx":662
*
* if self._filename != NULL: free(self._filename )
* filename = _my_encodeFilename(filename) # <<<<<<<<<<<<<<
* cdef bytes bmode = mode.encode('ascii')
* #cdef char* cfilename
*/
- __pyx_t_8 = ((PyObject *)__pyx_f_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = ((PyObject *)__pyx_f_5pysam_9csamtools__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_filename);
__pyx_v_filename = __pyx_t_8;
__pyx_t_8 = 0;
- /* "csamtools.pyx":663
+ /* "pysam/csamtools.pyx":663
* if self._filename != NULL: free(self._filename )
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<<
@@ -6739,7 +7338,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__pyx_v_bmode = ((PyObject*)__pyx_t_5);
__pyx_t_5 = 0;
- /* "csamtools.pyx":666
+ /* "pysam/csamtools.pyx":666
* #cdef char* cfilename
* #cfilename = filename.encode(_FILENAME_ENCODING)
* self._filename = strdup(filename) # <<<<<<<<<<<<<<
@@ -6747,9 +7346,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename = strdup(__pyx_t_12);
+ __pyx_v_self->_filename = strdup(__pyx_t_12);
- /* "csamtools.pyx":667
+ /* "pysam/csamtools.pyx":667
* #cfilename = filename.encode(_FILENAME_ENCODING)
* self._filename = strdup(filename)
* self.isstream = strcmp( filename, "-" ) == 0 # <<<<<<<<<<<<<<
@@ -6757,9 +7356,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
+ __pyx_v_self->isstream = (strcmp(__pyx_t_12, __pyx_k_26) == 0);
- /* "csamtools.pyx":669
+ /* "pysam/csamtools.pyx":669
* self.isstream = strcmp( filename, "-" ) == 0
*
* self.isbam = len(mode) > 1 and mode[1] == 'b' # <<<<<<<<<<<<<<
@@ -6767,19 +7366,26 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* self.isremote = strncmp(filename,"http:",5) == 0 or \
*/
__pyx_t_13 = PyObject_Length(__pyx_v_mode); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = (__pyx_t_13 > 1);
+ __pyx_t_5 = __Pyx_PyBool_FromLong((__pyx_t_13 > 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__b), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_n_s__b), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = __pyx_t_7;
+ __pyx_t_7 = 0;
} else {
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_8 = __pyx_t_5;
+ __pyx_t_5 = 0;
}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam = __pyx_t_11;
+ __pyx_t_9 = __Pyx_PyInt_AsInt(__pyx_t_8); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_self->isbam = __pyx_t_9;
- /* "csamtools.pyx":671
+ /* "pysam/csamtools.pyx":671
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*
* self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
@@ -6787,10 +7393,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = (strncmp(__pyx_t_12, __pyx_k_27, 5) == 0);
- if (!__pyx_t_11) {
+ __pyx_t_1 = (strncmp(__pyx_t_12, __pyx_k_27, 5) == 0);
+ if (!__pyx_t_1) {
- /* "csamtools.pyx":672
+ /* "pysam/csamtools.pyx":672
*
* self.isremote = strncmp(filename,"http:",5) == 0 or \
* strncmp(filename,"ftp:",4) == 0 # <<<<<<<<<<<<<<
@@ -6798,22 +7404,22 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* cdef char * ctext
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = (strncmp(__pyx_t_12, __pyx_k_28, 4) == 0);
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_10 = (strncmp(__pyx_t_12, __pyx_k_28, 4) == 0);
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_10 = __pyx_t_11;
+ __pyx_t_11 = __pyx_t_1;
}
- /* "csamtools.pyx":671
+ /* "pysam/csamtools.pyx":671
* self.isbam = len(mode) > 1 and mode[1] == 'b'
*
* self.isremote = strncmp(filename,"http:",5) == 0 or \ # <<<<<<<<<<<<<<
* strncmp(filename,"ftp:",4) == 0
*
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote = __pyx_t_10;
+ __pyx_v_self->isremote = __pyx_t_11;
- /* "csamtools.pyx":675
+ /* "pysam/csamtools.pyx":675
*
* cdef char * ctext
* ctext = NULL # <<<<<<<<<<<<<<
@@ -6822,63 +7428,66 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_ctext = NULL;
- /* "csamtools.pyx":677
+ /* "pysam/csamtools.pyx":677
* ctext = NULL
*
* if mode[0] == 'w': # <<<<<<<<<<<<<<
* # open file for writing
*
*/
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_n_s__w), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_10) {
+ if (__pyx_t_11) {
- /* "csamtools.pyx":681
+ /* "pysam/csamtools.pyx":681
*
* # header structure (used for writing)
* if template: # <<<<<<<<<<<<<<
* # copy header from another file
* header_to_write = template.samfile.header
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_11) {
- /* "csamtools.pyx":683
+ /* "pysam/csamtools.pyx":683
* if template:
* # copy header from another file
* header_to_write = template.samfile.header # <<<<<<<<<<<<<<
*
* elif header:
*/
- __pyx_v_header_to_write = __pyx_v_template->samfile->header;
- goto __pyx_L20;
+ __pyx_t_14 = __pyx_v_template->samfile->header;
+ __pyx_v_header_to_write = __pyx_t_14;
+ goto __pyx_L17;
}
- /* "csamtools.pyx":685
+ /* "pysam/csamtools.pyx":685
* header_to_write = template.samfile.header
*
* elif header: # <<<<<<<<<<<<<<
* header_to_write = self._buildHeader( header )
*
*/
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_11) {
- /* "csamtools.pyx":686
+ /* "pysam/csamtools.pyx":686
*
* elif header:
* header_to_write = self._buildHeader( header ) # <<<<<<<<<<<<<<
*
* else:
*/
- __pyx_v_header_to_write = ((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->_buildHeader(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), __pyx_v_header);
- goto __pyx_L20;
+ __pyx_v_header_to_write = ((struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->_buildHeader(__pyx_v_self, __pyx_v_header);
+ goto __pyx_L17;
}
/*else*/ {
- /* "csamtools.pyx":690
+ /* "pysam/csamtools.pyx":690
* else:
* # build header from a target names and lengths
* assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing" # <<<<<<<<<<<<<<
@@ -6886,20 +7495,20 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_10) {
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = __pyx_t_11;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_11) {
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __pyx_t_1;
} else {
- __pyx_t_1 = __pyx_t_10;
+ __pyx_t_10 = __pyx_t_11;
}
- if (unlikely(!__pyx_t_1)) {
+ if (unlikely(!__pyx_t_10)) {
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_29));
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":691
+ /* "pysam/csamtools.pyx":691
* # build header from a target names and lengths
* assert referencenames and referencelengths, "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing"
* assert len(referencenames) == len(referencelengths), "unequal names and lengths of reference sequences" # <<<<<<<<<<<<<<
@@ -6908,14 +7517,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
__pyx_t_13 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!(__pyx_t_13 == __pyx_t_14))) {
+ __pyx_t_15 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!(__pyx_t_13 == __pyx_t_15))) {
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_30));
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":694
+ /* "pysam/csamtools.pyx":694
*
* # allocate and fill header
* referencenames = [ _force_bytes(ref) for ref in referencenames ] # <<<<<<<<<<<<<<
@@ -6923,24 +7532,32 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* header_to_write.n_targets = len(referencenames)
*/
__pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __Pyx_GOTREF(__pyx_t_5);
if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
- __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_14 = 0;
- __pyx_t_15 = NULL;
+ __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
+ __pyx_t_16 = NULL;
} else {
- __pyx_t_14 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_16 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
- } else if (PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_14); __Pyx_INCREF(__pyx_t_7); __pyx_t_14++;
+ if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_7); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_7 = __pyx_t_15(__pyx_t_8);
+ __pyx_t_7 = __pyx_t_16(__pyx_t_8);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
@@ -6953,18 +7570,20 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_XDECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_7;
__pyx_t_7 = 0;
- __pyx_t_7 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_ref)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (unlikely(PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_5));
- __Pyx_DECREF(__pyx_v_referencenames);
- __pyx_v_referencenames = ((PyObject *)__pyx_t_5);
+ __pyx_t_8 = ((PyObject *)__pyx_t_5);
+ __Pyx_INCREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_v_referencenames);
+ __pyx_v_referencenames = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":695
+ /* "pysam/csamtools.pyx":695
* # allocate and fill header
* referencenames = [ _force_bytes(ref) for ref in referencenames ]
* header_to_write = bam_header_init() # <<<<<<<<<<<<<<
@@ -6973,17 +7592,17 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_header_to_write = bam_header_init();
- /* "csamtools.pyx":696
+ /* "pysam/csamtools.pyx":696
* referencenames = [ _force_bytes(ref) for ref in referencenames ]
* header_to_write = bam_header_init()
* header_to_write.n_targets = len(referencenames) # <<<<<<<<<<<<<<
* n = 0
* for x in referencenames: n += len(x) + 1
*/
- __pyx_t_14 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->n_targets = __pyx_t_14;
+ __pyx_t_15 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->n_targets = __pyx_t_15;
- /* "csamtools.pyx":697
+ /* "pysam/csamtools.pyx":697
* header_to_write = bam_header_init()
* header_to_write.n_targets = len(referencenames)
* n = 0 # <<<<<<<<<<<<<<
@@ -6993,7 +7612,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_INCREF(__pyx_int_0);
__pyx_v_n = __pyx_int_0;
- /* "csamtools.pyx":698
+ /* "pysam/csamtools.pyx":698
* header_to_write.n_targets = len(referencenames)
* n = 0
* for x in referencenames: n += len(x) + 1 # <<<<<<<<<<<<<<
@@ -7001,284 +7620,291 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
*/
if (PyList_CheckExact(__pyx_v_referencenames) || PyTuple_CheckExact(__pyx_v_referencenames)) {
- __pyx_t_5 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_5); __pyx_t_14 = 0;
- __pyx_t_15 = NULL;
+ __pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
+ __pyx_t_16 = NULL;
} else {
- __pyx_t_14 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_15 = Py_TYPE(__pyx_t_5)->tp_iternext;
+ __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_16 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_5)) {
- if (__pyx_t_14 >= PyList_GET_SIZE(__pyx_t_5)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
- } else if (PyTuple_CheckExact(__pyx_t_5)) {
- if (__pyx_t_14 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_14); __Pyx_INCREF(__pyx_t_8); __pyx_t_14++;
+ if (!__pyx_t_16 && PyList_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_5 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_5); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
+ if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_5 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_15); __Pyx_INCREF(__pyx_t_5); __pyx_t_15++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_5 = PySequence_ITEM(__pyx_t_8, __pyx_t_15); __pyx_t_15++; if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_8 = __pyx_t_15(__pyx_t_5);
- if (unlikely(!__pyx_t_8)) {
+ __pyx_t_5 = __pyx_t_16(__pyx_t_8);
+ if (unlikely(!__pyx_t_5)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_5);
}
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
__pyx_t_13 = PyObject_Length(__pyx_v_x); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_8); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_n, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_v_n);
__pyx_v_n = __pyx_t_7;
__pyx_t_7 = 0;
}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":699
+ /* "pysam/csamtools.pyx":699
* n = 0
* for x in referencenames: n += len(x) + 1
* header_to_write.target_name = <char**>calloc(n, sizeof(char*)) # <<<<<<<<<<<<<<
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets:
*/
- __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_16, (sizeof(char *))));
+ __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_name = ((char **)calloc(__pyx_t_17, (sizeof(char *))));
- /* "csamtools.pyx":700
+ /* "pysam/csamtools.pyx":700
* for x in referencenames: n += len(x) + 1
* header_to_write.target_name = <char**>calloc(n, sizeof(char*))
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t)) # <<<<<<<<<<<<<<
* for x from 0 <= x < header_to_write.n_targets:
* header_to_write.target_len[x] = referencelengths[x]
*/
- __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_16, (sizeof(uint32_t))));
+ __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_n); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 700; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_header_to_write->target_len = ((uint32_t *)calloc(__pyx_t_17, (sizeof(uint32_t))));
- /* "csamtools.pyx":701
+ /* "pysam/csamtools.pyx":701
* header_to_write.target_name = <char**>calloc(n, sizeof(char*))
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x]
*/
- __pyx_t_17 = __pyx_v_header_to_write->n_targets;
- for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18++) {
- __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_18 = __pyx_v_header_to_write->n_targets;
+ for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19++) {
+ __pyx_t_8 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":702
+ /* "pysam/csamtools.pyx":702
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets:
* header_to_write.target_len[x] = referencelengths[x] # <<<<<<<<<<<<<<
* name = referencenames[x]
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
*/
- __pyx_t_5 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_19 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_19 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_14 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_14 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_header_to_write->target_len[__pyx_t_14]) = __pyx_t_19;
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_20 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_20 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_15 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_15 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ (__pyx_v_header_to_write->target_len[__pyx_t_15]) = __pyx_t_20;
- /* "csamtools.pyx":703
+ /* "pysam/csamtools.pyx":703
* for x from 0 <= x < header_to_write.n_targets:
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x] # <<<<<<<<<<<<<<
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
* strncpy( header_to_write.target_name[x], name, len(name) )
*/
- __pyx_t_5 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_name);
- __pyx_v_name = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_name = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":704
+ /* "pysam/csamtools.pyx":704
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x]
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char)) # <<<<<<<<<<<<<<
* strncpy( header_to_write.target_name[x], name, len(name) )
*
*/
- __pyx_t_14 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_13 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- (__pyx_v_header_to_write->target_name[__pyx_t_13]) = ((char *)calloc((__pyx_t_14 + 1), (sizeof(char))));
+ (__pyx_v_header_to_write->target_name[__pyx_t_13]) = ((char *)calloc((__pyx_t_15 + 1), (sizeof(char))));
- /* "csamtools.pyx":705
+ /* "pysam/csamtools.pyx":705
* name = referencenames[x]
* header_to_write.target_name[x] = <char*>calloc(len(name)+1, sizeof(char))
* strncpy( header_to_write.target_name[x], name, len(name) ) # <<<<<<<<<<<<<<
*
* # Optionally, if there is no text, add a SAM compatible header to output
*/
- __pyx_t_14 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_14 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_15 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(__pyx_v_name); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = PyObject_Length(__pyx_v_name); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy((__pyx_v_header_to_write->target_name[__pyx_t_14]), __pyx_t_12, __pyx_t_13);
- __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy((__pyx_v_header_to_write->target_name[__pyx_t_15]), __pyx_t_12, __pyx_t_13);
+ __pyx_t_19 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_19 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "csamtools.pyx":701
+ /* "pysam/csamtools.pyx":701
* header_to_write.target_name = <char**>calloc(n, sizeof(char*))
* header_to_write.target_len = <uint32_t*>calloc(n, sizeof(uint32_t))
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* header_to_write.target_len[x] = referencelengths[x]
* name = referencenames[x]
*/
- __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":709
+ /* "pysam/csamtools.pyx":709
* # Optionally, if there is no text, add a SAM compatible header to output
* # file.
* if text is None and add_sq_text: # <<<<<<<<<<<<<<
* text = []
* for x from 0 <= x < header_to_write.n_targets:
*/
- __pyx_t_1 = (__pyx_v_text == Py_None);
- if (__pyx_t_1) {
- __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_add_sq_text); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_10 = (__pyx_v_text == Py_None);
+ if (__pyx_t_10) {
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_add_sq_text); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_t_11;
} else {
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_1 = __pyx_t_10;
}
- if (__pyx_t_11) {
+ if (__pyx_t_1) {
- /* "csamtools.pyx":710
+ /* "pysam/csamtools.pyx":710
* # file.
* if text is None and add_sq_text:
* text = [] # <<<<<<<<<<<<<<
* for x from 0 <= x < header_to_write.n_targets:
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
*/
- __pyx_t_5 = PyList_New(0); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = ((PyObject *)__pyx_t_5);
- __pyx_t_5 = 0;
+ __pyx_v_text = ((PyObject *)__pyx_t_8);
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":711
+ /* "pysam/csamtools.pyx":711
* if text is None and add_sq_text:
* text = []
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
* text = ''.join(text)
*/
- __pyx_t_17 = __pyx_v_header_to_write->n_targets;
- for (__pyx_t_18 = 0; __pyx_t_18 < __pyx_t_17; __pyx_t_18++) {
- __pyx_t_5 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_18 = __pyx_v_header_to_write->n_targets;
+ for (__pyx_t_19 = 0; __pyx_t_19 < __pyx_t_18; __pyx_t_19++) {
+ __pyx_t_8 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_x = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":712
+ /* "pysam/csamtools.pyx":712
* text = []
* for x from 0 <= x < header_to_write.n_targets:
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) ) # <<<<<<<<<<<<<<
* text = ''.join(text)
*
*/
- __pyx_t_5 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_referencenames, __pyx_v_x); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__pyx_t_7 = PyObject_GetItem(__pyx_v_referencelengths, __pyx_v_x); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_5 = 0;
+ __pyx_t_8 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_31), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_31), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_PyObject_Append(__pyx_v_text, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_text, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_18 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_18 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_19 = __Pyx_PyInt_AsLong(__pyx_v_x); if (unlikely((__pyx_t_19 == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- /* "csamtools.pyx":711
+ /* "pysam/csamtools.pyx":711
* if text is None and add_sq_text:
* text = []
* for x from 0 <= x < header_to_write.n_targets: # <<<<<<<<<<<<<<
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
* text = ''.join(text)
*/
- __pyx_t_8 = PyInt_FromLong(__pyx_t_18); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyInt_FromLong(__pyx_t_19); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_v_x);
- __pyx_v_x = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_x = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "csamtools.pyx":713
+ /* "pysam/csamtools.pyx":713
* for x from 0 <= x < header_to_write.n_targets:
* text.append( "@SQ\tSN:%s\tLN:%s\n" % (referencenames[x], referencelengths[x] ) )
* text = ''.join(text) # <<<<<<<<<<<<<<
*
* if text != None:
*/
- __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_text);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_text);
__Pyx_GIVEREF(__pyx_v_text);
- __pyx_t_5 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = __pyx_t_5;
- __pyx_t_5 = 0;
- goto __pyx_L27;
+ __pyx_v_text = __pyx_t_8;
+ __pyx_t_8 = 0;
+ goto __pyx_L24;
}
- __pyx_L27:;
+ __pyx_L24:;
- /* "csamtools.pyx":715
+ /* "pysam/csamtools.pyx":715
* text = ''.join(text)
*
* if text != None: # <<<<<<<<<<<<<<
* # copy without \0
* text = _force_bytes(text)
*/
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_text, Py_None, Py_NE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_11) {
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_text, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_1) {
- /* "csamtools.pyx":717
+ /* "pysam/csamtools.pyx":717
* if text != None:
* # copy without \0
* text = _force_bytes(text) # <<<<<<<<<<<<<<
* ctext = text
* header_to_write.l_text = strlen(ctext)
*/
- __pyx_t_5 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_text)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_text)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_v_text);
- __pyx_v_text = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_v_text = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":718
+ /* "pysam/csamtools.pyx":718
* # copy without \0
* text = _force_bytes(text)
* ctext = text # <<<<<<<<<<<<<<
@@ -7288,7 +7914,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__pyx_t_12 = PyBytes_AsString(__pyx_v_text); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_ctext = __pyx_t_12;
- /* "csamtools.pyx":719
+ /* "pysam/csamtools.pyx":719
* text = _force_bytes(text)
* ctext = text
* header_to_write.l_text = strlen(ctext) # <<<<<<<<<<<<<<
@@ -7297,7 +7923,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_header_to_write->l_text = strlen(__pyx_v_ctext);
- /* "csamtools.pyx":720
+ /* "pysam/csamtools.pyx":720
* ctext = text
* header_to_write.l_text = strlen(ctext)
* header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) ) # <<<<<<<<<<<<<<
@@ -7306,7 +7932,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_header_to_write->text = ((char *)calloc(strlen(__pyx_v_ctext), (sizeof(char))));
- /* "csamtools.pyx":721
+ /* "pysam/csamtools.pyx":721
* header_to_write.l_text = strlen(ctext)
* header_to_write.text = <char*>calloc( strlen(ctext), sizeof(char) )
* memcpy( header_to_write.text, ctext, strlen(ctext) ) # <<<<<<<<<<<<<<
@@ -7314,11 +7940,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* header_to_write.hash = NULL
*/
memcpy(__pyx_v_header_to_write->text, __pyx_v_ctext, strlen(__pyx_v_ctext));
- goto __pyx_L30;
+ goto __pyx_L27;
}
- __pyx_L30:;
+ __pyx_L27:;
- /* "csamtools.pyx":723
+ /* "pysam/csamtools.pyx":723
* memcpy( header_to_write.text, ctext, strlen(ctext) )
*
* header_to_write.hash = NULL # <<<<<<<<<<<<<<
@@ -7327,7 +7953,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_header_to_write->hash = NULL;
- /* "csamtools.pyx":724
+ /* "pysam/csamtools.pyx":724
*
* header_to_write.hash = NULL
* header_to_write.rg2lib = NULL # <<<<<<<<<<<<<<
@@ -7336,35 +7962,35 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_v_header_to_write->rg2lib = NULL;
}
- __pyx_L20:;
+ __pyx_L17:;
- /* "csamtools.pyx":728
+ /* "pysam/csamtools.pyx":728
* # open file. Header gets written to file at the same time for bam files
* # and sam files (in the latter case, the mode needs to be wh)
* store = StderrStore() # <<<<<<<<<<<<<<
* self.samfile = samopen( filename, bmode, header_to_write )
* store.release()
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_store = __pyx_t_7;
__pyx_t_7 = 0;
- /* "csamtools.pyx":729
+ /* "pysam/csamtools.pyx":729
* # and sam files (in the latter case, the mode needs to be wh)
* store = StderrStore()
* self.samfile = samopen( filename, bmode, header_to_write ) # <<<<<<<<<<<<<<
* store.release()
*
*/
- __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_21 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, __pyx_v_header_to_write);
+ __pyx_v_self->samfile = samopen(__pyx_t_21, __pyx_t_12, __pyx_v_header_to_write);
- /* "csamtools.pyx":730
+ /* "pysam/csamtools.pyx":730
* store = StderrStore()
* self.samfile = samopen( filename, bmode, header_to_write )
* store.release() # <<<<<<<<<<<<<<
@@ -7373,29 +7999,29 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
*/
__pyx_t_7 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":733
+ /* "pysam/csamtools.pyx":733
*
* # bam_header_destroy takes care of cleaning up of all the members
* if not template and header_to_write != NULL: # <<<<<<<<<<<<<<
* bam_header_destroy( header_to_write )
*
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = (!__pyx_t_11);
- if (__pyx_t_1) {
- __pyx_t_11 = (__pyx_v_header_to_write != NULL);
- __pyx_t_10 = __pyx_t_11;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = (!__pyx_t_1);
+ if (__pyx_t_10) {
+ __pyx_t_1 = (__pyx_v_header_to_write != NULL);
+ __pyx_t_11 = __pyx_t_1;
} else {
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_11 = __pyx_t_10;
}
- if (__pyx_t_10) {
+ if (__pyx_t_11) {
- /* "csamtools.pyx":734
+ /* "pysam/csamtools.pyx":734
* # bam_header_destroy takes care of cleaning up of all the members
* if not template and header_to_write != NULL:
* bam_header_destroy( header_to_write ) # <<<<<<<<<<<<<<
@@ -7403,26 +8029,28 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* elif mode[0] == "r":
*/
bam_header_destroy(__pyx_v_header_to_write);
- goto __pyx_L31;
+ goto __pyx_L28;
}
- __pyx_L31:;
- goto __pyx_L19;
+ __pyx_L28:;
+ goto __pyx_L16;
}
- /* "csamtools.pyx":736
+ /* "pysam/csamtools.pyx":736
* bam_header_destroy( header_to_write )
*
* elif mode[0] == "r": # <<<<<<<<<<<<<<
* # open file for reading
* if strncmp( filename, "-", 1) != 0 and \
*/
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (__pyx_t_10) {
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_11) {
- /* "csamtools.pyx":738
+ /* "pysam/csamtools.pyx":738
* elif mode[0] == "r":
* # open file for reading
* if strncmp( filename, "-", 1) != 0 and \ # <<<<<<<<<<<<<<
@@ -7430,480 +8058,520 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* not os.path.exists( filename ):
*/
__pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_10 = (strncmp(__pyx_t_12, __pyx_k_26, 1) != 0);
- if (__pyx_t_10) {
+ __pyx_t_11 = (strncmp(__pyx_t_12, __pyx_k_26, 1) != 0);
+ if (__pyx_t_11) {
- /* "csamtools.pyx":739
+ /* "pysam/csamtools.pyx":739
* # open file for reading
* if strncmp( filename, "-", 1) != 0 and \
* not self.isremote and \ # <<<<<<<<<<<<<<
* not os.path.exists( filename ):
* raise IOError( "file `%s` not found" % filename)
*/
- __pyx_t_1 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
- if (__pyx_t_1) {
+ __pyx_t_10 = (!__pyx_v_self->isremote);
+ if (__pyx_t_10) {
- /* "csamtools.pyx":740
+ /* "pysam/csamtools.pyx":740
* if strncmp( filename, "-", 1) != 0 and \
* not self.isremote and \
* not os.path.exists( filename ): # <<<<<<<<<<<<<<
* raise IOError( "file `%s` not found" % filename)
*
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__path); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__exists); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
- __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_21 = (!__pyx_t_11);
- __pyx_t_11 = __pyx_t_21;
+ __pyx_t_22 = (!__pyx_t_1);
+ __pyx_t_1 = __pyx_t_22;
} else {
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_1 = __pyx_t_10;
}
- __pyx_t_1 = __pyx_t_11;
+ __pyx_t_10 = __pyx_t_1;
} else {
- __pyx_t_1 = __pyx_t_10;
+ __pyx_t_10 = __pyx_t_11;
}
- if (__pyx_t_1) {
+ if (__pyx_t_10) {
- /* "csamtools.pyx":741
+ /* "pysam/csamtools.pyx":741
* not self.isremote and \
* not os.path.exists( filename ):
* raise IOError( "file `%s` not found" % filename) # <<<<<<<<<<<<<<
*
* # try to detect errors
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_32), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ goto __pyx_L29;
}
- __pyx_L32:;
+ __pyx_L29:;
- /* "csamtools.pyx":744
+ /* "pysam/csamtools.pyx":744
*
* # try to detect errors
* self.samfile = samopen( filename, bmode, NULL ) # <<<<<<<<<<<<<<
* if self.samfile == NULL:
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
*/
- __pyx_t_20 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_20 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyBytes_AsString(__pyx_v_filename); if (unlikely((__pyx_t_21 == (const char*)NULL) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_12 = PyBytes_AsString(((PyObject *)__pyx_v_bmode)); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = samopen(__pyx_t_20, __pyx_t_12, NULL);
+ __pyx_v_self->samfile = samopen(__pyx_t_21, __pyx_t_12, NULL);
- /* "csamtools.pyx":745
+ /* "pysam/csamtools.pyx":745
* # try to detect errors
* self.samfile = samopen( filename, bmode, NULL )
* if self.samfile == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode)
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
- if (__pyx_t_1) {
+ __pyx_t_10 = (__pyx_v_self->samfile == NULL);
+ if (__pyx_t_10) {
- /* "csamtools.pyx":746
+ /* "pysam/csamtools.pyx":746
* self.samfile = samopen( filename, bmode, NULL )
* if self.samfile == NULL:
* raise ValueError( "could not open file (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
*
* # bam files require a valid header
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_33), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L33;
+ goto __pyx_L30;
}
- __pyx_L33:;
+ __pyx_L30:;
- /* "csamtools.pyx":749
+ /* "pysam/csamtools.pyx":749
*
* # bam files require a valid header
* if self.isbam: # <<<<<<<<<<<<<<
* if self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ if (__pyx_v_self->isbam) {
- /* "csamtools.pyx":750
+ /* "pysam/csamtools.pyx":750
* # bam files require a valid header
* if self.isbam:
* if self.samfile.header == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode )
* else:
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
- if (__pyx_t_1) {
+ __pyx_t_10 = (__pyx_v_self->samfile->header == NULL);
+ if (__pyx_t_10) {
- /* "csamtools.pyx":751
+ /* "pysam/csamtools.pyx":751
* if self.isbam:
* if self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) # <<<<<<<<<<<<<<
* else:
* # in sam files it is optional (samfile full of unmapped reads)
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_34), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L35;
+ goto __pyx_L32;
}
- __pyx_L35:;
- goto __pyx_L34;
+ __pyx_L32:;
+ goto __pyx_L31;
}
/*else*/ {
- /* "csamtools.pyx":754
+ /* "pysam/csamtools.pyx":754
* else:
* # in sam files it is optional (samfile full of unmapped reads)
* if check_header and self.samfile.header == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode )
*
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
- __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_10) {
+ __pyx_t_11 = (__pyx_v_self->samfile->header == NULL);
+ __pyx_t_1 = __pyx_t_11;
} else {
- __pyx_t_11 = __pyx_t_1;
+ __pyx_t_1 = __pyx_t_10;
}
- if (__pyx_t_11) {
+ if (__pyx_t_1) {
- /* "csamtools.pyx":755
+ /* "pysam/csamtools.pyx":755
* # in sam files it is optional (samfile full of unmapped reads)
* if check_header and self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it SAM format?" % mode ) # <<<<<<<<<<<<<<
*
* # disabled for autodetection to work
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_35), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L36;
+ goto __pyx_L33;
}
- __pyx_L36:;
+ __pyx_L33:;
}
- __pyx_L34:;
+ __pyx_L31:;
- /* "csamtools.pyx":759
+ /* "pysam/csamtools.pyx":759
* # disabled for autodetection to work
* # needs to be disabled so that reading from sam-files without headers works
* if check_sq and self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
*
*/
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_11) {
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_1) {
+ __pyx_t_10 = (__pyx_v_self->samfile->header->n_targets == 0);
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_10 = __pyx_t_11;
+ __pyx_t_11 = __pyx_t_1;
}
- if (__pyx_t_10) {
+ if (__pyx_t_11) {
- /* "csamtools.pyx":760
+ /* "pysam/csamtools.pyx":760
* # needs to be disabled so that reading from sam-files without headers works
* if check_sq and self.samfile.header.n_targets == 0:
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode) # <<<<<<<<<<<<<<
*
* if self.samfile == NULL:
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_36), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L37;
+ goto __pyx_L34;
}
- __pyx_L37:;
- goto __pyx_L19;
+ __pyx_L34:;
+ goto __pyx_L16;
}
- __pyx_L19:;
+ __pyx_L16:;
- /* "csamtools.pyx":762
+ /* "pysam/csamtools.pyx":762
* raise ValueError( "file header is empty (mode='%s') - is it SAM/BAM format?" % mode)
*
* if self.samfile == NULL: # <<<<<<<<<<<<<<
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile == NULL);
- if (__pyx_t_10) {
+ __pyx_t_11 = (__pyx_v_self->samfile == NULL);
+ if (__pyx_t_11) {
- /* "csamtools.pyx":763
+ /* "pysam/csamtools.pyx":763
*
* if self.samfile == NULL:
* raise IOError("could not open file `%s`" % filename ) # <<<<<<<<<<<<<<
*
* # check for index and open if present
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_9), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_8, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_5, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L38;
+ goto __pyx_L35;
}
- __pyx_L38:;
+ __pyx_L35:;
- /* "csamtools.pyx":766
+ /* "pysam/csamtools.pyx":766
*
* # check for index and open if present
* if mode[0] == "r" and self.isbam: # <<<<<<<<<<<<<<
*
* if not self.isremote:
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_5, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_10) {
- __pyx_t_11 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam;
+ if (__pyx_t_11) {
+ __pyx_t_1 = __pyx_v_self->isbam;
} else {
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_1 = __pyx_t_11;
}
- if (__pyx_t_11) {
+ if (__pyx_t_1) {
- /* "csamtools.pyx":768
+ /* "pysam/csamtools.pyx":768
* if mode[0] == "r" and self.isbam:
*
* if not self.isremote: # <<<<<<<<<<<<<<
- * if not os.path.exists(filename + b".bai"):
- * self.index = NULL
+ * if not os.path.exists(filename + b".bai") \
+ * and not os.path.exists( filename[:-4] + b".bai"):
*/
- __pyx_t_11 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
- if (__pyx_t_11) {
+ __pyx_t_1 = (!__pyx_v_self->isremote);
+ if (__pyx_t_1) {
- /* "csamtools.pyx":769
+ /* "pysam/csamtools.pyx":769
*
* if not self.isremote:
- * if not os.path.exists(filename + b".bai"): # <<<<<<<<<<<<<<
+ * if not os.path.exists(filename + b".bai") \ # <<<<<<<<<<<<<<
+ * and not os.path.exists( filename[:-4] + b".bai"):
* self.index = NULL
- * else:
*/
__pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__path); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__exists); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5);
+ __Pyx_GIVEREF(__pyx_t_5);
+ __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_10 = (!__pyx_t_11);
- if (__pyx_t_10) {
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_11 = (!__pyx_t_1);
+ if (__pyx_t_11) {
- /* "csamtools.pyx":770
+ /* "pysam/csamtools.pyx":770
* if not self.isremote:
- * if not os.path.exists(filename + b".bai"):
+ * if not os.path.exists(filename + b".bai") \
+ * and not os.path.exists( filename[:-4] + b".bai"): # <<<<<<<<<<<<<<
+ * self.index = NULL
+ * else:
+ */
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__path); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__exists); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_filename, 0, -4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PyNumber_Add(__pyx_t_7, ((PyObject *)__pyx_kp_b_37)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_10 = (!__pyx_t_1);
+ __pyx_t_1 = __pyx_t_10;
+ } else {
+ __pyx_t_1 = __pyx_t_11;
+ }
+ if (__pyx_t_1) {
+
+ /* "pysam/csamtools.pyx":771
+ * if not os.path.exists(filename + b".bai") \
+ * and not os.path.exists( filename[:-4] + b".bai"):
* self.index = NULL # <<<<<<<<<<<<<<
* else:
* # returns NULL if there is no index or index could not be opened
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = NULL;
- goto __pyx_L41;
+ __pyx_v_self->index = NULL;
+ goto __pyx_L38;
}
/*else*/ {
- /* "csamtools.pyx":773
+ /* "pysam/csamtools.pyx":774
* else:
* # returns NULL if there is no index or index could not be opened
* self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
* if self.index == NULL:
* raise IOError("error while opening index `%s` " % filename )
*/
- __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12);
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->index = bam_index_load(__pyx_t_12);
- /* "csamtools.pyx":774
+ /* "pysam/csamtools.pyx":775
* # returns NULL if there is no index or index could not be opened
* self.index = bam_index_load(filename)
* if self.index == NULL: # <<<<<<<<<<<<<<
* raise IOError("error while opening index `%s` " % filename )
* else:
*/
- __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
- if (__pyx_t_10) {
+ __pyx_t_1 = (__pyx_v_self->index == NULL);
+ if (__pyx_t_1) {
- /* "csamtools.pyx":775
+ /* "pysam/csamtools.pyx":776
* self.index = bam_index_load(filename)
* if self.index == NULL:
* raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
* else:
* self.index = bam_index_load(filename)
*/
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L42;
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L39;
}
- __pyx_L42:;
+ __pyx_L39:;
}
- __pyx_L41:;
- goto __pyx_L40;
+ __pyx_L38:;
+ goto __pyx_L37;
}
/*else*/ {
- /* "csamtools.pyx":777
+ /* "pysam/csamtools.pyx":778
* raise IOError("error while opening index `%s` " % filename )
* else:
* self.index = bam_index_load(filename) # <<<<<<<<<<<<<<
* if self.index == NULL:
* raise IOError("error while opening index `%s` " % filename )
*/
- __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index = bam_index_load(__pyx_t_12);
+ __pyx_t_12 = PyBytes_AsString(__pyx_v_filename); if (unlikely((!__pyx_t_12) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->index = bam_index_load(__pyx_t_12);
- /* "csamtools.pyx":778
+ /* "pysam/csamtools.pyx":779
* else:
* self.index = bam_index_load(filename)
* if self.index == NULL: # <<<<<<<<<<<<<<
* raise IOError("error while opening index `%s` " % filename )
*
*/
- __pyx_t_10 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index == NULL);
- if (__pyx_t_10) {
+ __pyx_t_1 = (__pyx_v_self->index == NULL);
+ if (__pyx_t_1) {
- /* "csamtools.pyx":779
+ /* "pysam/csamtools.pyx":780
* self.index = bam_index_load(filename)
* if self.index == NULL:
* raise IOError("error while opening index `%s` " % filename ) # <<<<<<<<<<<<<<
*
* if not self.isstream:
*/
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_38), __pyx_v_filename); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L43;
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L40;
}
- __pyx_L43:;
+ __pyx_L40:;
}
- __pyx_L40:;
+ __pyx_L37:;
- /* "csamtools.pyx":781
+ /* "pysam/csamtools.pyx":782
* raise IOError("error while opening index `%s` " % filename )
*
* if not self.isstream: # <<<<<<<<<<<<<<
* self.start_offset = bam_tell( self.samfile.x.bam )
*
*/
- __pyx_t_10 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream);
- if (__pyx_t_10) {
+ __pyx_t_1 = (!__pyx_v_self->isstream);
+ if (__pyx_t_1) {
- /* "csamtools.pyx":782
+ /* "pysam/csamtools.pyx":783
*
* if not self.isstream:
* self.start_offset = bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
*
* def gettid( self, reference ):
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset = bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam);
- goto __pyx_L44;
+ __pyx_v_self->start_offset = bam_tell(__pyx_v_self->samfile->x.bam);
+ goto __pyx_L41;
}
- __pyx_L44:;
- goto __pyx_L39;
+ __pyx_L41:;
+ goto __pyx_L36;
}
- __pyx_L39:;
+ __pyx_L36:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -7912,7 +8580,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_msg);
@@ -7931,7 +8599,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
return __pyx_r;
}
-/* "csamtools.pyx":784
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_8gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_9gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("gettid (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_8gettid(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_reference));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":785
* self.start_offset = bam_tell( self.samfile.x.bam )
*
* def gettid( self, reference ): # <<<<<<<<<<<<<<
@@ -7939,9 +8619,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_3_open(PyObject *__pyx_v_self, PyO
* convert :term:`reference` name into numerical :term:`tid`
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_4gettid[] = "Samfile.gettid(self, reference)\n\n convert :term:`reference` name into numerical :term:`tid`\n\n returns -1 if reference is not known.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, PyObject *__pyx_v_reference) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8gettid(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -7953,49 +8631,49 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, Py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("gettid");
- __Pyx_TraceCall("gettid", __pyx_f[0], 784);
+ __Pyx_RefNannySetupContext("gettid", 0);
+ __Pyx_TraceCall("gettid", __pyx_f[0], 785);
__Pyx_INCREF(__pyx_v_reference);
- /* "csamtools.pyx":790
+ /* "pysam/csamtools.pyx":791
* returns -1 if reference is not known.
* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_39), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_39), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":791
+ /* "pysam/csamtools.pyx":792
* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* reference = _force_bytes(reference) # <<<<<<<<<<<<<<
* return pysam_reference2tid( self.samfile.header, reference )
*
*/
- __pyx_t_2 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_reference)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_reference)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_reference);
__pyx_v_reference = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":792
+ /* "pysam/csamtools.pyx":793
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference ) # <<<<<<<<<<<<<<
@@ -8003,8 +8681,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, Py
* def getrname( self, tid ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyBytes_AsString(__pyx_v_reference); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(pysam_reference2tid(__pyx_v_self->samfile->header, __pyx_t_5)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -8015,7 +8693,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, Py
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.gettid", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.gettid", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_reference);
@@ -8025,7 +8703,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":794
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_10getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("getrname (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_10getrname(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":795
* return pysam_reference2tid( self.samfile.header, reference )
*
* def getrname( self, tid ): # <<<<<<<<<<<<<<
@@ -8033,9 +8723,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4gettid(PyObject *__pyx_v_self, Py
* convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_5getrname[] = "Samfile.getrname(self, tid)\n\n convert numerical :term:`tid` into :term:`reference` name.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_tid) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -8047,92 +8735,90 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getrname");
- __Pyx_TraceCall("getrname", __pyx_f[0], 794);
+ __Pyx_RefNannySetupContext("getrname", 0);
+ __Pyx_TraceCall("getrname", __pyx_f[0], 795);
- /* "csamtools.pyx":797
+ /* "pysam/csamtools.pyx":798
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_40), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_40), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":798
+ /* "pysam/csamtools.pyx":799
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
* return _charptr_to_str(self.samfile.header.target_name[tid])
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_int_0, __pyx_v_tid, Py_LE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_int_0, __pyx_v_tid, Py_LE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_PyObject_IsTrue(__pyx_t_2)) {
__Pyx_DECREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_tid, __pyx_t_1, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "csamtools.pyx":799
+ /* "pysam/csamtools.pyx":800
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
* return _charptr_to_str(self.samfile.header.target_name[tid])
*
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_tid);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_tid);
__Pyx_GIVEREF(__pyx_v_tid);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":800
+ /* "pysam/csamtools.pyx":801
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
* return _charptr_to_str(self.samfile.header.target_name[tid]) # <<<<<<<<<<<<<<
@@ -8140,8 +8826,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self,
* cdef char * _getrname( self, int tid ): # TODO unused
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_tid); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyIndex_AsSsize_t(__pyx_v_tid); if (unlikely((__pyx_t_5 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_t_5])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -8152,7 +8838,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self,
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -8161,7 +8847,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "csamtools.pyx":802
+/* "pysam/csamtools.pyx":803
* return _charptr_to_str(self.samfile.header.target_name[tid])
*
* cdef char * _getrname( self, int tid ): # TODO unused # <<<<<<<<<<<<<<
@@ -8169,7 +8855,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_5getrname(PyObject *__pyx_v_self,
* convert numerical :term:`tid` into :term:`reference` name.'''
*/
-static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, int __pyx_v_tid) {
+static char *__pyx_f_5pysam_9csamtools_7Samfile__getrname(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, int __pyx_v_tid) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -8181,35 +8867,35 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_getrname");
- __Pyx_TraceCall("_getrname", __pyx_f[0], 802);
+ __Pyx_RefNannySetupContext("_getrname", 0);
+ __Pyx_TraceCall("_getrname", __pyx_f[0], 803);
- /* "csamtools.pyx":805
+ /* "pysam/csamtools.pyx":806
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_42), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_42), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L3;
}
__pyx_L3:;
- /* "csamtools.pyx":806
+ /* "pysam/csamtools.pyx":807
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
@@ -8223,44 +8909,44 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "csamtools.pyx":807
+ /* "pysam/csamtools.pyx":808
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) ) # <<<<<<<<<<<<<<
* return self.samfile.header.target_name[tid]
*
*/
- __pyx_t_2 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_2 = 0;
__pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L4;
}
__pyx_L4:;
- /* "csamtools.pyx":808
+ /* "pysam/csamtools.pyx":809
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
* return self.samfile.header.target_name[tid] # <<<<<<<<<<<<<<
@@ -8276,7 +8962,7 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_WriteUnraisable("csamtools.Samfile._getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.csamtools.Samfile._getrname", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -8284,51 +8970,22 @@ static char *__pyx_f_9csamtools_7Samfile__getrname(struct __pyx_obj_9csamtools_S
return __pyx_r;
}
-/* "csamtools.pyx":810
- * return self.samfile.header.target_name[tid]
- *
- * def _parseRegion( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_6_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_12_parseRegion[] = "Samfile._parseRegion(self, reference=None, start=None, end=None, region=None)\n\n parse region information.\n\n raise ValueError for for invalid regions.\n\n returns a tuple of flag, tid, start and end. Flag indicates\n whether some coordinates were supplied.\n\n Note that regions are 1-based, while start,end are python coordinates.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- int __pyx_v_rtid;
- PY_LONG_LONG __pyx_v_rstart;
- PY_LONG_LONG __pyx_v_rend;
- PyObject *__pyx_v_parts = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- PyObject *__pyx_t_5 = NULL;
- PY_LONG_LONG __pyx_t_6;
- int __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- Py_ssize_t __pyx_t_12;
- int __pyx_t_13;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_parseRegion");
- __Pyx_TraceCall("_parseRegion", __pyx_f[0], 810);
+ __Pyx_RefNannySetupContext("_parseRegion (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[4] = {0,0,0,0};
- /* "csamtools.pyx":811
+ /* "pysam/csamtools.pyx":812
*
* def _parseRegion( self,
* reference = None, # <<<<<<<<<<<<<<
@@ -8337,7 +8994,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
values[0] = ((PyObject *)Py_None);
- /* "csamtools.pyx":812
+ /* "pysam/csamtools.pyx":813
* def _parseRegion( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
@@ -8346,7 +9003,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
values[1] = ((PyObject *)Py_None);
- /* "csamtools.pyx":813
+ /* "pysam/csamtools.pyx":814
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
@@ -8355,7 +9012,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
values[2] = ((PyObject *)Py_None);
- /* "csamtools.pyx":814
+ /* "pysam/csamtools.pyx":815
* start = None,
* end = None,
* region = None ): # <<<<<<<<<<<<<<
@@ -8365,7 +9022,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
values[3] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -8374,7 +9032,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -8397,7 +9055,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parseRegion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -8416,16 +9074,55 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_parseRegion", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parseRegion", 0, 0, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":811
+ * return self.samfile.header.target_name[tid]
+ *
+ * def _parseRegion( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_12_parseRegion(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region) {
+ int __pyx_v_rtid;
+ PY_LONG_LONG __pyx_v_rstart;
+ PY_LONG_LONG __pyx_v_rend;
+ PyObject *__pyx_v_parts = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ PyObject *__pyx_t_5 = NULL;
+ PY_LONG_LONG __pyx_t_6;
+ int __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_parseRegion", 0);
+ __Pyx_TraceCall("_parseRegion", __pyx_f[0], 811);
__Pyx_INCREF(__pyx_v_reference);
__Pyx_INCREF(__pyx_v_region);
- /* "csamtools.pyx":833
+ /* "pysam/csamtools.pyx":834
* cdef long long rend
*
* rtid = -1 # <<<<<<<<<<<<<<
@@ -8434,7 +9131,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_v_rtid = -1;
- /* "csamtools.pyx":834
+ /* "pysam/csamtools.pyx":835
*
* rtid = -1
* rstart = 0 # <<<<<<<<<<<<<<
@@ -8443,29 +9140,28 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_v_rstart = 0;
- /* "csamtools.pyx":835
+ /* "pysam/csamtools.pyx":836
* rtid = -1
* rstart = 0
* rend = max_pos # <<<<<<<<<<<<<<
* if start != None:
* try:
*/
- __pyx_v_rend = __pyx_v_9csamtools_max_pos;
+ __pyx_v_rend = __pyx_v_5pysam_9csamtools_max_pos;
- /* "csamtools.pyx":836
+ /* "pysam/csamtools.pyx":837
* rstart = 0
* rend = max_pos
* if start != None: # <<<<<<<<<<<<<<
* try:
* rstart = start
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- /* "csamtools.pyx":837
+ /* "pysam/csamtools.pyx":838
* rend = max_pos
* if start != None:
* try: # <<<<<<<<<<<<<<
@@ -8479,24 +9175,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
__Pyx_XGOTREF(__pyx_t_5);
/*try:*/ {
- /* "csamtools.pyx":838
+ /* "pysam/csamtools.pyx":839
* if start != None:
* try:
* rstart = start # <<<<<<<<<<<<<<
* except OverflowError:
* raise ValueError( 'start out of range (%i)' % start )
*/
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L7_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_start); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__pyx_v_rstart = __pyx_t_6;
}
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- goto __pyx_L14_try_end;
- __pyx_L7_error:;
+ goto __pyx_L11_try_end;
+ __pyx_L4_error:;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":839
+ /* "pysam/csamtools.pyx":840
* try:
* rstart = start
* except OverflowError: # <<<<<<<<<<<<<<
@@ -8505,68 +9201,67 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
if (__pyx_t_7) {
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_9);
- /* "csamtools.pyx":840
+ /* "pysam/csamtools.pyx":841
* rstart = start
* except OverflowError:
* raise ValueError( 'start out of range (%i)' % start ) # <<<<<<<<<<<<<<
*
* if end != None:
*/
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_v_start); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_11));
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_Raise(__pyx_t_10, 0, 0, 0);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L9_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L8_exception_handled;
+ goto __pyx_L5_exception_handled;
}
- __pyx_L9_except_error:;
+ __pyx_L6_except_error:;
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
goto __pyx_L1_error;
- __pyx_L8_exception_handled:;
+ __pyx_L5_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_ExceptionReset(__pyx_t_3, __pyx_t_4, __pyx_t_5);
- __pyx_L14_try_end:;
+ __pyx_L11_try_end:;
}
- goto __pyx_L6;
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":842
+ /* "pysam/csamtools.pyx":843
* raise ValueError( 'start out of range (%i)' % start )
*
* if end != None: # <<<<<<<<<<<<<<
* try:
* rend = end
*/
- __pyx_t_9 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_2) {
- /* "csamtools.pyx":843
+ /* "pysam/csamtools.pyx":844
*
* if end != None:
* try: # <<<<<<<<<<<<<<
@@ -8580,28 +9275,28 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
__Pyx_XGOTREF(__pyx_t_3);
/*try:*/ {
- /* "csamtools.pyx":844
+ /* "pysam/csamtools.pyx":845
* if end != None:
* try:
* rend = end # <<<<<<<<<<<<<<
* except OverflowError:
* raise ValueError( 'end out of range (%i)' % end )
*/
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 844; __pyx_clineno = __LINE__; goto __pyx_L18_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_v_end); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L15_error;}
__pyx_v_rend = __pyx_t_6;
}
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L25_try_end;
- __pyx_L18_error:;
+ goto __pyx_L22_try_end;
+ __pyx_L15_error:;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "csamtools.pyx":845
+ /* "pysam/csamtools.pyx":846
* try:
* rend = end
* except OverflowError: # <<<<<<<<<<<<<<
@@ -8610,218 +9305,218 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_OverflowError);
if (__pyx_t_7) {
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_8, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":846
+ /* "pysam/csamtools.pyx":847
* rend = end
* except OverflowError:
* raise ValueError( 'end out of range (%i)' % end ) # <<<<<<<<<<<<<<
*
* if region:
*/
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_v_end); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_11));
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_Raise(__pyx_t_10, 0, 0, 0);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L20_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L17_except_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L19_exception_handled;
+ goto __pyx_L16_exception_handled;
}
- __pyx_L20_except_error:;
+ __pyx_L17_except_error:;
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
goto __pyx_L1_error;
- __pyx_L19_exception_handled:;
+ __pyx_L16_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_5);
__Pyx_XGIVEREF(__pyx_t_4);
__Pyx_XGIVEREF(__pyx_t_3);
__Pyx_ExceptionReset(__pyx_t_5, __pyx_t_4, __pyx_t_3);
- __pyx_L25_try_end:;
+ __pyx_L22_try_end:;
}
- goto __pyx_L17;
+ goto __pyx_L14;
}
- __pyx_L17:;
+ __pyx_L14:;
- /* "csamtools.pyx":848
+ /* "pysam/csamtools.pyx":849
* raise ValueError( 'end out of range (%i)' % end )
*
* if region: # <<<<<<<<<<<<<<
* region = _force_str(region)
* parts = re.split( "[:-]", region )
*/
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_2) {
- /* "csamtools.pyx":849
+ /* "pysam/csamtools.pyx":850
*
* if region:
* region = _force_str(region) # <<<<<<<<<<<<<<
* parts = re.split( "[:-]", region )
* reference = parts[0]
*/
- __pyx_t_1 = __pyx_f_9csamtools__force_str(__pyx_v_region); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 849; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools__force_str(__pyx_v_region); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":850
+ /* "pysam/csamtools.pyx":851
* if region:
* region = _force_str(region)
* parts = re.split( "[:-]", region ) # <<<<<<<<<<<<<<
* reference = parts[0]
* if len(parts) >= 2: rstart = int(parts[1]) - 1
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_43));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_parts = __pyx_t_9;
__pyx_t_9 = 0;
- /* "csamtools.pyx":851
+ /* "pysam/csamtools.pyx":852
* region = _force_str(region)
* parts = re.split( "[:-]", region )
* reference = parts[0] # <<<<<<<<<<<<<<
* if len(parts) >= 2: rstart = int(parts[1]) - 1
* if len(parts) >= 3: rend = int(parts[2])
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_v_reference);
__pyx_v_reference = __pyx_t_9;
__pyx_t_9 = 0;
- /* "csamtools.pyx":852
+ /* "pysam/csamtools.pyx":853
* parts = re.split( "[:-]", region )
* reference = parts[0]
* if len(parts) >= 2: rstart = int(parts[1]) - 1 # <<<<<<<<<<<<<<
* if len(parts) >= 3: rend = int(parts[2])
*
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = (__pyx_t_12 >= 2);
if (__pyx_t_2) {
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_parts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rstart = __pyx_t_6;
- goto __pyx_L29;
+ goto __pyx_L26;
}
- __pyx_L29:;
+ __pyx_L26:;
- /* "csamtools.pyx":853
+ /* "pysam/csamtools.pyx":854
* reference = parts[0]
* if len(parts) >= 2: rstart = int(parts[1]) - 1
* if len(parts) >= 3: rend = int(parts[2]) # <<<<<<<<<<<<<<
*
* if not reference: return 0, 0, 0, 0
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Length(__pyx_v_parts); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = (__pyx_t_12 >= 3);
if (__pyx_t_2) {
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_parts, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyInt_AsLongLong(__pyx_t_1); if (unlikely((__pyx_t_6 == (PY_LONG_LONG)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_rend = __pyx_t_6;
- goto __pyx_L30;
+ goto __pyx_L27;
}
- __pyx_L30:;
- goto __pyx_L28;
+ __pyx_L27:;
+ goto __pyx_L25;
}
- __pyx_L28:;
+ __pyx_L25:;
- /* "csamtools.pyx":855
+ /* "pysam/csamtools.pyx":856
* if len(parts) >= 3: rend = int(parts[2])
*
* if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
*
* rtid = self.gettid( reference )
*/
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_13 = (!__pyx_t_2);
if (__pyx_t_13) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(((PyObject *)__pyx_k_tuple_44));
__pyx_r = ((PyObject *)__pyx_k_tuple_44);
goto __pyx_L0;
- goto __pyx_L31;
+ goto __pyx_L28;
}
- __pyx_L31:;
+ __pyx_L28:;
- /* "csamtools.pyx":857
+ /* "pysam/csamtools.pyx":858
* if not reference: return 0, 0, 0, 0
*
* rtid = self.gettid( reference ) # <<<<<<<<<<<<<<
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__gettid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
- __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_7 = __Pyx_PyInt_AsInt(__pyx_t_8); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyInt_AsInt(__pyx_t_8); if (unlikely((__pyx_t_7 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_rtid = __pyx_t_7;
- /* "csamtools.pyx":858
+ /* "pysam/csamtools.pyx":859
*
* rtid = self.gettid( reference )
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference ) # <<<<<<<<<<<<<<
@@ -8830,24 +9525,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_t_13 = (__pyx_v_rtid < 0);
if (__pyx_t_13) {
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_45), __pyx_v_reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L32;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L29;
}
- __pyx_L32:;
+ __pyx_L29:;
- /* "csamtools.pyx":859
+ /* "pysam/csamtools.pyx":860
* rtid = self.gettid( reference )
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) ) # <<<<<<<<<<<<<<
@@ -8856,37 +9551,37 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_t_13 = (__pyx_v_rstart > __pyx_v_rend);
if (__pyx_t_13) {
- __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_8 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_46), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_46), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L33;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L30;
}
- __pyx_L33:;
+ __pyx_L30:;
- /* "csamtools.pyx":860
+ /* "pysam/csamtools.pyx":861
* if rtid < 0: raise ValueError( "invalid reference `%s`" % reference )
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
* if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart ) # <<<<<<<<<<<<<<
@@ -8895,31 +9590,31 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_t_13 = (0 <= __pyx_v_rstart);
if (__pyx_t_13) {
- __pyx_t_13 = (__pyx_v_rstart < __pyx_v_9csamtools_max_pos);
+ __pyx_t_13 = (__pyx_v_rstart < __pyx_v_5pysam_9csamtools_max_pos);
}
__pyx_t_2 = (!__pyx_t_13);
if (__pyx_t_2) {
- __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_17), __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L34;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L31;
}
- __pyx_L34:;
+ __pyx_L31:;
- /* "csamtools.pyx":861
+ /* "pysam/csamtools.pyx":862
* if rstart > rend: raise ValueError( 'invalid coordinates: start (%i) > end (%i)' % (rstart, rend) )
* if not 0 <= rstart < max_pos: raise ValueError( 'start out of range (%i)' % rstart )
* if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend ) # <<<<<<<<<<<<<<
@@ -8928,31 +9623,31 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
*/
__pyx_t_2 = (0 <= __pyx_v_rend);
if (__pyx_t_2) {
- __pyx_t_2 = (__pyx_v_rend <= __pyx_v_9csamtools_max_pos);
+ __pyx_t_2 = (__pyx_v_rend <= __pyx_v_5pysam_9csamtools_max_pos);
}
__pyx_t_13 = (!__pyx_t_2);
if (__pyx_t_13) {
- __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_18), __pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L35;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L32;
}
- __pyx_L35:;
+ __pyx_L32:;
- /* "csamtools.pyx":863
+ /* "pysam/csamtools.pyx":864
* if not 0 <= rend <= max_pos: raise ValueError( 'end out of range (%i)' % rend )
*
* return 1, rtid, rstart, rend # <<<<<<<<<<<<<<
@@ -8960,14 +9655,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
* def reset( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_9 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyLong_FromLongLong(__pyx_v_rstart); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyLong_FromLongLong(__pyx_v_rend); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+ __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_int_1);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_int_1);
__Pyx_GIVEREF(__pyx_int_1);
@@ -8992,7 +9687,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._parseRegion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_parts);
@@ -9004,7 +9699,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":865
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_14reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_15reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("reset (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_14reset(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":866
* return 1, rtid, rstart, rend
*
* def reset( self ): # <<<<<<<<<<<<<<
@@ -9012,9 +9719,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6_parseRegion(PyObject *__pyx_v_se
* return self.seek( self.start_offset, 0 )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_7reset[] = "Samfile.reset(self)\nreset file position to beginning of read section.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_14reset(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -9024,10 +9729,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYT
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset");
- __Pyx_TraceCall("reset", __pyx_f[0], 865);
+ __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_TraceCall("reset", __pyx_f[0], 866);
- /* "csamtools.pyx":867
+ /* "pysam/csamtools.pyx":868
* def reset( self ):
* '''reset file position to beginning of read section.'''
* return self.seek( self.start_offset, 0 ) # <<<<<<<<<<<<<<
@@ -9035,19 +9740,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYT
* def seek( self, uint64_t offset, int where = 0):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seek); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(__pyx_v_self->start_offset); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_int_0);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -9061,7 +9766,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYT
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Samfile.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -9070,47 +9775,31 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7reset(PyObject *__pyx_v_self, CYT
return __pyx_r;
}
-/* "csamtools.pyx":869
- * return self.seek( self.start_offset, 0 )
- *
- * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
- * '''
- * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_8seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_16seek[] = "Samfile.seek(self, uint64_t offset, int where=0)\n\n move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_17seek(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
uint64_t __pyx_v_offset;
int __pyx_v_where;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("seek");
- __Pyx_TraceCall("seek", __pyx_f[0], 869);
+ __Pyx_RefNannySetupContext("seek (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__offset,&__pyx_n_s__where,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__offset)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -9119,7 +9808,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyOb
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "seek") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -9129,107 +9818,133 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyOb
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_offset = __Pyx_PyInt_from_py_uint64_t(values[0]); if (unlikely((__pyx_v_offset == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_offset = __Pyx_PyInt_from_py_uint64_t(values[0]); if (unlikely((__pyx_v_offset == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
if (values[1]) {
- __pyx_v_where = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_where = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_where == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_where = ((int)0);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("seek", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_16seek(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_offset, __pyx_v_where);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":870
+ * return self.seek( self.start_offset, 0 )
+ *
+ * def seek( self, uint64_t offset, int where = 0): # <<<<<<<<<<<<<<
+ * '''
+ * move file pointer to position *offset*, see :meth:`pysam.Samfile.tell`.
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_16seek(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, uint64_t __pyx_v_offset, int __pyx_v_where) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("seek", 0);
+ __Pyx_TraceCall("seek", __pyx_f[0], 870);
- /* "csamtools.pyx":874
+ /* "pysam/csamtools.pyx":875
* '''
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":875
+ /* "pysam/csamtools.pyx":876
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":876
+ /* "pysam/csamtools.pyx":877
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam: # <<<<<<<<<<<<<<
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
*/
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
+ __pyx_t_4 = (!__pyx_v_self->isbam);
if (__pyx_t_4) {
- /* "csamtools.pyx":877
+ /* "pysam/csamtools.pyx":878
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
* if self.isstream:
* raise OSError("seek no available in streams")
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_49), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_49), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "csamtools.pyx":878
+ /* "pysam/csamtools.pyx":879
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
* if self.isstream: # <<<<<<<<<<<<<<
* raise OSError("seek no available in streams")
*
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) {
+ if (__pyx_v_self->isstream) {
- /* "csamtools.pyx":879
+ /* "pysam/csamtools.pyx":880
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
* raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
*
* return bam_seek( self.samfile.x.bam, offset, where )
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_OSError, ((PyObject *)__pyx_k_tuple_51), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_OSError, ((PyObject *)__pyx_k_tuple_51), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- __pyx_L8:;
+ __pyx_L5:;
- /* "csamtools.pyx":881
+ /* "pysam/csamtools.pyx":882
* raise OSError("seek no available in streams")
*
* return bam_seek( self.samfile.x.bam, offset, where ) # <<<<<<<<<<<<<<
@@ -9237,7 +9952,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyOb
* def tell( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_seek(__pyx_v_self->samfile->x.bam, __pyx_v_offset, __pyx_v_where)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -9248,7 +9963,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyOb
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.seek", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -9257,7 +9972,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyOb
return __pyx_r;
}
-/* "csamtools.pyx":883
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_18tell[] = "Samfile.tell(self)\n\n return current file position\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_19tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("tell (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_18tell(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":884
* return bam_seek( self.samfile.x.bam, offset, where )
*
* def tell( self ): # <<<<<<<<<<<<<<
@@ -9265,9 +9992,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8seek(PyObject *__pyx_v_self, PyOb
* return current file position
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_9tell[] = "Samfile.tell(self)\n\n return current file position\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_18tell(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -9278,69 +10003,69 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTH
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("tell");
- __Pyx_TraceCall("tell", __pyx_f[0], 883);
+ __Pyx_RefNannySetupContext("tell", 0);
+ __Pyx_TraceCall("tell", __pyx_f[0], 884);
- /* "csamtools.pyx":887
+ /* "pysam/csamtools.pyx":888
* return current file position
* '''
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":888
+ /* "pysam/csamtools.pyx":889
* '''
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_52), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_52), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":889
+ /* "pysam/csamtools.pyx":890
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam: # <<<<<<<<<<<<<<
* raise NotImplementedError("seek only available in bam files")
*
*/
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
+ __pyx_t_4 = (!__pyx_v_self->isbam);
if (__pyx_t_4) {
- /* "csamtools.pyx":890
+ /* "pysam/csamtools.pyx":891
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
*
* return bam_tell( self.samfile.x.bam )
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_53), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_53), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":892
+ /* "pysam/csamtools.pyx":893
* raise NotImplementedError("seek only available in bam files")
*
* return bam_tell( self.samfile.x.bam ) # <<<<<<<<<<<<<<
@@ -9348,7 +10073,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTH
* def fetch( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int64_t(bam_tell(__pyx_v_self->samfile->x.bam)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -9359,7 +10084,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTH
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.tell", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -9368,56 +10093,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_9tell(PyObject *__pyx_v_self, CYTH
return __pyx_r;
}
-/* "csamtools.pyx":894
- * return bam_tell( self.samfile.x.bam )
- *
- * def fetch( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_10fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\n [...]
-static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_20fetch[] = "Samfile.fetch(self, reference=None, start=None, end=None, region=None, callback=None, until_eof=False)\n\n fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can\n be supplied.\n\n Without *reference* or *region* all mapped reads will be fetched. The reads will be returned\ [...]
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_21fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_until_eof = 0;
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- int __pyx_v_reopen;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_t_15;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fetch");
- __Pyx_TraceCall("fetch", __pyx_f[0], 894);
+ __Pyx_RefNannySetupContext("fetch (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,&__pyx_n_s__until_eof,0};
PyObject* values[6] = {0,0,0,0,0,0};
- /* "csamtools.pyx":895
+ /* "pysam/csamtools.pyx":896
*
* def fetch( self,
* reference = None, # <<<<<<<<<<<<<<
@@ -9426,7 +10119,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
values[0] = ((PyObject *)Py_None);
- /* "csamtools.pyx":896
+ /* "pysam/csamtools.pyx":897
* def fetch( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
@@ -9435,7 +10128,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
values[1] = ((PyObject *)Py_None);
- /* "csamtools.pyx":897
+ /* "pysam/csamtools.pyx":898
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
@@ -9444,7 +10137,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
values[2] = ((PyObject *)Py_None);
- /* "csamtools.pyx":898
+ /* "pysam/csamtools.pyx":899
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
@@ -9453,7 +10146,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
values[3] = ((PyObject *)Py_None);
- /* "csamtools.pyx":899
+ /* "pysam/csamtools.pyx":900
* end = None,
* region = None,
* callback = None, # <<<<<<<<<<<<<<
@@ -9464,7 +10157,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
values[5] = __pyx_k_54;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 6: values[5] = PyTuple_GET_ITEM(__pyx_args, 5);
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
@@ -9475,7 +10169,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -9508,7 +10202,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -9531,57 +10225,99 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("fetch", 0, 0, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_20fetch(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_until_eof);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":895
+ * return bam_tell( self.samfile.x.bam )
+ *
+ * def fetch( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_until_eof) {
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ int __pyx_v_reopen;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_t_15;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("fetch", 0);
+ __Pyx_TraceCall("fetch", __pyx_f[0], 895);
- /* "csamtools.pyx":924
+ /* "pysam/csamtools.pyx":925
* cdef int rtid, rstart, rend, has_coord
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":925
+ /* "pysam/csamtools.pyx":926
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_55), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_55), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":927
+ /* "pysam/csamtools.pyx":928
* raise ValueError( "I/O operation on closed file" )
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
* if self.isstream: reopen = False
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -9594,28 +10330,29 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 4)) {
+ if (size > 4) __Pyx_RaiseTooManyValuesError(4);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
- if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
- if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
@@ -9625,58 +10362,67 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ Py_ssize_t i;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ for (i=0; i < 4; i++) {
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(item);
+ *(temps[i]) = item;
+ }
+ #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_7);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ for (index=0; index < 4; index++) {
+ PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(item);
+ *(temps[index]) = item;
+ }
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L8_unpacking_done;
- __pyx_L7_unpacking_failed:;
+ goto __pyx_L5_unpacking_done;
+ __pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L8_unpacking_done:;
+ __pyx_t_9 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5_unpacking_done:;
}
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_v_has_coord = __pyx_t_10;
__pyx_v_rtid = __pyx_t_11;
__pyx_v_rstart = __pyx_t_12;
__pyx_v_rend = __pyx_t_13;
- /* "csamtools.pyx":929
+ /* "pysam/csamtools.pyx":930
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*
* if self.isstream: reopen = False # <<<<<<<<<<<<<<
* else: reopen = True
*
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isstream) {
+ if (__pyx_v_self->isstream) {
__pyx_v_reopen = 0;
- goto __pyx_L9;
+ goto __pyx_L6;
}
/*else*/ {
- /* "csamtools.pyx":930
+ /* "pysam/csamtools.pyx":931
*
* if self.isstream: reopen = False
* else: reopen = True # <<<<<<<<<<<<<<
@@ -9685,37 +10431,37 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
__pyx_v_reopen = 1;
}
- __pyx_L9:;
+ __pyx_L6:;
- /* "csamtools.pyx":932
+ /* "pysam/csamtools.pyx":933
* else: reopen = True
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ if (__pyx_v_self->isbam) {
- /* "csamtools.pyx":933
+ /* "pysam/csamtools.pyx":934
*
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
* raise ValueError( "fetch called on bamfile without index" )
*
*/
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_14 = (!__pyx_t_4);
if (__pyx_t_14) {
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
+ __pyx_t_4 = (!__pyx_v_self->isremote);
__pyx_t_15 = __pyx_t_4;
} else {
__pyx_t_15 = __pyx_t_14;
@@ -9726,33 +10472,33 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
}
if (__pyx_t_14) {
- /* "csamtools.pyx":934
+ /* "pysam/csamtools.pyx":935
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_57), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_57), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 935; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 935; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L8;
}
- __pyx_L11:;
+ __pyx_L8:;
- /* "csamtools.pyx":936
+ /* "pysam/csamtools.pyx":937
* raise ValueError( "fetch called on bamfile without index" )
*
* if callback: # <<<<<<<<<<<<<<
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
*/
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- /* "csamtools.pyx":937
+ /* "pysam/csamtools.pyx":938
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
@@ -9761,41 +10507,41 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
__pyx_t_14 = (!__pyx_v_has_coord);
if (__pyx_t_14) {
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_59), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_59), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L13;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L10;
}
- __pyx_L13:;
+ __pyx_L10:;
- /* "csamtools.pyx":938
+ /* "pysam/csamtools.pyx":939
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* return bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_3 = (!__pyx_t_14);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_61), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_61), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L11;
}
- __pyx_L14:;
+ __pyx_L11:;
- /* "csamtools.pyx":939
+ /* "pysam/csamtools.pyx":940
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
* return bam_fetch(self.samfile.x.bam, # <<<<<<<<<<<<<<
@@ -9804,50 +10550,50 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
__Pyx_XDECREF(__pyx_r);
- /* "csamtools.pyx":945
+ /* "pysam/csamtools.pyx":946
* rend,
* <void*>callback,
* fetch_callback ) # <<<<<<<<<<<<<<
* else:
* if has_coord:
*/
- __pyx_t_5 = PyInt_FromLong(bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_5pysam_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L12;
+ goto __pyx_L9;
}
/*else*/ {
- /* "csamtools.pyx":947
+ /* "pysam/csamtools.pyx":948
* fetch_callback )
* else:
* if has_coord: # <<<<<<<<<<<<<<
- * return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
- * else:
+ * return IteratorRowRegion( self, rtid, rstart, rend,
+ * reopen=reopen )
*/
if (__pyx_v_has_coord) {
- /* "csamtools.pyx":948
+ /* "pysam/csamtools.pyx":949
* else:
* if has_coord:
- * return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen ) # <<<<<<<<<<<<<<
+ * return IteratorRowRegion( self, rtid, rstart, rend, # <<<<<<<<<<<<<<
+ * reopen=reopen )
* else:
- * if until_eof:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_7);
@@ -9857,34 +10603,42 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
__pyx_t_5 = 0;
__pyx_t_7 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":950
+ * if has_coord:
+ * return IteratorRowRegion( self, rtid, rstart, rend,
+ * reopen=reopen ) # <<<<<<<<<<<<<<
+ * else:
+ * if until_eof:
+ */
+ __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_r = __pyx_t_7;
__pyx_t_7 = 0;
goto __pyx_L0;
- goto __pyx_L15;
+ goto __pyx_L12;
}
/*else*/ {
- /* "csamtools.pyx":950
- * return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
+ /* "pysam/csamtools.pyx":952
+ * reopen=reopen )
* else:
* if until_eof: # <<<<<<<<<<<<<<
* return IteratorRowAll( self, reopen=reopen )
* else:
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "csamtools.pyx":951
+ /* "pysam/csamtools.pyx":953
* else:
* if until_eof:
* return IteratorRowAll( self, reopen=reopen ) # <<<<<<<<<<<<<<
@@ -9892,29 +10646,29 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
* # AH: check - reason why no reopen for AllRefs?
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_6 = PyDict_New(); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_6, ((PyObject *)__pyx_n_s__reopen), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L16;
+ goto __pyx_L13;
}
/*else*/ {
- /* "csamtools.pyx":954
+ /* "pysam/csamtools.pyx":956
* else:
* # AH: check - reason why no reopen for AllRefs?
* return IteratorRowAllRefs(self ) # , reopen=reopen ) # <<<<<<<<<<<<<<
@@ -9922,28 +10676,28 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
* if has_coord:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_r = __pyx_t_6;
__pyx_t_6 = 0;
goto __pyx_L0;
}
- __pyx_L16:;
+ __pyx_L13:;
}
- __pyx_L15:;
+ __pyx_L12:;
}
- __pyx_L12:;
- goto __pyx_L10;
+ __pyx_L9:;
+ goto __pyx_L7;
}
/*else*/ {
- /* "csamtools.pyx":956
+ /* "pysam/csamtools.pyx":958
* return IteratorRowAllRefs(self ) # , reopen=reopen )
* else:
* if has_coord: # <<<<<<<<<<<<<<
@@ -9952,105 +10706,105 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
*/
if (__pyx_v_has_coord) {
- /* "csamtools.pyx":957
+ /* "pysam/csamtools.pyx":959
* else:
* if has_coord:
* raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_63), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_63), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L17;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L14;
}
- __pyx_L17:;
+ __pyx_L14:;
- /* "csamtools.pyx":959
+ /* "pysam/csamtools.pyx":961
* raise ValueError ("fetching by region is not available for sam files" )
*
* if callback: # <<<<<<<<<<<<<<
* raise NotImplementedError( "callback not implemented yet" )
*
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "csamtools.pyx":960
+ /* "pysam/csamtools.pyx":962
*
* if callback:
* raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
*
* if self.samfile.header == NULL:
*/
- __pyx_t_6 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_65), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_65), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L18;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L15;
}
- __pyx_L18:;
+ __pyx_L15:;
- /* "csamtools.pyx":962
+ /* "pysam/csamtools.pyx":964
* raise NotImplementedError( "callback not implemented yet" )
*
* if self.samfile.header == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "fetch called for samfile without header")
*
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header == NULL);
+ __pyx_t_3 = (__pyx_v_self->samfile->header == NULL);
if (__pyx_t_3) {
- /* "csamtools.pyx":963
+ /* "pysam/csamtools.pyx":965
*
* if self.samfile.header == NULL:
* raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
*
* # check if targets are defined
*/
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_67), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_67), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 965; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_Raise(__pyx_t_6, 0, 0, 0);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L19;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 965; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L16;
}
- __pyx_L19:;
+ __pyx_L16:;
- /* "csamtools.pyx":967
+ /* "pysam/csamtools.pyx":969
* # check if targets are defined
* # give warning, sam_read1 segfaults
* if self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
* warnings.warn( "fetch called for samfile without header")
*
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
+ __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
if (__pyx_t_3) {
- /* "csamtools.pyx":968
+ /* "pysam/csamtools.pyx":970
* # give warning, sam_read1 segfaults
* if self.samfile.header.n_targets == 0:
* warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<<
*
* return IteratorRowAll( self, reopen=reopen )
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__warnings); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__warnings); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__warn); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__warn); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_68), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_68), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L20;
+ goto __pyx_L17;
}
- __pyx_L20:;
+ __pyx_L17:;
- /* "csamtools.pyx":970
+ /* "pysam/csamtools.pyx":972
* warnings.warn( "fetch called for samfile without header")
*
* return IteratorRowAll( self, reopen=reopen ) # <<<<<<<<<<<<<<
@@ -10058,18 +10812,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
* def mate( self,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowAll)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -10077,7 +10831,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
__pyx_t_7 = 0;
goto __pyx_L0;
}
- __pyx_L10:;
+ __pyx_L7:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -10088,7 +10842,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -10097,7 +10851,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":972
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_22mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_23mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("mate (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_22mate(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_read));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":974
* return IteratorRowAll( self, reopen=reopen )
*
* def mate( self, # <<<<<<<<<<<<<<
@@ -10105,119 +10876,119 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10fetch(PyObject *__pyx_v_self, Py
* '''return the mate of :class:`AlignedRead` *read*.
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_11mate[] = "Samfile.mate(self, AlignedRead read)\nreturn the mate of :class:`AlignedRead` *read*.\n\n Throws a ValueError if read is unpaired or the mate\n is unmapped.\n\n .. note::\n Calling this method will change the file position.\n This might interfere with any iterators that have\n not re-opened the file.\n\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read) {
uint32_t __pyx_v_flag;
- __pyx_t_9csamtools_MateData __pyx_v_mate_data;
+ __pyx_t_5pysam_9csamtools_MateData __pyx_v_mate_data;
int __pyx_v_x;
- struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_dest = 0;
+ struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_dest = 0;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ uint32_t __pyx_t_1;
+ int __pyx_t_2;
PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ bam1_t *__pyx_t_5;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("mate");
- __Pyx_TraceCall("mate", __pyx_f[0], 972);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("mate", 0);
+ __Pyx_TraceCall("mate", __pyx_f[0], 974);
- /* "csamtools.pyx":985
+ /* "pysam/csamtools.pyx":987
*
* '''
* cdef uint32_t flag = read._delegate.core.flag # <<<<<<<<<<<<<<
*
* if flag & BAM_FPAIRED == 0:
*/
- __pyx_v_flag = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.flag;
+ __pyx_t_1 = __pyx_v_read->_delegate->core.flag;
+ __pyx_v_flag = __pyx_t_1;
- /* "csamtools.pyx":987
+ /* "pysam/csamtools.pyx":989
* cdef uint32_t flag = read._delegate.core.flag
*
* if flag & BAM_FPAIRED == 0: # <<<<<<<<<<<<<<
* raise ValueError( "read %s: is unpaired" % (read.qname))
* if flag & BAM_FMUNMAP != 0:
*/
- __pyx_t_1 = ((__pyx_v_flag & 1) == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = ((__pyx_v_flag & 1) == 0);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":988
+ /* "pysam/csamtools.pyx":990
*
* if flag & BAM_FPAIRED == 0:
* raise ValueError( "read %s: is unpaired" % (read.qname)) # <<<<<<<<<<<<<<
* if flag & BAM_FMUNMAP != 0:
* raise ValueError( "mate %s: is unmapped" % (read.qname))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_3));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_69), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_Raise(__pyx_t_4, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":989
+ /* "pysam/csamtools.pyx":991
* if flag & BAM_FPAIRED == 0:
* raise ValueError( "read %s: is unpaired" % (read.qname))
* if flag & BAM_FMUNMAP != 0: # <<<<<<<<<<<<<<
* raise ValueError( "mate %s: is unmapped" % (read.qname))
*
*/
- __pyx_t_1 = ((__pyx_v_flag & 8) != 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = ((__pyx_v_flag & 8) != 0);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":990
+ /* "pysam/csamtools.pyx":992
* raise ValueError( "read %s: is unpaired" % (read.qname))
* if flag & BAM_FMUNMAP != 0:
* raise ValueError( "mate %s: is unmapped" % (read.qname)) # <<<<<<<<<<<<<<
*
* cdef MateData mate_data
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_read, __pyx_n_s__qname); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_read), __pyx_n_s__qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_3 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_70), __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __Pyx_Raise(__pyx_t_2, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":994
+ /* "pysam/csamtools.pyx":996
* cdef MateData mate_data
*
* mate_data.name = <char *>bam1_qname(read._delegate) # <<<<<<<<<<<<<<
* mate_data.mate = NULL
* # xor flags to get the other mate
*/
- __pyx_v_mate_data.name = ((char *)bam1_qname(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate));
+ __pyx_v_mate_data.name = ((char *)bam1_qname(__pyx_v_read->_delegate));
- /* "csamtools.pyx":995
+ /* "pysam/csamtools.pyx":997
*
* mate_data.name = <char *>bam1_qname(read._delegate)
* mate_data.mate = NULL # <<<<<<<<<<<<<<
@@ -10226,7 +10997,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO
*/
__pyx_v_mate_data.mate = NULL;
- /* "csamtools.pyx":997
+ /* "pysam/csamtools.pyx":999
* mate_data.mate = NULL
* # xor flags to get the other mate
* cdef int x = BAM_FREAD1 + BAM_FREAD2 # <<<<<<<<<<<<<<
@@ -10235,7 +11006,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO
*/
__pyx_v_x = 192;
- /* "csamtools.pyx":998
+ /* "pysam/csamtools.pyx":1000
* # xor flags to get the other mate
* cdef int x = BAM_FREAD1 + BAM_FREAD2
* mate_data.flag = ( flag ^ x) & x # <<<<<<<<<<<<<<
@@ -10244,64 +11015,65 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO
*/
__pyx_v_mate_data.flag = ((__pyx_v_flag ^ __pyx_v_x) & __pyx_v_x);
- /* "csamtools.pyx":1006
+ /* "pysam/csamtools.pyx":1008
* read._delegate.core.mpos + 1,
* <void*>&mate_data,
* mate_callback ) # <<<<<<<<<<<<<<
*
* if mate_data.mate == NULL:
*/
- bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mtid, ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos, (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read)->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_9csamtools_mate_callback);
+ bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_5pysam_9csamtools_mate_callback);
- /* "csamtools.pyx":1008
+ /* "pysam/csamtools.pyx":1010
* mate_callback )
*
* if mate_data.mate == NULL: # <<<<<<<<<<<<<<
* raise ValueError( "mate not found" )
*
*/
- __pyx_t_1 = (__pyx_v_mate_data.mate == NULL);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_mate_data.mate == NULL);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":1009
+ /* "pysam/csamtools.pyx":1011
*
* if mate_data.mate == NULL:
* raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_72), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_Raise(__pyx_t_2, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_72), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_Raise(__pyx_t_3, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
- /* "csamtools.pyx":1011
+ /* "pysam/csamtools.pyx":1013
* raise ValueError( "mate not found" )
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead) # <<<<<<<<<<<<<<
* dest._delegate = mate_data.mate
* return dest
*/
- __pyx_t_2 = __Pyx_tp_new(((PyObject*)__pyx_ptype_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (!(likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_dest = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_tp_new(((PyObject*)__pyx_ptype_5pysam_9csamtools_AlignedRead)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1013; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (!(likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5pysam_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1013; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_dest = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":1012
+ /* "pysam/csamtools.pyx":1014
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = mate_data.mate # <<<<<<<<<<<<<<
* return dest
*
*/
- __pyx_v_dest->_delegate = __pyx_v_mate_data.mate;
+ __pyx_t_5 = __pyx_v_mate_data.mate;
+ __pyx_v_dest->_delegate = __pyx_t_5;
- /* "csamtools.pyx":1013
+ /* "pysam/csamtools.pyx":1015
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
* dest._delegate = mate_data.mate
* return dest # <<<<<<<<<<<<<<
@@ -10316,9 +11088,9 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Samfile.mate", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.mate", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF((PyObject *)__pyx_v_dest);
@@ -10328,53 +11100,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11mate(PyObject *__pyx_v_self, PyO
return __pyx_r;
}
-/* "csamtools.pyx":1015
- * return dest
- *
- * def count( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_12count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file does not [...]
-static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_24count[] = "Samfile.count(self, reference=None, start=None, end=None, region=None, until_eof=False)\n*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*\n\n count reads :term:`region` using 0-based indexing. The region is specified by\n :term:`reference`, *start* and *end*. Alternatively, a samtools :term:`region` string can be supplied.\n\n Note that a :term:`TAM` file d [...]
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_25count(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_until_eof = 0;
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_counter;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_t_14;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("count");
- __Pyx_TraceCall("count", __pyx_f[0], 1015);
+ __Pyx_RefNannySetupContext("count (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__until_eof,0};
PyObject* values[5] = {0,0,0,0,0};
- /* "csamtools.pyx":1016
+ /* "pysam/csamtools.pyx":1018
*
* def count( self,
* reference = None, # <<<<<<<<<<<<<<
@@ -10383,7 +11125,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
*/
values[0] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1017
+ /* "pysam/csamtools.pyx":1019
* def count( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
@@ -10392,7 +11134,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
*/
values[1] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1018
+ /* "pysam/csamtools.pyx":1020
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
@@ -10401,7 +11143,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
*/
values[2] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1019
+ /* "pysam/csamtools.pyx":1021
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
@@ -10412,7 +11154,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
values[4] = __pyx_k_73;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -10422,7 +11165,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -10450,7 +11193,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "count") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1017; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -10471,58 +11214,98 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("count", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1015; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("count", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1017; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_24count(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_until_eof);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1017
+ * return dest
+ *
+ * def count( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_until_eof) {
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_counter;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_t_14;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("count", 0);
+ __Pyx_TraceCall("count", __pyx_f[0], 1017);
__Pyx_INCREF(__pyx_v_region);
- /* "csamtools.pyx":1033
+ /* "pysam/csamtools.pyx":1035
* cdef int rend
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1035; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":1034
+ /* "pysam/csamtools.pyx":1036
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_74), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_74), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1036
+ /* "pysam/csamtools.pyx":1038
* raise ValueError( "I/O operation on closed file" )
*
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
* cdef int counter
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -10535,28 +11318,29 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 4)) {
+ if (size > 4) __Pyx_RaiseTooManyValuesError(4);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
- if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
- if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
@@ -10566,36 +11350,45 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ Py_ssize_t i;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ for (i=0; i < 4; i++) {
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(item);
+ *(temps[i]) = item;
+ }
+ #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_7);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ for (index=0; index < 4; index++) {
+ PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(item);
+ *(temps[index]) = item;
+ }
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L8_unpacking_done;
- __pyx_L7_unpacking_failed:;
+ goto __pyx_L5_unpacking_done;
+ __pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L8_unpacking_done:;
+ __pyx_t_9 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5_unpacking_done:;
}
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_v_region);
__pyx_v_region = __pyx_t_1;
@@ -10604,7 +11397,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
__pyx_v_rstart = __pyx_t_11;
__pyx_v_rend = __pyx_t_12;
- /* "csamtools.pyx":1039
+ /* "pysam/csamtools.pyx":1041
*
* cdef int counter
* counter = 0; # <<<<<<<<<<<<<<
@@ -10613,35 +11406,35 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
*/
__pyx_v_counter = 0;
- /* "csamtools.pyx":1041
+ /* "pysam/csamtools.pyx":1043
* counter = 0;
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" )
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ if (__pyx_v_self->isbam) {
- /* "csamtools.pyx":1042
+ /* "pysam/csamtools.pyx":1044
*
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote: # <<<<<<<<<<<<<<
* raise ValueError( "fetch called on bamfile without index" )
*
*/
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_until_eof); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1044; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = (!__pyx_t_4);
if (__pyx_t_13) {
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isremote);
+ __pyx_t_4 = (!__pyx_v_self->isremote);
__pyx_t_14 = __pyx_t_4;
} else {
__pyx_t_14 = __pyx_t_13;
@@ -10652,84 +11445,84 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
}
if (__pyx_t_13) {
- /* "csamtools.pyx":1043
+ /* "pysam/csamtools.pyx":1045
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
*
* if not region:
*/
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_75), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_75), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L7;
}
- __pyx_L10:;
+ __pyx_L7:;
- /* "csamtools.pyx":1045
+ /* "pysam/csamtools.pyx":1047
* raise ValueError( "fetch called on bamfile without index" )
*
* if not region: # <<<<<<<<<<<<<<
* raise ValueError( "counting functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
*/
- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_region); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_13);
if (__pyx_t_3) {
- /* "csamtools.pyx":1046
+ /* "pysam/csamtools.pyx":1048
*
* if not region:
* raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
* bam_fetch(self.samfile.x.bam,
*/
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L8;
}
- __pyx_L11:;
+ __pyx_L8:;
- /* "csamtools.pyx":1047
+ /* "pysam/csamtools.pyx":1049
* if not region:
* raise ValueError( "counting functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_13 = (!__pyx_t_3);
if (__pyx_t_13) {
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_78), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_78), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L12;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L9;
}
- __pyx_L12:;
+ __pyx_L9:;
- /* "csamtools.pyx":1054
+ /* "pysam/csamtools.pyx":1056
* rend,
* <void*>&counter,
* count_callback ) # <<<<<<<<<<<<<<
* return counter
* else:
*/
- bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_9csamtools_count_callback);
+ bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_5pysam_9csamtools_count_callback);
- /* "csamtools.pyx":1055
+ /* "pysam/csamtools.pyx":1057
* <void*>&counter,
* count_callback )
* return counter # <<<<<<<<<<<<<<
@@ -10737,29 +11530,29 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
* raise ValueError ("count for a region is not available for sam files" )
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyInt_FromLong(__pyx_v_counter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1055; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyInt_FromLong(__pyx_v_counter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_r = __pyx_t_5;
__pyx_t_5 = 0;
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L6;
}
/*else*/ {
- /* "csamtools.pyx":1057
+ /* "pysam/csamtools.pyx":1059
* return counter
* else:
* raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
*
* def pileup( self,
*/
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_80), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_80), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L9:;
+ __pyx_L6:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -10770,7 +11563,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.count", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_region);
@@ -10780,56 +11573,26 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_12count(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":1059
- * raise ValueError ("count for a region is not available for sam files" )
- *
- * def pileup( self, # <<<<<<<<<<<<<<
- * reference = None,
- * start = None,
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_13pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be returned\n [...]
-static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_26pileup[] = "Samfile.pileup(self, reference=None, start=None, end=None, region=None, callback=None, **kwargs)\n\n perform a :term:`pileup` within a :term:`region`. The region is specified by\n :term:`reference`, *start* and *end* (using 0-based indexing).\n Alternatively, a samtools *region* string can be supplied.\n\n Without *reference* or *region* all reads will be used for the pileup. The reads will be retu [...]
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_27pileup(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_callback = 0;
PyObject *__pyx_v_kwargs = 0;
- int __pyx_v_rtid;
- int __pyx_v_rstart;
- int __pyx_v_rend;
- int __pyx_v_has_coord;
- bam_plbuf_t *__pyx_v_buf;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
- int __pyx_t_11;
- int __pyx_t_12;
- int __pyx_t_13;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("pileup");
- __Pyx_TraceCall("pileup", __pyx_f[0], 1059);
+ __Pyx_RefNannySetupContext("pileup (wrapper)", 0);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return NULL;
__Pyx_GOTREF(__pyx_v_kwargs);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__callback,0};
PyObject* values[5] = {0,0,0,0,0};
- /* "csamtools.pyx":1060
+ /* "pysam/csamtools.pyx":1062
*
* def pileup( self,
* reference = None, # <<<<<<<<<<<<<<
@@ -10838,7 +11601,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
values[0] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1061
+ /* "pysam/csamtools.pyx":1063
* def pileup( self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
@@ -10847,7 +11610,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
values[1] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1062
+ /* "pysam/csamtools.pyx":1064
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
@@ -10856,7 +11619,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
values[2] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1063
+ /* "pysam/csamtools.pyx":1065
* start = None,
* end = None,
* region = None, # <<<<<<<<<<<<<<
@@ -10865,7 +11628,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
values[3] = ((PyObject *)Py_None);
- /* "csamtools.pyx":1064
+ /* "pysam/csamtools.pyx":1066
* end = None,
* region = None,
* callback = None, # <<<<<<<<<<<<<<
@@ -10875,7 +11638,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
values[4] = ((PyObject *)Py_None);
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -10885,7 +11649,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
if (kw_args > 0) {
PyObject* value = PyDict_GetItem(__pyx_kwds, __pyx_n_s__reference);
@@ -10913,7 +11677,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "pileup") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1061; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -10934,58 +11698,99 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("pileup", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1061; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_26pileup(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_callback, __pyx_v_kwargs);
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1061
+ * raise ValueError ("count for a region is not available for sam files" )
+ *
+ * def pileup( self, # <<<<<<<<<<<<<<
+ * reference = None,
+ * start = None,
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_callback, PyObject *__pyx_v_kwargs) {
+ int __pyx_v_rtid;
+ int __pyx_v_rstart;
+ int __pyx_v_rend;
+ int __pyx_v_has_coord;
+ bam_plbuf_t *__pyx_v_buf;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *(*__pyx_t_9)(PyObject *);
+ int __pyx_t_10;
+ int __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_t_13;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("pileup", 0);
+ __Pyx_TraceCall("pileup", __pyx_f[0], 1061);
- /* "csamtools.pyx":1115
+ /* "pysam/csamtools.pyx":1117
* cdef bam_plbuf_t *buf
*
* if not self._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":1116
+ /* "pysam/csamtools.pyx":1118
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_81), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_81), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1118
+ /* "pysam/csamtools.pyx":1120
* raise ValueError( "I/O operation on closed file" )
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region ) # <<<<<<<<<<<<<<
*
* if self.isbam:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___parseRegion); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
__Pyx_GIVEREF(__pyx_v_reference);
@@ -10998,28 +11803,29 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 4)) {
+ if (size > 4) __Pyx_RaiseTooManyValuesError(4);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
- if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
- if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
@@ -11029,89 +11835,98 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ Py_ssize_t i;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ for (i=0; i < 4; i++) {
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(item);
+ *(temps[i]) = item;
+ }
+ #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L7_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_7);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ for (index=0; index < 4; index++) {
+ PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(item);
+ *(temps[index]) = item;
+ }
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L8_unpacking_done;
- __pyx_L7_unpacking_failed:;
+ goto __pyx_L5_unpacking_done;
+ __pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L8_unpacking_done:;
+ __pyx_t_9 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L5_unpacking_done:;
}
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_1); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_11 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_6); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_v_has_coord = __pyx_t_10;
__pyx_v_rtid = __pyx_t_11;
__pyx_v_rstart = __pyx_t_12;
__pyx_v_rend = __pyx_t_13;
- /* "csamtools.pyx":1120
+ /* "pysam/csamtools.pyx":1122
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*
* if self.isbam: # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
*
*/
- if (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam) {
+ if (__pyx_v_self->isbam) {
- /* "csamtools.pyx":1121
+ /* "pysam/csamtools.pyx":1123
*
* if self.isbam:
* if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_83), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_83), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L10;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L7;
}
- __pyx_L10:;
+ __pyx_L7:;
- /* "csamtools.pyx":1123
+ /* "pysam/csamtools.pyx":1125
* if not self._hasIndex(): raise ValueError( "no index available for pileup" )
*
* if callback: # <<<<<<<<<<<<<<
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
*
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "csamtools.pyx":1124
+ /* "pysam/csamtools.pyx":1126
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
@@ -11120,34 +11935,34 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
__pyx_t_3 = (!__pyx_v_has_coord);
if (__pyx_t_3) {
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_84), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_84), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L12;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L9;
}
- __pyx_L12:;
+ __pyx_L9:;
- /* "csamtools.pyx":1126
+ /* "pysam/csamtools.pyx":1128
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
*
* buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
* self.index, rtid, rstart, rend,
*/
- __pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
+ __pyx_v_buf = bam_plbuf_init(((bam_pileup_f)__pyx_f_5pysam_9csamtools_pileup_callback), ((void *)__pyx_v_callback));
- /* "csamtools.pyx":1129
+ /* "pysam/csamtools.pyx":1131
* bam_fetch(self.samfile.x.bam,
* self.index, rtid, rstart, rend,
* buf, pileup_fetch_callback ) # <<<<<<<<<<<<<<
*
* # finalize pileup
*/
- bam_fetch(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->x.bam, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_9csamtools_pileup_fetch_callback);
+ bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_5pysam_9csamtools_pileup_fetch_callback);
- /* "csamtools.pyx":1132
+ /* "pysam/csamtools.pyx":1134
*
* # finalize pileup
* bam_plbuf_push( NULL, buf) # <<<<<<<<<<<<<<
@@ -11156,7 +11971,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
bam_plbuf_push(NULL, __pyx_v_buf);
- /* "csamtools.pyx":1133
+ /* "pysam/csamtools.pyx":1135
* # finalize pileup
* bam_plbuf_push( NULL, buf)
* bam_plbuf_destroy(buf) # <<<<<<<<<<<<<<
@@ -11164,11 +11979,11 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
* if has_coord:
*/
bam_plbuf_destroy(__pyx_v_buf);
- goto __pyx_L11;
+ goto __pyx_L8;
}
/*else*/ {
- /* "csamtools.pyx":1135
+ /* "pysam/csamtools.pyx":1137
* bam_plbuf_destroy(buf)
* else:
* if has_coord: # <<<<<<<<<<<<<<
@@ -11177,7 +11992,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
*/
if (__pyx_v_has_coord) {
- /* "csamtools.pyx":1136
+ /* "pysam/csamtools.pyx":1138
* else:
* if has_coord:
* return IteratorColumnRegion( self, # <<<<<<<<<<<<<<
@@ -11185,70 +12000,78 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
* start = rstart,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_5 = PyDict_New(); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+
+ /* "pysam/csamtools.pyx":1142
+ * start = rstart,
+ * end = rend,
+ * **kwargs ) # <<<<<<<<<<<<<<
+ * else:
+ * return IteratorColumnAllRefs(self, **kwargs )
+ */
+ __pyx_t_5 = PyDict_Copy(((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- /* "csamtools.pyx":1137
+ /* "pysam/csamtools.pyx":1139
* if has_coord:
* return IteratorColumnRegion( self,
* tid = rtid, # <<<<<<<<<<<<<<
* start = rstart,
* end = rend,
*/
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rtid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid)))) {
+ __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__tid)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__tid), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "csamtools.pyx":1138
+ /* "pysam/csamtools.pyx":1140
* return IteratorColumnRegion( self,
* tid = rtid,
* start = rstart, # <<<<<<<<<<<<<<
* end = rend,
* **kwargs )
*/
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rstart); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start)))) {
+ __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__start)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__start), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "csamtools.pyx":1139
+ /* "pysam/csamtools.pyx":1141
* tid = rtid,
* start = rstart,
* end = rend, # <<<<<<<<<<<<<<
* **kwargs )
* else:
*/
- __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_rend); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PyDict_GetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end)))) {
+ __Pyx_RaiseDoubleKeywordsError("function", ((PyObject *)__pyx_n_s__end)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ if (PyDict_SetItem(__pyx_t_5, ((PyObject *)__pyx_n_s__end), __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
-
- /* "csamtools.pyx":1140
- * start = rstart,
- * end = rend,
- * **kwargs ) # <<<<<<<<<<<<<<
- * else:
- * return IteratorColumnAllRefs(self, **kwargs )
- */
- if (PyDict_Update(((PyObject *)__pyx_t_5), ((PyObject *)__pyx_v_kwargs)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorColumnRegion)), ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_r = __pyx_t_6;
__pyx_t_6 = 0;
goto __pyx_L0;
- goto __pyx_L13;
+ goto __pyx_L10;
}
/*else*/ {
- /* "csamtools.pyx":1142
+ /* "pysam/csamtools.pyx":1144
* **kwargs )
* else:
* return IteratorColumnAllRefs(self, **kwargs ) # <<<<<<<<<<<<<<
@@ -11256,39 +12079,42 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
* else:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_INCREF(__pyx_v_self);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_self);
- __Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_5 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_v_kwargs)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_v_self));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self));
+ __pyx_t_5 = ((PyObject *)__pyx_v_kwargs);
+ __Pyx_INCREF(__pyx_t_5);
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs)), ((PyObject *)__pyx_t_6), ((PyObject *)__pyx_t_5)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_r = __pyx_t_5;
- __pyx_t_5 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __pyx_r = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L0;
}
- __pyx_L13:;
+ __pyx_L10:;
}
- __pyx_L11:;
- goto __pyx_L9;
+ __pyx_L8:;
+ goto __pyx_L6;
}
/*else*/ {
- /* "csamtools.pyx":1145
+ /* "pysam/csamtools.pyx":1147
*
* else:
* raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
*
* def close( self ):
*/
- __pyx_t_5 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L9:;
+ __pyx_L6:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -11299,17 +12125,28 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.pileup", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":1147
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_28close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_29close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("close (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_28close(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1149
* raise NotImplementedError( "pileup of samfiles not implemented yet" )
*
* def close( self ): # <<<<<<<<<<<<<<
@@ -11317,55 +12154,53 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_13pileup(PyObject *__pyx_v_self, P
* closes the :class:`pysam.Samfile`.'''
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_14close[] = "Samfile.close(self)\n\n closes the :class:`pysam.Samfile`.";
-static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_28close(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("close");
- __Pyx_TraceCall("close", __pyx_f[0], 1147);
+ __Pyx_RefNannySetupContext("close", 0);
+ __Pyx_TraceCall("close", __pyx_f[0], 1149);
- /* "csamtools.pyx":1150
+ /* "pysam/csamtools.pyx":1152
* '''
* closes the :class:`pysam.Samfile`.'''
* if self.samfile != NULL: # <<<<<<<<<<<<<<
* samclose( self.samfile )
* bam_index_destroy(self.index);
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile != NULL);
+ __pyx_t_1 = (__pyx_v_self->samfile != NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":1151
+ /* "pysam/csamtools.pyx":1153
* closes the :class:`pysam.Samfile`.'''
* if self.samfile != NULL:
* samclose( self.samfile ) # <<<<<<<<<<<<<<
* bam_index_destroy(self.index);
* self.samfile = NULL
*/
- samclose(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile);
+ samclose(__pyx_v_self->samfile);
- /* "csamtools.pyx":1152
+ /* "pysam/csamtools.pyx":1154
* if self.samfile != NULL:
* samclose( self.samfile )
* bam_index_destroy(self.index); # <<<<<<<<<<<<<<
* self.samfile = NULL
*
*/
- bam_index_destroy(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index);
+ bam_index_destroy(__pyx_v_self->index);
- /* "csamtools.pyx":1153
+ /* "pysam/csamtools.pyx":1155
* samclose( self.samfile )
* bam_index_destroy(self.index);
* self.samfile = NULL # <<<<<<<<<<<<<<
*
* def __dealloc__( self ):
*/
- ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile = NULL;
- goto __pyx_L5;
+ __pyx_v_self->samfile = NULL;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
__Pyx_XGIVEREF(__pyx_r);
@@ -11374,7 +12209,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CY
return __pyx_r;
}
-/* "csamtools.pyx":1155
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":1157
* self.samfile = NULL
*
* def __dealloc__( self ): # <<<<<<<<<<<<<<
@@ -11382,8 +12226,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_14close(PyObject *__pyx_v_self, CY
* # note: no doc string
*/
-static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_7Samfile_30__dealloc__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
@@ -11392,57 +12235,57 @@ static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1155);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1157);
- /* "csamtools.pyx":1159
+ /* "pysam/csamtools.pyx":1161
* # note: no doc string
* # note: __del__ is not called.
* self.close() # <<<<<<<<<<<<<<
* bam_destroy1(self.b)
* if self._filename != NULL: free( self._filename )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":1160
+ /* "pysam/csamtools.pyx":1162
* # note: __del__ is not called.
* self.close()
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self._filename != NULL: free( self._filename )
*
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
+ bam_destroy1(__pyx_v_self->b);
- /* "csamtools.pyx":1161
+ /* "pysam/csamtools.pyx":1163
* self.close()
* bam_destroy1(self.b)
* if self._filename != NULL: free( self._filename ) # <<<<<<<<<<<<<<
*
* cpdef int write( self, AlignedRead read ) except -1:
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename != NULL);
+ __pyx_t_3 = (__pyx_v_self->_filename != NULL);
if (__pyx_t_3) {
- free(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename);
- goto __pyx_L5;
+ free(__pyx_v_self->_filename);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.__dealloc__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":1163
+/* "pysam/csamtools.pyx":1165
* if self._filename != NULL: free( self._filename )
*
* cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
@@ -11450,8 +12293,8 @@ static void __pyx_pf_9csamtools_7Samfile_15__dealloc__(PyObject *__pyx_v_self) {
* write a single :class:`pysam.AlignedRead` to disk.
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static int __pyx_f_5pysam_9csamtools_7Samfile_write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read, int __pyx_skip_dispatch) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -11464,24 +12307,24 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write");
- __Pyx_TraceCall("write", __pyx_f[0], 1163);
+ __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_TraceCall("write", __pyx_f[0], 1165);
/* Check if called by wrapper */
if (unlikely(__pyx_skip_dispatch)) ;
- /* Check if overriden in Python */
+ /* Check if overridden in Python */
else if (unlikely(Py_TYPE(((PyObject *)__pyx_v_self))->tp_dictoffset != 0)) {
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (void *)&__pyx_pf_9csamtools_7Samfile_16write)) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ if (!PyCFunction_Check(__pyx_t_1) || (PyCFunction_GET_FUNCTION(__pyx_t_1) != (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_33write)) {
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_read));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_read));
__Pyx_GIVEREF(((PyObject *)__pyx_v_read));
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_r = __pyx_t_4;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -11490,24 +12333,24 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "csamtools.pyx":1169
+ /* "pysam/csamtools.pyx":1171
* returns the number of bytes written.
* '''
* if not self._isOpen(): # <<<<<<<<<<<<<<
* return 0
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1169; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_6 = (!__pyx_t_5);
if (__pyx_t_6) {
- /* "csamtools.pyx":1170
+ /* "pysam/csamtools.pyx":1172
* '''
* if not self._isOpen():
* return 0 # <<<<<<<<<<<<<<
@@ -11520,7 +12363,7 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
}
__pyx_L3:;
- /* "csamtools.pyx":1172
+ /* "pysam/csamtools.pyx":1174
* return 0
*
* return samwrite( self.samfile, read._delegate ) # <<<<<<<<<<<<<<
@@ -11536,7 +12379,7 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_WriteUnraisable("csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -11544,7 +12387,24 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
return __pyx_r;
}
-/* "csamtools.pyx":1163
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_32write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_33write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("write (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_32write(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_read));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1165
* if self._filename != NULL: free( self._filename )
*
* cpdef int write( self, AlignedRead read ) except -1: # <<<<<<<<<<<<<<
@@ -11552,9 +12412,7 @@ static int __pyx_f_9csamtools_7Samfile_write(struct __pyx_obj_9csamtools_Samfile
* write a single :class:`pysam.AlignedRead` to disk.
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_16write[] = "Samfile.write(self, AlignedRead read) -> int\n\n write a single :class:`pysam.AlignedRead` to disk.\n\n returns the number of bytes written.\n ";
-static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, PyObject *__pyx_v_read) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_32write(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_read) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -11562,11 +12420,10 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, Py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("write");
- __Pyx_TraceCall("write", __pyx_f[0], 1163);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("write", 0);
+ __Pyx_TraceCall("write", __pyx_f[0], 1165);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_9csamtools_Samfile *)((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->__pyx_vtab)->write(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self), ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_read), 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *)__pyx_v_self->__pyx_vtab)->write(__pyx_v_self, __pyx_v_read, 1)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -11576,7 +12433,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, Py
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -11585,7 +12442,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":1174
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_34__enter__[] = "Samfile.__enter__(self)";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__enter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1176
* return samwrite( self.samfile, read._delegate )
*
* def __enter__(self): # <<<<<<<<<<<<<<
@@ -11593,16 +12462,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_16write(PyObject *__pyx_v_self, Py
*
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_17__enter__[] = "Samfile.__enter__(self)";
-static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_34__enter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__enter__");
- __Pyx_TraceCall("__enter__", __pyx_f[0], 1174);
+ __Pyx_RefNannySetupContext("__enter__", 0);
+ __Pyx_TraceCall("__enter__", __pyx_f[0], 1176);
- /* "csamtools.pyx":1175
+ /* "pysam/csamtools.pyx":1177
*
* def __enter__(self):
* return self # <<<<<<<<<<<<<<
@@ -11610,8 +12477,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self
* def __exit__(self, exc_type, exc_value, traceback):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -11622,36 +12489,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_17__enter__(PyObject *__pyx_v_self
return __pyx_r;
}
-/* "csamtools.pyx":1177
- * return self
- *
- * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
- * self.close()
- * return False
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_18__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
-static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- PyObject *__pyx_v_exc_type = 0;
- PyObject *__pyx_v_exc_value = 0;
- PyObject *__pyx_v_traceback = 0;
- PyObject *__pyx_r = NULL;
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_36__exit__[] = "Samfile.__exit__(self, exc_type, exc_value, traceback)";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ CYTHON_UNUSED PyObject *__pyx_v_exc_type = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_exc_value = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_traceback = 0;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__exit__");
- __Pyx_TraceCall("__exit__", __pyx_f[0], 1177);
+ __Pyx_RefNannySetupContext("__exit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__exc_type,&__pyx_n_s__exc_value,&__pyx_n_s__traceback,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -11659,26 +12513,23 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self,
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_type)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_value);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__exc_value)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__traceback);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__traceback)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__exit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -11693,28 +12544,52 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1177; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__exit__", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_exc_type, __pyx_v_exc_value, __pyx_v_traceback);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "csamtools.pyx":1178
+/* "pysam/csamtools.pyx":1179
+ * return self
+ *
+ * def __exit__(self, exc_type, exc_value, traceback): # <<<<<<<<<<<<<<
+ * self.close()
+ * return False
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_36__exit__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_exc_type, CYTHON_UNUSED PyObject *__pyx_v_exc_value, CYTHON_UNUSED PyObject *__pyx_v_traceback) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__exit__", 0);
+ __Pyx_TraceCall("__exit__", __pyx_f[0], 1179);
+
+ /* "pysam/csamtools.pyx":1180
*
* def __exit__(self, exc_type, exc_value, traceback):
* self.close() # <<<<<<<<<<<<<<
* return False
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":1179
+ /* "pysam/csamtools.pyx":1181
* def __exit__(self, exc_type, exc_value, traceback):
* self.close()
* return False # <<<<<<<<<<<<<<
@@ -11722,7 +12597,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self,
* ###############################################################
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -11733,7 +12608,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self,
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.__exit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -11742,7 +12617,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "csamtools.pyx":1188
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1190
* property filename:
* '''number of :term:`filename` associated with this object.'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -11750,8 +12636,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_18__exit__(PyObject *__pyx_v_self,
* return self._filename
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -11762,35 +12647,35 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1188);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1190);
- /* "csamtools.pyx":1189
+ /* "pysam/csamtools.pyx":1191
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self._filename
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_87), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_87), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1190
+ /* "pysam/csamtools.pyx":1192
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return self._filename # <<<<<<<<<<<<<<
@@ -11798,7 +12683,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_
* property nreferences:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1190; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_self->_filename); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -11809,7 +12694,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.filename.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -11818,7 +12703,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":1194
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1196
* property nreferences:
* '''number of :term:`reference` sequences in the file.'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -11826,8 +12722,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8filename___get__(PyObject *__pyx_
* return self.samfile.header.n_targets
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_11nreferences___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -11838,35 +12733,35 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1194);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1196);
- /* "csamtools.pyx":1195
+ /* "pysam/csamtools.pyx":1197
* '''number of :term:`reference` sequences in the file.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self.samfile.header.n_targets
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_88), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_88), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1196
+ /* "pysam/csamtools.pyx":1198
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return self.samfile.header.n_targets # <<<<<<<<<<<<<<
@@ -11874,7 +12769,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__
* property references:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->samfile->header->n_targets); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -11885,7 +12780,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.nreferences.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.nreferences.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -11894,7 +12789,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":1200
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1202
* property references:
* """tuple with the names of :term:`reference` sequences."""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -11902,8 +12808,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_11nreferences___get__(PyObject *__
* t = []
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_10references___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
PyObject *__pyx_r = NULL;
@@ -11918,73 +12823,70 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1200);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1202);
- /* "csamtools.pyx":1201
+ /* "pysam/csamtools.pyx":1203
* """tuple with the names of :term:`reference` sequences."""
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1202
+ /* "pysam/csamtools.pyx":1204
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = [] # <<<<<<<<<<<<<<
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_t = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1203
+ /* "pysam/csamtools.pyx":1205
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = []
* for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
* return tuple(t)
*/
- __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
- /* "csamtools.pyx":1204
+ /* "pysam/csamtools.pyx":1206
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) ) # <<<<<<<<<<<<<<
* return tuple(t)
*
*/
- if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools__charptr_to_str((__pyx_v_self->samfile->header->target_name[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- /* "csamtools.pyx":1205
+ /* "pysam/csamtools.pyx":1207
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( _charptr_to_str(self.samfile.header.target_name[x]) )
* return tuple(t) # <<<<<<<<<<<<<<
@@ -11992,10 +12894,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__p
* property lengths:
*/
__Pyx_XDECREF(__pyx_r);
- if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -12006,7 +12905,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__p
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.references.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.references.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_t);
@@ -12016,7 +12915,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":1211
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1213
* :attr:`pysam.Samfile.references`
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -12024,8 +12934,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_10references___get__(PyObject *__p
* t = []
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_7lengths___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_v_t = NULL;
long __pyx_v_x;
PyObject *__pyx_r = NULL;
@@ -12040,73 +12949,70 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1211);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1213);
- /* "csamtools.pyx":1212
+ /* "pysam/csamtools.pyx":1214
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_90), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_90), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1213
+ /* "pysam/csamtools.pyx":1215
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = [] # <<<<<<<<<<<<<<
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( self.samfile.header.target_len[x] )
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_t = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1214
+ /* "pysam/csamtools.pyx":1216
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* t = []
* for x from 0 <= x < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* t.append( self.samfile.header.target_len[x] )
* return tuple(t)
*/
- __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_5; __pyx_v_x++) {
- /* "csamtools.pyx":1215
+ /* "pysam/csamtools.pyx":1217
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( self.samfile.header.target_len[x] ) # <<<<<<<<<<<<<<
* return tuple(t)
*
*/
- if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t((__pyx_v_self->samfile->header->target_len[__pyx_v_x])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyList_Append(__pyx_v_t, __pyx_t_2); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
- /* "csamtools.pyx":1216
+ /* "pysam/csamtools.pyx":1218
* for x from 0 <= x < self.samfile.header.n_targets:
* t.append( self.samfile.header.target_len[x] )
* return tuple(t) # <<<<<<<<<<<<<<
@@ -12114,10 +13020,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v
* property mapped:
*/
__Pyx_XDECREF(__pyx_r);
- if (unlikely(((PyObject *)__pyx_v_t) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyList_AsTuple(__pyx_v_t)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -12128,7 +13031,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.lengths.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.lengths.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_t);
@@ -12138,7 +13041,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v
return __pyx_r;
}
-/* "csamtools.pyx":1221
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1223
* """total number of mapped reads in file.
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -12146,8 +13060,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_7lengths___get__(PyObject *__pyx_v
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6mapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
int __pyx_v_tid;
uint32_t __pyx_v_total;
PyObject *__pyx_r = NULL;
@@ -12161,53 +13074,79 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1221);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1223);
- /* "csamtools.pyx":1222
+ /* "pysam/csamtools.pyx":1224
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
- *
+ * if self.index == NULL:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_91), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_91), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1223
+ /* "pysam/csamtools.pyx":1225
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
+ * if self.index == NULL:
+ * raise ValueError( "mapping information not recorded in index or index not available")
+ */
+ __pyx_t_4 = (!__pyx_v_self->isbam);
+ if (__pyx_t_4) {
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_93), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
+ }
+ __pyx_L4:;
+
+ /* "pysam/csamtools.pyx":1226
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
+ * if self.index == NULL: # <<<<<<<<<<<<<<
+ * raise ValueError( "mapping information not recorded in index or index not available")
*
- * cdef int tid
*/
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
+ __pyx_t_4 = (__pyx_v_self->index == NULL);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_93), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":1227
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
+ * if self.index == NULL:
+ * raise ValueError( "mapping information not recorded in index or index not available") # <<<<<<<<<<<<<<
+ *
+ * cdef int tid
+ */
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_95), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- __pyx_L6:;
+ __pyx_L5:;
- /* "csamtools.pyx":1226
+ /* "pysam/csamtools.pyx":1230
*
* cdef int tid
* cdef uint32_t total = 0 # <<<<<<<<<<<<<<
@@ -12216,27 +13155,27 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_
*/
__pyx_v_total = 0;
- /* "csamtools.pyx":1227
+ /* "pysam/csamtools.pyx":1231
* cdef int tid
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* total += pysam_get_mapped( self.index, tid )
* return total
*/
- __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
- /* "csamtools.pyx":1228
+ /* "pysam/csamtools.pyx":1232
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets:
* total += pysam_get_mapped( self.index, tid ) # <<<<<<<<<<<<<<
* return total
*
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_mapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid));
+ __pyx_v_total = (__pyx_v_total + pysam_get_mapped(__pyx_v_self->index, __pyx_v_tid));
}
- /* "csamtools.pyx":1229
+ /* "pysam/csamtools.pyx":1233
* for tid from 0 <= tid < self.samfile.header.n_targets:
* total += pysam_get_mapped( self.index, tid )
* return total # <<<<<<<<<<<<<<
@@ -12244,7 +13183,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_
* property unmapped:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_total); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_total); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -12255,7 +13194,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.mapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.mapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -12264,7 +13203,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":1234
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1238
* """total number of unmapped reads in file.
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -12272,8 +13222,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6mapped___get__(PyObject *__pyx_v_
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_8unmapped___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
int __pyx_v_tid;
uint32_t __pyx_v_total;
PyObject *__pyx_r = NULL;
@@ -12287,53 +13236,53 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1234);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1238);
- /* "csamtools.pyx":1235
+ /* "pysam/csamtools.pyx":1239
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
* cdef int tid
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_94), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_96), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1236
+ /* "pysam/csamtools.pyx":1240
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
* cdef int tid
* cdef uint32_t total = 0
*/
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
+ __pyx_t_4 = (!__pyx_v_self->isbam);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_96), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_AttributeError, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":1238
+ /* "pysam/csamtools.pyx":1242
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
* cdef int tid
* cdef uint32_t total = 0 # <<<<<<<<<<<<<<
@@ -12342,36 +13291,36 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_
*/
__pyx_v_total = 0;
- /* "csamtools.pyx":1239
+ /* "pysam/csamtools.pyx":1243
* cdef int tid
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets: # <<<<<<<<<<<<<<
* total += pysam_get_unmapped( self.index, tid )
* # get unmapped reads without coordinates
*/
- __pyx_t_5 = ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets;
+ __pyx_t_5 = __pyx_v_self->samfile->header->n_targets;
for (__pyx_v_tid = 0; __pyx_v_tid < __pyx_t_5; __pyx_v_tid++) {
- /* "csamtools.pyx":1240
+ /* "pysam/csamtools.pyx":1244
* cdef uint32_t total = 0
* for tid from 0 <= tid < self.samfile.header.n_targets:
* total += pysam_get_unmapped( self.index, tid ) # <<<<<<<<<<<<<<
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 )
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, __pyx_v_tid));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, __pyx_v_tid));
}
- /* "csamtools.pyx":1242
+ /* "pysam/csamtools.pyx":1246
* total += pysam_get_unmapped( self.index, tid )
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 ) # <<<<<<<<<<<<<<
* return total
*
*/
- __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->index, -1));
+ __pyx_v_total = (__pyx_v_total + pysam_get_unmapped(__pyx_v_self->index, -1));
- /* "csamtools.pyx":1243
+ /* "pysam/csamtools.pyx":1247
* # get unmapped reads without coordinates
* total += pysam_get_unmapped( self.index, -1 )
* return total # <<<<<<<<<<<<<<
@@ -12379,7 +13328,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_
* property text:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_total); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_total); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -12390,7 +13339,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -12399,7 +13348,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":1247
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1251
* property text:
* '''full contents of the :term:`sam file` header as a string.'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -12407,8 +13367,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_8unmapped___get__(PyObject *__pyx_
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_4text___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -12419,35 +13378,35 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_se
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1247);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1251);
- /* "csamtools.pyx":1248
+ /* "pysam/csamtools.pyx":1252
* '''full contents of the :term:`sam file` header as a string.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1249
+ /* "pysam/csamtools.pyx":1253
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text) # <<<<<<<<<<<<<<
@@ -12455,7 +13414,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_se
* property header:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_from_string_and_size(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_from_string_and_size(__pyx_v_self->samfile->header->text, __pyx_v_self->samfile->header->l_text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1253; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -12466,7 +13425,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_se
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.text.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.text.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -12475,7 +13434,18 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":1255
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1259
* a two-level dictionary.
* '''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -12483,8 +13453,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_4text___get__(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6header___get__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_v_result = NULL;
PyObject *__pyx_v_t = NULL;
PyObject *__pyx_v_line = NULL;
@@ -12517,102 +13486,110 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1255);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1259);
- /* "csamtools.pyx":1256
+ /* "pysam/csamtools.pyx":1260
* '''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* result = {}
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_100), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1258
+ /* "pysam/csamtools.pyx":1262
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
*
* result = {} # <<<<<<<<<<<<<<
*
* if self.samfile.header.text != NULL:
*/
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_result = __pyx_t_2;
+ __pyx_v_result = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1260
+ /* "pysam/csamtools.pyx":1264
* result = {}
*
* if self.samfile.header.text != NULL: # <<<<<<<<<<<<<<
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
*/
- __pyx_t_4 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->text != NULL);
+ __pyx_t_4 = (__pyx_v_self->samfile->header->text != NULL);
if (__pyx_t_4) {
- /* "csamtools.pyx":1262
+ /* "pysam/csamtools.pyx":1266
* if self.samfile.header.text != NULL:
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text # <<<<<<<<<<<<<<
* for line in t.split("\n"):
* if not line.strip(): continue
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1262; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__text); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_t = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1263
+ /* "pysam/csamtools.pyx":1267
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
* for line in t.split("\n"): # <<<<<<<<<<<<<<
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_t, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_t, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_101), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_2)) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
- } else if (PyTuple_CheckExact(__pyx_t_2)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_1 = __pyx_t_6(__pyx_t_2);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -12622,28 +13599,28 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
__pyx_v_line = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1264
+ /* "pysam/csamtools.pyx":1268
* t = self.text
* for line in t.split("\n"):
* if not line.strip(): continue # <<<<<<<<<<<<<<
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t")
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- goto __pyx_L7_continue;
- goto __pyx_L9;
+ goto __pyx_L5_continue;
+ goto __pyx_L7;
}
- __pyx_L9:;
+ __pyx_L7:;
- /* "csamtools.pyx":1265
+ /* "pysam/csamtools.pyx":1269
* for line in t.split("\n"):
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
@@ -12651,55 +13628,55 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
* record = fields[0]
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_101), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_103), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(!__pyx_t_3)) {
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_102), __pyx_v_line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_104), __pyx_v_line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1266
+ /* "pysam/csamtools.pyx":1270
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t") # <<<<<<<<<<<<<<
* record = fields[0]
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
*/
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_103), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_105), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_fields);
__pyx_v_fields = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1267
+ /* "pysam/csamtools.pyx":1271
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t")
* record = fields[0] # <<<<<<<<<<<<<<
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
*
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_fields, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_fields, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_record);
__pyx_v_record = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1268
+ /* "pysam/csamtools.pyx":1272
* fields = line[1:].split("\t")
* record = fields[0]
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line) # <<<<<<<<<<<<<<
@@ -12707,142 +13684,149 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
* # treat comments
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(!__pyx_t_3)) {
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_104), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1271
+ /* "pysam/csamtools.pyx":1275
*
* # treat comments
* if record == "CO": # <<<<<<<<<<<<<<
* if record not in result: result[record] = []
* result[record].append( "\t".join( fields[1:] ) )
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":1272
+ /* "pysam/csamtools.pyx":1276
* # treat comments
* if record == "CO":
* if record not in result: result[record] = [] # <<<<<<<<<<<<<<
* result[record].append( "\t".join( fields[1:] ) )
* continue
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L11;
+ goto __pyx_L9;
}
- __pyx_L11:;
+ __pyx_L9:;
- /* "csamtools.pyx":1273
+ /* "pysam/csamtools.pyx":1277
* if record == "CO":
* if record not in result: result[record] = []
* result[record].append( "\t".join( fields[1:] ) ) # <<<<<<<<<<<<<<
* continue
- *
+ * # the following is clumsy as generators do not work?
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_7, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_7, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "csamtools.pyx":1274
+ /* "pysam/csamtools.pyx":1278
* if record not in result: result[record] = []
* result[record].append( "\t".join( fields[1:] ) )
* continue # <<<<<<<<<<<<<<
- *
* # the following is clumsy as generators do not work?
+ * x = {}
*/
- goto __pyx_L7_continue;
- goto __pyx_L10;
+ goto __pyx_L5_continue;
+ goto __pyx_L8;
}
- __pyx_L10:;
+ __pyx_L8:;
- /* "csamtools.pyx":1277
- *
+ /* "pysam/csamtools.pyx":1280
+ * continue
* # the following is clumsy as generators do not work?
* x = {} # <<<<<<<<<<<<<<
* for field in fields[1:]:
- * key, value = field.split(":",1)
+ * if ":" not in field:
*/
- __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1280; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_XDECREF(((PyObject *)__pyx_v_x));
- __pyx_v_x = __pyx_t_9;
+ __pyx_v_x = ((PyObject*)__pyx_t_9);
__pyx_t_9 = 0;
- /* "csamtools.pyx":1278
+ /* "pysam/csamtools.pyx":1281
* # the following is clumsy as generators do not work?
* x = {}
* for field in fields[1:]: # <<<<<<<<<<<<<<
- * key, value = field.split(":",1)
- * # uppercase keys must be valid
+ * if ":" not in field:
+ * raise ValueError("malformatted header: no ':' in field" )
*/
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_fields, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
__pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_10 = 0;
__pyx_t_11 = NULL;
} else {
- __pyx_t_10 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_11 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_8)) {
+ if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
- } else if (PyTuple_CheckExact(__pyx_t_8)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_10); __Pyx_INCREF(__pyx_t_9); __pyx_t_10++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_10); __pyx_t_10++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_9 = __pyx_t_11(__pyx_t_8);
if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1278; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -12852,59 +13836,94 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
__pyx_v_field = __pyx_t_9;
__pyx_t_9 = 0;
- /* "csamtools.pyx":1279
+ /* "pysam/csamtools.pyx":1282
* x = {}
* for field in fields[1:]:
+ * if ":" not in field: # <<<<<<<<<<<<<<
+ * raise ValueError("malformatted header: no ':' in field" )
+ * key, value = field.split(":",1)
+ */
+ __pyx_t_3 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_kp_s_107), __pyx_v_field, Py_NE)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__pyx_t_3) {
+
+ /* "pysam/csamtools.pyx":1283
+ * for field in fields[1:]:
+ * if ":" not in field:
+ * raise ValueError("malformatted header: no ':' in field" ) # <<<<<<<<<<<<<<
+ * key, value = field.split(":",1)
+ * # uppercase keys must be valid
+ */
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_Raise(__pyx_t_9, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L12;
+ }
+ __pyx_L12:;
+
+ /* "pysam/csamtools.pyx":1284
+ * if ":" not in field:
+ * raise ValueError("malformatted header: no ':' in field" )
* key, value = field.split(":",1) # <<<<<<<<<<<<<<
* # uppercase keys must be valid
* # lowercase are permitted for user fields
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_field, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_field, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_106), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
PyObject* sequence = __pyx_t_7;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_9 = PyList_GET_ITEM(sequence, 0);
__pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_1);
+ #else
+ __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ #endif
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_12 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L14_unpacking_failed;
+ index = 0; __pyx_t_9 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_9)) goto __pyx_L13_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L14_unpacking_failed;
+ index = 1; __pyx_t_1 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_1)) goto __pyx_L13_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- goto __pyx_L15_unpacking_done;
- __pyx_L14_unpacking_failed:;
+ goto __pyx_L14_unpacking_done;
+ __pyx_L13_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L15_unpacking_done:;
+ __pyx_t_13 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L14_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_key);
__pyx_v_key = __pyx_t_9;
@@ -12913,309 +13932,306 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
__pyx_v_value = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1282
+ /* "pysam/csamtools.pyx":1287
* # uppercase keys must be valid
* # lowercase are permitted for user fields
* if key in VALID_HEADER_FIELDS[record]: # <<<<<<<<<<<<<<
* x[key] = VALID_HEADER_FIELDS[record][key](value)
* elif not key.isupper():
*/
- __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_record); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_record); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_3 = ((PySequence_Contains(__pyx_t_1, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1282; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":1283
+ /* "pysam/csamtools.pyx":1288
* # lowercase are permitted for user fields
* if key in VALID_HEADER_FIELDS[record]:
* x[key] = VALID_HEADER_FIELDS[record][key](value) # <<<<<<<<<<<<<<
* elif not key.isupper():
* x[key] = value
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_key); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_t_7, __pyx_v_key); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L16;
+ goto __pyx_L15;
}
- /* "csamtools.pyx":1284
+ /* "pysam/csamtools.pyx":1289
* if key in VALID_HEADER_FIELDS[record]:
* x[key] = VALID_HEADER_FIELDS[record][key](value)
* elif not key.isupper(): # <<<<<<<<<<<<<<
* x[key] = value
* else:
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":1285
+ /* "pysam/csamtools.pyx":1290
* x[key] = VALID_HEADER_FIELDS[record][key](value)
* elif not key.isupper():
* x[key] = value # <<<<<<<<<<<<<<
* else:
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L16;
+ if (PyDict_SetItem(((PyObject *)__pyx_v_x), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L15;
}
/*else*/ {
- /* "csamtools.pyx":1287
+ /* "pysam/csamtools.pyx":1292
* x[key] = value
* else:
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) ) # <<<<<<<<<<<<<<
*
* if VALID_HEADER_TYPES[record] == dict:
*/
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_107), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_111), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_Raise(__pyx_t_9, 0, 0, 0);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L16:;
+ __pyx_L15:;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":1289
+ /* "pysam/csamtools.pyx":1294
* raise ValueError( "unknown field code '%s' in record '%s'" % (key, record) )
*
* if VALID_HEADER_TYPES[record] == dict: # <<<<<<<<<<<<<<
* if record in result:
* raise ValueError( "multiple '%s' lines are not permitted" % record )
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyDict_Type))), Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyDict_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1289; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_4) {
- /* "csamtools.pyx":1290
+ /* "pysam/csamtools.pyx":1295
*
* if VALID_HEADER_TYPES[record] == dict:
* if record in result: # <<<<<<<<<<<<<<
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = ((PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- /* "csamtools.pyx":1291
+ /* "pysam/csamtools.pyx":1296
* if VALID_HEADER_TYPES[record] == dict:
* if record in result:
* raise ValueError( "multiple '%s' lines are not permitted" % record ) # <<<<<<<<<<<<<<
* result[record] = x
* elif VALID_HEADER_TYPES[record] == list:
*/
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_108), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_112), __pyx_v_record); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L18;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L17;
}
- __pyx_L18:;
+ __pyx_L17:;
- /* "csamtools.pyx":1292
+ /* "pysam/csamtools.pyx":1297
* if record in result:
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x # <<<<<<<<<<<<<<
* elif VALID_HEADER_TYPES[record] == list:
* if record not in result: result[record] = []
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L17;
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_v_x)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L16;
}
- /* "csamtools.pyx":1293
+ /* "pysam/csamtools.pyx":1298
* raise ValueError( "multiple '%s' lines are not permitted" % record )
* result[record] = x
* elif VALID_HEADER_TYPES[record] == list: # <<<<<<<<<<<<<<
* if record not in result: result[record] = []
* result[record].append( x )
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetItem(__pyx_t_8, __pyx_v_record); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyList_Type))), Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)((PyObject*)(&PyList_Type))), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_4) {
- /* "csamtools.pyx":1294
+ /* "pysam/csamtools.pyx":1299
* result[record] = x
* elif VALID_HEADER_TYPES[record] == list:
* if record not in result: result[record] = [] # <<<<<<<<<<<<<<
* result[record].append( x )
*
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), __pyx_v_record))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_PyDict_Contains(__pyx_v_record, ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_v_record, ((PyObject *)__pyx_t_8)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- goto __pyx_L19;
+ goto __pyx_L18;
}
- __pyx_L19:;
+ __pyx_L18:;
- /* "csamtools.pyx":1295
+ /* "pysam/csamtools.pyx":1300
* elif VALID_HEADER_TYPES[record] == list:
* if record not in result: result[record] = []
* result[record].append( x ) # <<<<<<<<<<<<<<
*
* # if there are no SQ lines in the header, add the reference names
*/
- __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_v_record); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_8, ((PyObject *)__pyx_v_x)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_Append(__pyx_t_8, ((PyObject *)__pyx_v_x)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L17;
+ goto __pyx_L16;
}
- __pyx_L17:;
- __pyx_L7_continue:;
+ __pyx_L16:;
+ __pyx_L5_continue:;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":1303
+ /* "pysam/csamtools.pyx":1308
* # SQ lines, the SQ information is not part of the textual header and thus
* # are missing from the output. See issue 84.
* if "SQ" not in result: # <<<<<<<<<<<<<<
* sq = []
* for ref, length in zip( self.references, self.lengths ):
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_PyDict_Contains(((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_result), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- /* "csamtools.pyx":1304
+ /* "pysam/csamtools.pyx":1309
* # are missing from the output. See issue 84.
* if "SQ" not in result:
* sq = [] # <<<<<<<<<<<<<<
* for ref, length in zip( self.references, self.lengths ):
* sq.append( {'LN': length, 'SN': ref } )
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_sq = __pyx_t_2;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1309; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_sq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1305
+ /* "pysam/csamtools.pyx":1310
* if "SQ" not in result:
* sq = []
* for ref, length in zip( self.references, self.lengths ): # <<<<<<<<<<<<<<
* sq.append( {'LN': length, 'SN': ref } )
* result["SQ"] = sq
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__references); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__lengths); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_2 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
__pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__pyx_t_6 = Py_TYPE(__pyx_t_8)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_8)) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_8)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
- } else if (PyTuple_CheckExact(__pyx_t_8)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_5); __Pyx_INCREF(__pyx_t_9); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_8, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_9 = __pyx_t_6(__pyx_t_8);
if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -13223,45 +14239,54 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
}
if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_2 = PyList_GET_ITEM(sequence, 0);
__pyx_t_7 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ #endif
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L23_unpacking_failed;
+ index = 0; __pyx_t_2 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_2)) goto __pyx_L22_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L23_unpacking_failed;
+ index = 1; __pyx_t_7 = __pyx_t_13(__pyx_t_1); if (unlikely(!__pyx_t_7)) goto __pyx_L22_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_1), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_1), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L24_unpacking_done;
- __pyx_L23_unpacking_failed:;
+ goto __pyx_L23_unpacking_done;
+ __pyx_L22_unpacking_failed:;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L24_unpacking_done:;
+ __pyx_t_13 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L23_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_2;
@@ -13270,41 +14295,38 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
__pyx_v_length = __pyx_t_7;
__pyx_t_7 = 0;
- /* "csamtools.pyx":1306
+ /* "pysam/csamtools.pyx":1311
* sq = []
* for ref, length in zip( self.references, self.lengths ):
* sq.append( {'LN': length, 'SN': ref } ) # <<<<<<<<<<<<<<
* result["SQ"] = sq
*
*/
- if (unlikely(((PyObject *)__pyx_v_sq) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__LN), __pyx_v_length) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__SN), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_14 = PyList_Append(__pyx_v_sq, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__LN), __pyx_v_length) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__SN), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyList_Append(__pyx_v_sq, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":1307
+ /* "pysam/csamtools.pyx":1312
* for ref, length in zip( self.references, self.lengths ):
* sq.append( {'LN': length, 'SN': ref } )
* result["SQ"] = sq # <<<<<<<<<<<<<<
*
* return result
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_sq)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L20;
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_v_sq)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L19;
}
- __pyx_L20:;
- goto __pyx_L6;
+ __pyx_L19:;
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":1309
+ /* "pysam/csamtools.pyx":1314
* result["SQ"] = sq
*
* return result # <<<<<<<<<<<<<<
@@ -13325,7 +14347,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_12);
- __Pyx_AddTraceback("csamtools.Samfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.header.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
@@ -13346,63 +14368,40 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_6header___get__(PyObject *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":1311
- * return result
- *
- * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
- * '''build a header line from *fields* dictionary for *record*'''
- *
- */
-
-static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_19_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
-static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_38_buildLine[] = "Samfile._buildLine(self, fields, record)\nbuild a header line from *fields* dictionary for *record*";
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_fields = 0;
PyObject *__pyx_v_record = 0;
- PyObject *__pyx_v_line = NULL;
- PyObject *__pyx_v_key = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- Py_ssize_t __pyx_t_5;
- PyObject *(*__pyx_t_6)(PyObject *);
- PyObject *__pyx_t_7 = NULL;
- int __pyx_t_8;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildLine");
- __Pyx_TraceCall("_buildLine", __pyx_f[0], 1311);
+ __Pyx_RefNannySetupContext("_buildLine (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__fields,&__pyx_n_s__record,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fields)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1316; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_buildLine") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1316; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -13415,107 +14414,146 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1311; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_buildLine", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1316; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self), __pyx_v_fields, __pyx_v_record);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1316
+ * return result
+ *
+ * def _buildLine( self, fields, record ): # <<<<<<<<<<<<<<
+ * '''build a header line from *fields* dictionary for *record*'''
+ *
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_38_buildLine(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_fields, PyObject *__pyx_v_record) {
+ PyObject *__pyx_v_line = NULL;
+ PyObject *__pyx_v_key = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
+ PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_8;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_buildLine", 0);
+ __Pyx_TraceCall("_buildLine", __pyx_f[0], 1316);
- /* "csamtools.pyx":1315
+ /* "pysam/csamtools.pyx":1320
*
* # TODO: add checking for field and sort order
* line = ["@%s" % record ] # <<<<<<<<<<<<<<
* # comment
* if record == "CO":
*/
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_109), __pyx_v_record); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_113), __pyx_v_record); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_v_line = __pyx_t_2;
+ __pyx_v_line = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1317
+ /* "pysam/csamtools.pyx":1322
* line = ["@%s" % record ]
* # comment
* if record == "CO": # <<<<<<<<<<<<<<
* line.append( fields )
* # user tags
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_record, ((PyObject *)__pyx_n_s__CO), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":1318
+ /* "pysam/csamtools.pyx":1323
* # comment
* if record == "CO":
* line.append( fields ) # <<<<<<<<<<<<<<
* # user tags
* elif record.islower():
*/
- if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = PyList_Append(__pyx_v_line, __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ __pyx_t_4 = PyList_Append(__pyx_v_line, __pyx_v_fields); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- /* "csamtools.pyx":1320
+ /* "pysam/csamtools.pyx":1325
* line.append( fields )
* # user tags
* elif record.islower(): # <<<<<<<<<<<<<<
* for key in sorted(fields):
* line.append( "%s:%s" % (key, str(fields[key])))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__islower); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_record, __pyx_n_s__islower); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":1321
+ /* "pysam/csamtools.pyx":1326
* # user tags
* elif record.islower():
* for key in sorted(fields): # <<<<<<<<<<<<<<
* line.append( "%s:%s" % (key, str(fields[key])))
* # defined tags
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
- __pyx_t_2 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
__pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -13525,79 +14563,84 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1322
+ /* "pysam/csamtools.pyx":1327
* elif record.islower():
* for key in sorted(fields):
* line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
* # defined tags
* else:
*/
- if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_114), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L6;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":1326
+ /* "pysam/csamtools.pyx":1331
* else:
* # write fields of the specification
* for key in VALID_HEADER_ORDER[record]: # <<<<<<<<<<<<<<
* if key in fields:
* line.append( "%s:%s" % (key, str(fields[key])))
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
__pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -13607,56 +14650,53 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1327
+ /* "pysam/csamtools.pyx":1332
* # write fields of the specification
* for key in VALID_HEADER_ORDER[record]:
* if key in fields: # <<<<<<<<<<<<<<
* line.append( "%s:%s" % (key, str(fields[key])))
* # write user fields
*/
- __pyx_t_3 = ((PySequence_Contains(__pyx_v_fields, __pyx_v_key))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_v_fields, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "csamtools.pyx":1328
+ /* "pysam/csamtools.pyx":1333
* for key in VALID_HEADER_ORDER[record]:
* if key in fields:
* line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
* # write user fields
* for key in fields:
*/
- if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_114), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- goto __pyx_L11;
+ goto __pyx_L8;
}
- __pyx_L11:;
+ __pyx_L8:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":1330
+ /* "pysam/csamtools.pyx":1335
* line.append( "%s:%s" % (key, str(fields[key])))
* # write user fields
* for key in fields: # <<<<<<<<<<<<<<
@@ -13667,23 +14707,31 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
__pyx_t_1 = __pyx_v_fields; __Pyx_INCREF(__pyx_t_1); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_fields); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_fields); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -13693,65 +14741,62 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1331
+ /* "pysam/csamtools.pyx":1336
* # write user fields
* for key in fields:
* if not key.isupper(): # <<<<<<<<<<<<<<
* line.append( "%s:%s" % (key, str(fields[key])))
*
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_key, __pyx_n_s__isupper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_8 = (!__pyx_t_3);
if (__pyx_t_8) {
- /* "csamtools.pyx":1332
+ /* "pysam/csamtools.pyx":1337
* for key in fields:
* if not key.isupper():
* line.append( "%s:%s" % (key, str(fields[key]))) # <<<<<<<<<<<<<<
*
* return "\t".join( line )
*/
- if (unlikely(((PyObject *)__pyx_v_line) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_110), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_114), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_line, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L14;
+ goto __pyx_L11;
}
- __pyx_L14:;
+ __pyx_L11:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1334
+ /* "pysam/csamtools.pyx":1339
* line.append( "%s:%s" % (key, str(fields[key])))
*
* return "\t".join( line ) # <<<<<<<<<<<<<<
@@ -13759,14 +14804,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
* cdef bam_header_t * _buildHeader( self, new_header ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(((PyObject *)__pyx_v_line));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_line));
__Pyx_GIVEREF(((PyObject *)__pyx_v_line));
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -13780,7 +14825,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_AddTraceback("csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._buildLine", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_line);
@@ -13791,7 +14836,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":1336
+/* "pysam/csamtools.pyx":1341
* return "\t".join( line )
*
* cdef bam_header_t * _buildHeader( self, new_header ): # <<<<<<<<<<<<<<
@@ -13799,7 +14844,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_19_buildLine(PyObject *__pyx_v_sel
*
*/
-static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_new_header) {
+static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self, PyObject *__pyx_v_new_header) {
PyObject *__pyx_v_lines = NULL;
bam_header_t *__pyx_v_dest;
PyObject *__pyx_v_record = NULL;
@@ -13839,22 +14884,22 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_buildHeader");
- __Pyx_TraceCall("_buildHeader", __pyx_f[0], 1336);
+ __Pyx_RefNannySetupContext("_buildHeader", 0);
+ __Pyx_TraceCall("_buildHeader", __pyx_f[0], 1341);
- /* "csamtools.pyx":1342
+ /* "pysam/csamtools.pyx":1347
* '''
*
* lines = [] # <<<<<<<<<<<<<<
*
* # check if hash exists
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_lines = __pyx_t_1;
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_lines = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":1349
+ /* "pysam/csamtools.pyx":1354
* cdef bam_header_t * dest
*
* dest = bam_header_init() # <<<<<<<<<<<<<<
@@ -13863,37 +14908,45 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
*/
__pyx_v_dest = bam_header_init();
- /* "csamtools.pyx":1352
+ /* "pysam/csamtools.pyx":1357
*
* # first: defined tags
* for record in VALID_HEADERS: # <<<<<<<<<<<<<<
* if record in new_header:
* ttype = VALID_HEADER_TYPES[record]
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_2)) {
+ if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
- } else if (PyTuple_CheckExact(__pyx_t_2)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_1 = __pyx_t_4(__pyx_t_2);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -13903,72 +14956,71 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_v_record = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1353
+ /* "pysam/csamtools.pyx":1358
* # first: defined tags
* for record in VALID_HEADERS:
* if record in new_header: # <<<<<<<<<<<<<<
* ttype = VALID_HEADER_TYPES[record]
* data = new_header[record]
*/
- __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_v_new_header, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "csamtools.pyx":1354
+ /* "pysam/csamtools.pyx":1359
* for record in VALID_HEADERS:
* if record in new_header:
* ttype = VALID_HEADER_TYPES[record] # <<<<<<<<<<<<<<
* data = new_header[record]
* if type( data ) != type( ttype() ):
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_1, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_ttype);
__pyx_v_ttype = __pyx_t_6;
__pyx_t_6 = 0;
- /* "csamtools.pyx":1355
+ /* "pysam/csamtools.pyx":1360
* if record in new_header:
* ttype = VALID_HEADER_TYPES[record]
* data = new_header[record] # <<<<<<<<<<<<<<
* if type( data ) != type( ttype() ):
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
*/
- __pyx_t_6 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_data);
__pyx_v_data = __pyx_t_6;
__pyx_t_6 = 0;
- /* "csamtools.pyx":1356
+ /* "pysam/csamtools.pyx":1361
* ttype = VALID_HEADER_TYPES[record]
* data = new_header[record]
* if type( data ) != type( ttype() ): # <<<<<<<<<<<<<<
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
* if type( data ) is dict:
*/
- __pyx_t_6 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_6)), Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(__pyx_t_6)), Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
- /* "csamtools.pyx":1357
+ /* "pysam/csamtools.pyx":1362
* data = new_header[record]
* if type( data ) != type( ttype() ):
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) ) # <<<<<<<<<<<<<<
* if type( data ) is dict:
* lines.append( self._buildLine( data, record ) )
*/
- __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_v_ttype, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
@@ -13979,25 +15031,25 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
PyTuple_SET_ITEM(__pyx_t_6, 2, ((PyObject *)Py_TYPE(__pyx_t_1)));
__Pyx_GIVEREF(((PyObject *)Py_TYPE(__pyx_t_1)));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_111), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_115), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L6;
}
__pyx_L6:;
- /* "csamtools.pyx":1358
+ /* "pysam/csamtools.pyx":1363
* if type( data ) != type( ttype() ):
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
* if type( data ) is dict: # <<<<<<<<<<<<<<
@@ -14007,67 +15059,72 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_t_5 = (((PyObject *)Py_TYPE(__pyx_v_data)) == ((PyObject *)((PyObject*)(&PyDict_Type))));
if (__pyx_t_5) {
- /* "csamtools.pyx":1359
+ /* "pysam/csamtools.pyx":1364
* raise ValueError( "invalid type for record %s: %s, expected %s" % (record, type(data), type(ttype()) ) )
* if type( data ) is dict:
* lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
* else:
* for fields in new_header[record]:
*/
- if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L7;
}
/*else*/ {
- /* "csamtools.pyx":1361
+ /* "pysam/csamtools.pyx":1366
* lines.append( self._buildLine( data, record ) )
* else:
* for fields in new_header[record]: # <<<<<<<<<<<<<<
* lines.append( self._buildLine( fields, record ) )
*
*/
- __pyx_t_7 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
__pyx_t_6 = __pyx_t_7; __Pyx_INCREF(__pyx_t_6); __pyx_t_9 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_9 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = -1; __pyx_t_6 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_10 = Py_TYPE(__pyx_t_6)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_6)) {
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_6)) {
if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
- } else if (PyTuple_CheckExact(__pyx_t_6)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_6)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_6, __pyx_t_9); __Pyx_INCREF(__pyx_t_7); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_6, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_7 = __pyx_t_10(__pyx_t_6);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -14077,31 +15134,28 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_v_fields = __pyx_t_7;
__pyx_t_7 = 0;
- /* "csamtools.pyx":1362
+ /* "pysam/csamtools.pyx":1367
* else:
* for fields in new_header[record]:
* lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
*
* # then: user tags (lower case), sorted alphabetically
*/
- if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_11 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_11); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_11); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
@@ -14113,48 +15167,56 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":1365
+ /* "pysam/csamtools.pyx":1370
*
* # then: user tags (lower case), sorted alphabetically
* for record, data in sorted(new_header.items()): # <<<<<<<<<<<<<<
* if record in VALID_HEADERS: continue
* if type( data ) is dict:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_new_header, __pyx_n_s__items); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_new_header, __pyx_n_s__items); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_sorted, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
if (PyList_CheckExact(__pyx_t_6) || PyTuple_CheckExact(__pyx_t_6)) {
__pyx_t_2 = __pyx_t_6; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_2)) {
+ if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
- } else if (PyTuple_CheckExact(__pyx_t_2)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_6 = __pyx_t_4(__pyx_t_2);
if (unlikely(!__pyx_t_6)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -14162,29 +15224,37 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
PyObject* sequence = __pyx_t_6;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_11 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_11 = PyList_GET_ITEM(sequence, 0);
__pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_11);
__Pyx_INCREF(__pyx_t_1);
+ #else
+ __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ #endif
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_7)->tp_iternext;
@@ -14192,14 +15262,15 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_11);
index = 1; __pyx_t_1 = __pyx_t_12(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L12_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L13_unpacking_done;
__pyx_L12_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L13_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_record);
@@ -14209,16 +15280,16 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_v_data = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1366
+ /* "pysam/csamtools.pyx":1371
* # then: user tags (lower case), sorted alphabetically
* for record, data in sorted(new_header.items()):
* if record in VALID_HEADERS: continue # <<<<<<<<<<<<<<
* if type( data ) is dict:
* lines.append( self._buildLine( data, record ) )
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__VALID_HEADERS); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = ((PySequence_Contains(__pyx_t_6, __pyx_v_record))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_record, __pyx_t_6, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_5) {
goto __pyx_L10_continue;
@@ -14226,7 +15297,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__pyx_L14:;
- /* "csamtools.pyx":1367
+ /* "pysam/csamtools.pyx":1372
* for record, data in sorted(new_header.items()):
* if record in VALID_HEADERS: continue
* if type( data ) is dict: # <<<<<<<<<<<<<<
@@ -14236,67 +15307,72 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_t_5 = (((PyObject *)Py_TYPE(__pyx_v_data)) == ((PyObject *)((PyObject*)(&PyDict_Type))));
if (__pyx_t_5) {
- /* "csamtools.pyx":1368
+ /* "pysam/csamtools.pyx":1373
* if record in VALID_HEADERS: continue
* if type( data ) is dict:
* lines.append( self._buildLine( data, record ) ) # <<<<<<<<<<<<<<
* else:
* for fields in new_header[record]:
*/
- if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_11 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_11); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_11); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
goto __pyx_L15;
}
/*else*/ {
- /* "csamtools.pyx":1370
+ /* "pysam/csamtools.pyx":1375
* lines.append( self._buildLine( data, record ) )
* else:
* for fields in new_header[record]: # <<<<<<<<<<<<<<
* lines.append( self._buildLine( fields, record ) )
*
*/
- __pyx_t_11 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetItem(__pyx_v_new_header, __pyx_v_record); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
if (PyList_CheckExact(__pyx_t_11) || PyTuple_CheckExact(__pyx_t_11)) {
__pyx_t_1 = __pyx_t_11; __Pyx_INCREF(__pyx_t_1); __pyx_t_9 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_9 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_11); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_10 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_11 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_11 = PySequence_ITEM(__pyx_t_1, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_11 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_9); __Pyx_INCREF(__pyx_t_11); __pyx_t_9++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_11 = PySequence_ITEM(__pyx_t_1, __pyx_t_9); __pyx_t_9++; if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_11 = __pyx_t_10(__pyx_t_1);
if (unlikely(!__pyx_t_11)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -14306,31 +15382,28 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_v_fields = __pyx_t_11;
__pyx_t_11 = 0;
- /* "csamtools.pyx":1371
+ /* "pysam/csamtools.pyx":1376
* else:
* for fields in new_header[record]:
* lines.append( self._buildLine( fields, record ) ) # <<<<<<<<<<<<<<
*
* text = "\n".join(lines) + "\n"
*/
- if (unlikely(((PyObject *)__pyx_v_lines) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___buildLine); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
__Pyx_INCREF(__pyx_v_record);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_record);
__Pyx_GIVEREF(__pyx_v_record);
- __pyx_t_7 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyList_Append(__pyx_v_lines, __pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -14340,31 +15413,31 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":1373
+ /* "pysam/csamtools.pyx":1378
* lines.append( self._buildLine( fields, record ) )
*
* text = "\n".join(lines) + "\n" # <<<<<<<<<<<<<<
* if dest.text != NULL: free( dest.text )
* dest.text = <char*>calloc( len(text), sizeof(char))
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_v_lines));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_lines));
__Pyx_GIVEREF(((PyObject *)__pyx_v_lines));
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Add(__pyx_t_7, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_7, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_v_text = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1374
+ /* "pysam/csamtools.pyx":1379
*
* text = "\n".join(lines) + "\n"
* if dest.text != NULL: free( dest.text ) # <<<<<<<<<<<<<<
@@ -14378,105 +15451,113 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__pyx_L18:;
- /* "csamtools.pyx":1375
+ /* "pysam/csamtools.pyx":1380
* text = "\n".join(lines) + "\n"
* if dest.text != NULL: free( dest.text )
* dest.text = <char*>calloc( len(text), sizeof(char)) # <<<<<<<<<<<<<<
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii')
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest->text = ((char *)calloc(__pyx_t_3, (sizeof(char))));
- /* "csamtools.pyx":1376
+ /* "pysam/csamtools.pyx":1381
* if dest.text != NULL: free( dest.text )
* dest.text = <char*>calloc( len(text), sizeof(char))
* dest.l_text = len(text) # <<<<<<<<<<<<<<
* cdef bytes btext = text.encode('ascii')
* strncpy( dest.text, btext, dest.l_text )
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_text); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest->l_text = __pyx_t_3;
- /* "csamtools.pyx":1377
+ /* "pysam/csamtools.pyx":1382
* dest.text = <char*>calloc( len(text), sizeof(char))
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<<
* strncpy( dest.text, btext, dest.l_text )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_text, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_text, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_116), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_7))||((__pyx_t_7) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_7)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_btext = ((PyObject*)__pyx_t_7);
__pyx_t_7 = 0;
- /* "csamtools.pyx":1378
+ /* "pysam/csamtools.pyx":1383
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii')
* strncpy( dest.text, btext, dest.l_text ) # <<<<<<<<<<<<<<
*
* cdef bytes bseqname
*/
- __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_btext)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_btext)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
strncpy(__pyx_v_dest->text, __pyx_t_13, __pyx_v_dest->l_text);
- /* "csamtools.pyx":1382
+ /* "pysam/csamtools.pyx":1387
* cdef bytes bseqname
* # collect targets
* if "SQ" in new_header: # <<<<<<<<<<<<<<
* seqs = []
* for fields in new_header["SQ"]:
*/
- __pyx_t_5 = ((PySequence_Contains(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__SQ), __pyx_v_new_header, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "csamtools.pyx":1383
+ /* "pysam/csamtools.pyx":1388
* # collect targets
* if "SQ" in new_header:
* seqs = [] # <<<<<<<<<<<<<<
* for fields in new_header["SQ"]:
* try:
*/
- __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_v_seqs = __pyx_t_7;
+ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_v_seqs = ((PyObject*)__pyx_t_7);
__pyx_t_7 = 0;
- /* "csamtools.pyx":1384
+ /* "pysam/csamtools.pyx":1389
* if "SQ" in new_header:
* seqs = []
* for fields in new_header["SQ"]: # <<<<<<<<<<<<<<
* try:
* seqs.append( (fields["SN"], fields["LN"] ) )
*/
- __pyx_t_7 = PyObject_GetItem(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_new_header, ((PyObject *)__pyx_n_s__SQ)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
__pyx_t_1 = __pyx_t_7; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_7 = __pyx_t_4(__pyx_t_1);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -14486,7 +15567,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_v_fields = __pyx_t_7;
__pyx_t_7 = 0;
- /* "csamtools.pyx":1385
+ /* "pysam/csamtools.pyx":1390
* seqs = []
* for fields in new_header["SQ"]:
* try: # <<<<<<<<<<<<<<
@@ -14500,29 +15581,26 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
- /* "csamtools.pyx":1386
+ /* "pysam/csamtools.pyx":1391
* for fields in new_header["SQ"]:
* try:
* seqs.append( (fields["SN"], fields["LN"] ) ) # <<<<<<<<<<<<<<
* except KeyError:
* raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*/
- if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- }
- __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__SN)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1391; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, ((PyObject *)__pyx_n_s__LN)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1391; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1391; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_7 = 0;
__pyx_t_2 = 0;
- __pyx_t_8 = PyList_Append(__pyx_v_seqs, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1386; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
+ __pyx_t_8 = PyList_Append(__pyx_v_seqs, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1391; __pyx_clineno = __LINE__; goto __pyx_L22_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
}
__Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
@@ -14535,7 +15613,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "csamtools.pyx":1387
+ /* "pysam/csamtools.pyx":1392
* try:
* seqs.append( (fields["SN"], fields["LN"] ) )
* except KeyError: # <<<<<<<<<<<<<<
@@ -14544,41 +15622,41 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
*/
__pyx_t_17 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_17) {
- __Pyx_AddTraceback("csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1387; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_AddTraceback("pysam.csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1392; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_7);
- /* "csamtools.pyx":1388
+ /* "pysam/csamtools.pyx":1393
* seqs.append( (fields["SN"], fields["LN"] ) )
* except KeyError:
* raise KeyError( "incomplete sequence information in '%s'" % str(fields)) # <<<<<<<<<<<<<<
*
* dest.n_targets = len(seqs)
*/
- __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_11));
+ __pyx_t_11 = PyTuple_New(1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_11);
__Pyx_INCREF(__pyx_v_fields);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_fields);
__Pyx_GIVEREF(__pyx_v_fields);
- __pyx_t_18 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __pyx_t_18 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
- __pyx_t_11 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_113), __pyx_t_18); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __pyx_t_11 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_117), __pyx_t_18); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_11));
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_18));
+ __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __Pyx_GOTREF(__pyx_t_18);
PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11));
__Pyx_GIVEREF(((PyObject *)__pyx_t_11));
__pyx_t_11 = 0;
- __pyx_t_11 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ __pyx_t_11 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0;
__Pyx_Raise(__pyx_t_11, 0, 0, 0);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1388; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1393; __pyx_clineno = __LINE__; goto __pyx_L24_except_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
@@ -14600,20 +15678,17 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":1390
+ /* "pysam/csamtools.pyx":1395
* raise KeyError( "incomplete sequence information in '%s'" % str(fields))
*
* dest.n_targets = len(seqs) # <<<<<<<<<<<<<<
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*/
- if (unlikely(((PyObject *)__pyx_v_seqs) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs));
+ __pyx_t_3 = PyList_GET_SIZE(((PyObject *)__pyx_v_seqs)); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_dest->n_targets = __pyx_t_3;
- /* "csamtools.pyx":1391
+ /* "pysam/csamtools.pyx":1396
*
* dest.n_targets = len(seqs)
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) ) # <<<<<<<<<<<<<<
@@ -14622,7 +15697,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
*/
__pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *))));
- /* "csamtools.pyx":1392
+ /* "pysam/csamtools.pyx":1397
* dest.n_targets = len(seqs)
* dest.target_name = <char**>calloc( dest.n_targets, sizeof(char*) )
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) ) # <<<<<<<<<<<<<<
@@ -14631,7 +15706,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
*/
__pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t))));
- /* "csamtools.pyx":1394
+ /* "pysam/csamtools.pyx":1399
* dest.target_len = <uint32_t*>calloc( dest.n_targets, sizeof(uint32_t) )
*
* for x from 0 <= x < dest.n_targets: # <<<<<<<<<<<<<<
@@ -14641,40 +15716,48 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_t_19 = __pyx_v_dest->n_targets;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_19; __pyx_v_x++) {
- /* "csamtools.pyx":1395
+ /* "pysam/csamtools.pyx":1400
*
* for x from 0 <= x < dest.n_targets:
* seqname, seqlen = seqs[x] # <<<<<<<<<<<<<<
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii')
*/
- __pyx_t_1 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_seqs), __pyx_v_x, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
PyObject* sequence = __pyx_t_1;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_7 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_7);
__Pyx_INCREF(__pyx_t_2);
+ #else
+ __pyx_t_7 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ #endif
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_6 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_6)->tp_iternext;
@@ -14682,14 +15765,15 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_GOTREF(__pyx_t_7);
index = 1; __pyx_t_2 = __pyx_t_12(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L34_unpacking_failed;
__Pyx_GOTREF(__pyx_t_2);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L35_unpacking_done;
__pyx_L34_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1400; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L35_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_seqname);
@@ -14699,59 +15783,59 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__pyx_v_seqlen = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1396
+ /* "pysam/csamtools.pyx":1401
* for x from 0 <= x < dest.n_targets:
* seqname, seqlen = seqs[x]
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) ) # <<<<<<<<<<<<<<
* bseqname = seqname.encode('ascii')
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1396; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1401; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
(__pyx_v_dest->target_name[__pyx_v_x]) = ((char *)calloc((__pyx_t_3 + 1), (sizeof(char))));
- /* "csamtools.pyx":1397
+ /* "pysam/csamtools.pyx":1402
* seqname, seqlen = seqs[x]
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<<
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
* dest.target_len[x] = seqlen
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_seqname, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_seqname, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_114), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_118), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!(likely(PyBytes_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(PyBytes_CheckExact(__pyx_t_2))||((__pyx_t_2) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_2)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_XDECREF(((PyObject *)__pyx_v_bseqname));
__pyx_v_bseqname = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1398
+ /* "pysam/csamtools.pyx":1403
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii')
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 ) # <<<<<<<<<<<<<<
* dest.target_len[x] = seqlen
*
*/
- __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_bseqname)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_bseqname)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_seqname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1403; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
strncpy((__pyx_v_dest->target_name[__pyx_v_x]), __pyx_t_13, (__pyx_t_3 + 1));
- /* "csamtools.pyx":1399
+ /* "pysam/csamtools.pyx":1404
* bseqname = seqname.encode('ascii')
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
* dest.target_len[x] = seqlen # <<<<<<<<<<<<<<
*
* return dest
*/
- __pyx_t_20 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_seqlen); if (unlikely((__pyx_t_20 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1399; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_20 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_seqlen); if (unlikely((__pyx_t_20 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
(__pyx_v_dest->target_len[__pyx_v_x]) = __pyx_t_20;
}
goto __pyx_L19;
}
__pyx_L19:;
- /* "csamtools.pyx":1401
+ /* "pysam/csamtools.pyx":1406
* dest.target_len[x] = seqlen
*
* return dest # <<<<<<<<<<<<<<
@@ -14770,7 +15854,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_11);
__Pyx_XDECREF(__pyx_t_18);
- __Pyx_WriteUnraisable("csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.csamtools.Samfile._buildHeader", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_lines);
@@ -14789,7 +15873,18 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
return __pyx_r;
}
-/* "csamtools.pyx":1411
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_41__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1416
* ## Possible solutions: deprecate or open new file handle
* ###############################################################
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -14797,8 +15892,7 @@ static bam_header_t *__pyx_f_9csamtools_7Samfile__buildHeader(struct __pyx_obj_9
* if not self.isbam and self.samfile.header.n_targets == 0:
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_40__iter__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -14810,67 +15904,67 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self)
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1411);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1416);
- /* "csamtools.pyx":1412
+ /* "pysam/csamtools.pyx":1417
* ###############################################################
* def __iter__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header")
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_115), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_119), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1413
+ /* "pysam/csamtools.pyx":1418
* def __iter__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam and self.samfile.header.n_targets == 0: # <<<<<<<<<<<<<<
* raise NotImplementedError( "can not iterate over samfile without header")
* return self
*/
- __pyx_t_4 = (!((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->isbam);
+ __pyx_t_4 = (!__pyx_v_self->isbam);
if (__pyx_t_4) {
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile->header->n_targets == 0);
+ __pyx_t_3 = (__pyx_v_self->samfile->header->n_targets == 0);
__pyx_t_5 = __pyx_t_3;
} else {
__pyx_t_5 = __pyx_t_4;
}
if (__pyx_t_5) {
- /* "csamtools.pyx":1414
+ /* "pysam/csamtools.pyx":1419
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<<
* return self
*
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_121), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":1415
+ /* "pysam/csamtools.pyx":1420
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header")
* return self # <<<<<<<<<<<<<<
@@ -14878,8 +15972,8 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self)
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -14887,7 +15981,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self)
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.__iter__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -14896,7 +15990,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self)
return __pyx_r;
}
-/* "csamtools.pyx":1417
+/* "pysam/csamtools.pyx":1422
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
@@ -14904,14 +15998,14 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_20__iter__(PyObject *__pyx_v_self)
*
*/
-static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static bam1_t *__pyx_f_5pysam_9csamtools_7Samfile_getCurrent(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1417);
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1422);
- /* "csamtools.pyx":1418
+ /* "pysam/csamtools.pyx":1423
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
@@ -14928,7 +16022,7 @@ static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtool
return __pyx_r;
}
-/* "csamtools.pyx":1420
+/* "pysam/csamtools.pyx":1425
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
@@ -14936,14 +16030,14 @@ static bam1_t *__pyx_f_9csamtools_7Samfile_getCurrent(struct __pyx_obj_9csamtool
* cversion of iterator. Used by :class:`pysam.Samfile.IteratorColumn`.
*/
-static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile *__pyx_v_self) {
+static int __pyx_f_5pysam_9csamtools_7Samfile_cnext(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1420);
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1425);
- /* "csamtools.pyx":1425
+ /* "pysam/csamtools.pyx":1430
* '''
* cdef int ret
* return samread(self.samfile, self.b) # <<<<<<<<<<<<<<
@@ -14960,7 +16054,22 @@ static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile
return __pyx_r;
}
-/* "csamtools.pyx":1427
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_7Samfile_42__next__[] = "\n python version of next().\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_43__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7Samfile_42__next__(((struct __pyx_obj_5pysam_9csamtools_Samfile *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1432
* return samread(self.samfile, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -14968,10 +16077,7 @@ static int __pyx_f_9csamtools_7Samfile_cnext(struct __pyx_obj_9csamtools_Samfile
* python version of next().
*/
-static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_7Samfile_21__next__[] = "\n python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_7Samfile_21__next__;
-static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_42__next__(struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -14981,19 +16087,19 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self)
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1427);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1432);
- /* "csamtools.pyx":1432
+ /* "pysam/csamtools.pyx":1437
* """
* cdef int ret
* ret = samread(self.samfile, self.b) # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->samfile, ((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b);
+ __pyx_v_ret = samread(__pyx_v_self->samfile, __pyx_v_self->b);
- /* "csamtools.pyx":1433
+ /* "pysam/csamtools.pyx":1438
* cdef int ret
* ret = samread(self.samfile, self.b)
* if (ret > 0): # <<<<<<<<<<<<<<
@@ -15003,7 +16109,7 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self)
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "csamtools.pyx":1434
+ /* "pysam/csamtools.pyx":1439
* ret = samread(self.samfile, self.b)
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
@@ -15011,16 +16117,16 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self)
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_Samfile *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":1436
+ /* "pysam/csamtools.pyx":1441
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -15028,15 +16134,15 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self)
* ##-------------------------------------------------------------------
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.Samfile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Samfile.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -15045,42 +16151,24 @@ static PyObject *__pyx_pf_9csamtools_7Samfile_21__next__(PyObject *__pyx_v_self)
return __pyx_r;
}
-/* "csamtools.pyx":1481
- * """
- *
- * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
-
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_tid;
int __pyx_v_beg;
int __pyx_v_end;
int __pyx_v_reopen;
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1481);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__beg,&__pyx_n_s__end,&__pyx_n_s__reopen,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -15090,28 +16178,24 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__beg)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
if (kw_args > 0) {
@@ -15120,7 +16204,7 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -15133,93 +16217,127 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
- __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_beg = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_beg == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
+ __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_beg = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_beg == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
if (values[4]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
+
+ /* "pysam/csamtools.pyx":1486
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
__pyx_v_reopen = ((int)1);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 4, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_beg, __pyx_v_end, __pyx_v_reopen);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static int __pyx_pf_5pysam_9csamtools_17IteratorRowRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_beg, int __pyx_v_end, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ samfile_t *__pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1486);
- /* "csamtools.pyx":1483
+ /* "pysam/csamtools.pyx":1488
* def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":1484
+ /* "pysam/csamtools.pyx":1489
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* if not samfile._hasIndex():
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_118), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1486
+ /* "pysam/csamtools.pyx":1491
* raise ValueError( "I/O operation on closed file" )
*
* if not samfile._hasIndex(): # <<<<<<<<<<<<<<
* raise ValueError( "no index available for iteration" )
*
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "csamtools.pyx":1487
+ /* "pysam/csamtools.pyx":1492
*
* if not samfile._hasIndex():
* raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
*
* # makes sure that samfile stays alive as long as the
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_120), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_124), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "csamtools.pyx":1491
+ /* "pysam/csamtools.pyx":1496
* # makes sure that samfile stays alive as long as the
* # iterator is alive
* self.samfile = samfile # <<<<<<<<<<<<<<
@@ -15228,11 +16346,11 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "csamtools.pyx":1493
+ /* "pysam/csamtools.pyx":1498
* self.samfile = samfile
*
* if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
@@ -15242,11 +16360,11 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L8;
+ goto __pyx_L5;
}
/*else*/ {
- /* "csamtools.pyx":1494
+ /* "pysam/csamtools.pyx":1499
*
* if samfile.isbam: mode = b"rb"
* else: mode = b"r" # <<<<<<<<<<<<<<
@@ -15256,9 +16374,9 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L8:;
+ __pyx_L5:;
- /* "csamtools.pyx":1498
+ /* "pysam/csamtools.pyx":1503
* # reopen the file - note that this makes the iterator
* # slow and causes pileup to slow down significantly.
* if reopen: # <<<<<<<<<<<<<<
@@ -15267,46 +16385,46 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
*/
if (__pyx_v_reopen) {
- /* "csamtools.pyx":1499
+ /* "pysam/csamtools.pyx":1504
* # slow and causes pileup to slow down significantly.
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_store = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1500
+ /* "pysam/csamtools.pyx":1505
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* store.release()
* assert self.fp != NULL
*/
- __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "csamtools.pyx":1501
+ /* "pysam/csamtools.pyx":1506
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
* assert self.fp != NULL
* self.owns_samfile = True
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":1502
+ /* "pysam/csamtools.pyx":1507
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
@@ -15314,77 +16432,78 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp != NULL))) {
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1503
+ /* "pysam/csamtools.pyx":1508
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = self.samfile.samfile
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L9;
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L6;
}
/*else*/ {
- /* "csamtools.pyx":1505
+ /* "pysam/csamtools.pyx":1510
* self.owns_samfile = True
* else:
* self.fp = self.samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->samfile;
+ __pyx_t_6 = __pyx_v_self->samfile->samfile;
+ __pyx_v_self->fp = __pyx_t_6;
- /* "csamtools.pyx":1506
+ /* "pysam/csamtools.pyx":1511
* else:
* self.fp = self.samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* self.retval = 0
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile = 0;
+ __pyx_v_self->owns_samfile = 0;
}
- __pyx_L9:;
+ __pyx_L6:;
- /* "csamtools.pyx":1508
+ /* "pysam/csamtools.pyx":1513
* self.owns_samfile = False
*
* self.retval = 0 # <<<<<<<<<<<<<<
*
* self.iter = bam_iter_query(self.samfile.index,
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval = 0;
+ __pyx_v_self->retval = 0;
- /* "csamtools.pyx":1510
+ /* "pysam/csamtools.pyx":1515
* self.retval = 0
*
* self.iter = bam_iter_query(self.samfile.index, # <<<<<<<<<<<<<<
* tid,
* beg,
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter = bam_iter_query(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
+ __pyx_v_self->iter = bam_iter_query(__pyx_v_self->samfile->index, __pyx_v_tid, __pyx_v_beg, __pyx_v_end);
- /* "csamtools.pyx":1514
+ /* "pysam/csamtools.pyx":1519
* beg,
* end)
* self.b = bam_init1() # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b = bam_init1();
+ __pyx_v_self->b = bam_init1();
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
@@ -15394,7 +16513,18 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":1516
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1521
* self.b = bam_init1()
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -15402,15 +16532,14 @@ static int __pyx_pf_9csamtools_17IteratorRowRegion___cinit__(PyObject *__pyx_v_s
*
*/
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1516);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1521);
- /* "csamtools.pyx":1517
+ /* "pysam/csamtools.pyx":1522
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -15418,8 +16547,8 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__p
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -15430,7 +16559,7 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":1519
+/* "pysam/csamtools.pyx":1524
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
@@ -15438,14 +16567,14 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_1__iter__(PyObject *__p
*
*/
-static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static bam1_t *__pyx_f_5pysam_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1519);
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1524);
- /* "csamtools.pyx":1520
+ /* "pysam/csamtools.pyx":1525
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
@@ -15462,7 +16591,7 @@ static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_ob
return __pyx_r;
}
-/* "csamtools.pyx":1522
+/* "pysam/csamtools.pyx":1527
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
@@ -15470,14 +16599,14 @@ static bam1_t *__pyx_f_9csamtools_17IteratorRowRegion_getCurrent(struct __pyx_ob
* self.retval = bam_iter_read( self.fp.x.bam,
*/
-static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamtools_IteratorRowRegion *__pyx_v_self) {
+static int __pyx_f_5pysam_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1522);
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1527);
- /* "csamtools.pyx":1524
+ /* "pysam/csamtools.pyx":1529
* cdef int cnext(self):
* '''cversion of iterator. Used by IteratorColumn'''
* self.retval = bam_iter_read( self.fp.x.bam, # <<<<<<<<<<<<<<
@@ -15492,7 +16621,22 @@ static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamto
return __pyx_r;
}
-/* "csamtools.pyx":1528
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__[] = "python version of next().\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1533
* self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -15500,10 +16644,7 @@ static int __pyx_f_9csamtools_17IteratorRowRegion_cnext(struct __pyx_obj_9csamto
* """
*/
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_17IteratorRowRegion_2__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
-static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_17IteratorRowRegion_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -15512,34 +16653,34 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1528);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1533);
- /* "csamtools.pyx":1531
+ /* "pysam/csamtools.pyx":1536
* """python version of next().
* """
* self.cnext() # <<<<<<<<<<<<<<
* if self.retval < 0: raise StopIteration
* return makeAlignedRead( self.b )
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
- /* "csamtools.pyx":1532
+ /* "pysam/csamtools.pyx":1537
* """
* self.cnext()
* if self.retval < 0: raise StopIteration # <<<<<<<<<<<<<<
* return makeAlignedRead( self.b )
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->retval < 0);
+ __pyx_t_1 = (__pyx_v_self->retval < 0);
if (__pyx_t_1) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1533
+ /* "pysam/csamtools.pyx":1538
* self.cnext()
* if self.retval < 0: raise StopIteration
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
@@ -15547,7 +16688,7 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__p
* def __dealloc__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -15557,7 +16698,7 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__p
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -15566,7 +16707,16 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":1535
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":1540
* return makeAlignedRead( self.b )
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -15574,91 +16724,71 @@ static PyObject *__pyx_pf_9csamtools_17IteratorRowRegion_2__next__(PyObject *__p
* bam_iter_destroy( self.iter )
*/
-static void __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_17IteratorRowRegion_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1535);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1540);
- /* "csamtools.pyx":1536
+ /* "pysam/csamtools.pyx":1541
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* bam_iter_destroy( self.iter )
* if self.owns_samfile: samclose( self.fp )
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->b);
+ bam_destroy1(__pyx_v_self->b);
- /* "csamtools.pyx":1537
+ /* "pysam/csamtools.pyx":1542
* def __dealloc__(self):
* bam_destroy1(self.b)
* bam_iter_destroy( self.iter ) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_iter_destroy(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->iter);
+ bam_iter_destroy(__pyx_v_self->iter);
- /* "csamtools.pyx":1538
+ /* "pysam/csamtools.pyx":1543
* bam_destroy1(self.b)
* bam_iter_destroy( self.iter )
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* cdef class IteratorRowAll(IteratorRow):
*/
- if (((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_v_self)->fp);
- goto __pyx_L5;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":1550
- * """
- *
- * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
-
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_reopen;
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1550);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -15667,7 +16797,7 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -15677,57 +16807,91 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
if (values[1]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
+
+ /* "pysam/csamtools.pyx":1555
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
__pyx_v_reopen = ((int)1);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static int __pyx_pf_5pysam_9csamtools_14IteratorRowAll___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ samfile_t *__pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1555);
- /* "csamtools.pyx":1552
+ /* "pysam/csamtools.pyx":1557
* def __cinit__(self, Samfile samfile, int reopen = True ):
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":1553
+ /* "pysam/csamtools.pyx":1558
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* if samfile.isbam: mode = b"rb"
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_121), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_125), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1555
+ /* "pysam/csamtools.pyx":1560
* raise ValueError( "I/O operation on closed file" )
*
* if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
@@ -15737,11 +16901,11 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L7;
+ goto __pyx_L4;
}
/*else*/ {
- /* "csamtools.pyx":1556
+ /* "pysam/csamtools.pyx":1561
*
* if samfile.isbam: mode = b"rb"
* else: mode = b"r" # <<<<<<<<<<<<<<
@@ -15751,9 +16915,9 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "csamtools.pyx":1559
+ /* "pysam/csamtools.pyx":1564
*
* # reopen the file to avoid iterator conflict
* if reopen: # <<<<<<<<<<<<<<
@@ -15762,46 +16926,46 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
*/
if (__pyx_v_reopen) {
- /* "csamtools.pyx":1560
+ /* "pysam/csamtools.pyx":1565
* # reopen the file to avoid iterator conflict
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_store = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":1561
+ /* "pysam/csamtools.pyx":1566
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* store.release()
* assert self.fp != NULL
*/
- __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "csamtools.pyx":1562
+ /* "pysam/csamtools.pyx":1567
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
* assert self.fp != NULL
* self.owns_samfile = True
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":1563
+ /* "pysam/csamtools.pyx":1568
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
@@ -15809,59 +16973,60 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp != NULL))) {
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1564
+ /* "pysam/csamtools.pyx":1569
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = samfile.samfile
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L8;
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L5;
}
/*else*/ {
- /* "csamtools.pyx":1566
+ /* "pysam/csamtools.pyx":1571
* self.owns_samfile = True
* else:
* self.fp = samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
+ __pyx_t_6 = __pyx_v_samfile->samfile;
+ __pyx_v_self->fp = __pyx_t_6;
- /* "csamtools.pyx":1567
+ /* "pysam/csamtools.pyx":1572
* else:
* self.fp = samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* # allocate memory for alignment
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile = 0;
+ __pyx_v_self->owns_samfile = 0;
}
- __pyx_L8:;
+ __pyx_L5:;
- /* "csamtools.pyx":1570
+ /* "pysam/csamtools.pyx":1575
*
* # allocate memory for alignment
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAll.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
@@ -15871,7 +17036,18 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
return __pyx_r;
}
-/* "csamtools.pyx":1572
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1577
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -15879,15 +17055,14 @@ static int __pyx_pf_9csamtools_14IteratorRowAll___cinit__(PyObject *__pyx_v_self
*
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1572);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1577);
- /* "csamtools.pyx":1573
+ /* "pysam/csamtools.pyx":1578
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -15895,8 +17070,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -15907,7 +17082,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":1575
+/* "pysam/csamtools.pyx":1580
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
@@ -15915,14 +17090,14 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_1__iter__(PyObject *__pyx_
*
*/
-static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+static bam1_t *__pyx_f_5pysam_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1575);
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1580);
- /* "csamtools.pyx":1576
+ /* "pysam/csamtools.pyx":1581
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
@@ -15939,7 +17114,7 @@ static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9
return __pyx_r;
}
-/* "csamtools.pyx":1578
+/* "pysam/csamtools.pyx":1583
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
@@ -15947,14 +17122,14 @@ static bam1_t *__pyx_f_9csamtools_14IteratorRowAll_getCurrent(struct __pyx_obj_9
* return samread(self.fp, self.b)
*/
-static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools_IteratorRowAll *__pyx_v_self) {
+static int __pyx_f_5pysam_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1578);
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1583);
- /* "csamtools.pyx":1580
+ /* "pysam/csamtools.pyx":1585
* cdef int cnext(self):
* '''cversion of iterator. Used by IteratorColumn'''
* return samread(self.fp, self.b) # <<<<<<<<<<<<<<
@@ -15971,7 +17146,22 @@ static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* "csamtools.pyx":1582
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1587
* return samread(self.fp, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -15979,10 +17169,7 @@ static int __pyx_f_9csamtools_14IteratorRowAll_cnext(struct __pyx_obj_9csamtools
*
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorRowAll_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
-static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorRowAll_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -15992,19 +17179,19 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1582);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1587);
- /* "csamtools.pyx":1588
+ /* "pysam/csamtools.pyx":1593
* """
* cdef int ret
* ret = samread(self.fp, self.b) # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp, ((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
+ __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_self->b);
- /* "csamtools.pyx":1589
+ /* "pysam/csamtools.pyx":1594
* cdef int ret
* ret = samread(self.fp, self.b)
* if (ret > 0): # <<<<<<<<<<<<<<
@@ -16014,7 +17201,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "csamtools.pyx":1590
+ /* "pysam/csamtools.pyx":1595
* ret = samread(self.fp, self.b)
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
@@ -16022,16 +17209,16 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":1592
+ /* "pysam/csamtools.pyx":1597
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -16039,15 +17226,15 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_
* def __dealloc__(self):
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAll.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAll.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -16056,7 +17243,16 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":1594
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":1599
* raise StopIteration
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -16064,100 +17260,113 @@ static PyObject *__pyx_pf_9csamtools_14IteratorRowAll_2__next__(PyObject *__pyx_
* if self.owns_samfile: samclose( self.fp )
*/
-static void __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_14IteratorRowAll_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1594);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1599);
- /* "csamtools.pyx":1595
+ /* "pysam/csamtools.pyx":1600
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->b);
+ bam_destroy1(__pyx_v_self->b);
- /* "csamtools.pyx":1596
+ /* "pysam/csamtools.pyx":1601
* def __dealloc__(self):
* bam_destroy1(self.b)
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* cdef class IteratorRowAllRefs(IteratorRow):
*/
- if (((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IteratorRowAll *)__pyx_v_self)->fp);
- goto __pyx_L5;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":1602
- * """
- *
- * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
- * assert samfile._isOpen()
- * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
- */
-
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1602);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1607; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1607; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self), __pyx_v_samfile);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1607
+ * """
+ *
+ * def __cinit__(self, Samfile samfile): # <<<<<<<<<<<<<<
+ * assert samfile._isOpen()
+ * if not samfile._hasIndex(): raise ValueError("no index available for fetch")
+ */
+
+static int __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1607);
- /* "csamtools.pyx":1603
+ /* "pysam/csamtools.pyx":1608
*
* def __cinit__(self, Samfile samfile):
* assert samfile._isOpen() # <<<<<<<<<<<<<<
@@ -16165,45 +17374,45 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_
* self.samfile = samfile
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (unlikely(!__pyx_t_3)) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1604
+ /* "pysam/csamtools.pyx":1609
* def __cinit__(self, Samfile samfile):
* assert samfile._isOpen()
* if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
* self.samfile = samfile
* self.tid = -1
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___hasIndex); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_126), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1605
+ /* "pysam/csamtools.pyx":1610
* assert samfile._isOpen()
* if not samfile._hasIndex(): raise ValueError("no index available for fetch")
* self.samfile = samfile # <<<<<<<<<<<<<<
@@ -16212,25 +17421,25 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "csamtools.pyx":1606
+ /* "pysam/csamtools.pyx":1611
* if not samfile._hasIndex(): raise ValueError("no index available for fetch")
* self.samfile = samfile
* self.tid = -1 # <<<<<<<<<<<<<<
*
* def nextiter(self):
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = -1;
+ __pyx_v_self->tid = -1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -16238,7 +17447,19 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":1608
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter[] = "IteratorRowAllRefs.nextiter(self)";
+static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("nextiter (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1613
* self.tid = -1
*
* def nextiter(self): # <<<<<<<<<<<<<<
@@ -16246,9 +17467,7 @@ static int __pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(PyObject *__pyx_v_
*
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter[] = "IteratorRowAllRefs.nextiter(self)";
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -16257,23 +17476,23 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("nextiter");
- __Pyx_TraceCall("nextiter", __pyx_f[0], 1608);
+ __Pyx_RefNannySetupContext("nextiter", 0);
+ __Pyx_TraceCall("nextiter", __pyx_f[0], 1613);
- /* "csamtools.pyx":1609
+ /* "pysam/csamtools.pyx":1614
*
* def nextiter(self):
* self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29) # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
- __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile));
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_int_0);
@@ -16283,13 +17502,13 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__
PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_int_536870912);
__Pyx_GIVEREF(__pyx_int_536870912);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_GIVEREF(__pyx_t_1);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter));
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_1);
+ __Pyx_GOTREF(__pyx_v_self->rowiter);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->rowiter));
+ __pyx_v_self->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_t_1);
__pyx_t_1 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -16297,7 +17516,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.nextiter", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.nextiter", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -16306,7 +17525,18 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":1611
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1616
* self.rowiter = IteratorRowRegion(self.samfile, self.tid, 0, 1<<29)
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -16314,15 +17544,14 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter(PyObject *__
*
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_4__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1611);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1616);
- /* "csamtools.pyx":1612
+ /* "pysam/csamtools.pyx":1617
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -16330,8 +17559,8 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__
* def __next__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -16342,7 +17571,22 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":1614
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1619
* return self
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -16350,10 +17594,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__(PyObject *__
*
*/
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
-static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_18IteratorRowAllRefs_6__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -16365,34 +17606,34 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1614);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1619);
- /* "csamtools.pyx":1620
+ /* "pysam/csamtools.pyx":1625
* """
* # Create an initial iterator
* if self.tid==-1: # <<<<<<<<<<<<<<
* if not self.samfile.nreferences:
* raise StopIteration
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid == -1);
+ __pyx_t_1 = (__pyx_v_self->tid == -1);
if (__pyx_t_1) {
- /* "csamtools.pyx":1621
+ /* "pysam/csamtools.pyx":1626
* # Create an initial iterator
* if self.tid==-1:
* if not self.samfile.nreferences: # <<<<<<<<<<<<<<
* raise StopIteration
* self.tid = 0
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = (!__pyx_t_1);
if (__pyx_t_3) {
- /* "csamtools.pyx":1622
+ /* "pysam/csamtools.pyx":1627
* if self.tid==-1:
* if not self.samfile.nreferences:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -16400,38 +17641,38 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
* self.nextiter()
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":1623
+ /* "pysam/csamtools.pyx":1628
* if not self.samfile.nreferences:
* raise StopIteration
* self.tid = 0 # <<<<<<<<<<<<<<
* self.nextiter()
*
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = 0;
+ __pyx_v_self->tid = 0;
- /* "csamtools.pyx":1624
+ /* "pysam/csamtools.pyx":1629
* raise StopIteration
* self.tid = 0
* self.nextiter() # <<<<<<<<<<<<<<
*
* while 1:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1626
+ /* "pysam/csamtools.pyx":1631
* self.nextiter()
*
* while 1: # <<<<<<<<<<<<<<
@@ -16441,26 +17682,26 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
while (1) {
if (!1) break;
- /* "csamtools.pyx":1627
+ /* "pysam/csamtools.pyx":1632
*
* while 1:
* self.rowiter.cnext() # <<<<<<<<<<<<<<
*
* # If current iterator is not exhausted, return aligned read
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorRowRegion *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter);
+ ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *)__pyx_v_self->rowiter->__pyx_vtab)->cnext(__pyx_v_self->rowiter);
- /* "csamtools.pyx":1630
+ /* "pysam/csamtools.pyx":1635
*
* # If current iterator is not exhausted, return aligned read
* if self.rowiter.retval>0: # <<<<<<<<<<<<<<
* return makeAlignedRead(self.rowiter.b)
*
*/
- __pyx_t_3 = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->retval > 0);
+ __pyx_t_3 = (__pyx_v_self->rowiter->retval > 0);
if (__pyx_t_3) {
- /* "csamtools.pyx":1631
+ /* "pysam/csamtools.pyx":1636
* # If current iterator is not exhausted, return aligned read
* if self.rowiter.retval>0:
* return makeAlignedRead(self.rowiter.b) # <<<<<<<<<<<<<<
@@ -16468,61 +17709,60 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
* self.tid += 1
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->rowiter->b); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L9;
+ goto __pyx_L7;
}
- __pyx_L9:;
+ __pyx_L7:;
- /* "csamtools.pyx":1633
+ /* "pysam/csamtools.pyx":1638
* return makeAlignedRead(self.rowiter.b)
*
* self.tid += 1 # <<<<<<<<<<<<<<
*
* # Otherwise, proceed to next reference or stop
*/
- ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid = (((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid + 1);
+ __pyx_v_self->tid = (__pyx_v_self->tid + 1);
- /* "csamtools.pyx":1636
+ /* "pysam/csamtools.pyx":1641
*
* # Otherwise, proceed to next reference or stop
* if self.tid<self.samfile.nreferences: # <<<<<<<<<<<<<<
* self.nextiter()
* else:
*/
- __pyx_t_4 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)__pyx_v_self)->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self->samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_4, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1636; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":1637
+ /* "pysam/csamtools.pyx":1642
* # Otherwise, proceed to next reference or stop
* if self.tid<self.samfile.nreferences:
* self.nextiter() # <<<<<<<<<<<<<<
* else:
* raise StopIteration
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__nextiter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1637; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L10;
+ goto __pyx_L8;
}
/*else*/ {
- /* "csamtools.pyx":1639
+ /* "pysam/csamtools.pyx":1644
* self.nextiter()
* else:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -16530,9 +17770,9 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
* cdef class IteratorRowSelection(IteratorRow):
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L10:;
+ __pyx_L8:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -16541,7 +17781,7 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IteratorRowAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -16550,40 +17790,22 @@ static PyObject *__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":1647
- * """
- *
- * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
- *
- * if not samfile._isOpen():
- */
-
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
PyObject *__pyx_v_positions = 0;
int __pyx_v_reopen;
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_t_4;
- char *__pyx_t_5;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1647);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__positions,&__pyx_n_s__reopen,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -16591,16 +17813,14 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__positions);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__positions)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (kw_args > 0) {
@@ -16609,7 +17829,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -16620,91 +17840,125 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
__pyx_v_positions = values[1];
if (values[2]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
+
+ /* "pysam/csamtools.pyx":1652
+ * """
+ *
+ * def __cinit__(self, Samfile samfile, positions, int reopen = True ): # <<<<<<<<<<<<<<
+ *
+ * if not samfile._isOpen():
+ */
__pyx_v_reopen = ((int)1);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self), __pyx_v_samfile, __pyx_v_positions, __pyx_v_reopen);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static int __pyx_pf_5pysam_9csamtools_20IteratorRowSelection___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_positions, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ char *__pyx_t_5;
+ samfile_t *__pyx_t_6;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1652);
- /* "csamtools.pyx":1649
+ /* "pysam/csamtools.pyx":1654
* def __cinit__(self, Samfile samfile, positions, int reopen = True ):
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "csamtools.pyx":1650
+ /* "pysam/csamtools.pyx":1655
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* if not samfile._isOpen():
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_123), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_127), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1652
+ /* "pysam/csamtools.pyx":1657
* raise ValueError( "I/O operation on closed file" )
*
* if not samfile._isOpen(): # <<<<<<<<<<<<<<
* raise ValueError( "I/O operation on closed file" )
*
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s___isOpen); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "csamtools.pyx":1653
+ /* "pysam/csamtools.pyx":1658
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* assert samfile.isbam, "can only use this iterator on bam files"
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_124), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_128), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "csamtools.pyx":1655
+ /* "pysam/csamtools.pyx":1660
* raise ValueError( "I/O operation on closed file" )
*
* assert samfile.isbam, "can only use this iterator on bam files" # <<<<<<<<<<<<<<
@@ -16713,12 +17967,12 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
if (unlikely(!__pyx_v_samfile->isbam)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_125));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_129));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1656
+ /* "pysam/csamtools.pyx":1661
*
* assert samfile.isbam, "can only use this iterator on bam files"
* mode = b"rb" # <<<<<<<<<<<<<<
@@ -16728,7 +17982,7 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- /* "csamtools.pyx":1659
+ /* "pysam/csamtools.pyx":1664
*
* # reopen the file to avoid iterator conflict
* if reopen: # <<<<<<<<<<<<<<
@@ -16737,46 +17991,46 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
*/
if (__pyx_v_reopen) {
- /* "csamtools.pyx":1660
+ /* "pysam/csamtools.pyx":1665
* # reopen the file to avoid iterator conflict
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1665; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_store = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1661
+ /* "pysam/csamtools.pyx":1666
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* store.release()
* assert self.fp != NULL
*/
- __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1661; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
+ __pyx_t_5 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_5) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_5, NULL);
- /* "csamtools.pyx":1662
+ /* "pysam/csamtools.pyx":1667
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
* assert self.fp != NULL
* self.owns_samfile = True
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":1663
+ /* "pysam/csamtools.pyx":1668
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
@@ -16784,54 +18038,55 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp != NULL))) {
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1668; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":1664
+ /* "pysam/csamtools.pyx":1669
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = samfile.samfile
*/
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L8;
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L5;
}
/*else*/ {
- /* "csamtools.pyx":1666
+ /* "pysam/csamtools.pyx":1671
* self.owns_samfile = True
* else:
* self.fp = samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
+ __pyx_t_6 = __pyx_v_samfile->samfile;
+ __pyx_v_self->fp = __pyx_t_6;
- /* "csamtools.pyx":1667
+ /* "pysam/csamtools.pyx":1672
* else:
* self.fp = samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* # allocate memory for alignment
*/
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile = 0;
+ __pyx_v_self->owns_samfile = 0;
}
- __pyx_L8:;
+ __pyx_L5:;
- /* "csamtools.pyx":1670
+ /* "pysam/csamtools.pyx":1675
*
* # allocate memory for alignment
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t)) # <<<<<<<<<<<<<<
*
* self.positions = positions
*/
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ __pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "csamtools.pyx":1672
+ /* "pysam/csamtools.pyx":1677
* self.b = <bam1_t*>calloc(1, sizeof(bam1_t))
*
* self.positions = positions # <<<<<<<<<<<<<<
@@ -16840,25 +18095,25 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
*/
__Pyx_INCREF(__pyx_v_positions);
__Pyx_GIVEREF(__pyx_v_positions);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
- __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions);
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->positions = __pyx_v_positions;
+ __Pyx_GOTREF(__pyx_v_self->positions);
+ __Pyx_DECREF(__pyx_v_self->positions);
+ __pyx_v_self->positions = __pyx_v_positions;
- /* "csamtools.pyx":1673
+ /* "pysam/csamtools.pyx":1678
*
* self.positions = positions
* self.current_pos = 0 # <<<<<<<<<<<<<<
*
* def __iter__(self):
*/
- ((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->current_pos = 0;
+ __pyx_v_self->current_pos = 0;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowSelection.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
@@ -16868,7 +18123,18 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":1675
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1680
* self.current_pos = 0
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -16876,15 +18142,14 @@ static int __pyx_pf_9csamtools_20IteratorRowSelection___cinit__(PyObject *__pyx_
*
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1675);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1680);
- /* "csamtools.pyx":1676
+ /* "pysam/csamtools.pyx":1681
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -16892,8 +18157,8 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *
* cdef bam1_t * getCurrent( self ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -16904,7 +18169,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *
return __pyx_r;
}
-/* "csamtools.pyx":1678
+/* "pysam/csamtools.pyx":1683
* return self
*
* cdef bam1_t * getCurrent( self ): # <<<<<<<<<<<<<<
@@ -16912,14 +18177,14 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_1__iter__(PyObject *
*
*/
-static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static bam1_t *__pyx_f_5pysam_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
bam1_t *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getCurrent");
- __Pyx_TraceCall("getCurrent", __pyx_f[0], 1678);
+ __Pyx_RefNannySetupContext("getCurrent", 0);
+ __Pyx_TraceCall("getCurrent", __pyx_f[0], 1683);
- /* "csamtools.pyx":1679
+ /* "pysam/csamtools.pyx":1684
*
* cdef bam1_t * getCurrent( self ):
* return self.b # <<<<<<<<<<<<<<
@@ -16936,7 +18201,7 @@ static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx
return __pyx_r;
}
-/* "csamtools.pyx":1681
+/* "pysam/csamtools.pyx":1686
* return self.b
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
@@ -16944,7 +18209,7 @@ static bam1_t *__pyx_f_9csamtools_20IteratorRowSelection_getCurrent(struct __pyx
*
*/
-static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csamtools_IteratorRowSelection *__pyx_v_self) {
+static int __pyx_f_5pysam_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -16955,10 +18220,10 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1681);
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1686);
- /* "csamtools.pyx":1685
+ /* "pysam/csamtools.pyx":1690
*
* # end iteration if out of positions
* if self.current_pos >= len(self.positions): return -1 # <<<<<<<<<<<<<<
@@ -16967,7 +18232,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
*/
__pyx_t_1 = __pyx_v_self->positions;
__Pyx_INCREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (__pyx_v_self->current_pos >= __pyx_t_2);
if (__pyx_t_3) {
@@ -16977,20 +18242,20 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
}
__pyx_L3:;
- /* "csamtools.pyx":1687
+ /* "pysam/csamtools.pyx":1692
* if self.current_pos >= len(self.positions): return -1
*
* bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 ) # <<<<<<<<<<<<<<
* self.current_pos += 1
* return samread(self.fp, self.b)
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_self->positions, __pyx_v_self->current_pos, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_self->positions, __pyx_v_self->current_pos, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyInt_from_py_uint64_t(__pyx_t_1); if (unlikely((__pyx_t_4 == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyInt_from_py_uint64_t(__pyx_t_1); if (unlikely((__pyx_t_4 == (uint64_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
bam_seek(__pyx_v_self->fp->x.bam, __pyx_t_4, 0);
- /* "csamtools.pyx":1688
+ /* "pysam/csamtools.pyx":1693
*
* bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
* self.current_pos += 1 # <<<<<<<<<<<<<<
@@ -16999,7 +18264,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
*/
__pyx_v_self->current_pos = (__pyx_v_self->current_pos + 1);
- /* "csamtools.pyx":1689
+ /* "pysam/csamtools.pyx":1694
* bam_seek( self.fp.x.bam, self.positions[self.current_pos], 0 )
* self.current_pos += 1
* return samread(self.fp, self.b) # <<<<<<<<<<<<<<
@@ -17013,7 +18278,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_WriteUnraisable("csamtools.IteratorRowSelection.cnext", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_WriteUnraisable("pysam.csamtools.IteratorRowSelection.cnext", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -17021,7 +18286,22 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
return __pyx_r;
}
-/* "csamtools.pyx":1691
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1696
* return samread(self.fp, self.b)
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -17029,10 +18309,7 @@ static int __pyx_f_9csamtools_20IteratorRowSelection_cnext(struct __pyx_obj_9csa
*
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_20IteratorRowSelection_2__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
-static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorRowSelection_4__next__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
int __pyx_v_ret;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -17042,19 +18319,19 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1691);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1696);
- /* "csamtools.pyx":1697
+ /* "pysam/csamtools.pyx":1702
* """
*
* cdef int ret = self.cnext() # <<<<<<<<<<<<<<
* if (ret > 0):
* return makeAlignedRead( self.b )
*/
- __pyx_v_ret = ((struct __pyx_vtabstruct_9csamtools_IteratorRowSelection *)((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->__pyx_vtab)->cnext(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __pyx_v_ret = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self->__pyx_vtab)->cnext(__pyx_v_self);
- /* "csamtools.pyx":1698
+ /* "pysam/csamtools.pyx":1703
*
* cdef int ret = self.cnext()
* if (ret > 0): # <<<<<<<<<<<<<<
@@ -17064,7 +18341,7 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *
__pyx_t_1 = (__pyx_v_ret > 0);
if (__pyx_t_1) {
- /* "csamtools.pyx":1699
+ /* "pysam/csamtools.pyx":1704
* cdef int ret = self.cnext()
* if (ret > 0):
* return makeAlignedRead( self.b ) # <<<<<<<<<<<<<<
@@ -17072,16 +18349,16 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *
* raise StopIteration
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_makeAlignedRead(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makeAlignedRead(__pyx_v_self->b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":1701
+ /* "pysam/csamtools.pyx":1706
* return makeAlignedRead( self.b )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -17089,15 +18366,15 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *
* def __dealloc__(self):
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1701; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorRowSelection.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorRowSelection.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -17106,7 +18383,16 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *
return __pyx_r;
}
-/* "csamtools.pyx":1703
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":1708
* raise StopIteration
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -17114,40 +18400,39 @@ static PyObject *__pyx_pf_9csamtools_20IteratorRowSelection_2__next__(PyObject *
* if self.owns_samfile: samclose( self.fp )
*/
-static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_20IteratorRowSelection_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1703);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1708);
- /* "csamtools.pyx":1704
+ /* "pysam/csamtools.pyx":1709
*
* def __dealloc__(self):
* bam_destroy1(self.b) # <<<<<<<<<<<<<<
* if self.owns_samfile: samclose( self.fp )
*
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->b);
+ bam_destroy1(__pyx_v_self->b);
- /* "csamtools.pyx":1705
+ /* "pysam/csamtools.pyx":1710
* def __dealloc__(self):
* bam_destroy1(self.b)
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* ##-------------------------------------------------------------------
*/
- if (((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IteratorRowSelection *)__pyx_v_self)->fp);
- goto __pyx_L5;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":1710
+/* "pysam/csamtools.pyx":1715
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef int __advance_all( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
@@ -17155,24 +18440,24 @@ static void __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(PyObject *__
* '''
*/
-static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_9csamtools___iterdata *__pyx_v_d;
+static int __pyx_f_5pysam_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_5pysam_9csamtools___iterdata *__pyx_v_d;
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_all");
- __Pyx_TraceCall("__advance_all", __pyx_f[0], 1710);
+ __Pyx_RefNannySetupContext("__advance_all", 0);
+ __Pyx_TraceCall("__advance_all", __pyx_f[0], 1715);
- /* "csamtools.pyx":1714
+ /* "pysam/csamtools.pyx":1719
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
*/
- __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
- /* "csamtools.pyx":1715
+ /* "pysam/csamtools.pyx":1720
* cdef __iterdata * d
* d = <__iterdata*>data
* return bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -17189,7 +18474,7 @@ static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":1717
+/* "pysam/csamtools.pyx":1722
* return bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* cdef int __advance_snpcalls( void * data, bam1_t * b ): # <<<<<<<<<<<<<<
@@ -17197,8 +18482,8 @@ static int __pyx_f_9csamtools___advance_all(void *__pyx_v_data, bam1_t *__pyx_v_
* the samtools pileup.
*/
-static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
- __pyx_t_9csamtools___iterdata *__pyx_v_d;
+static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__pyx_v_b) {
+ __pyx_t_5pysam_9csamtools___iterdata *__pyx_v_d;
int __pyx_v_ret;
int __pyx_v_skip;
int __pyx_v_q;
@@ -17210,27 +18495,28 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
int __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ int32_t __pyx_t_4;
PyObject *__pyx_t_5 = NULL;
PyObject *__pyx_t_6 = NULL;
- long __pyx_t_7;
+ PyObject *__pyx_t_7 = NULL;
+ long __pyx_t_8;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__advance_snpcalls");
- __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1717);
+ __Pyx_RefNannySetupContext("__advance_snpcalls", 0);
+ __Pyx_TraceCall("__advance_snpcalls", __pyx_f[0], 1722);
- /* "csamtools.pyx":1722
+ /* "pysam/csamtools.pyx":1727
* '''
* cdef __iterdata * d
* d = <__iterdata*>data # <<<<<<<<<<<<<<
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*/
- __pyx_v_d = ((__pyx_t_9csamtools___iterdata *)__pyx_v_data);
+ __pyx_v_d = ((__pyx_t_5pysam_9csamtools___iterdata *)__pyx_v_data);
- /* "csamtools.pyx":1724
+ /* "pysam/csamtools.pyx":1729
* d = <__iterdata*>data
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -17239,7 +18525,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_ret = bam_iter_read(__pyx_v_d->samfile->x.bam, __pyx_v_d->iter, __pyx_v_b);
- /* "csamtools.pyx":1725
+ /* "pysam/csamtools.pyx":1730
*
* cdef int ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
* cdef int skip = 0 # <<<<<<<<<<<<<<
@@ -17248,7 +18534,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_skip = 0;
- /* "csamtools.pyx":1727
+ /* "pysam/csamtools.pyx":1732
* cdef int skip = 0
* cdef int q
* cdef int is_cns = 1 # <<<<<<<<<<<<<<
@@ -17257,7 +18543,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_is_cns = 1;
- /* "csamtools.pyx":1728
+ /* "pysam/csamtools.pyx":1733
* cdef int q
* cdef int is_cns = 1
* cdef int is_nobaq = 0 # <<<<<<<<<<<<<<
@@ -17266,7 +18552,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_is_nobaq = 0;
- /* "csamtools.pyx":1729
+ /* "pysam/csamtools.pyx":1734
* cdef int is_cns = 1
* cdef int is_nobaq = 0
* cdef int capQ_thres = 0 # <<<<<<<<<<<<<<
@@ -17275,7 +18561,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_capQ_thres = 0;
- /* "csamtools.pyx":1732
+ /* "pysam/csamtools.pyx":1737
*
* # reload sequence
* if d.fastafile != NULL and b.core.tid != d.tid: # <<<<<<<<<<<<<<
@@ -17291,7 +18577,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
if (__pyx_t_3) {
- /* "csamtools.pyx":1733
+ /* "pysam/csamtools.pyx":1738
* # reload sequence
* if d.fastafile != NULL and b.core.tid != d.tid:
* if d.seq != NULL: free(d.seq) # <<<<<<<<<<<<<<
@@ -17305,25 +18591,26 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L4:;
- /* "csamtools.pyx":1734
+ /* "pysam/csamtools.pyx":1739
* if d.fastafile != NULL and b.core.tid != d.tid:
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid # <<<<<<<<<<<<<<
* d.seq = faidx_fetch_seq(d.fastafile,
* d.samfile.header.target_name[d.tid],
*/
- __pyx_v_d->tid = __pyx_v_b->core.tid;
+ __pyx_t_4 = __pyx_v_b->core.tid;
+ __pyx_v_d->tid = __pyx_t_4;
- /* "csamtools.pyx":1735
+ /* "pysam/csamtools.pyx":1740
* if d.seq != NULL: free(d.seq)
* d.tid = b.core.tid
* d.seq = faidx_fetch_seq(d.fastafile, # <<<<<<<<<<<<<<
* d.samfile.header.target_name[d.tid],
* 0, max_pos,
*/
- __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_9csamtools_max_pos, (&__pyx_v_d->seq_len));
+ __pyx_v_d->seq = faidx_fetch_seq(__pyx_v_d->fastafile, (__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid]), 0, __pyx_v_5pysam_9csamtools_max_pos, (&__pyx_v_d->seq_len));
- /* "csamtools.pyx":1739
+ /* "pysam/csamtools.pyx":1744
* 0, max_pos,
* &d.seq_len)
* if d.seq == NULL: # <<<<<<<<<<<<<<
@@ -17333,47 +18620,47 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
__pyx_t_3 = (__pyx_v_d->seq == NULL);
if (__pyx_t_3) {
- /* "csamtools.pyx":1741
+ /* "pysam/csamtools.pyx":1746
* if d.seq == NULL:
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
* (d.samfile.header.target_name[d.tid], # <<<<<<<<<<<<<<
* d.tid))
*
*/
- __pyx_t_4 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_5 = PyBytes_FromString((__pyx_v_d->samfile->header->target_name[__pyx_v_d->tid])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- /* "csamtools.pyx":1742
+ /* "pysam/csamtools.pyx":1747
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
* (d.samfile.header.target_name[d.tid],
* d.tid)) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_5 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_4));
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_5);
- __Pyx_GIVEREF(__pyx_t_5);
- __pyx_t_4 = 0;
- __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_126), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_5));
+ __pyx_t_6 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_5, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_130), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = 0;
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_6, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
}
__pyx_L5:;
@@ -17381,7 +18668,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L3:;
- /* "csamtools.pyx":1745
+ /* "pysam/csamtools.pyx":1750
*
*
* while ret >= 0: # <<<<<<<<<<<<<<
@@ -17392,7 +18679,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
__pyx_t_3 = (__pyx_v_ret >= 0);
if (!__pyx_t_3) break;
- /* "csamtools.pyx":1747
+ /* "pysam/csamtools.pyx":1752
* while ret >= 0:
*
* skip = 0 # <<<<<<<<<<<<<<
@@ -17401,7 +18688,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_skip = 0;
- /* "csamtools.pyx":1750
+ /* "pysam/csamtools.pyx":1755
*
* # realign read - changes base qualities
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq ) # <<<<<<<<<<<<<<
@@ -17426,7 +18713,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L8:;
- /* "csamtools.pyx":1752
+ /* "pysam/csamtools.pyx":1757
* if d.seq != NULL and is_cns and not is_nobaq: bam_prob_realn( b, d.seq )
*
* if d.seq != NULL and capQ_thres > 10: # <<<<<<<<<<<<<<
@@ -17442,7 +18729,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
if (__pyx_t_2) {
- /* "csamtools.pyx":1753
+ /* "pysam/csamtools.pyx":1758
*
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
@@ -17451,7 +18738,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
*/
__pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
- /* "csamtools.pyx":1754
+ /* "pysam/csamtools.pyx":1759
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1 # <<<<<<<<<<<<<<
@@ -17464,7 +18751,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
goto __pyx_L10;
}
- /* "csamtools.pyx":1755
+ /* "pysam/csamtools.pyx":1760
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q # <<<<<<<<<<<<<<
@@ -17481,20 +18768,20 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L9:;
- /* "csamtools.pyx":1756
+ /* "pysam/csamtools.pyx":1761
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1 # <<<<<<<<<<<<<<
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*
*/
- __pyx_t_7 = (__pyx_v_b->core.flag & 4);
- if (__pyx_t_7) {
+ __pyx_t_8 = (__pyx_v_b->core.flag & 4);
+ if (__pyx_t_8) {
__pyx_v_skip = 1;
goto __pyx_L11;
}
- /* "csamtools.pyx":1757
+ /* "pysam/csamtools.pyx":1762
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1 # <<<<<<<<<<<<<<
@@ -17513,7 +18800,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L11:;
- /* "csamtools.pyx":1759
+ /* "pysam/csamtools.pyx":1764
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
*
* if not skip: break # <<<<<<<<<<<<<<
@@ -17527,7 +18814,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L12:;
- /* "csamtools.pyx":1762
+ /* "pysam/csamtools.pyx":1767
* # additional filters
*
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
@@ -17538,7 +18825,7 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
}
__pyx_L7_break:;
- /* "csamtools.pyx":1764
+ /* "pysam/csamtools.pyx":1769
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* return ret # <<<<<<<<<<<<<<
@@ -17551,10 +18838,10 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_WriteUnraisable("csamtools.__advance_snpcalls", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_WriteUnraisable("pysam.csamtools.__advance_snpcalls", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -17562,70 +18849,85 @@ static int __pyx_f_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1_t *__p
return __pyx_r;
}
-/* "csamtools.pyx":1813
- * '''
- *
- * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- * self.mask = kwargs.get("mask", BAM_DEF_MASK )
- */
-
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1813);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1818
+ * '''
+ *
+ * def __cinit__( self, Samfile samfile, **kwargs ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ * self.mask = kwargs.get("mask", BAM_DEF_MASK )
+ */
+
+static int __pyx_pf_5pysam_9csamtools_14IteratorColumn___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1818);
- /* "csamtools.pyx":1814
+ /* "pysam/csamtools.pyx":1819
*
* def __cinit__( self, Samfile samfile, **kwargs ):
* self.samfile = samfile # <<<<<<<<<<<<<<
@@ -17634,151 +18936,149 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "csamtools.pyx":1815
+ /* "pysam/csamtools.pyx":1820
* def __cinit__( self, Samfile samfile, **kwargs ):
* self.samfile = samfile
* self.mask = kwargs.get("mask", BAM_DEF_MASK ) # <<<<<<<<<<<<<<
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None )
*/
- if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__mask), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__mask), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->mask = __pyx_t_3;
+ __pyx_v_self->mask = __pyx_t_3;
- /* "csamtools.pyx":1816
+ /* "pysam/csamtools.pyx":1821
* self.samfile = samfile
* self.mask = kwargs.get("mask", BAM_DEF_MASK )
* self.fastafile = kwargs.get( "fastafile", None ) # <<<<<<<<<<<<<<
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 )
*/
- if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__fastafile), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__fastafile), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!(likely(((__pyx_t_2) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_2, __pyx_ptype_5pysam_9csamtools_Fastafile))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_t_2);
+ __Pyx_GOTREF(__pyx_v_self->fastafile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
+ __pyx_v_self->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":1817
+ /* "pysam/csamtools.pyx":1822
* self.mask = kwargs.get("mask", BAM_DEF_MASK )
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None ) # <<<<<<<<<<<<<<
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL
*/
- if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__stepper), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__stepper), Py_None); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
- __Pyx_DECREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper);
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->stepper = __pyx_t_2;
+ __Pyx_GOTREF(__pyx_v_self->stepper);
+ __Pyx_DECREF(__pyx_v_self->stepper);
+ __pyx_v_self->stepper = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":1818
+ /* "pysam/csamtools.pyx":1823
* self.fastafile = kwargs.get( "fastafile", None )
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 ) # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
* self.tid = 0
*/
- if (unlikely(((PyObject *)__pyx_v_kwargs) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "get"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__max_depth), __pyx_int_8000); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItemDefault(((PyObject *)__pyx_v_kwargs), ((PyObject *)__pyx_n_s__max_depth), __pyx_int_8000); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->max_depth = __pyx_t_3;
+ __pyx_v_self->max_depth = __pyx_t_3;
- /* "csamtools.pyx":1819
+ /* "pysam/csamtools.pyx":1824
* self.stepper = kwargs.get( "stepper", None )
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
* self.tid = 0
* self.pos = 0
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
+ __pyx_v_self->iterdata.seq = NULL;
- /* "csamtools.pyx":1820
+ /* "pysam/csamtools.pyx":1825
* self.max_depth = kwargs.get( "max_depth", 8000 )
* self.iterdata.seq = NULL
* self.tid = 0 # <<<<<<<<<<<<<<
* self.pos = 0
* self.n_plp = 0
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->tid = 0;
+ __pyx_v_self->tid = 0;
- /* "csamtools.pyx":1821
+ /* "pysam/csamtools.pyx":1826
* self.iterdata.seq = NULL
* self.tid = 0
* self.pos = 0 # <<<<<<<<<<<<<<
* self.n_plp = 0
* self.plp = NULL
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pos = 0;
+ __pyx_v_self->pos = 0;
- /* "csamtools.pyx":1822
+ /* "pysam/csamtools.pyx":1827
* self.tid = 0
* self.pos = 0
* self.n_plp = 0 # <<<<<<<<<<<<<<
* self.plp = NULL
* self.pileup_iter = <bam_plp_t>NULL
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->n_plp = 0;
+ __pyx_v_self->n_plp = 0;
- /* "csamtools.pyx":1823
+ /* "pysam/csamtools.pyx":1828
* self.pos = 0
* self.n_plp = 0
* self.plp = NULL # <<<<<<<<<<<<<<
* self.pileup_iter = <bam_plp_t>NULL
*
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->plp = NULL;
+ __pyx_v_self->plp = NULL;
- /* "csamtools.pyx":1824
+ /* "pysam/csamtools.pyx":1829
* self.n_plp = 0
* self.plp = NULL
* self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
*
*
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
+ __pyx_v_self->pileup_iter = NULL;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":1827
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1832
*
*
* def __iter__(self): # <<<<<<<<<<<<<<
@@ -17786,15 +19086,14 @@ static int __pyx_pf_9csamtools_14IteratorColumn___cinit__(PyObject *__pyx_v_self
*
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_2__iter__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__iter__");
- __Pyx_TraceCall("__iter__", __pyx_f[0], 1827);
+ __Pyx_RefNannySetupContext("__iter__", 0);
+ __Pyx_TraceCall("__iter__", __pyx_f[0], 1832);
- /* "csamtools.pyx":1828
+ /* "pysam/csamtools.pyx":1833
*
* def __iter__(self):
* return self # <<<<<<<<<<<<<<
@@ -17802,8 +19101,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_
* cdef int cnext(self):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(__pyx_v_self);
- __pyx_r = __pyx_v_self;
+ __Pyx_INCREF(((PyObject *)__pyx_v_self));
+ __pyx_r = ((PyObject *)__pyx_v_self);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -17814,7 +19113,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":1830
+/* "pysam/csamtools.pyx":1835
* return self
*
* cdef int cnext(self): # <<<<<<<<<<<<<<
@@ -17822,14 +19121,14 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_1__iter__(PyObject *__pyx_
*
*/
-static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+static int __pyx_f_5pysam_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("cnext");
- __Pyx_TraceCall("cnext", __pyx_f[0], 1830);
+ __Pyx_RefNannySetupContext("cnext", 0);
+ __Pyx_TraceCall("cnext", __pyx_f[0], 1835);
- /* "csamtools.pyx":1836
+ /* "pysam/csamtools.pyx":1841
* It has been re-implemented to permit for filtering.
* '''
* self.plp = bam_plp_auto( self.pileup_iter, # <<<<<<<<<<<<<<
@@ -17844,7 +19143,7 @@ static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools
return __pyx_r;
}
-/* "csamtools.pyx":1841
+/* "pysam/csamtools.pyx":1846
* &self.n_plp )
*
* cdef char * getSequence( self ): # <<<<<<<<<<<<<<
@@ -17852,14 +19151,14 @@ static int __pyx_f_9csamtools_14IteratorColumn_cnext(struct __pyx_obj_9csamtools
* '''
*/
-static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self) {
+static char *__pyx_f_5pysam_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
char *__pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("getSequence");
- __Pyx_TraceCall("getSequence", __pyx_f[0], 1841);
+ __Pyx_RefNannySetupContext("getSequence", 0);
+ __Pyx_TraceCall("getSequence", __pyx_f[0], 1846);
- /* "csamtools.pyx":1844
+ /* "pysam/csamtools.pyx":1849
* '''return current reference sequence underlying the iterator.
* '''
* return self.iterdata.seq # <<<<<<<<<<<<<<
@@ -17876,7 +19175,18 @@ static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9c
return __pyx_r;
}
-/* "csamtools.pyx":1848
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1853
* property seq_len:
* '''current sequence length.'''
* def __get__(self): return self.iterdata.seq_len # <<<<<<<<<<<<<<
@@ -17884,8 +19194,7 @@ static char *__pyx_f_9csamtools_14IteratorColumn_getSequence(struct __pyx_obj_9c
* def addReference( self, Fastafile fastafile ):
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_7seq_len___get__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -17893,10 +19202,10 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 1848);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 1853);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->iterdata.seq_len); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1853; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -17906,7 +19215,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IteratorColumn.seq_len.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.seq_len.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -17915,7 +19224,24 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":1850
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_14IteratorColumn_4addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("addReference (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_5pysam_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)__pyx_v_fastafile));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1855
* def __get__(self): return self.iterdata.seq_len
*
* def addReference( self, Fastafile fastafile ): # <<<<<<<<<<<<<<
@@ -17923,78 +19249,81 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(PyObject
* add reference sequences in *fastafile* to iterator.'''
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorColumn_2addReference[] = "IteratorColumn.addReference(self, Fastafile fastafile)\n\n add reference sequences in *fastafile* to iterator.";
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__pyx_v_self, PyObject *__pyx_v_fastafile) {
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_4addReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Fastafile *__pyx_v_fastafile) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
+ faidx_t *__pyx_t_2;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("addReference");
- __Pyx_TraceCall("addReference", __pyx_f[0], 1850);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fastafile), __pyx_ptype_9csamtools_Fastafile, 1, "fastafile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("addReference", 0);
+ __Pyx_TraceCall("addReference", __pyx_f[0], 1855);
- /* "csamtools.pyx":1853
+ /* "pysam/csamtools.pyx":1858
* '''
* add reference sequences in *fastafile* to iterator.'''
* self.fastafile = fastafile # <<<<<<<<<<<<<<
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1
*/
- __Pyx_INCREF(__pyx_v_fastafile);
- __Pyx_GIVEREF(__pyx_v_fastafile);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)__pyx_v_fastafile);
+ __Pyx_INCREF(((PyObject *)__pyx_v_fastafile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_fastafile));
+ __Pyx_GOTREF(__pyx_v_self->fastafile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->fastafile));
+ __pyx_v_self->fastafile = __pyx_v_fastafile;
- /* "csamtools.pyx":1854
+ /* "pysam/csamtools.pyx":1859
* add reference sequences in *fastafile* to iterator.'''
* self.fastafile = fastafile
* if self.iterdata.seq != NULL: free(self.iterdata.seq) # <<<<<<<<<<<<<<
* self.iterdata.tid = -1
* self.iterdata.fastafile = self.fastafile.fastafile
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
+ __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
if (__pyx_t_1) {
- free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
- goto __pyx_L5;
+ free(__pyx_v_self->iterdata.seq);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1855
+ /* "pysam/csamtools.pyx":1860
* self.fastafile = fastafile
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
* self.iterdata.fastafile = self.fastafile.fastafile
*
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.tid = -1;
+ __pyx_v_self->iterdata.tid = -1;
- /* "csamtools.pyx":1856
+ /* "pysam/csamtools.pyx":1861
* if self.iterdata.seq != NULL: free(self.iterdata.seq)
* self.iterdata.tid = -1
* self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
*
* def hasReference( self ):
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.fastafile = ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile->fastafile;
+ __pyx_t_2 = __pyx_v_self->fastafile->fastafile;
+ __pyx_v_self->iterdata.fastafile = __pyx_t_2;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.IteratorColumn.addReference", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
__Pyx_TraceReturn(__pyx_r);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":1858
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_14IteratorColumn_6hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
+static PyObject *__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("hasReference (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1863
* self.iterdata.fastafile = self.fastafile.fastafile
*
* def hasReference( self ): # <<<<<<<<<<<<<<
@@ -18002,16 +19331,14 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_2addReference(PyObject *__
* return true if iterator is associated with a reference'''
*/
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_14IteratorColumn_3hasReference[] = "IteratorColumn.hasReference(self)\n\n return true if iterator is associated with a reference";
-static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_14IteratorColumn_6hasReference(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("hasReference");
- __Pyx_TraceCall("hasReference", __pyx_f[0], 1858);
+ __Pyx_RefNannySetupContext("hasReference", 0);
+ __Pyx_TraceCall("hasReference", __pyx_f[0], 1863);
- /* "csamtools.pyx":1861
+ /* "pysam/csamtools.pyx":1866
* '''
* return true if iterator is associated with a reference'''
* return self.fastafile # <<<<<<<<<<<<<<
@@ -18019,8 +19346,8 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__
* cdef setMask( self, mask ):
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile));
- __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->fastafile);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->fastafile));
+ __pyx_r = ((PyObject *)__pyx_v_self->fastafile);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -18031,7 +19358,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":1863
+/* "pysam/csamtools.pyx":1868
* return self.fastafile
*
* cdef setMask( self, mask ): # <<<<<<<<<<<<<<
@@ -18039,7 +19366,7 @@ static PyObject *__pyx_pf_9csamtools_14IteratorColumn_3hasReference(PyObject *__
*
*/
-static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_mask) {
+static PyObject *__pyx_f_5pysam_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_mask) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -18047,20 +19374,20 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9c
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setMask");
- __Pyx_TraceCall("setMask", __pyx_f[0], 1863);
+ __Pyx_RefNannySetupContext("setMask", 0);
+ __Pyx_TraceCall("setMask", __pyx_f[0], 1868);
- /* "csamtools.pyx":1868
+ /* "pysam/csamtools.pyx":1873
* reads with bits set in *mask* will be skipped.
* '''
* self.mask = mask # <<<<<<<<<<<<<<
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
*/
- __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_mask); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_mask); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_self->mask = __pyx_t_1;
- /* "csamtools.pyx":1869
+ /* "pysam/csamtools.pyx":1874
* '''
* self.mask = mask
* bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
@@ -18072,7 +19399,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9c
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.IteratorColumn.setMask", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.setMask", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -18081,7 +19408,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9c
return __pyx_r;
}
-/* "csamtools.pyx":1871
+/* "pysam/csamtools.pyx":1876
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
@@ -18089,7 +19416,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setMask(struct __pyx_obj_9c
* int start,
*/
-static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args) {
+static PyObject *__pyx_f_5pysam_9csamtools_14IteratorColumn_setupIteratorData(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args) {
int __pyx_v_reopen = ((int)0);
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -18098,38 +19425,41 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
- int __pyx_t_6;
- int __pyx_t_7;
+ samfile_t *__pyx_t_6;
+ bam_iter_t __pyx_t_7;
int __pyx_t_8;
+ faidx_t *__pyx_t_9;
+ int __pyx_t_10;
+ int __pyx_t_11;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setupIteratorData");
- __Pyx_TraceCall("setupIteratorData", __pyx_f[0], 1871);
+ __Pyx_RefNannySetupContext("setupIteratorData", 0);
+ __Pyx_TraceCall("setupIteratorData", __pyx_f[0], 1876);
if (__pyx_optional_args) {
if (__pyx_optional_args->__pyx_n > 0) {
__pyx_v_reopen = __pyx_optional_args->reopen;
}
}
- /* "csamtools.pyx":1878
+ /* "pysam/csamtools.pyx":1883
* '''setup the iterator structure'''
*
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen ) # <<<<<<<<<<<<<<
* self.iterdata.samfile = self.samfile.samfile
* self.iterdata.iter = self.iter.iter
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_start); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(__pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyInt_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong(__pyx_v_reopen); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = PyTuple_New(5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
@@ -18145,34 +19475,36 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
__pyx_t_2 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_GIVEREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_v_self->iter);
__Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
- __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_4);
+ __pyx_v_self->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_t_4);
__pyx_t_4 = 0;
- /* "csamtools.pyx":1879
+ /* "pysam/csamtools.pyx":1884
*
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
* self.iterdata.samfile = self.samfile.samfile # <<<<<<<<<<<<<<
* self.iterdata.iter = self.iter.iter
* self.iterdata.seq = NULL
*/
- __pyx_v_self->iterdata.samfile = __pyx_v_self->samfile->samfile;
+ __pyx_t_6 = __pyx_v_self->samfile->samfile;
+ __pyx_v_self->iterdata.samfile = __pyx_t_6;
- /* "csamtools.pyx":1880
+ /* "pysam/csamtools.pyx":1885
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen )
* self.iterdata.samfile = self.samfile.samfile
* self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
* self.iterdata.tid = -1
*/
- __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
+ __pyx_t_7 = __pyx_v_self->iter->iter;
+ __pyx_v_self->iterdata.iter = __pyx_t_7;
- /* "csamtools.pyx":1881
+ /* "pysam/csamtools.pyx":1886
* self.iterdata.samfile = self.samfile.samfile
* self.iterdata.iter = self.iter.iter
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
@@ -18181,7 +19513,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
*/
__pyx_v_self->iterdata.seq = NULL;
- /* "csamtools.pyx":1882
+ /* "pysam/csamtools.pyx":1887
* self.iterdata.iter = self.iter.iter
* self.iterdata.seq = NULL
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
@@ -18190,32 +19522,32 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
*/
__pyx_v_self->iterdata.tid = -1;
- /* "csamtools.pyx":1884
+ /* "pysam/csamtools.pyx":1889
* self.iterdata.tid = -1
*
* if self.fastafile != None: # <<<<<<<<<<<<<<
* self.iterdata.fastafile = self.fastafile.fastafile
* else:
*/
- __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_self->fastafile), Py_None, Py_NE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(((PyObject *)__pyx_v_self->fastafile), Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (__pyx_t_6) {
+ if (__pyx_t_8) {
- /* "csamtools.pyx":1885
+ /* "pysam/csamtools.pyx":1890
*
* if self.fastafile != None:
* self.iterdata.fastafile = self.fastafile.fastafile # <<<<<<<<<<<<<<
* else:
* self.iterdata.fastafile = NULL
*/
- __pyx_v_self->iterdata.fastafile = __pyx_v_self->fastafile->fastafile;
+ __pyx_t_9 = __pyx_v_self->fastafile->fastafile;
+ __pyx_v_self->iterdata.fastafile = __pyx_t_9;
goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":1887
+ /* "pysam/csamtools.pyx":1892
* self.iterdata.fastafile = self.fastafile.fastafile
* else:
* self.iterdata.fastafile = NULL # <<<<<<<<<<<<<<
@@ -18226,82 +19558,85 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
}
__pyx_L3:;
- /* "csamtools.pyx":1889
+ /* "pysam/csamtools.pyx":1894
* self.iterdata.fastafile = NULL
*
* if self.stepper == None or self.stepper == "all": # <<<<<<<<<<<<<<
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
* elif self.stepper == "samtools":
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, Py_None, Py_EQ); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (!__pyx_t_6) {
- __pyx_t_7 = __Pyx_PyString_Equals(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = __pyx_t_7;
+ if (!__pyx_t_8) {
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__all), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_11 = __pyx_t_10;
} else {
- __pyx_t_8 = __pyx_t_6;
+ __pyx_t_11 = __pyx_t_8;
}
- if (__pyx_t_8) {
+ if (__pyx_t_11) {
- /* "csamtools.pyx":1890
+ /* "pysam/csamtools.pyx":1895
*
* if self.stepper == None or self.stepper == "all":
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata ) # <<<<<<<<<<<<<<
* elif self.stepper == "samtools":
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
*/
- __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_all), (&__pyx_v_self->iterdata));
+ __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_5pysam_9csamtools___advance_all), (&__pyx_v_self->iterdata));
goto __pyx_L4;
}
- /* "csamtools.pyx":1891
+ /* "pysam/csamtools.pyx":1896
* if self.stepper == None or self.stepper == "all":
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
* elif self.stepper == "samtools": # <<<<<<<<<<<<<<
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
* else:
*/
- __pyx_t_8 = __Pyx_PyString_Equals(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__samtools), Py_EQ); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_8) {
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_self->stepper, ((PyObject *)__pyx_n_s__samtools), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ if (__pyx_t_11) {
- /* "csamtools.pyx":1892
+ /* "pysam/csamtools.pyx":1897
* self.pileup_iter = bam_plp_init( &__advance_all, &self.iterdata )
* elif self.stepper == "samtools":
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata ) # <<<<<<<<<<<<<<
* else:
* raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
*/
- __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_9csamtools___advance_snpcalls), (&__pyx_v_self->iterdata));
+ __pyx_v_self->pileup_iter = bam_plp_init((&__pyx_f_5pysam_9csamtools___advance_snpcalls), (&__pyx_v_self->iterdata));
goto __pyx_L4;
}
/*else*/ {
- /* "csamtools.pyx":1894
+ /* "pysam/csamtools.pyx":1899
* self.pileup_iter = bam_plp_init( &__advance_snpcalls, &self.iterdata )
* else:
* raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper) # <<<<<<<<<<<<<<
*
* if self.max_depth:
*/
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_127), __pyx_v_self->stepper); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_131), __pyx_v_self->stepper); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L4:;
- /* "csamtools.pyx":1896
+ /* "pysam/csamtools.pyx":1901
* raise ValueError( "unknown stepper option `%s` in IteratorColumn" % self.stepper)
*
* if self.max_depth: # <<<<<<<<<<<<<<
@@ -18310,7 +19645,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
*/
if (__pyx_v_self->max_depth) {
- /* "csamtools.pyx":1897
+ /* "pysam/csamtools.pyx":1902
*
* if self.max_depth:
* bam_plp_set_maxcnt( self.pileup_iter, self.max_depth ) # <<<<<<<<<<<<<<
@@ -18322,7 +19657,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
}
__pyx_L5:;
- /* "csamtools.pyx":1899
+ /* "pysam/csamtools.pyx":1904
* bam_plp_set_maxcnt( self.pileup_iter, self.max_depth )
*
* bam_plp_set_mask( self.pileup_iter, self.mask ) # <<<<<<<<<<<<<<
@@ -18339,7 +19674,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.IteratorColumn.setupIteratorData", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.setupIteratorData", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -18348,7 +19683,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
return __pyx_r;
}
-/* "csamtools.pyx":1901
+/* "pysam/csamtools.pyx":1906
* bam_plp_set_mask( self.pileup_iter, self.mask )
*
* cdef reset( self, tid, start, end ): # <<<<<<<<<<<<<<
@@ -18356,29 +19691,30 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_setupIteratorData(struct __
*
*/
-static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_end) {
+static PyObject *__pyx_f_5pysam_9csamtools_14IteratorColumn_reset(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self, PyObject *__pyx_v_tid, PyObject *__pyx_v_start, PyObject *__pyx_v_end) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
- int __pyx_t_4;
+ bam_iter_t __pyx_t_4;
+ int __pyx_t_5;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("reset");
- __Pyx_TraceCall("reset", __pyx_f[0], 1901);
+ __Pyx_RefNannySetupContext("reset", 0);
+ __Pyx_TraceCall("reset", __pyx_f[0], 1906);
- /* "csamtools.pyx":1907
+ /* "pysam/csamtools.pyx":1912
* having to incur the full set-up costs.
* '''
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 ) # <<<<<<<<<<<<<<
* self.iterdata.iter = self.iter.iter
*
*/
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_self->samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
@@ -18391,59 +19727,59 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
__Pyx_INCREF(__pyx_v_end);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_end);
__Pyx_GIVEREF(__pyx_v_end);
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowRegion)), ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_GIVEREF(__pyx_t_3);
__Pyx_GOTREF(__pyx_v_self->iter);
__Pyx_DECREF(((PyObject *)__pyx_v_self->iter));
- __pyx_v_self->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)__pyx_t_3);
+ __pyx_v_self->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)__pyx_t_3);
__pyx_t_3 = 0;
- /* "csamtools.pyx":1908
+ /* "pysam/csamtools.pyx":1913
* '''
* self.iter = IteratorRowRegion( self.samfile, tid, start, end, reopen = 0 )
* self.iterdata.iter = self.iter.iter # <<<<<<<<<<<<<<
*
* # invalidate sequence if different tid
*/
- __pyx_v_self->iterdata.iter = __pyx_v_self->iter->iter;
+ __pyx_t_4 = __pyx_v_self->iter->iter;
+ __pyx_v_self->iterdata.iter = __pyx_t_4;
- /* "csamtools.pyx":1911
+ /* "pysam/csamtools.pyx":1916
*
* # invalidate sequence if different tid
* if self.tid != tid: # <<<<<<<<<<<<<<
* if self.iterdata.seq != NULL: free( self.iterdata.seq )
* self.iterdata.seq = NULL
*/
- __pyx_t_3 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_v_tid, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_v_tid, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_4) {
+ if (__pyx_t_5) {
- /* "csamtools.pyx":1912
+ /* "pysam/csamtools.pyx":1917
* # invalidate sequence if different tid
* if self.tid != tid:
* if self.iterdata.seq != NULL: free( self.iterdata.seq ) # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
* self.iterdata.tid = -1
*/
- __pyx_t_4 = (__pyx_v_self->iterdata.seq != NULL);
- if (__pyx_t_4) {
+ __pyx_t_5 = (__pyx_v_self->iterdata.seq != NULL);
+ if (__pyx_t_5) {
free(__pyx_v_self->iterdata.seq);
goto __pyx_L4;
}
__pyx_L4:;
- /* "csamtools.pyx":1913
+ /* "pysam/csamtools.pyx":1918
* if self.tid != tid:
* if self.iterdata.seq != NULL: free( self.iterdata.seq )
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
@@ -18452,7 +19788,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
*/
__pyx_v_self->iterdata.seq = NULL;
- /* "csamtools.pyx":1914
+ /* "pysam/csamtools.pyx":1919
* if self.iterdata.seq != NULL: free( self.iterdata.seq )
* self.iterdata.seq = NULL
* self.iterdata.tid = -1 # <<<<<<<<<<<<<<
@@ -18464,7 +19800,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
}
__pyx_L3:;
- /* "csamtools.pyx":1917
+ /* "pysam/csamtools.pyx":1922
*
* # self.pileup_iter = bam_plp_init( &__advancepileup, &self.iterdata )
* bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
@@ -18479,7 +19815,7 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IteratorColumn.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumn.reset", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -18488,7 +19824,16 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
return __pyx_r;
}
-/* "csamtools.pyx":1919
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":1924
* bam_plp_reset(self.pileup_iter)
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -18496,123 +19841,109 @@ static PyObject *__pyx_f_9csamtools_14IteratorColumn_reset(struct __pyx_obj_9csa
* # not been fully consumed
*/
-static void __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_14IteratorColumn_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *__pyx_v_self) {
__Pyx_RefNannyDeclarations
int __pyx_t_1;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1919);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 1924);
- /* "csamtools.pyx":1922
+ /* "pysam/csamtools.pyx":1927
* # reset in order to avoid memory leak messages for iterators that have
* # not been fully consumed
* if self.pileup_iter != <bam_plp_t>NULL: # <<<<<<<<<<<<<<
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter)
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter != ((bam_plp_t)NULL));
+ __pyx_t_1 = (__pyx_v_self->pileup_iter != NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":1923
+ /* "pysam/csamtools.pyx":1928
* # not been fully consumed
* if self.pileup_iter != <bam_plp_t>NULL:
* bam_plp_reset(self.pileup_iter) # <<<<<<<<<<<<<<
* bam_plp_destroy(self.pileup_iter)
* self.pileup_iter = <bam_plp_t>NULL
*/
- bam_plp_reset(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
+ bam_plp_reset(__pyx_v_self->pileup_iter);
- /* "csamtools.pyx":1924
+ /* "pysam/csamtools.pyx":1929
* if self.pileup_iter != <bam_plp_t>NULL:
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter) # <<<<<<<<<<<<<<
* self.pileup_iter = <bam_plp_t>NULL
*
*/
- bam_plp_destroy(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter);
+ bam_plp_destroy(__pyx_v_self->pileup_iter);
- /* "csamtools.pyx":1925
+ /* "pysam/csamtools.pyx":1930
* bam_plp_reset(self.pileup_iter)
* bam_plp_destroy(self.pileup_iter)
* self.pileup_iter = <bam_plp_t>NULL # <<<<<<<<<<<<<<
*
* if self.iterdata.seq != NULL:
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->pileup_iter = ((bam_plp_t)NULL);
- goto __pyx_L5;
+ __pyx_v_self->pileup_iter = NULL;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":1927
+ /* "pysam/csamtools.pyx":1932
* self.pileup_iter = <bam_plp_t>NULL
*
* if self.iterdata.seq != NULL: # <<<<<<<<<<<<<<
* free(self.iterdata.seq)
* self.iterdata.seq = NULL
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq != NULL);
+ __pyx_t_1 = (__pyx_v_self->iterdata.seq != NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":1928
+ /* "pysam/csamtools.pyx":1933
*
* if self.iterdata.seq != NULL:
* free(self.iterdata.seq) # <<<<<<<<<<<<<<
* self.iterdata.seq = NULL
*
*/
- free(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq);
+ free(__pyx_v_self->iterdata.seq);
- /* "csamtools.pyx":1929
+ /* "pysam/csamtools.pyx":1934
* if self.iterdata.seq != NULL:
* free(self.iterdata.seq)
* self.iterdata.seq = NULL # <<<<<<<<<<<<<<
*
* cdef class IteratorColumnRegion(IteratorColumn):
*/
- ((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self)->iterdata.seq = NULL;
- goto __pyx_L6;
+ __pyx_v_self->iterdata.seq = NULL;
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":1934
- * '''iterates over a region only.
- * '''
- * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
- * int tid = 0,
- * int start = 0,
- */
-
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_tid;
int __pyx_v_start;
int __pyx_v_end;
int __pyx_v_truncate;
- PyObject *__pyx_v_kwargs = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1934);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__truncate,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 5: values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
@@ -18622,10 +19953,9 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -18649,7 +19979,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1939; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -18662,27 +19992,27 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
if (values[1]) {
- __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1935; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_tid = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_tid == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1940; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_tid = ((int)0);
}
if (values[2]) {
- __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1936; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_start = __Pyx_PyInt_AsInt(values[2]); if (unlikely((__pyx_v_start == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1941; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
__pyx_v_start = ((int)0);
}
if (values[3]) {
- __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_end = __Pyx_PyInt_AsInt(values[3]); if (unlikely((__pyx_v_end == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
- __pyx_v_end = __pyx_k_128;
+ __pyx_v_end = __pyx_k_132;
}
if (values[4]) {
- __pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1938; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_truncate = __Pyx_PyInt_AsInt(values[4]); if (unlikely((__pyx_v_truncate == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1943; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
- /* "csamtools.pyx":1938
+ /* "pysam/csamtools.pyx":1943
* int start = 0,
* int end = max_pos,
* int truncate = False, # <<<<<<<<<<<<<<
@@ -18694,16 +20024,45 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1939; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self), __pyx_v_samfile, __pyx_v_tid, __pyx_v_start, __pyx_v_end, __pyx_v_truncate, __pyx_v_kwargs);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1939
+ * '''iterates over a region only.
+ * '''
+ * def __cinit__(self, Samfile samfile, # <<<<<<<<<<<<<<
+ * int tid = 0,
+ * int start = 0,
+ */
+
+static int __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self, CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, int __pyx_v_truncate, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_2;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1939);
- /* "csamtools.pyx":1942
+ /* "pysam/csamtools.pyx":1947
*
* # initialize iterator
* self.setupIteratorData( tid, start, end, 1 ) # <<<<<<<<<<<<<<
@@ -18712,51 +20071,65 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_
*/
__pyx_t_2.__pyx_n = 1;
__pyx_t_2.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_tid, __pyx_v_start, __pyx_v_end, &__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":1943
+ /* "pysam/csamtools.pyx":1948
* # initialize iterator
* self.setupIteratorData( tid, start, end, 1 )
* self.start = start # <<<<<<<<<<<<<<
* self.end = end
* self.truncate = truncate
*/
- ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start = __pyx_v_start;
+ __pyx_v_self->start = __pyx_v_start;
- /* "csamtools.pyx":1944
+ /* "pysam/csamtools.pyx":1949
* self.setupIteratorData( tid, start, end, 1 )
* self.start = start
* self.end = end # <<<<<<<<<<<<<<
* self.truncate = truncate
*
*/
- ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end = __pyx_v_end;
+ __pyx_v_self->end = __pyx_v_end;
- /* "csamtools.pyx":1945
+ /* "pysam/csamtools.pyx":1950
* self.start = start
* self.end = end
* self.truncate = truncate # <<<<<<<<<<<<<<
*
* def __next__(self):
*/
- ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate = __pyx_v_truncate;
+ __pyx_v_self->truncate = __pyx_v_truncate;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":1947
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__[] = "python version of next().\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1952
* self.truncate = truncate
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -18764,10 +20137,7 @@ static int __pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(PyObject *__pyx_
* """
*/
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
-static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_20IteratorColumnRegion_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -18776,10 +20146,10 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1947);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1952);
- /* "csamtools.pyx":1951
+ /* "pysam/csamtools.pyx":1956
* """
*
* while 1: # <<<<<<<<<<<<<<
@@ -18789,52 +20159,52 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *
while (1) {
if (!1) break;
- /* "csamtools.pyx":1952
+ /* "pysam/csamtools.pyx":1957
*
* while 1:
* self.cnext() # <<<<<<<<<<<<<<
* if self.n_plp < 0:
* raise ValueError("error during iteration" )
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion *)((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
- /* "csamtools.pyx":1953
+ /* "pysam/csamtools.pyx":1958
* while 1:
* self.cnext()
* if self.n_plp < 0: # <<<<<<<<<<<<<<
* raise ValueError("error during iteration" )
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp < 0);
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
- /* "csamtools.pyx":1954
+ /* "pysam/csamtools.pyx":1959
* self.cnext()
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
*
* if self.plp == NULL:
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_130), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_134), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
- /* "csamtools.pyx":1956
+ /* "pysam/csamtools.pyx":1961
* raise ValueError("error during iteration" )
*
* if self.plp == NULL: # <<<<<<<<<<<<<<
* raise StopIteration
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp == NULL);
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.plp == NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":1957
+ /* "pysam/csamtools.pyx":1962
*
* if self.plp == NULL:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -18842,53 +20212,53 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *
* if self.truncate:
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L8;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L6;
}
- __pyx_L8:;
+ __pyx_L6:;
- /* "csamtools.pyx":1959
+ /* "pysam/csamtools.pyx":1964
* raise StopIteration
*
* if self.truncate: # <<<<<<<<<<<<<<
- * if self.start < self.pos: continue
+ * if self.start > self.pos: continue
* if self.pos >= self.end: raise StopIteration
*/
- if (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->truncate) {
+ if (__pyx_v_self->truncate) {
- /* "csamtools.pyx":1960
+ /* "pysam/csamtools.pyx":1965
*
* if self.truncate:
- * if self.start < self.pos: continue # <<<<<<<<<<<<<<
+ * if self.start > self.pos: continue # <<<<<<<<<<<<<<
* if self.pos >= self.end: raise StopIteration
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->start < ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos);
+ __pyx_t_1 = (__pyx_v_self->start > __pyx_v_self->__pyx_base.pos);
if (__pyx_t_1) {
- goto __pyx_L5_continue;
- goto __pyx_L10;
+ goto __pyx_L3_continue;
+ goto __pyx_L8;
}
- __pyx_L10:;
+ __pyx_L8:;
- /* "csamtools.pyx":1961
+ /* "pysam/csamtools.pyx":1966
* if self.truncate:
- * if self.start < self.pos: continue
+ * if self.start > self.pos: continue
* if self.pos >= self.end: raise StopIteration # <<<<<<<<<<<<<<
*
* return makePileupProxy( &self.plp,
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos >= ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->end);
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.pos >= __pyx_v_self->end);
if (__pyx_t_1) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L11;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L9;
}
- __pyx_L11:;
- goto __pyx_L9;
+ __pyx_L9:;
+ goto __pyx_L7;
}
- __pyx_L9:;
+ __pyx_L7:;
- /* "csamtools.pyx":1963
+ /* "pysam/csamtools.pyx":1968
* if self.pos >= self.end: raise StopIteration
*
* return makePileupProxy( &self.plp, # <<<<<<<<<<<<<<
@@ -18897,26 +20267,26 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *
*/
__Pyx_XDECREF(__pyx_r);
- /* "csamtools.pyx":1966
+ /* "pysam/csamtools.pyx":1971
* self.tid,
* self.pos,
* self.n_plp ) # <<<<<<<<<<<<<<
*
* cdef class IteratorColumnAllRefs(IteratorColumn):
*/
- __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1963; __pyx_clineno = __LINE [...]
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- __pyx_L5_continue:;
+ __pyx_L3_continue:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IteratorColumnRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -18925,90 +20295,105 @@ static PyObject *__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__(PyObject *
return __pyx_r;
}
-/* "csamtools.pyx":1972
- * """
- *
- * def __cinit__(self, # <<<<<<<<<<<<<<
- * Samfile samfile,
- * **kwargs ):
- */
-
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
- PyObject *__pyx_v_kwargs = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
+ CYTHON_UNUSED PyObject *__pyx_v_kwargs = 0;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- int __pyx_t_3;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__cinit__");
- __Pyx_TraceCall("__cinit__", __pyx_f[0], 1972);
+ __Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
__pyx_v_kwargs = PyDict_New(); if (unlikely(!__pyx_v_kwargs)) return -1;
__Pyx_GOTREF(__pyx_v_kwargs);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, PyTuple_GET_SIZE(__pyx_args), "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
- __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self), __pyx_v_samfile, __pyx_v_kwargs);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_XDECREF(__pyx_v_kwargs);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "csamtools.pyx":1977
+/* "pysam/csamtools.pyx":1977
+ * """
+ *
+ * def __cinit__(self, # <<<<<<<<<<<<<<
+ * Samfile samfile,
+ * **kwargs ):
+ */
+
+static int __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs___cinit__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, CYTHON_UNUSED PyObject *__pyx_v_kwargs) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__cinit__", 0);
+ __Pyx_TraceCall("__cinit__", __pyx_f[0], 1977);
+
+ /* "pysam/csamtools.pyx":1982
*
* # no iteration over empty files
* if not samfile.nreferences: raise StopIteration # <<<<<<<<<<<<<<
*
* # initialize iterator
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (!__pyx_t_2);
if (__pyx_t_3) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":1980
+ /* "pysam/csamtools.pyx":1985
*
* # initialize iterator
* self.setupIteratorData( self.tid, 0, max_pos, 1 ) # <<<<<<<<<<<<<<
@@ -19017,7 +20402,7 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx
*/
__pyx_t_4.__pyx_n = 1;
__pyx_t_4.reopen = 1;
- __pyx_t_1 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1980; __pyx_clineno = __LINE__; g [...]
+ __pyx_t_1 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_5pysam_9csamtools_max_pos, &__pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -19025,16 +20410,30 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
- __Pyx_XDECREF(__pyx_v_kwargs);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":1982
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__[] = "python version of next().\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":1987
* self.setupIteratorData( self.tid, 0, max_pos, 1 )
*
* def __next__(self): # <<<<<<<<<<<<<<
@@ -19042,25 +20441,22 @@ static int __pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(PyObject *__pyx
* """
*/
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__[] = "python version of next().\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
-static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
PyObject *__pyx_t_2 = NULL;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
- struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_5;
+ struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData __pyx_t_5;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__next__");
- __Pyx_TraceCall("__next__", __pyx_f[0], 1982);
+ __Pyx_RefNannySetupContext("__next__", 0);
+ __Pyx_TraceCall("__next__", __pyx_f[0], 1987);
- /* "csamtools.pyx":1986
+ /* "pysam/csamtools.pyx":1991
* """
*
* while 1: # <<<<<<<<<<<<<<
@@ -19070,52 +20466,52 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
while (1) {
if (!1) break;
- /* "csamtools.pyx":1987
+ /* "pysam/csamtools.pyx":1992
*
* while 1:
* self.cnext() # <<<<<<<<<<<<<<
*
* if self.n_plp < 0:
*/
- ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self));
+ ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.cnext(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self));
- /* "csamtools.pyx":1989
+ /* "pysam/csamtools.pyx":1994
* self.cnext()
*
* if self.n_plp < 0: # <<<<<<<<<<<<<<
* raise ValueError("error during iteration" )
*
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp < 0);
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
- /* "csamtools.pyx":1990
+ /* "pysam/csamtools.pyx":1995
*
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
*
* # return result, if within same reference
*/
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_131), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_135), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
- /* "csamtools.pyx":1993
+ /* "pysam/csamtools.pyx":1998
*
* # return result, if within same reference
* if self.plp != NULL: # <<<<<<<<<<<<<<
* return makePileupProxy( &self.plp,
* self.tid,
*/
- __pyx_t_1 = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp != NULL);
+ __pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL);
if (__pyx_t_1) {
- /* "csamtools.pyx":1994
+ /* "pysam/csamtools.pyx":1999
* # return result, if within same reference
* if self.plp != NULL:
* return makePileupProxy( &self.plp, # <<<<<<<<<<<<<<
@@ -19124,51 +20520,50 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
*/
__Pyx_XDECREF(__pyx_r);
- /* "csamtools.pyx":1997
+ /* "pysam/csamtools.pyx":2002
* self.tid,
* self.pos,
* self.n_plp ) # <<<<<<<<<<<<<<
*
* # otherwise, proceed to next reference or stop
*/
- __pyx_t_2 = __pyx_f_9csamtools_makePileupProxy((&((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.plp), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.pos, ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1994; __pyx_clineno = [...]
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
goto __pyx_L0;
- goto __pyx_L8;
+ goto __pyx_L6;
}
- __pyx_L8:;
+ __pyx_L6:;
- /* "csamtools.pyx":2000
+ /* "pysam/csamtools.pyx":2005
*
* # otherwise, proceed to next reference or stop
* self.tid += 1 # <<<<<<<<<<<<<<
* if self.tid < self.samfile.nreferences:
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
*/
- ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid = (((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid + 1);
+ __pyx_v_self->__pyx_base.tid = (__pyx_v_self->__pyx_base.tid + 1);
- /* "csamtools.pyx":2001
+ /* "pysam/csamtools.pyx":2006
* # otherwise, proceed to next reference or stop
* self.tid += 1
* if self.tid < self.samfile.nreferences: # <<<<<<<<<<<<<<
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
* else:
*/
- __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_self->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(((PyObject *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self->__pyx_base.samfile), __pyx_n_s__nreferences); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_4 = PyObject_RichCompare(__pyx_t_2, __pyx_t_3, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2001; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_1) {
- /* "csamtools.pyx":2002
+ /* "pysam/csamtools.pyx":2007
* self.tid += 1
* if self.tid < self.samfile.nreferences:
* self.setupIteratorData( self.tid, 0, max_pos, 0 ) # <<<<<<<<<<<<<<
@@ -19177,14 +20572,14 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
*/
__pyx_t_5.__pyx_n = 1;
__pyx_t_5.reopen = 0;
- __pyx_t_4 = ((struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs *)((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_9csamtools_IteratorColumn *)__pyx_v_self), ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)__pyx_v_self)->__pyx_base.tid, 0, __pyx_v_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2002; __pyx_clineno = __LINE_ [...]
+ __pyx_t_4 = ((struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *)__pyx_v_self->__pyx_base.__pyx_vtab)->__pyx_base.setupIteratorData(((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)__pyx_v_self), __pyx_v_self->__pyx_base.tid, 0, __pyx_v_5pysam_9csamtools_max_pos, &__pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L9;
+ goto __pyx_L7;
}
/*else*/ {
- /* "csamtools.pyx":2004
+ /* "pysam/csamtools.pyx":2009
* self.setupIteratorData( self.tid, 0, max_pos, 0 )
* else:
* raise StopIteration # <<<<<<<<<<<<<<
@@ -19192,9 +20587,9 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
* ##-------------------------------------------------------------------
*/
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L9:;
+ __pyx_L7:;
}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -19203,7 +20598,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IteratorColumnAllRefs.__next__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -19212,7 +20607,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":2009
+/* "pysam/csamtools.pyx":2014
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_start(bam1_t *src) except -1: # <<<<<<<<<<<<<<
@@ -19220,7 +20615,7 @@ static PyObject *__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__(PyObject
* cdef uint32_t k
*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src) {
+static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx_v_src) {
uint32_t *__pyx_v_cigar_p;
uint32_t __pyx_v_op;
uint32_t __pyx_v_k;
@@ -19231,12 +20626,11 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
int __pyx_t_2;
int __pyx_t_3;
int __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_start");
- __Pyx_TraceCall("query_start", __pyx_f[0], 2009);
+ __Pyx_RefNannySetupContext("query_start", 0);
+ __Pyx_TraceCall("query_start", __pyx_f[0], 2014);
- /* "csamtools.pyx":2012
+ /* "pysam/csamtools.pyx":2017
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
* cdef uint32_t start_offset = 0 # <<<<<<<<<<<<<<
@@ -19245,7 +20639,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
__pyx_v_start_offset = 0;
- /* "csamtools.pyx":2014
+ /* "pysam/csamtools.pyx":2019
* cdef uint32_t start_offset = 0
*
* if src.core.n_cigar: # <<<<<<<<<<<<<<
@@ -19254,7 +20648,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
if (__pyx_v_src->core.n_cigar) {
- /* "csamtools.pyx":2015
+ /* "pysam/csamtools.pyx":2020
*
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
@@ -19263,7 +20657,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2016
+ /* "pysam/csamtools.pyx":2021
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
@@ -19273,7 +20667,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
__pyx_t_1 = __pyx_v_src->core.n_cigar;
for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) {
- /* "csamtools.pyx":2017
+ /* "pysam/csamtools.pyx":2022
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -19282,7 +20676,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "csamtools.pyx":2022
+ /* "pysam/csamtools.pyx":2027
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -19291,7 +20685,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
switch (__pyx_v_op) {
- /* "csamtools.pyx":2018
+ /* "pysam/csamtools.pyx":2023
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
@@ -19300,7 +20694,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
case 5:
- /* "csamtools.pyx":2019
+ /* "pysam/csamtools.pyx":2024
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -19316,19 +20710,16 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
}
if (__pyx_t_4) {
- /* "csamtools.pyx":2020
+ /* "pysam/csamtools.pyx":2025
* if op==BAM_CHARD_CLIP:
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
* return -1
* elif op==BAM_CSOFT_CLIP:
*/
- __pyx_t_5 = __pyx_builtin_ValueError;
- __Pyx_INCREF(__pyx_t_5);
- PyErr_SetString(__pyx_t_5, __pyx_k_132);
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_136);
- /* "csamtools.pyx":2021
+ /* "pysam/csamtools.pyx":2026
* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
@@ -19342,7 +20733,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
__pyx_L6:;
break;
- /* "csamtools.pyx":2022
+ /* "pysam/csamtools.pyx":2027
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -19351,7 +20742,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
*/
case 4:
- /* "csamtools.pyx":2023
+ /* "pysam/csamtools.pyx":2028
* return -1
* elif op==BAM_CSOFT_CLIP:
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
@@ -19362,7 +20753,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
break;
default:
- /* "csamtools.pyx":2025
+ /* "pysam/csamtools.pyx":2030
* start_offset += cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
@@ -19378,7 +20769,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
}
__pyx_L3:;
- /* "csamtools.pyx":2027
+ /* "pysam/csamtools.pyx":2032
* break
*
* return start_offset # <<<<<<<<<<<<<<
@@ -19395,7 +20786,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
return __pyx_r;
}
-/* "csamtools.pyx":2032
+/* "pysam/csamtools.pyx":2037
* ##-------------------------------------------------------------------
* ##-------------------------------------------------------------------
* cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
@@ -19403,41 +20794,42 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_start(bam1_t *__pyx_v_src)
* cdef uint32_t k
*/
-static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
+static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v_src) {
uint32_t *__pyx_v_cigar_p;
uint32_t __pyx_v_op;
uint32_t __pyx_v_k;
uint32_t __pyx_v_end_offset;
int32_t __pyx_r;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
+ int32_t __pyx_t_1;
int __pyx_t_2;
int __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_4;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("query_end");
- __Pyx_TraceCall("query_end", __pyx_f[0], 2032);
+ __Pyx_RefNannySetupContext("query_end", 0);
+ __Pyx_TraceCall("query_end", __pyx_f[0], 2037);
- /* "csamtools.pyx":2035
+ /* "pysam/csamtools.pyx":2040
* cdef uint32_t * cigar_p, op
* cdef uint32_t k
* cdef uint32_t end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
* if src.core.n_cigar>1:
*/
- __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
+ __pyx_t_1 = __pyx_v_src->core.l_qseq;
+ __pyx_v_end_offset = __pyx_t_1;
- /* "csamtools.pyx":2037
+ /* "pysam/csamtools.pyx":2042
* cdef uint32_t end_offset = src.core.l_qseq
*
* if src.core.n_cigar>1: # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar > 1);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.n_cigar > 1);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2038
+ /* "pysam/csamtools.pyx":2043
*
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
@@ -19446,7 +20838,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2039
+ /* "pysam/csamtools.pyx":2044
* if src.core.n_cigar>1:
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1: # <<<<<<<<<<<<<<
@@ -19455,7 +20847,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
*/
for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
- /* "csamtools.pyx":2040
+ /* "pysam/csamtools.pyx":2045
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -19464,7 +20856,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "csamtools.pyx":2045
+ /* "pysam/csamtools.pyx":2050
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -19473,7 +20865,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
*/
switch (__pyx_v_op) {
- /* "csamtools.pyx":2041
+ /* "pysam/csamtools.pyx":2046
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
@@ -19482,35 +20874,32 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
*/
case 5:
- /* "csamtools.pyx":2042
+ /* "pysam/csamtools.pyx":2047
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
*/
- __pyx_t_1 = (__pyx_v_end_offset != 0);
- if (__pyx_t_1) {
- __pyx_t_2 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
- __pyx_t_3 = __pyx_t_2;
+ __pyx_t_2 = (__pyx_v_end_offset != 0);
+ if (__pyx_t_2) {
+ __pyx_t_3 = (__pyx_v_end_offset != __pyx_v_src->core.l_qseq);
+ __pyx_t_4 = __pyx_t_3;
} else {
- __pyx_t_3 = __pyx_t_1;
+ __pyx_t_4 = __pyx_t_2;
}
- if (__pyx_t_3) {
+ if (__pyx_t_4) {
- /* "csamtools.pyx":2043
+ /* "pysam/csamtools.pyx":2048
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
* return -1
* elif op==BAM_CSOFT_CLIP:
*/
- __pyx_t_4 = __pyx_builtin_ValueError;
- __Pyx_INCREF(__pyx_t_4);
- PyErr_SetString(__pyx_t_4, __pyx_k_132);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_136);
- /* "csamtools.pyx":2044
+ /* "pysam/csamtools.pyx":2049
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
@@ -19524,7 +20913,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
__pyx_L6:;
break;
- /* "csamtools.pyx":2045
+ /* "pysam/csamtools.pyx":2050
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -19533,7 +20922,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
*/
case 4:
- /* "csamtools.pyx":2046
+ /* "pysam/csamtools.pyx":2051
* return -1
* elif op==BAM_CSOFT_CLIP:
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
@@ -19544,7 +20933,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
break;
default:
- /* "csamtools.pyx":2048
+ /* "pysam/csamtools.pyx":2053
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
@@ -19560,29 +20949,30 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
}
__pyx_L3:;
- /* "csamtools.pyx":2050
+ /* "pysam/csamtools.pyx":2055
* break
*
* if end_offset==0: # <<<<<<<<<<<<<<
* end_offset = src.core.l_qseq
*
*/
- __pyx_t_3 = (__pyx_v_end_offset == 0);
- if (__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_end_offset == 0);
+ if (__pyx_t_4) {
- /* "csamtools.pyx":2051
+ /* "pysam/csamtools.pyx":2056
*
* if end_offset==0:
* end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
*
* return end_offset
*/
- __pyx_v_end_offset = __pyx_v_src->core.l_qseq;
+ __pyx_t_1 = __pyx_v_src->core.l_qseq;
+ __pyx_v_end_offset = __pyx_t_1;
goto __pyx_L7;
}
__pyx_L7:;
- /* "csamtools.pyx":2053
+ /* "pysam/csamtools.pyx":2058
* end_offset = src.core.l_qseq
*
* return end_offset # <<<<<<<<<<<<<<
@@ -19599,7 +20989,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
return __pyx_r;
}
-/* "csamtools.pyx":2056
+/* "pysam/csamtools.pyx":2061
*
*
* cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
@@ -19607,7 +20997,7 @@ static CYTHON_INLINE int32_t __pyx_f_9csamtools_query_end(bam1_t *__pyx_v_src) {
* cdef uint32_t k
*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
uint8_t *__pyx_v_p;
uint32_t __pyx_v_k;
char *__pyx_v_s;
@@ -19622,10 +21012,10 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_seq_range");
- __Pyx_TraceCall("get_seq_range", __pyx_f[0], 2056);
+ __Pyx_RefNannySetupContext("get_seq_range", 0);
+ __Pyx_TraceCall("get_seq_range", __pyx_f[0], 2061);
- /* "csamtools.pyx":2061
+ /* "pysam/csamtools.pyx":2066
* cdef char * s
*
* if not src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -19635,7 +21025,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
__pyx_t_1 = (!__pyx_v_src->core.l_qseq);
if (__pyx_t_1) {
- /* "csamtools.pyx":2062
+ /* "pysam/csamtools.pyx":2067
*
* if not src.core.l_qseq:
* return None # <<<<<<<<<<<<<<
@@ -19650,29 +21040,29 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
}
__pyx_L3:;
- /* "csamtools.pyx":2064
+ /* "pysam/csamtools.pyx":2069
* return None
*
* seq = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
* s = <char*>seq
* p = bam1_seq(src)
*/
- __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2069; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":2065
+ /* "pysam/csamtools.pyx":2070
*
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq # <<<<<<<<<<<<<<
* p = bam1_seq(src)
*
*/
- __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2065; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_s = ((char *)__pyx_t_3);
- /* "csamtools.pyx":2066
+ /* "pysam/csamtools.pyx":2071
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq
* p = bam1_seq(src) # <<<<<<<<<<<<<<
@@ -19681,7 +21071,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "csamtools.pyx":2068
+ /* "pysam/csamtools.pyx":2073
* p = bam1_seq(src)
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
@@ -19691,17 +21081,17 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "csamtools.pyx":2071
+ /* "pysam/csamtools.pyx":2076
* # equivalent to bam_nt16_rev_table[bam1_seqi(s, i)] (see bam.c)
* # note: do not use string literal as it will be a python string
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf] # <<<<<<<<<<<<<<
*
* return seq
*/
- (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
+ (__pyx_v_s[(__pyx_v_k - __pyx_v_start)]) = (__pyx_v_5pysam_9csamtools_bam_nt16_rev_table[(((__pyx_v_p[__Pyx_div_long(__pyx_v_k, 2)]) >> (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))) & 0xf)]);
}
- /* "csamtools.pyx":2073
+ /* "pysam/csamtools.pyx":2078
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf]
*
* return seq # <<<<<<<<<<<<<<
@@ -19717,7 +21107,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.get_seq_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.get_seq_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_seq);
@@ -19727,7 +21117,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":2076
+/* "pysam/csamtools.pyx":2081
*
*
* cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
@@ -19735,7 +21125,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_seq_range(bam1_t *__pyx_v_
* cdef uint32_t k
*/
-static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *__pyx_v_src, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
uint8_t *__pyx_v_p;
uint32_t __pyx_v_k;
char *__pyx_v_q;
@@ -19750,10 +21140,10 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("get_qual_range");
- __Pyx_TraceCall("get_qual_range", __pyx_f[0], 2076);
+ __Pyx_RefNannySetupContext("get_qual_range", 0);
+ __Pyx_TraceCall("get_qual_range", __pyx_f[0], 2081);
- /* "csamtools.pyx":2081
+ /* "pysam/csamtools.pyx":2086
* cdef char * q
*
* p = bam1_qual(src) # <<<<<<<<<<<<<<
@@ -19762,7 +21152,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "csamtools.pyx":2082
+ /* "pysam/csamtools.pyx":2087
*
* p = bam1_qual(src)
* if p[0] == 0xff: # <<<<<<<<<<<<<<
@@ -19772,7 +21162,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
__pyx_t_1 = ((__pyx_v_p[0]) == 0xff);
if (__pyx_t_1) {
- /* "csamtools.pyx":2083
+ /* "pysam/csamtools.pyx":2088
* p = bam1_qual(src)
* if p[0] == 0xff:
* return None # <<<<<<<<<<<<<<
@@ -19787,29 +21177,29 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
}
__pyx_L3:;
- /* "csamtools.pyx":2085
+ /* "pysam/csamtools.pyx":2090
* return None
*
* qual = PyBytes_FromStringAndSize(NULL, end - start) # <<<<<<<<<<<<<<
* q = <char*>qual
*
*/
- __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)PyBytes_FromStringAndSize(NULL, (__pyx_v_end - __pyx_v_start))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_qual = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "csamtools.pyx":2086
+ /* "pysam/csamtools.pyx":2091
*
* qual = PyBytes_FromStringAndSize(NULL, end - start)
* q = <char*>qual # <<<<<<<<<<<<<<
*
* for k from start <= k < end:
*/
- __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2091; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_q = ((char *)__pyx_t_3);
- /* "csamtools.pyx":2088
+ /* "pysam/csamtools.pyx":2093
* q = <char*>qual
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
@@ -19819,7 +21209,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "csamtools.pyx":2090
+ /* "pysam/csamtools.pyx":2095
* for k from start <= k < end:
* ## equivalent to t[i] + 33 (see bam.c)
* q[k-start] = p[k] + 33 # <<<<<<<<<<<<<<
@@ -19829,7 +21219,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
(__pyx_v_q[(__pyx_v_k - __pyx_v_start)]) = ((__pyx_v_p[__pyx_v_k]) + 33);
}
- /* "csamtools.pyx":2092
+ /* "pysam/csamtools.pyx":2097
* q[k-start] = p[k] + 33
*
* return qual # <<<<<<<<<<<<<<
@@ -19845,7 +21235,7 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.get_qual_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.get_qual_range", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qual);
@@ -19855,7 +21245,21 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
return __pyx_r;
}
-/* "csamtools.pyx":2124
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2129
*
* # Now only called when instances are created from Python
* def __init__(self): # <<<<<<<<<<<<<<
@@ -19863,52 +21267,48 @@ static CYTHON_INLINE PyObject *__pyx_f_9csamtools_get_qual_range(bam1_t *__pyx_v
* self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) )
*/
-static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead___init__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 2124);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 2129);
- /* "csamtools.pyx":2126
+ /* "pysam/csamtools.pyx":2131
* def __init__(self):
* # see bam_init1
* self._delegate = <bam1_t*>calloc( 1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
* # allocate some memory
* # If size is 0, calloc does not return a pointer that can be passed to free()
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
+ __pyx_v_self->_delegate = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "csamtools.pyx":2130
+ /* "pysam/csamtools.pyx":2135
* # If size is 0, calloc does not return a pointer that can be passed to free()
* # so allocate 40 bytes for a new read
* self._delegate.m_data = 40 # <<<<<<<<<<<<<<
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
* self._delegate.data_len = 0
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data = 40;
+ __pyx_v_self->_delegate->m_data = 40;
- /* "csamtools.pyx":2131
+ /* "pysam/csamtools.pyx":2136
* # so allocate 40 bytes for a new read
* self._delegate.m_data = 40
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 ) # <<<<<<<<<<<<<<
* self._delegate.data_len = 0
*
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data = ((uint8_t *)calloc(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->m_data, 1));
+ __pyx_v_self->_delegate->data = ((uint8_t *)calloc(__pyx_v_self->_delegate->m_data, 1));
- /* "csamtools.pyx":2132
+ /* "pysam/csamtools.pyx":2137
* self._delegate.m_data = 40
* self._delegate.data = <uint8_t *>calloc( self._delegate.m_data, 1 )
* self._delegate.data_len = 0 # <<<<<<<<<<<<<<
*
* def __dealloc__(self):
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->data_len = 0;
+ __pyx_v_self->_delegate->data_len = 0;
__pyx_r = 0;
__Pyx_TraceReturn(Py_None);
@@ -19916,7 +21316,16 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":2134
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":2139
* self._delegate.data_len = 0
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -19924,27 +21333,41 @@ static int __pyx_pf_9csamtools_11AlignedRead___init__(PyObject *__pyx_v_self, Py
*
*/
-static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_11AlignedRead_2__dealloc__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 2134);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 2139);
- /* "csamtools.pyx":2135
+ /* "pysam/csamtools.pyx":2140
*
* def __dealloc__(self):
* bam_destroy1(self._delegate) # <<<<<<<<<<<<<<
*
* def __str__(self):
*/
- bam_destroy1(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate);
+ bam_destroy1(__pyx_v_self->_delegate);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-/* "csamtools.pyx":2137
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11AlignedRead_4__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
+struct wrapperbase __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__;
+#endif
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2142
* bam_destroy1(self._delegate)
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -19952,10 +21375,7 @@ static void __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(PyObject *__pyx_v_sel
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_2__str__[] = "return string representation of alignment.\n\n The representation is an approximate :term:`sam` format.\n\n An aligned read might not be associated with a :term:`Samfile`.\n As a result :term:`tid` is shown instead of the reference name.\n\n Similarly, the tags field is returned in its parsed state.\n ";
-struct wrapperbase __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4__str__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_v_seq = NULL;
PyObject *__pyx_v_qual = NULL;
PyObject *__pyx_r = NULL;
@@ -19977,97 +21397,96 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_se
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 2137);
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 2142);
- /* "csamtools.pyx":2149
+ /* "pysam/csamtools.pyx":2154
* # sam-parsing is done in sam.c/bam_format1_core which
* # requires a valid header.
* if sys.version_info[0] < 3: # <<<<<<<<<<<<<<
* seq = self.seq
* qual = self.qual
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__version_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__version_info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_3, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_3, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":2150
+ /* "pysam/csamtools.pyx":2155
* # requires a valid header.
* if sys.version_info[0] < 3:
* seq = self.seq # <<<<<<<<<<<<<<
* qual = self.qual
* else:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_seq = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":2151
+ /* "pysam/csamtools.pyx":2156
* if sys.version_info[0] < 3:
* seq = self.seq
* qual = self.qual # <<<<<<<<<<<<<<
* else:
* seq = self.seq.decode('ascii')
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2153
+ /* "pysam/csamtools.pyx":2158
* qual = self.qual
* else:
* seq = self.seq.decode('ascii') # <<<<<<<<<<<<<<
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname,
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__seq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_133), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_137), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_seq = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":2154
+ /* "pysam/csamtools.pyx":2159
* else:
* seq = self.seq.decode('ascii')
* qual = self.qual.decode('ascii') # <<<<<<<<<<<<<<
* return "\t".join(map(str, (self.qname,
* self.flag,
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__decode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_134), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_138), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2155
+ /* "pysam/csamtools.pyx":2160
* seq = self.seq.decode('ascii')
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname, # <<<<<<<<<<<<<<
@@ -20075,102 +21494,102 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_se
* self.rname,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qname); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":2156
+ /* "pysam/csamtools.pyx":2161
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname,
* self.flag, # <<<<<<<<<<<<<<
* self.rname,
* self.pos,
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- /* "csamtools.pyx":2157
+ /* "pysam/csamtools.pyx":2162
* return "\t".join(map(str, (self.qname,
* self.flag,
* self.rname, # <<<<<<<<<<<<<<
* self.pos,
* self.mapq,
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rname); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- /* "csamtools.pyx":2158
+ /* "pysam/csamtools.pyx":2163
* self.flag,
* self.rname,
* self.pos, # <<<<<<<<<<<<<<
* self.mapq,
* self.cigar,
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "csamtools.pyx":2159
+ /* "pysam/csamtools.pyx":2164
* self.rname,
* self.pos,
* self.mapq, # <<<<<<<<<<<<<<
* self.cigar,
* self.mrnm,
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "csamtools.pyx":2160
+ /* "pysam/csamtools.pyx":2165
* self.pos,
* self.mapq,
* self.cigar, # <<<<<<<<<<<<<<
* self.mrnm,
* self.mpos,
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- /* "csamtools.pyx":2161
+ /* "pysam/csamtools.pyx":2166
* self.mapq,
* self.cigar,
* self.mrnm, # <<<<<<<<<<<<<<
* self.mpos,
* self.rlen,
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2161; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mrnm); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- /* "csamtools.pyx":2162
+ /* "pysam/csamtools.pyx":2167
* self.cigar,
* self.mrnm,
* self.mpos, # <<<<<<<<<<<<<<
* self.rlen,
* seq,
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mpos); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2167; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- /* "csamtools.pyx":2163
+ /* "pysam/csamtools.pyx":2168
* self.mrnm,
* self.mpos,
* self.rlen, # <<<<<<<<<<<<<<
* seq,
* qual,
*/
- __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__rlen); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- /* "csamtools.pyx":2166
+ /* "pysam/csamtools.pyx":2171
* seq,
* qual,
* self.tags ))) # <<<<<<<<<<<<<<
*
* def compare(self, AlignedRead other):
*/
- __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2166; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tags); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
- __pyx_t_13 = PyTuple_New(12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ __pyx_t_13 = PyTuple_New(12); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_4);
@@ -20207,23 +21626,23 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_se
__pyx_t_10 = 0;
__pyx_t_11 = 0;
__pyx_t_12 = 0;
- __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_12));
+ __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_12, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_12, 1, ((PyObject *)__pyx_t_13));
__Pyx_GIVEREF(((PyObject *)__pyx_t_13));
__pyx_t_13 = 0;
- __pyx_t_13 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
- __pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_12));
+ __pyx_t_12 = PyTuple_New(1); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_12);
PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_13);
__Pyx_GIVEREF(__pyx_t_13);
__pyx_t_13 = 0;
- __pyx_t_13 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
@@ -20246,7 +21665,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_se
__Pyx_XDECREF(__pyx_t_11);
__Pyx_XDECREF(__pyx_t_12);
__Pyx_XDECREF(__pyx_t_13);
- __Pyx_AddTraceback("csamtools.AlignedRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_seq);
@@ -20257,7 +21676,24 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2168
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11AlignedRead_6compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("compare (wrapper)", 0);
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_other));
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2173
* self.tags )))
*
* def compare(self, AlignedRead other): # <<<<<<<<<<<<<<
@@ -20265,53 +21701,53 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_2__str__(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_3compare[] = "AlignedRead.compare(self, AlignedRead other)\nreturn -1,0,1, if contents in this are binary <,=,> to *other*";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_self, PyObject *__pyx_v_other) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6compare(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_other) {
int __pyx_v_retval;
bam1_t *__pyx_v_t;
bam1_t *__pyx_v_o;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("compare");
- __Pyx_TraceCall("compare", __pyx_f[0], 2168);
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_other), __pyx_ptype_9csamtools_AlignedRead, 1, "other", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2168; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_RefNannySetupContext("compare", 0);
+ __Pyx_TraceCall("compare", __pyx_f[0], 2173);
- /* "csamtools.pyx":2174
+ /* "pysam/csamtools.pyx":2179
* cdef bam1_t *t, *o
*
* t = self._delegate # <<<<<<<<<<<<<<
* o = other._delegate
*
*/
- __pyx_v_t = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_t = __pyx_t_1;
- /* "csamtools.pyx":2175
+ /* "pysam/csamtools.pyx":2180
*
* t = self._delegate
* o = other._delegate # <<<<<<<<<<<<<<
*
* # uncomment for debugging purposes
*/
- __pyx_v_o = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_other)->_delegate;
+ __pyx_t_1 = __pyx_v_other->_delegate;
+ __pyx_v_o = __pyx_t_1;
- /* "csamtools.pyx":2187
+ /* "pysam/csamtools.pyx":2192
*
* # Fast-path test for object identity
* if t==o: # <<<<<<<<<<<<<<
* return 0
*
*/
- __pyx_t_1 = (__pyx_v_t == __pyx_v_o);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_t == __pyx_v_o);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2188
+ /* "pysam/csamtools.pyx":2193
* # Fast-path test for object identity
* if t==o:
* return 0 # <<<<<<<<<<<<<<
@@ -20322,11 +21758,11 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
__Pyx_INCREF(__pyx_int_0);
__pyx_r = __pyx_int_0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2190
+ /* "pysam/csamtools.pyx":2195
* return 0
*
* retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t)) # <<<<<<<<<<<<<<
@@ -20335,7 +21771,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
*/
__pyx_v_retval = memcmp((&__pyx_v_t->core), (&__pyx_v_o->core), (sizeof(bam1_core_t)));
- /* "csamtools.pyx":2192
+ /* "pysam/csamtools.pyx":2197
* retval = memcmp(&t.core, &o.core, sizeof(bam1_core_t))
*
* if retval: return retval # <<<<<<<<<<<<<<
@@ -20344,16 +21780,16 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
*/
if (__pyx_v_retval) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2192; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":2193
+ /* "pysam/csamtools.pyx":2198
*
* if retval: return retval
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len) # <<<<<<<<<<<<<<
@@ -20362,7 +21798,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
*/
__pyx_v_retval = ((__pyx_v_t->data_len > __pyx_v_o->data_len) - (__pyx_v_t->data_len < __pyx_v_o->data_len));
- /* "csamtools.pyx":2194
+ /* "pysam/csamtools.pyx":2199
* if retval: return retval
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
* if retval: return retval # <<<<<<<<<<<<<<
@@ -20371,16 +21807,16 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
*/
if (__pyx_v_retval) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
- goto __pyx_L7;
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
- /* "csamtools.pyx":2195
+ /* "pysam/csamtools.pyx":2200
* retval = (t.data_len > o.data_len) - (t.data_len < o.data_len) # cmp(t.data_len, o.data_len)
* if retval: return retval
* return memcmp(t.data, o.data, t.data_len) # <<<<<<<<<<<<<<
@@ -20388,17 +21824,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
* # Disabled so long as __cmp__ is a special method
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyInt_FromLong(memcmp(__pyx_v_t->data, __pyx_v_o->data, __pyx_v_t->data_len)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyInt_FromLong(memcmp(__pyx_v_t->data, __pyx_v_o->data, __pyx_v_t->data_len)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.compare", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -20407,7 +21843,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2198
+/* Python wrapper */
+static Py_hash_t __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self); /*proto*/
+static Py_hash_t __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__(PyObject *__pyx_v_self) {
+ Py_hash_t __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__hash__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2203
*
* # Disabled so long as __cmp__ is a special method
* def __hash__(self): # <<<<<<<<<<<<<<
@@ -20415,15 +21862,14 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3compare(PyObject *__pyx_v_se
*
*/
-static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_self); /*proto*/
-static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_self) {
+static Py_hash_t __pyx_pf_5pysam_9csamtools_11AlignedRead_8__hash__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
Py_hash_t __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__hash__");
- __Pyx_TraceCall("__hash__", __pyx_f[0], 2198);
+ __Pyx_RefNannySetupContext("__hash__", 0);
+ __Pyx_TraceCall("__hash__", __pyx_f[0], 2203);
- /* "csamtools.pyx":2199
+ /* "pysam/csamtools.pyx":2204
* # Disabled so long as __cmp__ is a special method
* def __hash__(self):
* return _Py_HashPointer(<void *>self) # <<<<<<<<<<<<<<
@@ -20441,7 +21887,18 @@ static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2203
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2208
* property qname:
* """the query name (None if not present)"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -20449,47 +21906,48 @@ static Py_hash_t __pyx_pf_9csamtools_11AlignedRead_4__hash__(PyObject *__pyx_v_s
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2203);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2208);
- /* "csamtools.pyx":2205
+ /* "pysam/csamtools.pyx":2210
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.l_qname == 0: return None
* return _charptr_to_str(<char *>bam1_qname( src ))
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2206
+ /* "pysam/csamtools.pyx":2211
* cdef bam1_t * src
* src = self._delegate
* if src.core.l_qname == 0: return None # <<<<<<<<<<<<<<
* return _charptr_to_str(<char *>bam1_qname( src ))
*
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qname == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.l_qname == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2207
+ /* "pysam/csamtools.pyx":2212
* src = self._delegate
* if src.core.l_qname == 0: return None
* return _charptr_to_str(<char *>bam1_qname( src )) # <<<<<<<<<<<<<<
@@ -20497,17 +21955,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__py
* def __set__(self, qname ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools__charptr_to_str(((char *)bam1_qname(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools__charptr_to_str(((char *)bam1_qname(__pyx_v_src))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -20516,7 +21974,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2209
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2214
* return _charptr_to_str(<char *>bam1_qname( src ))
*
* def __set__(self, qname ): # <<<<<<<<<<<<<<
@@ -20524,8 +21993,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qname___get__(PyObject *__py
* qname = _force_bytes(qname)
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5qname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qname) {
bam1_t *__pyx_v_src;
int __pyx_v_l;
char *__pyx_v_p;
@@ -20536,28 +22004,28 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- char *__pyx_t_6;
+ bam1_t *__pyx_t_6;
+ char *__pyx_t_7;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2209);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2214);
__Pyx_INCREF(__pyx_v_qname);
- /* "csamtools.pyx":2210
+ /* "pysam/csamtools.pyx":2215
*
* def __set__(self, qname ):
* if qname == None or len(qname) == 0: return # <<<<<<<<<<<<<<
* qname = _force_bytes(qname)
* cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_qname, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2215; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
} else {
@@ -20566,33 +22034,34 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2211
+ /* "pysam/csamtools.pyx":2216
* def __set__(self, qname ):
* if qname == None or len(qname) == 0: return
* qname = _force_bytes(qname) # <<<<<<<<<<<<<<
* cdef bam1_t * src
* cdef int l
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_qname)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_qname)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_qname);
__pyx_v_qname = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":2216
+ /* "pysam/csamtools.pyx":2221
* cdef char * p
*
* src = self._delegate # <<<<<<<<<<<<<<
* p = bam1_qname( src )
*
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_6 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_6;
- /* "csamtools.pyx":2217
+ /* "pysam/csamtools.pyx":2222
*
* src = self._delegate
* p = bam1_qname( src ) # <<<<<<<<<<<<<<
@@ -20601,17 +22070,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
*/
__pyx_v_p = bam1_qname(__pyx_v_src);
- /* "csamtools.pyx":2220
+ /* "pysam/csamtools.pyx":2225
*
* # the qname is \0 terminated
* l = len(qname) + 1 # <<<<<<<<<<<<<<
* pysam_bam_update( src,
* src.core.l_qname,
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_qname); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_l = (__pyx_t_3 + 1);
- /* "csamtools.pyx":2224
+ /* "pysam/csamtools.pyx":2229
* src.core.l_qname,
* l,
* <uint8_t*>p ) # <<<<<<<<<<<<<<
@@ -20620,7 +22089,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
*/
pysam_bam_update(__pyx_v_src, __pyx_v_src->core.l_qname, __pyx_v_l, ((uint8_t *)__pyx_v_p));
- /* "csamtools.pyx":2226
+ /* "pysam/csamtools.pyx":2231
* <uint8_t*>p )
*
* src.core.l_qname = l # <<<<<<<<<<<<<<
@@ -20629,7 +22098,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
*/
__pyx_v_src->core.l_qname = __pyx_v_l;
- /* "csamtools.pyx":2230
+ /* "pysam/csamtools.pyx":2235
* # re-acquire pointer to location in memory
* # as it might have moved
* p = bam1_qname(src) # <<<<<<<<<<<<<<
@@ -20638,21 +22107,21 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
*/
__pyx_v_p = bam1_qname(__pyx_v_src);
- /* "csamtools.pyx":2232
+ /* "pysam/csamtools.pyx":2237
* p = bam1_qname(src)
*
* strncpy( p, qname, l ) # <<<<<<<<<<<<<<
*
* property cigar:
*/
- __pyx_t_6 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- strncpy(__pyx_v_p, __pyx_t_6, __pyx_v_l);
+ __pyx_t_7 = PyBytes_AsString(__pyx_v_qname); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ strncpy(__pyx_v_p, __pyx_t_7, __pyx_v_l);
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.qname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qname);
@@ -20661,7 +22130,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2259
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2272
*
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -20669,8 +22149,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(PyObject *__pyx_v_s
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
uint32_t *__pyx_v_cigar_p;
bam1_t *__pyx_v_src;
PyObject *__pyx_v_op = 0;
@@ -20679,56 +22158,58 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py
int __pyx_v_k;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- uint32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ uint32_t __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2259);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2272);
- /* "csamtools.pyx":2265
+ /* "pysam/csamtools.pyx":2278
* cdef int k
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return None
*
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2266
+ /* "pysam/csamtools.pyx":2279
*
* src = self._delegate
* if src.core.n_cigar == 0: return None # <<<<<<<<<<<<<<
*
* cigar = []
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2268
+ /* "pysam/csamtools.pyx":2281
* if src.core.n_cigar == 0: return None
*
* cigar = [] # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_cigar = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_cigar = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2269
+ /* "pysam/csamtools.pyx":2282
*
* cigar = []
* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
@@ -20737,64 +22218,64 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2270
+ /* "pysam/csamtools.pyx":2283
* cigar = []
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_3 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
+ __pyx_t_4 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "csamtools.pyx":2271
+ /* "pysam/csamtools.pyx":2284
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l))
*/
- __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) & 15)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_op = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2272
+ /* "pysam/csamtools.pyx":2285
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
* cigar.append((op, l))
* return cigar
*/
- __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2285; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_l = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2273
+ /* "pysam/csamtools.pyx":2286
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l)) # <<<<<<<<<<<<<<
* return cigar
*
*/
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_op);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_op);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_op);
__Pyx_GIVEREF(__pyx_v_op);
__Pyx_INCREF(__pyx_v_l);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_l);
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_l);
__Pyx_GIVEREF(__pyx_v_l);
- __pyx_t_4 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_5 = __Pyx_PyObject_Append(__pyx_v_cigar, ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2286; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
- /* "csamtools.pyx":2274
+ /* "pysam/csamtools.pyx":2287
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l))
* return cigar # <<<<<<<<<<<<<<
@@ -20809,9 +22290,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_5);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigar.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_op);
@@ -20823,7 +22304,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2276
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_values));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2289
* return cigar
*
* def __set__(self, values ): # <<<<<<<<<<<<<<
@@ -20831,8 +22323,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5cigar___get__(PyObject *__py
* cdef uint32_t * p
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_values) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_values) {
uint32_t *__pyx_v_p;
bam1_t *__pyx_v_src;
PyObject *__pyx_v_op = 0;
@@ -20845,33 +22336,33 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- PyObject *(*__pyx_t_6)(PyObject *);
- PyObject *__pyx_t_7 = NULL;
+ bam1_t *__pyx_t_6;
+ PyObject *(*__pyx_t_7)(PyObject *);
PyObject *__pyx_t_8 = NULL;
PyObject *__pyx_t_9 = NULL;
PyObject *__pyx_t_10 = NULL;
- PyObject *(*__pyx_t_11)(PyObject *);
- uint32_t __pyx_t_12;
+ PyObject *__pyx_t_11 = NULL;
+ PyObject *(*__pyx_t_12)(PyObject *);
+ uint32_t __pyx_t_13;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2276);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2289);
- /* "csamtools.pyx":2277
+ /* "pysam/csamtools.pyx":2290
*
* def __set__(self, values ):
* if values == None or len(values) == 0: return # <<<<<<<<<<<<<<
* cdef uint32_t * p
* cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_values, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2277; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
} else {
@@ -20880,11 +22371,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2283
+ /* "pysam/csamtools.pyx":2296
* cdef int k
*
* k = 0 # <<<<<<<<<<<<<<
@@ -20893,16 +22384,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
*/
__pyx_v_k = 0;
- /* "csamtools.pyx":2285
+ /* "pysam/csamtools.pyx":2298
* k = 0
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* # get location of cigar string
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_6 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_6;
- /* "csamtools.pyx":2288
+ /* "pysam/csamtools.pyx":2301
*
* # get location of cigar string
* p = bam1_cigar(src) # <<<<<<<<<<<<<<
@@ -20911,16 +22403,16 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2293
+ /* "pysam/csamtools.pyx":2306
* pysam_bam_update( src,
* src.core.n_cigar * 4,
* len(values) * 4, # <<<<<<<<<<<<<<
* <uint8_t*>p )
*
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2306; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":2294
+ /* "pysam/csamtools.pyx":2307
* src.core.n_cigar * 4,
* len(values) * 4,
* <uint8_t*>p ) # <<<<<<<<<<<<<<
@@ -20929,17 +22421,17 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
*/
pysam_bam_update(__pyx_v_src, (__pyx_v_src->core.n_cigar * 4), (__pyx_t_3 * 4), ((uint8_t *)__pyx_v_p));
- /* "csamtools.pyx":2297
+ /* "pysam/csamtools.pyx":2310
*
* # length is number of cigar operations, not bytes
* src.core.n_cigar = len(values) # <<<<<<<<<<<<<<
*
* # re-acquire pointer to location in memory
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_src->core.n_cigar = __pyx_t_3;
- /* "csamtools.pyx":2301
+ /* "pysam/csamtools.pyx":2314
* # re-acquire pointer to location in memory
* # as it might have moved
* p = bam1_cigar(src) # <<<<<<<<<<<<<<
@@ -20948,7 +22440,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2304
+ /* "pysam/csamtools.pyx":2317
*
* # insert cigar operations
* for op, l in values: # <<<<<<<<<<<<<<
@@ -20957,96 +22449,113 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
*/
if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
__pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
- __pyx_t_6 = NULL;
+ __pyx_t_7 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ __pyx_t_7 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_7 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_7 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_8); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_7 = __pyx_t_6(__pyx_t_1);
- if (unlikely(!__pyx_t_7)) {
+ __pyx_t_8 = __pyx_t_7(__pyx_t_1);
+ if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_GOTREF(__pyx_t_8);
}
- if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
- PyObject* sequence = __pyx_t_7;
+ if ((likely(PyTuple_CheckExact(__pyx_t_8))) || (PyList_CheckExact(__pyx_t_8))) {
+ PyObject* sequence = __pyx_t_8;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_8 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_8);
__Pyx_INCREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- } else {
- Py_ssize_t index = -1;
- __pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_t_10);
+ #else
+ __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
+ #endif
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ } else
+ {
+ Py_ssize_t index = -1;
+ __pyx_t_11 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
+ index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_10);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_op);
- __pyx_v_op = __pyx_t_8;
- __pyx_t_8 = 0;
- __Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_9;
+ __pyx_v_op = __pyx_t_9;
__pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_v_l);
+ __pyx_v_l = __pyx_t_10;
+ __pyx_t_10 = 0;
- /* "csamtools.pyx":2305
+ /* "pysam/csamtools.pyx":2318
* # insert cigar operations
* for op, l in values:
* p[k] = l << BAM_CIGAR_SHIFT | op # <<<<<<<<<<<<<<
* k += 1
*
*/
- __pyx_t_7 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = PyNumber_Or(__pyx_t_7, __pyx_v_op); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_12 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_9); if (unlikely((__pyx_t_12 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- (__pyx_v_p[__pyx_v_k]) = __pyx_t_12;
+ __pyx_t_8 = PyNumber_Lshift(__pyx_v_l, __pyx_int_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyNumber_Or(__pyx_t_8, __pyx_v_op); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_13 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_10); if (unlikely((__pyx_t_13 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ (__pyx_v_p[__pyx_v_k]) = __pyx_t_13;
- /* "csamtools.pyx":2306
+ /* "pysam/csamtools.pyx":2319
* for op, l in values:
* p[k] = l << BAM_CIGAR_SHIFT | op
* k += 1 # <<<<<<<<<<<<<<
@@ -21057,7 +22566,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":2309
+ /* "pysam/csamtools.pyx":2322
*
* ## setting the cigar string also updates the "bin" attribute
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, p)) # <<<<<<<<<<<<<<
@@ -21070,11 +22579,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.AlignedRead.cigar.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigar.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_op);
@@ -21084,7 +22593,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2316
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2338
* Returns the empty string if not present.
* '''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -21092,8 +22612,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(PyObject *__pyx_v_s
* if c == None: return ""
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_v_c = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_v_y = NULL;
@@ -21115,74 +22634,81 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObjec
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2316);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2338);
- /* "csamtools.pyx":2317
+ /* "pysam/csamtools.pyx":2339
* '''
* def __get__(self):
* c = self.cigar # <<<<<<<<<<<<<<
* if c == None: return ""
- * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
+ * # reverse order
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_c = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":2318
+ /* "pysam/csamtools.pyx":2340
* def __get__(self):
* c = self.cigar
* if c == None: return "" # <<<<<<<<<<<<<<
- * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
- *
+ * # reverse order
+ * else: return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c])
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_c, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_c, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_16));
__pyx_r = ((PyObject *)__pyx_kp_s_16);
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2319
- * c = self.cigar
+ /* "pysam/csamtools.pyx":2342
* if c == None: return ""
- * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c]) # <<<<<<<<<<<<<<
+ * # reverse order
+ * else: return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c]) # <<<<<<<<<<<<<<
*
* def __set__(self, cigar):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
if (PyList_CheckExact(__pyx_v_c) || PyTuple_CheckExact(__pyx_v_c)) {
__pyx_t_4 = __pyx_v_c; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_c); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_v_c); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_4)) {
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
- } else if (PyTuple_CheckExact(__pyx_t_4)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_7); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_7 = __pyx_t_6(__pyx_t_4);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -21190,45 +22716,54 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObjec
}
if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
PyObject* sequence = __pyx_t_7;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_8 = PyList_GET_ITEM(sequence, 0);
__pyx_t_9 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_8);
__Pyx_INCREF(__pyx_t_9);
+ #else
+ __pyx_t_8 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ #endif
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L8_unpacking_failed;
+ index = 0; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = NULL;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ __pyx_t_11 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_8;
@@ -21236,31 +22771,31 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObjec
__Pyx_XDECREF(__pyx_v_y);
__pyx_v_y = __pyx_t_9;
__pyx_t_9 = 0;
- __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromLong((__pyx_v_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyIndex_AsSsize_t(__pyx_v_x); if (unlikely((__pyx_t_12 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromLong((__pyx_v_5pysam_9csamtools_CODE2CIGAR[__pyx_t_12])); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_y);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_y);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_y);
__Pyx_GIVEREF(__pyx_v_y);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_135), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_139), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(((PyObject *)__pyx_t_3));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
@@ -21268,7 +22803,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObjec
__pyx_t_3 = 0;
goto __pyx_L0;
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -21280,7 +22815,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObjec
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.AlignedRead.cigarstring.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigarstring.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_c);
@@ -21292,16 +22827,26 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(PyObjec
return __pyx_r;
}
-/* "csamtools.pyx":2321
- * else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_cigar));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2344
+ * else: return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c])
*
* def __set__(self, cigar): # <<<<<<<<<<<<<<
* if cigar == None or len(cigar) == 0: self.cigar = []
* parts = CIGAR_REGEX.findall( cigar )
*/
-static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_cigar) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11cigarstring_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_cigar) {
PyObject *__pyx_v_parts = NULL;
PyObject *__pyx_v_x = NULL;
PyObject *__pyx_v_y = NULL;
@@ -21323,90 +22868,97 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2321);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2344);
- /* "csamtools.pyx":2322
+ /* "pysam/csamtools.pyx":2345
*
* def __set__(self, cigar):
* if cigar == None or len(cigar) == 0: self.cigar = [] # <<<<<<<<<<<<<<
* parts = CIGAR_REGEX.findall( cigar )
- * self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ]
+ * # reverse order
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_cigar, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_cigar, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_cigar); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_cigar); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
} else {
__pyx_t_5 = __pyx_t_2;
}
if (__pyx_t_5) {
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2323
+ /* "pysam/csamtools.pyx":2346
* def __set__(self, cigar):
* if cigar == None or len(cigar) == 0: self.cigar = []
* parts = CIGAR_REGEX.findall( cigar ) # <<<<<<<<<<<<<<
- * self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ]
- *
+ * # reverse order
+ * self.cigar = [ (CIGAR2CODE[ord(y)], int(x)) for x,y in parts ]
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR_REGEX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR_REGEX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__findall); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__findall); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_cigar);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_cigar);
__Pyx_GIVEREF(__pyx_v_cigar);
- __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_parts = __pyx_t_7;
__pyx_t_7 = 0;
- /* "csamtools.pyx":2324
- * if cigar == None or len(cigar) == 0: self.cigar = []
+ /* "pysam/csamtools.pyx":2348
* parts = CIGAR_REGEX.findall( cigar )
- * self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ] # <<<<<<<<<<<<<<
+ * # reverse order
+ * self.cigar = [ (CIGAR2CODE[ord(y)], int(x)) for x,y in parts ] # <<<<<<<<<<<<<<
*
* property seq:
*/
- __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = PyList_New(0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
if (PyList_CheckExact(__pyx_v_parts) || PyTuple_CheckExact(__pyx_v_parts)) {
__pyx_t_1 = __pyx_v_parts; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
__pyx_t_8 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_parts); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_parts); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_1)) {
+ if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
- } else if (PyTuple_CheckExact(__pyx_t_1)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_6); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_6 = __pyx_t_8(__pyx_t_1);
if (unlikely(!__pyx_t_6)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -21414,45 +22966,54 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__
}
if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
PyObject* sequence = __pyx_t_6;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_9 = PyList_GET_ITEM(sequence, 0);
__pyx_t_10 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_10);
+ #else
+ __pyx_t_9 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ #endif
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_11 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L8_unpacking_failed;
+ index = 0; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L8_unpacking_failed;
+ index = 1; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_9;
@@ -21460,42 +23021,45 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__
__Pyx_XDECREF(__pyx_v_y);
__pyx_v_y = __pyx_t_10;
__pyx_t_10 = 0;
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR2CODE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__CIGAR2CODE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __Pyx_INCREF(__pyx_v_x);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_x);
- __Pyx_GIVEREF(__pyx_v_x);
- __pyx_t_9 = PyObject_Call(__pyx_builtin_ord, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_INCREF(__pyx_v_y);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_y);
+ __Pyx_GIVEREF(__pyx_v_y);
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_ord, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetItem(__pyx_t_6, __pyx_t_9); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetItem(__pyx_t_6, __pyx_t_9); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
- __Pyx_INCREF(__pyx_v_y);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_y);
- __Pyx_GIVEREF(__pyx_v_y);
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_INCREF(__pyx_v_x);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_x);
+ __Pyx_GIVEREF(__pyx_v_x);
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_10 = 0;
__pyx_t_6 = 0;
- if (unlikely(PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_9))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_7, (PyObject*)__pyx_t_9))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__cigar, ((PyObject *)__pyx_t_7)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_t_7);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ if (PyObject_SetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__cigar, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = 0;
goto __pyx_L0;
@@ -21506,7 +23070,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("csamtools.AlignedRead.cigarstring.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.cigarstring.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_parts);
@@ -21517,7 +23081,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":2330
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2354
*
* In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -21525,47 +23100,48 @@ static int __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(PyObject *__
* cdef char * s
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3seq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2330);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2354);
- /* "csamtools.pyx":2333
+ /* "pysam/csamtools.pyx":2357
* cdef bam1_t * src
* cdef char * s
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2335
+ /* "pysam/csamtools.pyx":2359
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* return get_seq_range(src, 0, src.core.l_qseq)
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2337
+ /* "pysam/csamtools.pyx":2361
* if src.core.l_qseq == 0: return None
*
* return get_seq_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
@@ -21573,17 +23149,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_
* def __set__(self,seq):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_get_seq_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.seq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.seq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -21592,7 +23168,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":2339
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_seq));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2363
* return get_seq_range(src, 0, src.core.l_qseq)
*
* def __set__(self,seq): # <<<<<<<<<<<<<<
@@ -21600,8 +23187,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3seq___get__(PyObject *__pyx_
* # if no quality information is present, the first byte says 0xff.
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_seq) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3seq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_seq) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_p;
char *__pyx_v_s;
@@ -21616,30 +23202,30 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
Py_ssize_t __pyx_t_3;
int __pyx_t_4;
int __pyx_t_5;
- int __pyx_t_6;
- char *__pyx_t_7;
- long __pyx_t_8;
+ bam1_t *__pyx_t_6;
+ int __pyx_t_7;
+ char *__pyx_t_8;
+ long __pyx_t_9;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2339);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2363);
__Pyx_INCREF(__pyx_v_seq);
- /* "csamtools.pyx":2343
+ /* "pysam/csamtools.pyx":2367
* # if no quality information is present, the first byte says 0xff.
*
* if seq == None or len(seq) == 0: return # <<<<<<<<<<<<<<
* seq = _force_bytes(seq)
* cdef bam1_t * src
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_seq, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
} else {
@@ -21648,43 +23234,44 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
if (__pyx_t_5) {
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2344
+ /* "pysam/csamtools.pyx":2368
*
* if seq == None or len(seq) == 0: return
* seq = _force_bytes(seq) # <<<<<<<<<<<<<<
* cdef bam1_t * src
* cdef uint8_t * p
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_seq)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_seq)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_seq);
__pyx_v_seq = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":2350
+ /* "pysam/csamtools.pyx":2374
* cdef int l, k, nbytes_new, nbytes_old
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* l = len(seq)
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_6 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_6;
- /* "csamtools.pyx":2352
+ /* "pysam/csamtools.pyx":2376
* src = self._delegate
*
* l = len(seq) # <<<<<<<<<<<<<<
*
* # as the sequence is stored in half-bytes, the total length (sequence
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_seq); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_l = __pyx_t_3;
- /* "csamtools.pyx":2356
+ /* "pysam/csamtools.pyx":2380
* # as the sequence is stored in half-bytes, the total length (sequence
* # plus quality scores) is (l+1)/2 + l
* nbytes_new = (l+1)/2 + l # <<<<<<<<<<<<<<
@@ -21693,7 +23280,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_nbytes_new = (__Pyx_div_long((__pyx_v_l + 1), 2) + __pyx_v_l);
- /* "csamtools.pyx":2357
+ /* "pysam/csamtools.pyx":2381
* # plus quality scores) is (l+1)/2 + l
* nbytes_new = (l+1)/2 + l
* nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq # <<<<<<<<<<<<<<
@@ -21702,7 +23289,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_nbytes_old = (__Pyx_div_long((__pyx_v_src->core.l_qseq + 1), 2) + __pyx_v_src->core.l_qseq);
- /* "csamtools.pyx":2359
+ /* "pysam/csamtools.pyx":2383
* nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
* # acquire pointer to location in memory
* p = bam1_seq( src ) # <<<<<<<<<<<<<<
@@ -21711,7 +23298,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "csamtools.pyx":2360
+ /* "pysam/csamtools.pyx":2384
* # acquire pointer to location in memory
* p = bam1_seq( src )
* src.core.l_qseq = l # <<<<<<<<<<<<<<
@@ -21720,7 +23307,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_src->core.l_qseq = __pyx_v_l;
- /* "csamtools.pyx":2365
+ /* "pysam/csamtools.pyx":2389
* nbytes_old,
* nbytes_new,
* p) # <<<<<<<<<<<<<<
@@ -21729,7 +23316,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
pysam_bam_update(__pyx_v_src, __pyx_v_nbytes_old, __pyx_v_nbytes_new, __pyx_v_p);
- /* "csamtools.pyx":2368
+ /* "pysam/csamtools.pyx":2392
* # re-acquire pointer to location in memory
* # as it might have moved
* p = bam1_seq( src ) # <<<<<<<<<<<<<<
@@ -21738,50 +23325,50 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "csamtools.pyx":2369
+ /* "pysam/csamtools.pyx":2393
* # as it might have moved
* p = bam1_seq( src )
* for k from 0 <= k < nbytes_new: p[k] = 0 # <<<<<<<<<<<<<<
* # convert to C string
* s = seq
*/
- __pyx_t_6 = __pyx_v_nbytes_new;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
+ __pyx_t_7 = __pyx_v_nbytes_new;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_7; __pyx_v_k++) {
(__pyx_v_p[__pyx_v_k]) = 0;
}
- /* "csamtools.pyx":2371
+ /* "pysam/csamtools.pyx":2395
* for k from 0 <= k < nbytes_new: p[k] = 0
* # convert to C string
* s = seq # <<<<<<<<<<<<<<
* for k from 0 <= k < l:
* p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
*/
- __pyx_t_7 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_s = __pyx_t_7;
+ __pyx_t_8 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_8) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2395; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = __pyx_t_8;
- /* "csamtools.pyx":2372
+ /* "pysam/csamtools.pyx":2396
* # convert to C string
* s = seq
* for k from 0 <= k < l: # <<<<<<<<<<<<<<
* p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
*
*/
- __pyx_t_6 = __pyx_v_l;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_6; __pyx_v_k++) {
+ __pyx_t_7 = __pyx_v_l;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_7; __pyx_v_k++) {
- /* "csamtools.pyx":2373
+ /* "pysam/csamtools.pyx":2397
* s = seq
* for k from 0 <= k < l:
* p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2) # <<<<<<<<<<<<<<
*
* # erase qualities
*/
- __pyx_t_8 = __Pyx_div_long(__pyx_v_k, 2);
- (__pyx_v_p[__pyx_t_8]) = ((__pyx_v_p[__pyx_t_8]) | (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))));
+ __pyx_t_9 = __Pyx_div_long(__pyx_v_k, 2);
+ (__pyx_v_p[__pyx_t_9]) = ((__pyx_v_p[__pyx_t_9]) | (pysam_translate_sequence((__pyx_v_s[__pyx_v_k])) << (4 * (1 - __Pyx_mod_long(__pyx_v_k, 2)))));
}
- /* "csamtools.pyx":2376
+ /* "pysam/csamtools.pyx":2400
*
* # erase qualities
* p = bam1_qual( src ) # <<<<<<<<<<<<<<
@@ -21790,7 +23377,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "csamtools.pyx":2377
+ /* "pysam/csamtools.pyx":2401
* # erase qualities
* p = bam1_qual( src )
* p[0] = 0xff # <<<<<<<<<<<<<<
@@ -21803,7 +23390,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.seq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.seq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_seq);
@@ -21812,7 +23399,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":2384
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2408
*
* In Python 3, this property is of type bytes and assigning a unicode string to it consisting of ASCII characters only will work, but is inefficient."""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -21820,47 +23418,48 @@ static int __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(PyObject *__pyx_v_sel
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2384);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2408);
- /* "csamtools.pyx":2389
+ /* "pysam/csamtools.pyx":2413
* cdef char * q
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2391
+ /* "pysam/csamtools.pyx":2415
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* return get_qual_range(src, 0, src.core.l_qseq)
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2393
+ /* "pysam/csamtools.pyx":2417
* if src.core.l_qseq == 0: return None
*
* return get_qual_range(src, 0, src.core.l_qseq) # <<<<<<<<<<<<<<
@@ -21868,17 +23467,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx
* def __set__(self,qual):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_get_qual_range(__pyx_v_src, 0, __pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -21887,7 +23486,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2395
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2419
* return get_qual_range(src, 0, src.core.l_qseq)
*
* def __set__(self,qual): # <<<<<<<<<<<<<<
@@ -21895,8 +23505,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qual___get__(PyObject *__pyx
* cdef bam1_t * src
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4qual_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_p;
char *__pyx_v_q;
@@ -21904,33 +23513,35 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
int __pyx_v_l;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- Py_ssize_t __pyx_t_3;
- int __pyx_t_4;
+ bam1_t *__pyx_t_1;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
+ Py_ssize_t __pyx_t_4;
int __pyx_t_5;
- char *__pyx_t_6;
- PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_6;
+ char *__pyx_t_7;
PyObject *__pyx_t_8 = NULL;
- int __pyx_t_9;
+ PyObject *__pyx_t_9 = NULL;
+ int __pyx_t_10;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2395);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2419);
__Pyx_INCREF(__pyx_v_qual);
- /* "csamtools.pyx":2402
+ /* "pysam/csamtools.pyx":2426
* cdef int k
*
* src = self._delegate # <<<<<<<<<<<<<<
* p = bam1_qual( src )
* if qual == None or len(qual) == 0:
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2403
+ /* "pysam/csamtools.pyx":2427
*
* src = self._delegate
* p = bam1_qual( src ) # <<<<<<<<<<<<<<
@@ -21939,27 +23550,26 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "csamtools.pyx":2404
+ /* "pysam/csamtools.pyx":2428
* src = self._delegate
* p = bam1_qual( src )
* if qual == None or len(qual) == 0: # <<<<<<<<<<<<<<
* # if absent - set to 0xff
* p[0] = 0xff
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (!__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2404; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = (__pyx_t_3 == 0);
- __pyx_t_5 = __pyx_t_4;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_qual, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (!__pyx_t_3) {
+ __pyx_t_4 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__pyx_t_4 == 0);
+ __pyx_t_6 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_2;
+ __pyx_t_6 = __pyx_t_3;
}
- if (__pyx_t_5) {
+ if (__pyx_t_6) {
- /* "csamtools.pyx":2406
+ /* "pysam/csamtools.pyx":2430
* if qual == None or len(qual) == 0:
* # if absent - set to 0xff
* p[0] = 0xff # <<<<<<<<<<<<<<
@@ -21968,7 +23578,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
*/
(__pyx_v_p[0]) = 0xff;
- /* "csamtools.pyx":2407
+ /* "pysam/csamtools.pyx":2431
* # if absent - set to 0xff
* p[0] = 0xff
* return # <<<<<<<<<<<<<<
@@ -21977,91 +23587,91 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
*/
__pyx_r = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2408
+ /* "pysam/csamtools.pyx":2432
* p[0] = 0xff
* return
* qual = _force_bytes(qual) # <<<<<<<<<<<<<<
* cdef int l
* # convert to C string
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_qual)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_qual)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_qual);
- __pyx_v_qual = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_qual = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "csamtools.pyx":2411
+ /* "pysam/csamtools.pyx":2435
* cdef int l
* # convert to C string
* q = qual # <<<<<<<<<<<<<<
* l = len(qual)
* if src.core.l_qseq != l:
*/
- __pyx_t_6 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2411; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_q = __pyx_t_6;
+ __pyx_t_7 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2435; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_q = __pyx_t_7;
- /* "csamtools.pyx":2412
+ /* "pysam/csamtools.pyx":2436
* # convert to C string
* q = qual
* l = len(qual) # <<<<<<<<<<<<<<
* if src.core.l_qseq != l:
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_l = __pyx_t_3;
+ __pyx_t_4 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_l = __pyx_t_4;
- /* "csamtools.pyx":2413
+ /* "pysam/csamtools.pyx":2437
* q = qual
* l = len(qual)
* if src.core.l_qseq != l: # <<<<<<<<<<<<<<
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
* assert src.core.l_qseq == l
*/
- __pyx_t_5 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
- if (__pyx_t_5) {
+ __pyx_t_6 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
+ if (__pyx_t_6) {
- /* "csamtools.pyx":2414
+ /* "pysam/csamtools.pyx":2438
* l = len(qual)
* if src.core.l_qseq != l:
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq)) # <<<<<<<<<<<<<<
* assert src.core.l_qseq == l
* for k from 0 <= k < l:
*/
- __pyx_t_1 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_1 = 0;
- __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_136), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = __Pyx_PyInt_to_py_int32_t(__pyx_v_src->core.l_qseq); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_2 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L6;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L6:;
+ __pyx_L4:;
- /* "csamtools.pyx":2415
+ /* "pysam/csamtools.pyx":2439
* if src.core.l_qseq != l:
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
* assert src.core.l_qseq == l # <<<<<<<<<<<<<<
@@ -22071,21 +23681,21 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
#ifndef CYTHON_WITHOUT_ASSERTIONS
if (unlikely(!(__pyx_v_src->core.l_qseq == __pyx_v_l))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":2416
+ /* "pysam/csamtools.pyx":2440
* raise ValueError("quality and sequence mismatch: %i != %i" % (l, src.core.l_qseq))
* assert src.core.l_qseq == l
* for k from 0 <= k < l: # <<<<<<<<<<<<<<
* p[k] = <uint8_t>q[k] - 33
*
*/
- __pyx_t_9 = __pyx_v_l;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_9; __pyx_v_k++) {
+ __pyx_t_10 = __pyx_v_l;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_10; __pyx_v_k++) {
- /* "csamtools.pyx":2417
+ /* "pysam/csamtools.pyx":2441
* assert src.core.l_qseq == l
* for k from 0 <= k < l:
* p[k] = <uint8_t>q[k] - 33 # <<<<<<<<<<<<<<
@@ -22098,10 +23708,10 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_AddTraceback("csamtools.AlignedRead.qual.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qual.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qual);
@@ -22110,7 +23720,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2431
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2455
* were not considered for alignment may have been retained."""
*
* def __get__(self): # <<<<<<<<<<<<<<
@@ -22118,70 +23739,71 @@ static int __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(PyObject *__pyx_v_se
* cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5query___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- int32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ int32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2431);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2455);
- /* "csamtools.pyx":2436
+ /* "pysam/csamtools.pyx":2460
* cdef char * s
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2438
+ /* "pysam/csamtools.pyx":2462
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* start = query_start(src)
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2440
+ /* "pysam/csamtools.pyx":2464
* if src.core.l_qseq == 0: return None
*
* start = query_start(src) # <<<<<<<<<<<<<<
* end = query_end(src)
*
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_start = __pyx_t_2;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_start = __pyx_t_3;
- /* "csamtools.pyx":2441
+ /* "pysam/csamtools.pyx":2465
*
* start = query_start(src)
* end = query_end(src) # <<<<<<<<<<<<<<
*
* return get_seq_range(src, start, end)
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_end = __pyx_t_2;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_end = __pyx_t_3;
- /* "csamtools.pyx":2443
+ /* "pysam/csamtools.pyx":2467
* end = query_end(src)
*
* return get_seq_range(src, start, end) # <<<<<<<<<<<<<<
@@ -22189,17 +23811,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__py
* property qqual:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_9csamtools_get_seq_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_4 = __pyx_f_5pysam_9csamtools_get_seq_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_r = __pyx_t_4;
+ __pyx_t_4 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.AlignedRead.query.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.query.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -22208,7 +23830,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2449
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2473
*
* In Python 3, this property is of type bytes."""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -22216,70 +23849,71 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5query___get__(PyObject *__py
* cdef uint32_t start, end
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5qqual___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- int32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ int32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2449);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2473);
- /* "csamtools.pyx":2453
+ /* "pysam/csamtools.pyx":2477
* cdef uint32_t start, end
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* if src.core.l_qseq == 0: return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2455
+ /* "pysam/csamtools.pyx":2479
* src = self._delegate
*
* if src.core.l_qseq == 0: return None # <<<<<<<<<<<<<<
*
* start = query_start(src)
*/
- __pyx_t_1 = (__pyx_v_src->core.l_qseq == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.l_qseq == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2457
+ /* "pysam/csamtools.pyx":2481
* if src.core.l_qseq == 0: return None
*
* start = query_start(src) # <<<<<<<<<<<<<<
* end = query_end(src)
*
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_start = __pyx_t_2;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_start = __pyx_t_3;
- /* "csamtools.pyx":2458
+ /* "pysam/csamtools.pyx":2482
*
* start = query_start(src)
* end = query_end(src) # <<<<<<<<<<<<<<
*
* return get_qual_range(src, start, end)
*/
- __pyx_t_2 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_end = __pyx_t_2;
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_end = __pyx_t_3;
- /* "csamtools.pyx":2460
+ /* "pysam/csamtools.pyx":2484
* end = query_end(src)
*
* return get_qual_range(src, start, end) # <<<<<<<<<<<<<<
@@ -22287,17 +23921,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__py
* property qstart:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = __pyx_f_9csamtools_get_qual_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_4 = __pyx_f_5pysam_9csamtools_get_qual_range(__pyx_v_src, __pyx_v_start, __pyx_v_end); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_r = __pyx_t_4;
+ __pyx_t_4 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.AlignedRead.qqual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qqual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -22306,7 +23940,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2464
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2488
* property qstart:
* """start index of the aligned query portion of the sequence (0-based, inclusive)"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -22314,8 +23959,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5qqual___get__(PyObject *__py
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_6qstart___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -22324,10 +23968,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2464);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2488);
- /* "csamtools.pyx":2465
+ /* "pysam/csamtools.pyx":2489
* """start index of the aligned query portion of the sequence (0-based, inclusive)"""
* def __get__(self):
* return query_start(self._delegate) # <<<<<<<<<<<<<<
@@ -22335,8 +23979,8 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__p
* property qend:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_start(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -22346,7 +23990,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__p
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qstart.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qstart.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -22355,7 +23999,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":2469
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2493
* property qend:
* """end index of the aligned query portion of the sequence (0-based, exclusive)"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -22363,8 +24018,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6qstart___get__(PyObject *__p
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -22373,10 +24027,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2469);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2493);
- /* "csamtools.pyx":2470
+ /* "pysam/csamtools.pyx":2494
* """end index of the aligned query portion of the sequence (0-based, exclusive)"""
* def __get__(self):
* return query_end(self._delegate) # <<<<<<<<<<<<<<
@@ -22384,8 +24038,8 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx
* property qlen:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_end(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_self->_delegate); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = __pyx_t_2;
__pyx_t_2 = 0;
@@ -22395,7 +24049,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.qend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -22404,7 +24058,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2474
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2498
* property qlen:
* """Length of the aligned query sequence"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -22412,31 +24077,32 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qend___get__(PyObject *__pyx
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4qlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int32_t __pyx_t_1;
+ bam1_t *__pyx_t_1;
int32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ int32_t __pyx_t_3;
+ PyObject *__pyx_t_4 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2474);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2498);
- /* "csamtools.pyx":2476
+ /* "pysam/csamtools.pyx":2500
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* return query_end(src)-query_start(src)
*
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2477
+ /* "pysam/csamtools.pyx":2501
* cdef bam1_t * src
* src = self._delegate
* return query_end(src)-query_start(src) # <<<<<<<<<<<<<<
@@ -22444,19 +24110,19 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx
* property tags:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __pyx_f_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyInt_FromLong((__pyx_t_1 - __pyx_t_2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_r = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = __pyx_f_5pysam_9csamtools_query_end(__pyx_v_src); if (unlikely(__pyx_t_2 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools_query_start(__pyx_v_src); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyInt_FromLong((__pyx_t_2 - __pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_r = __pyx_t_4;
+ __pyx_t_4 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.AlignedRead.qlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.qlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -22465,7 +24131,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2494
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2518
* multiple times.
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -22473,8 +24150,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4qlen___get__(PyObject *__pyx
* cdef bam1_t * src
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_s;
char __pyx_v_auxtag[3];
@@ -22485,56 +24161,58 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
PyObject *__pyx_v_value = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- char __pyx_t_3;
- int __pyx_t_4;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ char __pyx_t_4;
int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- Py_ssize_t __pyx_t_7;
- PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_6;
+ PyObject *__pyx_t_7 = NULL;
+ Py_ssize_t __pyx_t_8;
PyObject *__pyx_t_9 = NULL;
PyObject *__pyx_t_10 = NULL;
- PyObject *(*__pyx_t_11)(PyObject *);
- uint8_t __pyx_t_12;
- int32_t __pyx_t_13;
- int __pyx_t_14;
+ PyObject *__pyx_t_11 = NULL;
+ PyObject *(*__pyx_t_12)(PyObject *);
+ uint8_t __pyx_t_13;
+ int32_t __pyx_t_14;
+ int __pyx_t_15;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2494);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2518);
- /* "csamtools.pyx":2503
+ /* "pysam/csamtools.pyx":2527
* cdef int32_t nvalues
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.l_aux == 0: return []
* s = bam1_aux( src )
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2504
+ /* "pysam/csamtools.pyx":2528
*
* src = self._delegate
* if src.l_aux == 0: return [] # <<<<<<<<<<<<<<
* s = bam1_aux( src )
* result = []
*/
- __pyx_t_1 = (__pyx_v_src->l_aux == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->l_aux == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2528; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2505
+ /* "pysam/csamtools.pyx":2529
* src = self._delegate
* if src.l_aux == 0: return []
* s = bam1_aux( src ) # <<<<<<<<<<<<<<
@@ -22543,19 +24221,19 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
__pyx_v_s = bam1_aux(__pyx_v_src);
- /* "csamtools.pyx":2506
+ /* "pysam/csamtools.pyx":2530
* if src.l_aux == 0: return []
* s = bam1_aux( src )
* result = [] # <<<<<<<<<<<<<<
* auxtag[2] = 0
* while s < (src.data + src.data_len):
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_result = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_result = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2507
+ /* "pysam/csamtools.pyx":2531
* s = bam1_aux( src )
* result = []
* auxtag[2] = 0 # <<<<<<<<<<<<<<
@@ -22564,7 +24242,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
(__pyx_v_auxtag[2]) = 0;
- /* "csamtools.pyx":2508
+ /* "pysam/csamtools.pyx":2532
* result = []
* auxtag[2] = 0
* while s < (src.data + src.data_len): # <<<<<<<<<<<<<<
@@ -22572,10 +24250,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* auxtag[0] = s[0]
*/
while (1) {
- __pyx_t_1 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
- if (!__pyx_t_1) break;
+ __pyx_t_2 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
+ if (!__pyx_t_2) break;
- /* "csamtools.pyx":2510
+ /* "pysam/csamtools.pyx":2534
* while s < (src.data + src.data_len):
* # get tag
* auxtag[0] = s[0] # <<<<<<<<<<<<<<
@@ -22584,7 +24262,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
(__pyx_v_auxtag[0]) = (__pyx_v_s[0]);
- /* "csamtools.pyx":2511
+ /* "pysam/csamtools.pyx":2535
* # get tag
* auxtag[0] = s[0]
* auxtag[1] = s[1] # <<<<<<<<<<<<<<
@@ -22593,7 +24271,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
(__pyx_v_auxtag[1]) = (__pyx_v_s[1]);
- /* "csamtools.pyx":2512
+ /* "pysam/csamtools.pyx":2536
* auxtag[0] = s[0]
* auxtag[1] = s[1]
* s += 2 # <<<<<<<<<<<<<<
@@ -22602,7 +24280,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
__pyx_v_s = (__pyx_v_s + 2);
- /* "csamtools.pyx":2513
+ /* "pysam/csamtools.pyx":2537
* auxtag[1] = s[1]
* s += 2
* auxtype = s[0] # <<<<<<<<<<<<<<
@@ -22611,38 +24289,38 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
__pyx_v_auxtype = (__pyx_v_s[0]);
- /* "csamtools.pyx":2514
+ /* "pysam/csamtools.pyx":2538
* s += 2
* auxtype = s[0]
* if auxtype in ('c', 'C'): # <<<<<<<<<<<<<<
* value = <int>bam_aux2i(s)
* s += 1
*/
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = ((int)(__pyx_t_3 == 'c'));
- if (!__pyx_t_1) {
- __pyx_t_4 = ((int)(__pyx_t_3 == 'C'));
- __pyx_t_5 = __pyx_t_4;
+ __pyx_t_4 = __pyx_v_auxtype;
+ __pyx_t_2 = ((int)(__pyx_t_4 == 'c'));
+ if (!__pyx_t_2) {
+ __pyx_t_5 = ((int)(__pyx_t_4 == 'C'));
+ __pyx_t_6 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_1;
+ __pyx_t_6 = __pyx_t_2;
}
- __pyx_t_1 = __pyx_t_5;
- if (__pyx_t_1) {
+ __pyx_t_2 = __pyx_t_6;
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2515
+ /* "pysam/csamtools.pyx":2539
* auxtype = s[0]
* if auxtype in ('c', 'C'):
* value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype in ('s', 'S'):
*/
- __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2516
+ /* "pysam/csamtools.pyx":2540
* if auxtype in ('c', 'C'):
* value = <int>bam_aux2i(s)
* s += 1 # <<<<<<<<<<<<<<
@@ -22650,41 +24328,41 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* value = <int>bam_aux2i(s)
*/
__pyx_v_s = (__pyx_v_s + 1);
- goto __pyx_L8;
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2517
+ /* "pysam/csamtools.pyx":2541
* value = <int>bam_aux2i(s)
* s += 1
* elif auxtype in ('s', 'S'): # <<<<<<<<<<<<<<
* value = <int>bam_aux2i(s)
* s += 2
*/
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = ((int)(__pyx_t_3 == 's'));
- if (!__pyx_t_1) {
- __pyx_t_5 = ((int)(__pyx_t_3 == 'S'));
- __pyx_t_4 = __pyx_t_5;
+ __pyx_t_4 = __pyx_v_auxtype;
+ __pyx_t_2 = ((int)(__pyx_t_4 == 's'));
+ if (!__pyx_t_2) {
+ __pyx_t_6 = ((int)(__pyx_t_4 == 'S'));
+ __pyx_t_5 = __pyx_t_6;
} else {
- __pyx_t_4 = __pyx_t_1;
+ __pyx_t_5 = __pyx_t_2;
}
- __pyx_t_1 = __pyx_t_4;
- if (__pyx_t_1) {
+ __pyx_t_2 = __pyx_t_5;
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2518
+ /* "pysam/csamtools.pyx":2542
* s += 1
* elif auxtype in ('s', 'S'):
* value = <int>bam_aux2i(s) # <<<<<<<<<<<<<<
* s += 2
* elif auxtype in ('i', 'I'):
*/
- __pyx_t_2 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2519
+ /* "pysam/csamtools.pyx":2543
* elif auxtype in ('s', 'S'):
* value = <int>bam_aux2i(s)
* s += 2 # <<<<<<<<<<<<<<
@@ -22692,41 +24370,41 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* value = <int32_t>bam_aux2i(s)
*/
__pyx_v_s = (__pyx_v_s + 2);
- goto __pyx_L8;
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2520
+ /* "pysam/csamtools.pyx":2544
* value = <int>bam_aux2i(s)
* s += 2
* elif auxtype in ('i', 'I'): # <<<<<<<<<<<<<<
* value = <int32_t>bam_aux2i(s)
* s += 4
*/
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = ((int)(__pyx_t_3 == 'i'));
- if (!__pyx_t_1) {
- __pyx_t_4 = ((int)(__pyx_t_3 == 'I'));
- __pyx_t_5 = __pyx_t_4;
+ __pyx_t_4 = __pyx_v_auxtype;
+ __pyx_t_2 = ((int)(__pyx_t_4 == 'i'));
+ if (!__pyx_t_2) {
+ __pyx_t_5 = ((int)(__pyx_t_4 == 'I'));
+ __pyx_t_6 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_1;
+ __pyx_t_6 = __pyx_t_2;
}
- __pyx_t_1 = __pyx_t_5;
- if (__pyx_t_1) {
+ __pyx_t_2 = __pyx_t_6;
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2521
+ /* "pysam/csamtools.pyx":2545
* s += 2
* elif auxtype in ('i', 'I'):
* value = <int32_t>bam_aux2i(s) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'f':
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2522
+ /* "pysam/csamtools.pyx":2546
* elif auxtype in ('i', 'I'):
* value = <int32_t>bam_aux2i(s)
* s += 4 # <<<<<<<<<<<<<<
@@ -22734,33 +24412,33 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* value = <float>bam_aux2f(s)
*/
__pyx_v_s = (__pyx_v_s + 4);
- goto __pyx_L8;
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2523
+ /* "pysam/csamtools.pyx":2547
* value = <int32_t>bam_aux2i(s)
* s += 4
* elif auxtype == 'f': # <<<<<<<<<<<<<<
* value = <float>bam_aux2f(s)
* s += 4
*/
- __pyx_t_1 = (__pyx_v_auxtype == 'f');
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_auxtype == 'f');
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2524
+ /* "pysam/csamtools.pyx":2548
* s += 4
* elif auxtype == 'f':
* value = <float>bam_aux2f(s) # <<<<<<<<<<<<<<
* s += 4
* elif auxtype == 'd':
*/
- __pyx_t_2 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2525
+ /* "pysam/csamtools.pyx":2549
* elif auxtype == 'f':
* value = <float>bam_aux2f(s)
* s += 4 # <<<<<<<<<<<<<<
@@ -22768,33 +24446,33 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* value = <double>bam_aux2d(s)
*/
__pyx_v_s = (__pyx_v_s + 4);
- goto __pyx_L8;
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2526
+ /* "pysam/csamtools.pyx":2550
* value = <float>bam_aux2f(s)
* s += 4
* elif auxtype == 'd': # <<<<<<<<<<<<<<
* value = <double>bam_aux2d(s)
* s += 8
*/
- __pyx_t_1 = (__pyx_v_auxtype == 'd');
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_auxtype == 'd');
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2527
+ /* "pysam/csamtools.pyx":2551
* s += 4
* elif auxtype == 'd':
* value = <double>bam_aux2d(s) # <<<<<<<<<<<<<<
* s += 8
* elif auxtype == 'A':
*/
- __pyx_t_2 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2528
+ /* "pysam/csamtools.pyx":2552
* elif auxtype == 'd':
* value = <double>bam_aux2d(s)
* s += 8 # <<<<<<<<<<<<<<
@@ -22802,36 +24480,36 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* value = "%c" % <char>bam_aux2A(s)
*/
__pyx_v_s = (__pyx_v_s + 8);
- goto __pyx_L8;
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2529
+ /* "pysam/csamtools.pyx":2553
* value = <double>bam_aux2d(s)
* s += 8
* elif auxtype == 'A': # <<<<<<<<<<<<<<
* value = "%c" % <char>bam_aux2A(s)
* s += 1
*/
- __pyx_t_1 = (__pyx_v_auxtype == 'A');
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_auxtype == 'A');
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2530
+ /* "pysam/csamtools.pyx":2554
* s += 8
* elif auxtype == 'A':
* value = "%c" % <char>bam_aux2A(s) # <<<<<<<<<<<<<<
* s += 1
* elif auxtype in ('Z', 'H'):
*/
- __pyx_t_2 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_s))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), __pyx_t_2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_141), __pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = ((PyObject *)__pyx_t_6);
- __pyx_t_6 = 0;
+ __pyx_v_value = ((PyObject *)__pyx_t_7);
+ __pyx_t_7 = 0;
- /* "csamtools.pyx":2531
+ /* "pysam/csamtools.pyx":2555
* elif auxtype == 'A':
* value = "%c" % <char>bam_aux2A(s)
* s += 1 # <<<<<<<<<<<<<<
@@ -22839,63 +24517,63 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* value = _charptr_to_str(<char*>bam_aux2Z(s))
*/
__pyx_v_s = (__pyx_v_s + 1);
- goto __pyx_L8;
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2532
+ /* "pysam/csamtools.pyx":2556
* value = "%c" % <char>bam_aux2A(s)
* s += 1
* elif auxtype in ('Z', 'H'): # <<<<<<<<<<<<<<
* value = _charptr_to_str(<char*>bam_aux2Z(s))
* # +1 for NULL terminated string
*/
- __pyx_t_3 = __pyx_v_auxtype;
- __pyx_t_1 = ((int)(__pyx_t_3 == 'Z'));
- if (!__pyx_t_1) {
- __pyx_t_5 = ((int)(__pyx_t_3 == 'H'));
- __pyx_t_4 = __pyx_t_5;
+ __pyx_t_4 = __pyx_v_auxtype;
+ __pyx_t_2 = ((int)(__pyx_t_4 == 'Z'));
+ if (!__pyx_t_2) {
+ __pyx_t_6 = ((int)(__pyx_t_4 == 'H'));
+ __pyx_t_5 = __pyx_t_6;
} else {
- __pyx_t_4 = __pyx_t_1;
+ __pyx_t_5 = __pyx_t_2;
}
- __pyx_t_1 = __pyx_t_4;
- if (__pyx_t_1) {
+ __pyx_t_2 = __pyx_t_5;
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2533
+ /* "pysam/csamtools.pyx":2557
* s += 1
* elif auxtype in ('Z', 'H'):
* value = _charptr_to_str(<char*>bam_aux2Z(s)) # <<<<<<<<<<<<<<
* # +1 for NULL terminated string
* s += len(value) + 1
*/
- __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_s))); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_7 = __pyx_f_5pysam_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_s))); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_value = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "csamtools.pyx":2535
+ /* "pysam/csamtools.pyx":2559
* value = _charptr_to_str(<char*>bam_aux2Z(s))
* # +1 for NULL terminated string
* s += len(value) + 1 # <<<<<<<<<<<<<<
* elif auxtype == 'B':
* s += 1
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_s = (__pyx_v_s + (__pyx_t_7 + 1));
- goto __pyx_L8;
+ __pyx_t_8 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_s = (__pyx_v_s + (__pyx_t_8 + 1));
+ goto __pyx_L6;
}
- /* "csamtools.pyx":2536
+ /* "pysam/csamtools.pyx":2560
* # +1 for NULL terminated string
* s += len(value) + 1
* elif auxtype == 'B': # <<<<<<<<<<<<<<
* s += 1
* byte_size, nvalues, value = convertBinaryTagToList( s )
*/
- __pyx_t_1 = (__pyx_v_auxtype == 'B');
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_auxtype == 'B');
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2537
+ /* "pysam/csamtools.pyx":2561
* s += len(value) + 1
* elif auxtype == 'B':
* s += 1 # <<<<<<<<<<<<<<
@@ -22904,73 +24582,84 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "csamtools.pyx":2538
+ /* "pysam/csamtools.pyx":2562
* elif auxtype == 'B':
* s += 1
* byte_size, nvalues, value = convertBinaryTagToList( s ) # <<<<<<<<<<<<<<
* # 5 for 1 char and 1 int
* s += 5 + ( nvalues * byte_size) - 1
*/
- __pyx_t_6 = __pyx_f_9csamtools_convertBinaryTagToList(__pyx_v_s); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if ((likely(PyTuple_CheckExact(__pyx_t_6))) || (PyList_CheckExact(__pyx_t_6))) {
- PyObject* sequence = __pyx_t_6;
+ __pyx_t_7 = __pyx_f_5pysam_9csamtools_convertBinaryTagToList(__pyx_v_s); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if ((likely(PyTuple_CheckExact(__pyx_t_7))) || (PyList_CheckExact(__pyx_t_7))) {
+ PyObject* sequence = __pyx_t_7;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 3)) {
+ if (size > 3) __Pyx_RaiseTooManyValuesError(3);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
- if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_8 = PyTuple_GET_ITEM(sequence, 1);
- __pyx_t_9 = PyTuple_GET_ITEM(sequence, 2);
+ __pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_10 = PyTuple_GET_ITEM(sequence, 2);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
- if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_8 = PyList_GET_ITEM(sequence, 1);
- __pyx_t_9 = PyList_GET_ITEM(sequence, 2);
+ __pyx_t_3 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_9 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_10 = PyList_GET_ITEM(sequence, 2);
}
- __Pyx_INCREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- } else {
- Py_ssize_t index = -1;
- __pyx_t_10 = PyObject_GetIter(__pyx_t_6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_t_10);
+ #else
+ __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_11 = Py_TYPE(__pyx_t_10)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_2)) goto __pyx_L9_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_8 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_8)) goto __pyx_L9_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_8);
- index = 2; __pyx_t_9 = __pyx_t_11(__pyx_t_10); if (unlikely(!__pyx_t_9)) goto __pyx_L9_unpacking_failed;
+ #endif
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ } else
+ {
+ Py_ssize_t index = -1;
+ __pyx_t_11 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
+ index = 0; __pyx_t_3 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_3)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_3);
+ index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_11(__pyx_t_10), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- goto __pyx_L10_unpacking_done;
- __pyx_L9_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L10_unpacking_done:;
+ index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L7_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_10);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L8_unpacking_done;
+ __pyx_L7_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L8_unpacking_done:;
}
- __pyx_t_12 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_2); if (unlikely((__pyx_t_12 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_13 = __Pyx_PyInt_from_py_int32_t(__pyx_t_8); if (unlikely((__pyx_t_13 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_v_byte_size = __pyx_t_12;
- __pyx_v_nvalues = __pyx_t_13;
+ __pyx_t_13 = __Pyx_PyInt_from_py_uint8_t(__pyx_t_3); if (unlikely((__pyx_t_13 == (uint8_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_14 = __Pyx_PyInt_from_py_int32_t(__pyx_t_9); if (unlikely((__pyx_t_14 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_v_byte_size = __pyx_t_13;
+ __pyx_v_nvalues = __pyx_t_14;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_value = __pyx_t_10;
+ __pyx_t_10 = 0;
- /* "csamtools.pyx":2540
+ /* "pysam/csamtools.pyx":2564
* byte_size, nvalues, value = convertBinaryTagToList( s )
* # 5 for 1 char and 1 int
* s += 5 + ( nvalues * byte_size) - 1 # <<<<<<<<<<<<<<
@@ -22978,11 +24667,11 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* s += 1
*/
__pyx_v_s = (__pyx_v_s + ((5 + (__pyx_v_nvalues * __pyx_v_byte_size)) - 1));
- goto __pyx_L8;
+ goto __pyx_L6;
}
- __pyx_L8:;
+ __pyx_L6:;
- /* "csamtools.pyx":2542
+ /* "pysam/csamtools.pyx":2566
* s += 5 + ( nvalues * byte_size) - 1
*
* s += 1 # <<<<<<<<<<<<<<
@@ -22991,31 +24680,29 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
*/
__pyx_v_s = (__pyx_v_s + 1);
- /* "csamtools.pyx":2544
+ /* "pysam/csamtools.pyx":2568
* s += 1
*
* result.append( (_charptr_to_str(auxtag), value) ) # <<<<<<<<<<<<<<
*
* return result
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = __pyx_f_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_7 = __pyx_f_5pysam_9csamtools__charptr_to_str(__pyx_v_auxtag); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ if (unlikely(!__pyx_v_value)) { __Pyx_RaiseUnboundLocalError("value"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2568; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_6 = 0;
- __pyx_t_14 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2544; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_15 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_10)); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2568; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
}
- /* "csamtools.pyx":2546
+ /* "pysam/csamtools.pyx":2570
* result.append( (_charptr_to_str(auxtag), value) )
*
* return result # <<<<<<<<<<<<<<
@@ -23030,12 +24717,12 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_6);
- __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.AlignedRead.tags.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_11);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tags.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
@@ -23046,7 +24733,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2548
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tags));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2572
* return result
*
* def __set__(self, tags): # <<<<<<<<<<<<<<
@@ -23054,8 +24752,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tags___get__(PyObject *__pyx
* cdef uint8_t * s
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tags) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tags_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tags) {
bam1_t *__pyx_v_src;
uint8_t *__pyx_v_s;
char *__pyx_v_temp;
@@ -23073,75 +24770,77 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
PyObject *__pyx_v_fmt = NULL;
PyObject *__pyx_v_total_size = NULL;
PyObject *__pyx_v_buffer = NULL;
+ PyObject *__pyx_v_p = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
+ bam1_t *__pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
- Py_ssize_t __pyx_t_4;
- PyObject *(*__pyx_t_5)(PyObject *);
- PyObject *__pyx_t_6 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+ PyObject *(*__pyx_t_6)(PyObject *);
PyObject *__pyx_t_7 = NULL;
PyObject *__pyx_t_8 = NULL;
- PyObject *(*__pyx_t_9)(PyObject *);
- int __pyx_t_10;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *(*__pyx_t_10)(PyObject *);
int __pyx_t_11;
- Py_ssize_t __pyx_t_12;
- PyObject *__pyx_t_13 = NULL;
+ int __pyx_t_12;
+ Py_ssize_t __pyx_t_13;
PyObject *__pyx_t_14 = NULL;
- int __pyx_t_15;
- size_t __pyx_t_16;
- int __pyx_t_17;
- char *__pyx_t_18;
+ PyObject *__pyx_t_15 = NULL;
+ int __pyx_t_16;
+ size_t __pyx_t_17;
+ int __pyx_t_18;
+ char *__pyx_t_19;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2548);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2572);
- /* "csamtools.pyx":2554
+ /* "pysam/csamtools.pyx":2578
* cdef char * temp
*
* src = self._delegate # <<<<<<<<<<<<<<
*
* fmts, args = ["<"], []
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2556
+ /* "pysam/csamtools.pyx":2580
* src = self._delegate
*
* fmts, args = ["<"], [] # <<<<<<<<<<<<<<
*
* if tags != None:
*/
- __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_138));
- PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_138));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138));
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_fmts = __pyx_t_1;
- __pyx_t_1 = 0;
- __pyx_v_args = __pyx_t_2;
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2580; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_142));
+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_142));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_142));
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2580; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_fmts = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
+ __pyx_v_args = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2558
+ /* "pysam/csamtools.pyx":2582
* fmts, args = ["<"], []
*
* if tags != None: # <<<<<<<<<<<<<<
*
* # map samtools code to python.struct code and byte size
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_tags, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_3) {
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_tags, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (__pyx_t_4) {
- /* "csamtools.pyx":2561
+ /* "pysam/csamtools.pyx":2585
*
* # map samtools code to python.struct code and byte size
* for pytag, value in tags: # <<<<<<<<<<<<<<
@@ -23149,111 +24848,128 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
* pytag = pytag.encode('ascii')
*/
if (PyList_CheckExact(__pyx_v_tags) || PyTuple_CheckExact(__pyx_v_tags)) {
- __pyx_t_2 = __pyx_v_tags; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
- __pyx_t_5 = NULL;
+ __pyx_t_3 = __pyx_v_tags; __Pyx_INCREF(__pyx_t_3); __pyx_t_5 = 0;
+ __pyx_t_6 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_tags); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_5 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_tags); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = Py_TYPE(__pyx_t_3)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
- } else if (PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
+ if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_3)) {
+ if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_3)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_3)) {
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_1 = __pyx_t_5(__pyx_t_2);
- if (unlikely(!__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_6(__pyx_t_3);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_2);
}
- if ((likely(PyTuple_CheckExact(__pyx_t_1))) || (PyList_CheckExact(__pyx_t_1))) {
- PyObject* sequence = __pyx_t_1;
+ if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
+ PyObject* sequence = __pyx_t_2;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_7 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_7 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_7 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- } else {
- Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_INCREF(__pyx_t_8);
+ #else
+ __pyx_t_7 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_8 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L8_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_6);
- index = 1; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L8_unpacking_failed;
+ #endif
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ } else
+ {
+ Py_ssize_t index = -1;
+ __pyx_t_9 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
+ index = 0; __pyx_t_7 = __pyx_t_10(__pyx_t_9); if (unlikely(!__pyx_t_7)) goto __pyx_L6_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ index = 1; __pyx_t_8 = __pyx_t_10(__pyx_t_9); if (unlikely(!__pyx_t_8)) goto __pyx_L6_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_8);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_10(__pyx_t_9), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = NULL;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ goto __pyx_L7_unpacking_done;
+ __pyx_L6_unpacking_failed:;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_10 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L7_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_pytag);
- __pyx_v_pytag = __pyx_t_6;
- __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_7;
+ __pyx_v_pytag = __pyx_t_7;
__pyx_t_7 = 0;
+ __Pyx_XDECREF(__pyx_v_value);
+ __pyx_v_value = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "csamtools.pyx":2562
+ /* "pysam/csamtools.pyx":2586
* # map samtools code to python.struct code and byte size
* for pytag, value in tags:
* if not type(pytag) is bytes: # <<<<<<<<<<<<<<
* pytag = pytag.encode('ascii')
* t = type(value)
*/
- __pyx_t_3 = (((PyObject *)Py_TYPE(__pyx_v_pytag)) == ((PyObject *)((PyObject*)(&PyBytes_Type))));
- __pyx_t_10 = (!__pyx_t_3);
- if (__pyx_t_10) {
+ __pyx_t_4 = (((PyObject *)Py_TYPE(__pyx_v_pytag)) == ((PyObject *)((PyObject*)(&PyBytes_Type))));
+ __pyx_t_11 = (!__pyx_t_4);
+ if (__pyx_t_11) {
- /* "csamtools.pyx":2563
+ /* "pysam/csamtools.pyx":2587
* for pytag, value in tags:
* if not type(pytag) is bytes:
* pytag = pytag.encode('ascii') # <<<<<<<<<<<<<<
* t = type(value)
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_pytag, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_pytag, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_143), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_pytag);
- __pyx_v_pytag = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L10;
+ __pyx_v_pytag = __pyx_t_8;
+ __pyx_t_8 = 0;
+ goto __pyx_L8;
}
- __pyx_L10:;
+ __pyx_L8:;
- /* "csamtools.pyx":2564
+ /* "pysam/csamtools.pyx":2588
* if not type(pytag) is bytes:
* pytag = pytag.encode('ascii')
* t = type(value) # <<<<<<<<<<<<<<
@@ -23264,23 +24980,23 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
__Pyx_XDECREF(((PyObject *)__pyx_v_t));
__pyx_v_t = ((PyObject*)((PyObject *)Py_TYPE(__pyx_v_value)));
- /* "csamtools.pyx":2566
+ /* "pysam/csamtools.pyx":2590
* t = type(value)
*
* if t is tuple or t is list: # <<<<<<<<<<<<<<
* # binary tags - treat separately
* pytype = 'B'
*/
- __pyx_t_10 = (__pyx_v_t == ((PyObject*)(&PyTuple_Type)));
- if (!__pyx_t_10) {
- __pyx_t_3 = (__pyx_v_t == ((PyObject*)(&PyList_Type)));
- __pyx_t_11 = __pyx_t_3;
+ __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyTuple_Type)));
+ if (!__pyx_t_11) {
+ __pyx_t_4 = (__pyx_v_t == ((PyObject*)(&PyList_Type)));
+ __pyx_t_12 = __pyx_t_4;
} else {
- __pyx_t_11 = __pyx_t_10;
+ __pyx_t_12 = __pyx_t_11;
}
- if (__pyx_t_11) {
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2568
+ /* "pysam/csamtools.pyx":2592
* if t is tuple or t is list:
* # binary tags - treat separately
* pytype = 'B' # <<<<<<<<<<<<<<
@@ -23291,1032 +25007,1021 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
__Pyx_XDECREF(__pyx_v_pytype);
__pyx_v_pytype = ((PyObject *)__pyx_n_s__B);
- /* "csamtools.pyx":2570
+ /* "pysam/csamtools.pyx":2594
* pytype = 'B'
* # get data type - first value determines type
* if type(value[0]) is float: # <<<<<<<<<<<<<<
* datafmt, datatype = "f", "f"
* else:
*/
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_value, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_11 = (((PyObject *)Py_TYPE(__pyx_t_7)) == ((PyObject *)((PyObject*)(&PyFloat_Type))));
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_11) {
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_value, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_12 = (((PyObject *)Py_TYPE(__pyx_t_8)) == ((PyObject *)((PyObject*)(&PyFloat_Type))));
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2571
+ /* "pysam/csamtools.pyx":2595
* # get data type - first value determines type
* if type(value[0]) is float:
* datafmt, datatype = "f", "f" # <<<<<<<<<<<<<<
* else:
* mi, ma = min(value), max(value)
*/
- __pyx_t_7 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_1 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_8 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_datafmt = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L12;
+ __pyx_v_datatype = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L10;
}
/*else*/ {
- /* "csamtools.pyx":2573
+ /* "pysam/csamtools.pyx":2597
* datafmt, datatype = "f", "f"
* else:
* mi, ma = min(value), max(value) # <<<<<<<<<<<<<<
* absmax = max( abs(mi), abs(ma) )
* # signed ints
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_7 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_6 = PyObject_Call(__pyx_builtin_max, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_max, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_mi);
- __pyx_v_mi = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_mi = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_ma);
- __pyx_v_ma = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_ma = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "csamtools.pyx":2574
+ /* "pysam/csamtools.pyx":2598
* else:
* mi, ma = min(value), max(value)
* absmax = max( abs(mi), abs(ma) ) # <<<<<<<<<<<<<<
* # signed ints
* if mi < 0:
*/
- __pyx_t_6 = PyNumber_Absolute(__pyx_v_ma); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyNumber_Absolute(__pyx_v_mi); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Absolute(__pyx_v_ma); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_RichCompare(__pyx_t_6, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Absolute(__pyx_v_mi); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (__pyx_t_11) {
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_1 = __pyx_t_6;
- } else {
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_7, __pyx_t_8, Py_GT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ if (__pyx_t_12) {
__Pyx_INCREF(__pyx_t_7);
- __pyx_t_1 = __pyx_t_7;
+ __pyx_t_2 = __pyx_t_7;
+ } else {
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_2 = __pyx_t_8;
}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_7 = __pyx_t_2;
+ __Pyx_INCREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_absmax);
- __pyx_v_absmax = __pyx_t_1;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_v_absmax = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "csamtools.pyx":2576
+ /* "pysam/csamtools.pyx":2600
* absmax = max( abs(mi), abs(ma) )
* # signed ints
* if mi < 0: # <<<<<<<<<<<<<<
* if mi >= -127: datafmt, datatype = "b", 'c'
* elif mi >= -32767: datafmt, datatype = "h", 's'
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_11) {
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2577
+ /* "pysam/csamtools.pyx":2601
* # signed ints
* if mi < 0:
* if mi >= -127: datafmt, datatype = "b", 'c' # <<<<<<<<<<<<<<
* elif mi >= -32767: datafmt, datatype = "h", 's'
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_11) {
- __pyx_t_1 = ((PyObject *)__pyx_n_s__b);
- __Pyx_INCREF(__pyx_t_1);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__c);
- __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_127, Py_GE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__b);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__c);
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_datafmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L14;
+ __pyx_v_datatype = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L12;
}
- /* "csamtools.pyx":2578
+ /* "pysam/csamtools.pyx":2602
* if mi < 0:
* if mi >= -127: datafmt, datatype = "b", 'c'
* elif mi >= -32767: datafmt, datatype = "h", 's' # <<<<<<<<<<<<<<
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "i", 'i'
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_11) {
- __pyx_t_6 = ((PyObject *)__pyx_n_s__h);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_1 = ((PyObject *)__pyx_n_s__s);
- __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_mi, __pyx_int_neg_32767, Py_GE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__h);
+ __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__s);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_datafmt = __pyx_t_2;
+ __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L14;
+ __pyx_v_datatype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L12;
}
- /* "csamtools.pyx":2579
+ /* "pysam/csamtools.pyx":2603
* if mi >= -127: datafmt, datatype = "b", 'c'
* elif mi >= -32767: datafmt, datatype = "h", 's'
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: datafmt, datatype = "i", 'i'
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_11) {
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L14;
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_neg_2147483648, Py_LT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_144), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_Raise(__pyx_t_7, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L12;
}
/*else*/ {
- /* "csamtools.pyx":2580
+ /* "pysam/csamtools.pyx":2604
* elif mi >= -32767: datafmt, datatype = "h", 's'
* elif absmax < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "i", 'i' # <<<<<<<<<<<<<<
*
* # unsigned ints
*/
- __pyx_t_1 = ((PyObject *)__pyx_n_s__i);
- __Pyx_INCREF(__pyx_t_1);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__i);
- __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_datafmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_datatype = __pyx_t_2;
+ __pyx_t_2 = 0;
}
- __pyx_L14:;
- goto __pyx_L13;
+ __pyx_L12:;
+ goto __pyx_L11;
}
/*else*/ {
- /* "csamtools.pyx":2584
+ /* "pysam/csamtools.pyx":2608
* # unsigned ints
* else:
* if absmax <= 255: datafmt, datatype = "B", 'C' # <<<<<<<<<<<<<<
* elif absmax <= 65535: datafmt, datatype = "H", 'S'
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_11) {
- __pyx_t_6 = ((PyObject *)__pyx_n_s__B);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_1 = ((PyObject *)__pyx_n_s__C);
- __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_255, Py_LE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__B);
+ __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__C);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_datafmt = __pyx_t_2;
+ __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L15;
+ __pyx_v_datatype = __pyx_t_7;
+ __pyx_t_7 = 0;
+ goto __pyx_L13;
}
- /* "csamtools.pyx":2585
+ /* "pysam/csamtools.pyx":2609
* else:
* if absmax <= 255: datafmt, datatype = "B", 'C'
* elif absmax <= 65535: datafmt, datatype = "H", 'S' # <<<<<<<<<<<<<<
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "I", 'I'
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_11) {
- __pyx_t_1 = ((PyObject *)__pyx_n_s__H);
- __Pyx_INCREF(__pyx_t_1);
- __pyx_t_6 = ((PyObject *)__pyx_n_s__S);
- __Pyx_INCREF(__pyx_t_6);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_65535, Py_LE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__H);
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__S);
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_datafmt = __pyx_t_7;
+ __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_6;
- __pyx_t_6 = 0;
- goto __pyx_L15;
+ __pyx_v_datatype = __pyx_t_2;
+ __pyx_t_2 = 0;
+ goto __pyx_L13;
}
- /* "csamtools.pyx":2586
+ /* "pysam/csamtools.pyx":2610
* if absmax <= 255: datafmt, datatype = "B", 'C'
* elif absmax <= 65535: datafmt, datatype = "H", 'S'
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: datafmt, datatype = "I", 'I'
*
*/
- __pyx_t_6 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (__pyx_t_11) {
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_6));
- __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __Pyx_Raise(__pyx_t_6, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2586; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L15;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_absmax, __pyx_int_4294967295, Py_GT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_144), __pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L13;
}
/*else*/ {
- /* "csamtools.pyx":2587
+ /* "pysam/csamtools.pyx":2611
* elif absmax <= 65535: datafmt, datatype = "H", 'S'
* elif absmax > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: datafmt, datatype = "I", 'I' # <<<<<<<<<<<<<<
*
* datafmt = "2sccI%i%s" % (len(value), datafmt)
*/
- __pyx_t_6 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_6);
- __pyx_t_1 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_1);
+ __pyx_t_2 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_7 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_datafmt = __pyx_t_2;
+ __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_datatype);
- __pyx_v_datatype = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_datatype = __pyx_t_7;
+ __pyx_t_7 = 0;
}
- __pyx_L15:;
+ __pyx_L13:;
}
- __pyx_L13:;
+ __pyx_L11:;
}
- __pyx_L12:;
+ __pyx_L10:;
- /* "csamtools.pyx":2589
+ /* "pysam/csamtools.pyx":2613
* else: datafmt, datatype = "I", 'I'
*
* datafmt = "2sccI%i%s" % (len(value), datafmt) # <<<<<<<<<<<<<<
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
+ __Pyx_GIVEREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_datafmt);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_v_datafmt);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_datafmt);
__Pyx_GIVEREF(__pyx_v_datafmt);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_141), ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2589; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_7 = 0;
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_145), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_datafmt);
- __pyx_v_datafmt = ((PyObject *)__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_v_datafmt = ((PyObject *)__pyx_t_7);
+ __pyx_t_7 = 0;
- /* "csamtools.pyx":2590
+ /* "pysam/csamtools.pyx":2614
*
* datafmt = "2sccI%i%s" % (len(value), datafmt)
* args.extend( [pytag[:2], # <<<<<<<<<<<<<<
* pytype.encode('ascii'),
* datatype.encode('ascii'),
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
- /* "csamtools.pyx":2593
+ /* "pysam/csamtools.pyx":2617
* pytype.encode('ascii'),
* datatype.encode('ascii'),
* len(value)] + list(value) ) # <<<<<<<<<<<<<<
* fmts.append( datafmt )
* continue
*/
- __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
- /* "csamtools.pyx":2591
+ /* "pysam/csamtools.pyx":2615
* datafmt = "2sccI%i%s" % (len(value), datafmt)
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* datatype.encode('ascii'),
* len(value)] + list(value) )
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_142), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_146), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":2592
+ /* "pysam/csamtools.pyx":2616
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
* datatype.encode('ascii'), # <<<<<<<<<<<<<<
* len(value)] + list(value) )
* fmts.append( datafmt )
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_datatype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_13 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_143), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_datatype, __pyx_n_s__encode); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_14 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_147), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":2593
+ /* "pysam/csamtools.pyx":2617
* pytype.encode('ascii'),
* datatype.encode('ascii'),
* len(value)] + list(value) ) # <<<<<<<<<<<<<<
* fmts.append( datafmt )
* continue
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_12); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_14 = PyList_New(4); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_14));
- PyList_SET_ITEM(__pyx_t_14, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- PyList_SET_ITEM(__pyx_t_14, 1, __pyx_t_8);
+ __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_13); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_15 = PyList_New(4); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ PyList_SET_ITEM(__pyx_t_15, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_15, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ PyList_SET_ITEM(__pyx_t_15, 2, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ PyList_SET_ITEM(__pyx_t_15, 3, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
- PyList_SET_ITEM(__pyx_t_14, 2, __pyx_t_13);
- __Pyx_GIVEREF(__pyx_t_13);
- PyList_SET_ITEM(__pyx_t_14, 3, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_6 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_14 = 0;
__pyx_t_8 = 0;
- __pyx_t_13 = 0;
- __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_13 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Add(((PyObject *)__pyx_t_14), __pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_13));
- PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __pyx_t_8 = PyNumber_Add(((PyObject *)__pyx_t_15), __pyx_t_14); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "csamtools.pyx":2594
+ /* "pysam/csamtools.pyx":2618
* datatype.encode('ascii'),
* len(value)] + list(value) )
* fmts.append( datafmt ) # <<<<<<<<<<<<<<
* continue
*
*/
- if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2594; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyList_Append(__pyx_v_fmts, __pyx_v_datafmt); if (unlikely(__pyx_t_16 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":2595
+ /* "pysam/csamtools.pyx":2619
* len(value)] + list(value) )
* fmts.append( datafmt )
* continue # <<<<<<<<<<<<<<
*
* if t is float:
*/
- goto __pyx_L6_continue;
- goto __pyx_L11;
+ goto __pyx_L4_continue;
+ goto __pyx_L9;
}
- __pyx_L11:;
+ __pyx_L9:;
- /* "csamtools.pyx":2597
+ /* "pysam/csamtools.pyx":2621
* continue
*
* if t is float: # <<<<<<<<<<<<<<
* fmt, pytype = "2scf", 'f'
* elif t is int:
*/
- __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyFloat_Type)));
- if (__pyx_t_11) {
+ __pyx_t_12 = (__pyx_v_t == ((PyObject*)(&PyFloat_Type)));
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2598
+ /* "pysam/csamtools.pyx":2622
*
* if t is float:
* fmt, pytype = "2scf", 'f' # <<<<<<<<<<<<<<
* elif t is int:
* # negative values
*/
- __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scf);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_13 = ((PyObject *)__pyx_n_s__f);
- __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scf);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_14 = ((PyObject *)__pyx_n_s__f);
+ __Pyx_INCREF(__pyx_t_14);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_fmt = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_13;
- __pyx_t_13 = 0;
- goto __pyx_L16;
+ __pyx_v_pytype = __pyx_t_14;
+ __pyx_t_14 = 0;
+ goto __pyx_L14;
}
- /* "csamtools.pyx":2599
+ /* "pysam/csamtools.pyx":2623
* if t is float:
* fmt, pytype = "2scf", 'f'
* elif t is int: # <<<<<<<<<<<<<<
* # negative values
* if value < 0:
*/
- __pyx_t_11 = (__pyx_v_t == ((PyObject*)(&PyInt_Type)));
- if (__pyx_t_11) {
+ __pyx_t_12 = (__pyx_v_t == ((PyObject*)(&PyInt_Type)));
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2601
+ /* "pysam/csamtools.pyx":2625
* elif t is int:
* # negative values
* if value < 0: # <<<<<<<<<<<<<<
* if value >= -127: fmt, pytype = "2scb", 'c'
* elif value >= -32767: fmt, pytype = "2sch", 's'
*/
- __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- if (__pyx_t_11) {
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2602
+ /* "pysam/csamtools.pyx":2626
* # negative values
* if value < 0:
* if value >= -127: fmt, pytype = "2scb", 'c' # <<<<<<<<<<<<<<
* elif value >= -32767: fmt, pytype = "2sch", 's'
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_127, Py_GE); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- if (__pyx_t_11) {
- __pyx_t_13 = ((PyObject *)__pyx_kp_s__2scb);
- __Pyx_INCREF(__pyx_t_13);
- __pyx_t_7 = ((PyObject *)__pyx_n_s__c);
- __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_127, Py_GE); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_14 = ((PyObject *)__pyx_kp_s__2scb);
+ __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_8 = ((PyObject *)__pyx_n_s__c);
+ __Pyx_INCREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_13;
- __pyx_t_13 = 0;
+ __pyx_v_fmt = __pyx_t_14;
+ __pyx_t_14 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L18;
+ __pyx_v_pytype = __pyx_t_8;
+ __pyx_t_8 = 0;
+ goto __pyx_L16;
}
- /* "csamtools.pyx":2603
+ /* "pysam/csamtools.pyx":2627
* if value < 0:
* if value >= -127: fmt, pytype = "2scb", 'c'
* elif value >= -32767: fmt, pytype = "2sch", 's' # <<<<<<<<<<<<<<
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2sci", 'i'
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_32767, Py_GE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_11) {
- __pyx_t_7 = ((PyObject *)__pyx_kp_s__2sch);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_13 = ((PyObject *)__pyx_n_s__s);
- __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_32767, Py_GE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_8 = ((PyObject *)__pyx_kp_s__2sch);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_14 = ((PyObject *)__pyx_n_s__s);
+ __Pyx_INCREF(__pyx_t_14);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_fmt = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_13;
- __pyx_t_13 = 0;
- goto __pyx_L18;
+ __pyx_v_pytype = __pyx_t_14;
+ __pyx_t_14 = 0;
+ goto __pyx_L16;
}
- /* "csamtools.pyx":2604
+ /* "pysam/csamtools.pyx":2628
* if value >= -127: fmt, pytype = "2scb", 'c'
* elif value >= -32767: fmt, pytype = "2sch", 's'
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: fmt, pytype = "2sci", 'i'
* # positive values
*/
- __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_2147483648, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- if (__pyx_t_11) {
- __pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_13));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_13));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_13));
- __pyx_t_13 = 0;
- __pyx_t_13 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_Raise(__pyx_t_13, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L18;
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_neg_2147483648, Py_LT); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_144), __pyx_v_value); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_14));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_14));
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_Raise(__pyx_t_14, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L16;
}
/*else*/ {
- /* "csamtools.pyx":2605
+ /* "pysam/csamtools.pyx":2629
* elif value >= -32767: fmt, pytype = "2sch", 's'
* elif value < -2147483648: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2sci", 'i' # <<<<<<<<<<<<<<
* # positive values
* else:
*/
- __pyx_t_13 = ((PyObject *)__pyx_kp_s__2sci);
- __Pyx_INCREF(__pyx_t_13);
- __pyx_t_7 = ((PyObject *)__pyx_n_s__i);
- __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_14 = ((PyObject *)__pyx_kp_s__2sci);
+ __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_8 = ((PyObject *)__pyx_n_s__i);
+ __Pyx_INCREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_13;
- __pyx_t_13 = 0;
+ __pyx_v_fmt = __pyx_t_14;
+ __pyx_t_14 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_pytype = __pyx_t_8;
+ __pyx_t_8 = 0;
}
- __pyx_L18:;
- goto __pyx_L17;
+ __pyx_L16:;
+ goto __pyx_L15;
}
/*else*/ {
- /* "csamtools.pyx":2608
+ /* "pysam/csamtools.pyx":2632
* # positive values
* else:
* if value <= 255: fmt, pytype = "2scB", 'C' # <<<<<<<<<<<<<<
* elif value <= 65535: fmt, pytype = "2scH", 'S'
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_255, Py_LE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_11) {
- __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scB);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_13 = ((PyObject *)__pyx_n_s__C);
- __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_value, __pyx_int_255, Py_LE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scB);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_14 = ((PyObject *)__pyx_n_s__C);
+ __Pyx_INCREF(__pyx_t_14);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_fmt = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_13;
- __pyx_t_13 = 0;
- goto __pyx_L19;
+ __pyx_v_pytype = __pyx_t_14;
+ __pyx_t_14 = 0;
+ goto __pyx_L17;
}
- /* "csamtools.pyx":2609
+ /* "pysam/csamtools.pyx":2633
* else:
* if value <= 255: fmt, pytype = "2scB", 'C'
* elif value <= 65535: fmt, pytype = "2scH", 'S' # <<<<<<<<<<<<<<
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2scI", 'I'
*/
- __pyx_t_13 = PyObject_RichCompare(__pyx_v_value, __pyx_int_65535, Py_LE); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- if (__pyx_t_11) {
- __pyx_t_13 = ((PyObject *)__pyx_kp_s__2scH);
- __Pyx_INCREF(__pyx_t_13);
- __pyx_t_7 = ((PyObject *)__pyx_n_s__S);
- __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_value, __pyx_int_65535, Py_LE); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_14 = ((PyObject *)__pyx_kp_s__2scH);
+ __Pyx_INCREF(__pyx_t_14);
+ __pyx_t_8 = ((PyObject *)__pyx_n_s__S);
+ __Pyx_INCREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_13;
- __pyx_t_13 = 0;
+ __pyx_v_fmt = __pyx_t_14;
+ __pyx_t_14 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L19;
+ __pyx_v_pytype = __pyx_t_8;
+ __pyx_t_8 = 0;
+ goto __pyx_L17;
}
- /* "csamtools.pyx":2610
+ /* "pysam/csamtools.pyx":2634
* if value <= 255: fmt, pytype = "2scB", 'C'
* elif value <= 65535: fmt, pytype = "2scH", 'S'
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value ) # <<<<<<<<<<<<<<
* else: fmt, pytype = "2scI", 'I'
* else:
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_value, __pyx_int_4294967295, Py_GT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_11) {
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_140), __pyx_v_value); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_13));
- PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __Pyx_Raise(__pyx_t_7, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L19;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_value, __pyx_int_4294967295, Py_GT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (__pyx_t_12) {
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_144), __pyx_v_value); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __Pyx_Raise(__pyx_t_8, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L17;
}
/*else*/ {
- /* "csamtools.pyx":2611
+ /* "pysam/csamtools.pyx":2635
* elif value <= 65535: fmt, pytype = "2scH", 'S'
* elif value > 4294967295: raise ValueError( "integer %i out of range of BAM/SAM specification" % value )
* else: fmt, pytype = "2scI", 'I' # <<<<<<<<<<<<<<
* else:
* # Note: hex strings (H) are not supported yet
*/
- __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scI);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_13 = ((PyObject *)__pyx_n_s__I);
- __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scI);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_14 = ((PyObject *)__pyx_n_s__I);
+ __Pyx_INCREF(__pyx_t_14);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_fmt = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_13;
- __pyx_t_13 = 0;
+ __pyx_v_pytype = __pyx_t_14;
+ __pyx_t_14 = 0;
}
- __pyx_L19:;
+ __pyx_L17:;
}
- __pyx_L17:;
- goto __pyx_L16;
+ __pyx_L15:;
+ goto __pyx_L14;
}
/*else*/ {
- /* "csamtools.pyx":2614
+ /* "pysam/csamtools.pyx":2638
* else:
* # Note: hex strings (H) are not supported yet
* if t is not bytes: # <<<<<<<<<<<<<<
* value = value.encode('ascii')
* if len(value) == 1:
*/
- __pyx_t_11 = (__pyx_v_t != ((PyObject*)(&PyBytes_Type)));
- if (__pyx_t_11) {
+ __pyx_t_12 = (__pyx_v_t != ((PyObject*)(&PyBytes_Type)));
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2615
+ /* "pysam/csamtools.pyx":2639
* # Note: hex strings (H) are not supported yet
* if t is not bytes:
* value = value.encode('ascii') # <<<<<<<<<<<<<<
* if len(value) == 1:
* fmt, pytype = "2scc", 'A'
*/
- __pyx_t_13 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__encode); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_7 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_k_tuple_144), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
+ __pyx_t_14 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__encode); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_8 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_k_tuple_148), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_7;
- __pyx_t_7 = 0;
- goto __pyx_L20;
+ __pyx_v_value = __pyx_t_8;
+ __pyx_t_8 = 0;
+ goto __pyx_L18;
}
- __pyx_L20:;
+ __pyx_L18:;
- /* "csamtools.pyx":2616
+ /* "pysam/csamtools.pyx":2640
* if t is not bytes:
* value = value.encode('ascii')
* if len(value) == 1: # <<<<<<<<<<<<<<
* fmt, pytype = "2scc", 'A'
* else:
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_11 = (__pyx_t_12 == 1);
- if (__pyx_t_11) {
+ __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = (__pyx_t_13 == 1);
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2617
+ /* "pysam/csamtools.pyx":2641
* value = value.encode('ascii')
* if len(value) == 1:
* fmt, pytype = "2scc", 'A' # <<<<<<<<<<<<<<
* else:
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
*/
- __pyx_t_7 = ((PyObject *)__pyx_kp_s__2scc);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_13 = ((PyObject *)__pyx_n_s__A);
- __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_8 = ((PyObject *)__pyx_kp_s__2scc);
+ __Pyx_INCREF(__pyx_t_8);
+ __pyx_t_14 = ((PyObject *)__pyx_n_s__A);
+ __Pyx_INCREF(__pyx_t_14);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_fmt = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_13;
- __pyx_t_13 = 0;
- goto __pyx_L21;
+ __pyx_v_pytype = __pyx_t_14;
+ __pyx_t_14 = 0;
+ goto __pyx_L19;
}
/*else*/ {
- /* "csamtools.pyx":2619
+ /* "pysam/csamtools.pyx":2643
* fmt, pytype = "2scc", 'A'
* else:
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z' # <<<<<<<<<<<<<<
*
* args.extend( [pytag[:2],
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_13 = PyInt_FromSsize_t((__pyx_t_12 + 1)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_145), __pyx_t_13); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_13 = ((PyObject *)__pyx_n_s__Z);
- __Pyx_INCREF(__pyx_t_13);
+ __pyx_t_13 = PyObject_Length(__pyx_v_value); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyInt_FromSsize_t((__pyx_t_13 + 1)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_149), __pyx_t_14); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_14 = ((PyObject *)__pyx_n_s__Z);
+ __Pyx_INCREF(__pyx_t_14);
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = ((PyObject *)__pyx_t_7);
- __pyx_t_7 = 0;
+ __pyx_v_fmt = ((PyObject *)__pyx_t_8);
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_pytype);
- __pyx_v_pytype = __pyx_t_13;
- __pyx_t_13 = 0;
+ __pyx_v_pytype = __pyx_t_14;
+ __pyx_t_14 = 0;
}
- __pyx_L21:;
+ __pyx_L19:;
}
- __pyx_L16:;
+ __pyx_L14:;
- /* "csamtools.pyx":2621
+ /* "pysam/csamtools.pyx":2645
* fmt, pytype = "2sc%is" % (len(value)+1), 'Z'
*
* args.extend( [pytag[:2], # <<<<<<<<<<<<<<
* pytype.encode('ascii'),
* value ] )
*/
- __pyx_t_13 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
- __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_14 = PyObject_GetAttr(((PyObject *)__pyx_v_args), __pyx_n_s__extend); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_pytag, 0, 2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
- /* "csamtools.pyx":2622
+ /* "pysam/csamtools.pyx":2646
*
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* value ] )
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_146), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_pytype, __pyx_n_s__encode); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_15 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_150), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "csamtools.pyx":2623
+ /* "pysam/csamtools.pyx":2647
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
* value ] ) # <<<<<<<<<<<<<<
*
* fmts.append( fmt )
*/
- __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
+ __pyx_t_7 = PyList_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ PyList_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ PyList_SET_ITEM(__pyx_t_7, 1, __pyx_t_15);
+ __Pyx_GIVEREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_value);
- PyList_SET_ITEM(__pyx_t_1, 2, __pyx_v_value);
+ PyList_SET_ITEM(__pyx_t_7, 2, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
+ __pyx_t_8 = 0;
+ __pyx_t_15 = 0;
+ __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_t_7));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
- __pyx_t_14 = 0;
- __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_14));
- PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "csamtools.pyx":2625
+ /* "pysam/csamtools.pyx":2649
* value ] )
*
* fmts.append( fmt ) # <<<<<<<<<<<<<<
*
* fmt = "".join(fmts)
*/
- if (unlikely(((PyObject *)__pyx_v_fmts) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_15 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L6_continue:;
+ __pyx_t_16 = PyList_Append(__pyx_v_fmts, __pyx_v_fmt); if (unlikely(__pyx_t_16 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L4_continue:;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":2627
+ /* "pysam/csamtools.pyx":2651
* fmts.append( fmt )
*
* fmt = "".join(fmts) # <<<<<<<<<<<<<<
* total_size = struct.calcsize(fmt)
* buffer = ctypes.create_string_buffer(total_size)
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_16), __pyx_n_s__join); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(((PyObject *)__pyx_v_fmts));
- PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_fmts));
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_fmts));
__Pyx_GIVEREF(((PyObject *)__pyx_v_fmts));
- __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_15 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_fmt);
- __pyx_v_fmt = __pyx_t_14;
- __pyx_t_14 = 0;
+ __pyx_v_fmt = __pyx_t_15;
+ __pyx_t_15 = 0;
- /* "csamtools.pyx":2628
+ /* "pysam/csamtools.pyx":2652
*
* fmt = "".join(fmts)
* total_size = struct.calcsize(fmt) # <<<<<<<<<<<<<<
* buffer = ctypes.create_string_buffer(total_size)
* struct.pack_into( fmt,
*/
- __pyx_t_14 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_14, __pyx_n_s__calcsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ __pyx_t_15 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_15, __pyx_n_s__calcsize); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ __pyx_t_15 = PyTuple_New(1); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_fmt);
- PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_fmt);
+ PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_fmt);
__Pyx_GIVEREF(__pyx_v_fmt);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __pyx_v_total_size = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __pyx_v_total_size = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2629
+ /* "pysam/csamtools.pyx":2653
* fmt = "".join(fmts)
* total_size = struct.calcsize(fmt)
* buffer = ctypes.create_string_buffer(total_size) # <<<<<<<<<<<<<<
* struct.pack_into( fmt,
* buffer,
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__ctypes); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_14 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s_147); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__ctypes); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s_151); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_total_size);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_total_size);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_total_size);
__Pyx_GIVEREF(__pyx_v_total_size);
- __pyx_t_1 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_v_buffer = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_t_7 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_v_buffer = __pyx_t_7;
+ __pyx_t_7 = 0;
- /* "csamtools.pyx":2630
+ /* "pysam/csamtools.pyx":2654
* total_size = struct.calcsize(fmt)
* buffer = ctypes.create_string_buffer(total_size)
* struct.pack_into( fmt, # <<<<<<<<<<<<<<
* buffer,
* 0,
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__pack_into); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__struct); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__pack_into); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "csamtools.pyx":2631
+ /* "pysam/csamtools.pyx":2655
* buffer = ctypes.create_string_buffer(total_size)
* struct.pack_into( fmt,
* buffer, # <<<<<<<<<<<<<<
* 0,
* *args )
*/
- __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_fmt);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fmt);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_fmt);
__Pyx_GIVEREF(__pyx_v_fmt);
__Pyx_INCREF(__pyx_v_buffer);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_buffer);
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_buffer);
__Pyx_GIVEREF(__pyx_v_buffer);
__Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_int_0);
+ PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_int_0);
__Pyx_GIVEREF(__pyx_int_0);
- /* "csamtools.pyx":2633
+ /* "pysam/csamtools.pyx":2657
* buffer,
* 0,
* *args ) # <<<<<<<<<<<<<<
*
* # delete the old data and allocate new space.
*/
- __pyx_t_14 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PySequence_Tuple(((PyObject *)__pyx_v_args)); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_15));
+ __pyx_t_14 = PyNumber_Add(((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_15)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_14));
- __pyx_t_13 = PyNumber_Add(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_14)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_13));
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
+ __pyx_t_15 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- goto __pyx_L5;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L3;
}
- __pyx_L5:;
- if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2640; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L3:;
- /* "csamtools.pyx":2641
+ /* "pysam/csamtools.pyx":2664
+ * pysam_bam_update( src,
+ * src.l_aux,
+ * total_size, # <<<<<<<<<<<<<<
+ * bam1_aux( src ) )
+ *
+ */
+ if (unlikely(!__pyx_v_total_size)) { __Pyx_RaiseUnboundLocalError("total_size"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":2665
* src.l_aux,
* total_size,
* bam1_aux( src ) ) # <<<<<<<<<<<<<<
*
* src.l_aux = total_size
*/
- pysam_bam_update(__pyx_v_src, __pyx_v_src->l_aux, __pyx_t_16, bam1_aux(__pyx_v_src));
+ pysam_bam_update(__pyx_v_src, __pyx_v_src->l_aux, __pyx_t_17, bam1_aux(__pyx_v_src));
- /* "csamtools.pyx":2643
+ /* "pysam/csamtools.pyx":2667
* bam1_aux( src ) )
*
* src.l_aux = total_size # <<<<<<<<<<<<<<
*
* # copy data only if there is any
*/
- __pyx_t_17 = __Pyx_PyInt_AsInt(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_src->l_aux = __pyx_t_17;
+ __pyx_t_18 = __Pyx_PyInt_AsInt(__pyx_v_total_size); if (unlikely((__pyx_t_18 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_src->l_aux = __pyx_t_18;
- /* "csamtools.pyx":2646
+ /* "pysam/csamtools.pyx":2670
*
* # copy data only if there is any
* if total_size != 0: # <<<<<<<<<<<<<<
*
* # get location of new data
*/
- __pyx_t_14 = PyObject_RichCompare(__pyx_v_total_size, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- if (__pyx_t_11) {
+ __pyx_t_15 = PyObject_RichCompare(__pyx_v_total_size, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_15); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_15); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (__pyx_t_12) {
- /* "csamtools.pyx":2649
+ /* "pysam/csamtools.pyx":2673
*
* # get location of new data
* s = bam1_aux( src ) # <<<<<<<<<<<<<<
@@ -24324,44 +26029,54 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
* # check if there is direct path from buffer.raw to tmp
*/
__pyx_v_s = bam1_aux(__pyx_v_src);
- if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_14 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":2652
+ /* "pysam/csamtools.pyx":2676
*
* # check if there is direct path from buffer.raw to tmp
- * temp = buffer.raw # <<<<<<<<<<<<<<
+ * p = buffer.raw # <<<<<<<<<<<<<<
+ * # create handle to make sure buffer stays alive long
+ * # enough for memcpy, see issue 129
+ */
+ if (unlikely(!__pyx_v_buffer)) { __Pyx_RaiseUnboundLocalError("buffer"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_15 = PyObject_GetAttr(__pyx_v_buffer, __pyx_n_s__raw); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_v_p = __pyx_t_15;
+ __pyx_t_15 = 0;
+
+ /* "pysam/csamtools.pyx":2679
+ * # create handle to make sure buffer stays alive long
+ * # enough for memcpy, see issue 129
+ * temp = p # <<<<<<<<<<<<<<
* memcpy( s, temp, total_size )
*
*/
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_18 = PyBytes_AsString(__pyx_t_14); if (unlikely((!__pyx_t_18) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- __pyx_v_temp = __pyx_t_18;
+ __pyx_t_19 = PyBytes_AsString(__pyx_v_p); if (unlikely((!__pyx_t_19) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_temp = __pyx_t_19;
- /* "csamtools.pyx":2653
- * # check if there is direct path from buffer.raw to tmp
- * temp = buffer.raw
+ /* "pysam/csamtools.pyx":2680
+ * # enough for memcpy, see issue 129
+ * temp = p
* memcpy( s, temp, total_size ) # <<<<<<<<<<<<<<
*
* property flag:
*/
- __pyx_t_16 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_16 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- memcpy(__pyx_v_s, __pyx_v_temp, __pyx_t_16);
- goto __pyx_L22;
+ __pyx_t_17 = __Pyx_PyInt_AsSize_t(__pyx_v_total_size); if (unlikely((__pyx_t_17 == (size_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ memcpy(__pyx_v_s, __pyx_v_temp, __pyx_t_17);
+ goto __pyx_L20;
}
- __pyx_L22:;
+ __pyx_L20:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
- __Pyx_XDECREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_14);
- __Pyx_AddTraceback("csamtools.AlignedRead.tags.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_15);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tags.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_fmts);
@@ -24378,12 +26093,24 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
__Pyx_XDECREF(__pyx_v_fmt);
__Pyx_XDECREF(__pyx_v_total_size);
__Pyx_XDECREF(__pyx_v_buffer);
+ __Pyx_XDECREF(__pyx_v_p);
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":2657
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2684
* property flag:
* """properties flag"""
* def __get__(self): return self._delegate.core.flag # <<<<<<<<<<<<<<
@@ -24391,8 +26118,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4flag___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -24400,10 +26126,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2657);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2684);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -24413,7 +26139,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.flag.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.flag.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24422,7 +26148,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2658
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_flag));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2685
* """properties flag"""
* def __get__(self): return self._delegate.core.flag
* def __set__(self, flag): self._delegate.core.flag = flag # <<<<<<<<<<<<<<
@@ -24430,8 +26167,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4flag___get__(PyObject *__pyx
* property rname:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_flag) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4flag_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_flag) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
@@ -24439,15 +26175,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_se
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2658);
- __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_flag); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2685);
+ __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_flag); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.flag = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.flag.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.flag.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -24455,7 +26191,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2676
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2703
*
* """
* def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
@@ -24463,8 +26210,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(PyObject *__pyx_v_se
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rname___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -24472,10 +26218,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2676);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2703);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -24485,7 +26231,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__py
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.rname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rname.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24494,7 +26240,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2677
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2704
* """
* def __get__(self): return self._delegate.core.tid
* def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
@@ -24502,8 +26259,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rname___get__(PyObject *__py
* property tid:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rname_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -24511,15 +26267,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_s
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2677);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2704);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.rname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rname.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -24527,7 +26283,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2690
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2717
*
* """
* def __get__(self): return self._delegate.core.tid # <<<<<<<<<<<<<<
@@ -24535,8 +26302,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(PyObject *__pyx_v_s
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3tid___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -24544,10 +26310,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2690);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2717);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2717; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -24557,7 +26323,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24566,7 +26332,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":2691
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2718
* """
* def __get__(self): return self._delegate.core.tid
* def __set__(self, tid): self._delegate.core.tid = tid # <<<<<<<<<<<<<<
@@ -24574,8 +26351,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3tid___get__(PyObject *__pyx_
* property pos:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_tid) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3tid_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -24583,15 +26359,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_sel
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2691);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.tid = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2718);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_tid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.tid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.tid.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tid.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -24599,7 +26375,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":2695
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2722
* property pos:
* """0-based leftmost coordinate"""
* def __get__(self): return self._delegate.core.pos # <<<<<<<<<<<<<<
@@ -24607,8 +26394,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(PyObject *__pyx_v_sel
* ## setting the cigar string also updates the "bin" attribute
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3pos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -24616,10 +26402,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2695);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2722);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2695; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -24629,7 +26415,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24638,7 +26424,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":2696
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_pos));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2723
* """0-based leftmost coordinate"""
* def __get__(self): return self._delegate.core.pos
* def __set__(self, pos): # <<<<<<<<<<<<<<
@@ -24646,29 +26443,30 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3pos___get__(PyObject *__pyx_
* cdef bam1_t * src
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_pos) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3pos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_pos) {
bam1_t *__pyx_v_src;
int __pyx_r;
__Pyx_RefNannyDeclarations
- int32_t __pyx_t_1;
+ bam1_t *__pyx_t_1;
+ int32_t __pyx_t_2;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2696);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2723);
- /* "csamtools.pyx":2699
+ /* "pysam/csamtools.pyx":2726
* ## setting the cigar string also updates the "bin" attribute
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar:
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2700
+ /* "pysam/csamtools.pyx":2727
* cdef bam1_t * src
* src = self._delegate
* if src.core.n_cigar: # <<<<<<<<<<<<<<
@@ -24677,7 +26475,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_sel
*/
if (__pyx_v_src->core.n_cigar) {
- /* "csamtools.pyx":2701
+ /* "pysam/csamtools.pyx":2728
* src = self._delegate
* if src.core.n_cigar:
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) ) # <<<<<<<<<<<<<<
@@ -24685,11 +26483,11 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_sel
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
*/
__pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)));
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2703
+ /* "pysam/csamtools.pyx":2730
* src.core.bin = bam_reg2bin( src.core.pos, bam_calend( &src.core, bam1_cigar(src)) )
* else:
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1) # <<<<<<<<<<<<<<
@@ -24698,22 +26496,22 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_sel
*/
__pyx_v_src->core.bin = bam_reg2bin(__pyx_v_src->core.pos, (__pyx_v_src->core.pos + 1));
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2704
+ /* "pysam/csamtools.pyx":2731
* else:
* src.core.bin = bam_reg2bin( src.core.pos, src.core.pos + 1)
* self._delegate.core.pos = pos # <<<<<<<<<<<<<<
* property bin:
* """properties bin"""
*/
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2704; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos = __pyx_t_1;
+ __pyx_t_2 = __Pyx_PyInt_from_py_int32_t(__pyx_v_pos); if (unlikely((__pyx_t_2 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.pos = __pyx_t_2;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.pos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -24721,7 +26519,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":2707
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2734
* property bin:
* """properties bin"""
* def __get__(self): return self._delegate.core.bin # <<<<<<<<<<<<<<
@@ -24729,8 +26538,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(PyObject *__pyx_v_sel
* property rlen:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_3bin___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -24738,10 +26546,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2707);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2734);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.bin); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -24751,7 +26559,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.bin.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.bin.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24760,7 +26568,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":2708
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_bin));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2735
* """properties bin"""
* def __get__(self): return self._delegate.core.bin
* def __set__(self, bin): self._delegate.core.bin = bin # <<<<<<<<<<<<<<
@@ -24768,8 +26587,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_3bin___get__(PyObject *__pyx_
* '''length of the read (read only). Returns 0 if not given.'''
*/
-static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_bin) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_3bin_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_bin) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
@@ -24777,15 +26595,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_sel
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2708);
- __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_bin); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.bin = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2735);
+ __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_bin); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.bin = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.bin.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.bin.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -24793,7 +26611,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":2711
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2738
* property rlen:
* '''length of the read (read only). Returns 0 if not given.'''
* def __get__(self): return self._delegate.core.l_qseq # <<<<<<<<<<<<<<
@@ -24801,8 +26630,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(PyObject *__pyx_v_sel
* '''aligned reference position of the read on the reference genome.
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4rlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -24810,10 +26638,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2711);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2738);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.l_qseq); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -24823,7 +26651,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.rlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24832,7 +26660,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2717
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2744
* aend points to one past the last aligned residue.
* Returns None if not available.'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -24840,55 +26679,56 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4rlen___get__(PyObject *__pyx
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4aend___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
+ bam1_t *__pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_t_4;
int __pyx_t_5;
+ int __pyx_t_6;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2717);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2744);
- /* "csamtools.pyx":2719
+ /* "pysam/csamtools.pyx":2746
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2720
+ /* "pysam/csamtools.pyx":2747
* cdef bam1_t * src
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
* return None
* return bam_calend(&src.core, bam1_cigar(src))
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_And(__pyx_t_2, __pyx_int_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!__pyx_t_3) {
- __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
- __pyx_t_5 = __pyx_t_4;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2747; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (!__pyx_t_4) {
+ __pyx_t_5 = (__pyx_v_src->core.n_cigar == 0);
+ __pyx_t_6 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_3;
+ __pyx_t_6 = __pyx_t_4;
}
- if (__pyx_t_5) {
+ if (__pyx_t_6) {
- /* "csamtools.pyx":2721
+ /* "pysam/csamtools.pyx":2748
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None # <<<<<<<<<<<<<<
@@ -24899,11 +26739,11 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2722
+ /* "pysam/csamtools.pyx":2749
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
* return bam_calend(&src.core, bam1_cigar(src)) # <<<<<<<<<<<<<<
@@ -24911,18 +26751,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx
* property alen:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.aend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.aend.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -24931,7 +26771,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2727
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2754
* '''aligned length of the read on the reference genome. Returns None if
* not available.'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -24939,55 +26790,56 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4aend___get__(PyObject *__pyx
* src = self._delegate
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4alen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
bam1_t *__pyx_v_src;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
+ bam1_t *__pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_t_4;
int __pyx_t_5;
+ int __pyx_t_6;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2727);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2754);
- /* "csamtools.pyx":2729
+ /* "pysam/csamtools.pyx":2756
* def __get__(self):
* cdef bam1_t * src
* src = self._delegate # <<<<<<<<<<<<<<
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2730
+ /* "pysam/csamtools.pyx":2757
* cdef bam1_t * src
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0: # <<<<<<<<<<<<<<
* return None
* return bam_calend(&src.core,
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_And(__pyx_t_2, __pyx_int_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (!__pyx_t_3) {
- __pyx_t_4 = (__pyx_v_src->core.n_cigar == 0);
- __pyx_t_5 = __pyx_t_4;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2757; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ if (!__pyx_t_4) {
+ __pyx_t_5 = (__pyx_v_src->core.n_cigar == 0);
+ __pyx_t_6 = __pyx_t_5;
} else {
- __pyx_t_5 = __pyx_t_3;
+ __pyx_t_6 = __pyx_t_4;
}
- if (__pyx_t_5) {
+ if (__pyx_t_6) {
- /* "csamtools.pyx":2731
+ /* "pysam/csamtools.pyx":2758
* src = self._delegate
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None # <<<<<<<<<<<<<<
@@ -24998,11 +26850,11 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx
__Pyx_INCREF(Py_None);
__pyx_r = Py_None;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2732
+ /* "pysam/csamtools.pyx":2759
* if (self.flag & BAM_FUNMAP) or src.core.n_cigar == 0:
* return None
* return bam_calend(&src.core, # <<<<<<<<<<<<<<
@@ -25011,25 +26863,25 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx
*/
__Pyx_XDECREF(__pyx_r);
- /* "csamtools.pyx":2734
+ /* "pysam/csamtools.pyx":2761
* return bam_calend(&src.core,
* bam1_cigar(src)) - \
* self._delegate.core.pos # <<<<<<<<<<<<<<
*
* property mapq:
*/
- __pyx_t_2 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.pos)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyInt_FromLong((bam_calend((&__pyx_v_src->core), bam1_cigar(__pyx_v_src)) - __pyx_v_self->_delegate->core.pos)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = __pyx_t_3;
+ __pyx_t_3 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.alen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.alen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25038,7 +26890,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2738
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2765
* property mapq:
* """mapping quality"""
* def __get__(self): return self._delegate.core.qual # <<<<<<<<<<<<<<
@@ -25046,8 +26909,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4alen___get__(PyObject *__pyx
*
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25055,10 +26917,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2738);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2765);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_delegate->core.qual); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2765; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25068,7 +26930,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mapq.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25077,7 +26939,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2739
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_qual));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2766
* """mapping quality"""
* def __get__(self): return self._delegate.core.qual
* def __set__(self, qual): self._delegate.core.qual = qual # <<<<<<<<<<<<<<
@@ -25085,8 +26958,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mapq___get__(PyObject *__pyx
* property mrnm:
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_qual) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mapq_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_qual) {
int __pyx_r;
__Pyx_RefNannyDeclarations
uint32_t __pyx_t_1;
@@ -25094,15 +26966,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_se
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2739);
- __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.qual = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2766);
+ __pyx_t_1 = __Pyx_PyInt_from_py_uint32_t(__pyx_v_qual); if (unlikely((__pyx_t_1 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.qual = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mapq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mapq.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25110,7 +26982,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2745
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2772
* deprecated, use RNEXT instead.
* """
* def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
@@ -25118,8 +27001,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(PyObject *__pyx_v_se
* property rnext:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25127,10 +27009,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2745);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2772);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25140,7 +27022,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mrnm.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25149,88 +27031,26 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2746
- * """
- * def __get__(self): return self._delegate.core.mtid
- * def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
- * property rnext:
- * """the :term:`reference` id of the mate """
- */
-
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
- int32_t __pyx_t_1;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2746);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2746; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mrnm.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":2749
- * property rnext:
- * """the :term:`reference` id of the mate """
- * def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
- * def __set__(self, mtid): self._delegate.core.mtid = mtid
- * property mpos:
- */
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5rnext___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2749);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2749; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.rnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":2750
- * """the :term:`reference` id of the mate """
+/* "pysam/csamtools.pyx":2773
+ * """
* def __get__(self): return self._delegate.core.mtid
* def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
- * property mpos:
- * """the position of the mate
+ * property rnext:
+ * """the :term:`reference` id of the mate """
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mrnm_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -25238,15 +27058,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_s
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2750);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2750; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mtid = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2773);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.rnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mrnm.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25254,88 +27074,26 @@ static int __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2754
- * """the position of the mate
- * deprecated, use PNEXT instead."""
- * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
- * def __set__(self, mpos): self._delegate.core.mpos = mpos
- * property pnext:
- */
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4mpos___get__(PyObject *__pyx_v_self) {
- PyObject *__pyx_r = NULL;
- __Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2754);
- __Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_r = __pyx_t_1;
- __pyx_t_1 = 0;
- goto __pyx_L0;
-
- __pyx_r = Py_None; __Pyx_INCREF(Py_None);
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = NULL;
- __pyx_L0:;
- __Pyx_XGIVEREF(__pyx_r);
- __Pyx_TraceReturn(__pyx_r);
- __Pyx_RefNannyFinishContext();
- return __pyx_r;
-}
-
-/* "csamtools.pyx":2755
- * deprecated, use PNEXT instead."""
- * def __get__(self): return self._delegate.core.mpos
- * def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
- * property pnext:
- * """the position of the mate"""
- */
-
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
- int __pyx_r;
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- int32_t __pyx_t_1;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2755);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2755; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
-
- __pyx_r = 0;
- goto __pyx_L0;
- __pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mpos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
- __pyx_r = -1;
- __pyx_L0:;
- __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "csamtools.pyx":2758
- * property pnext:
- * """the position of the mate"""
- * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
- * def __set__(self, mpos): self._delegate.core.mpos = mpos
- * property isize:
+/* "pysam/csamtools.pyx":2776
+ * property rnext:
+ * """the :term:`reference` id of the mate """
+ * def __get__(self): return self._delegate.core.mtid # <<<<<<<<<<<<<<
+ * def __set__(self, mtid): self._delegate.core.mtid = mtid
+ * property mpos:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25343,10 +27101,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2758);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2776);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2758; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mtid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25356,7 +27114,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__py
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.pnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25365,7 +27123,202 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2759
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mtid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mtid));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2777
+ * """the :term:`reference` id of the mate """
+ * def __get__(self): return self._delegate.core.mtid
+ * def __set__(self, mtid): self._delegate.core.mtid = mtid # <<<<<<<<<<<<<<
+ * property mpos:
+ * """the position of the mate
+ */
+
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5rnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mtid) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2777);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mtid); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mtid = __pyx_t_1;
+
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.rnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2781
+ * """the position of the mate
+ * deprecated, use PNEXT instead."""
+ * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos
+ * property pnext:
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2781);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2782
+ * deprecated, use PNEXT instead."""
+ * def __get__(self): return self._delegate.core.mpos
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
+ * property pnext:
+ * """the position of the mate"""
+ */
+
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4mpos_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ int32_t __pyx_t_1;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2782);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
+
+ __pyx_r = 0;
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mpos.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_TraceReturn(Py_None);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2785
+ * property pnext:
+ * """the position of the mate"""
+ * def __get__(self): return self._delegate.core.mpos # <<<<<<<<<<<<<<
+ * def __set__(self, mpos): self._delegate.core.mpos = mpos
+ * property isize:
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2785);
+ __Pyx_XDECREF(__pyx_r);
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.mpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = __pyx_t_1;
+ __pyx_t_1 = 0;
+ goto __pyx_L0;
+
+ __pyx_r = Py_None; __Pyx_INCREF(Py_None);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __Pyx_XDECREF(__pyx_t_1);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pnext.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __pyx_r = NULL;
+ __pyx_L0:;
+ __Pyx_XGIVEREF(__pyx_r);
+ __Pyx_TraceReturn(__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_mpos));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2786
* """the position of the mate"""
* def __get__(self): return self._delegate.core.mpos
* def __set__(self, mpos): self._delegate.core.mpos = mpos # <<<<<<<<<<<<<<
@@ -25373,8 +27326,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5pnext___get__(PyObject *__py
* """the insert size
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_mpos) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5pnext_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_mpos) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -25382,15 +27334,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_s
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2759);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.mpos = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2786);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_mpos); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.mpos = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.pnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.pnext.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25398,7 +27350,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2763
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2790
* """the insert size
* deprecated: use tlen instead"""
* def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
@@ -25406,8 +27369,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(PyObject *__pyx_v_s
* property tlen:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_5isize___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25415,10 +27377,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2763);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2790);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25428,7 +27390,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__py
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.isize.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.isize.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25437,7 +27399,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":2764
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2791
* deprecated: use tlen instead"""
* def __get__(self): return self._delegate.core.isize
* def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
@@ -25445,8 +27418,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5isize___get__(PyObject *__py
* """the insert size"""
*/
-static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5isize_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -25454,15 +27426,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_s
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2764);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2791);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.isize = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.isize.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.isize.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25470,7 +27442,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_s
return __pyx_r;
}
-/* "csamtools.pyx":2767
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2794
* property tlen:
* """the insert size"""
* def __get__(self): return self._delegate.core.isize # <<<<<<<<<<<<<<
@@ -25478,8 +27461,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(PyObject *__pyx_v_s
* property is_paired:
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25487,10 +27469,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2767);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2794);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_delegate->core.isize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2794; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25500,7 +27482,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.tlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tlen.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25509,7 +27491,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2768
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_isize));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2795
* """the insert size"""
* def __get__(self): return self._delegate.core.isize
* def __set__(self, isize): self._delegate.core.isize = isize # <<<<<<<<<<<<<<
@@ -25517,8 +27510,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_4tlen___get__(PyObject *__pyx
* """true if read is paired in sequencing"""
*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_isize) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_4tlen_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_isize) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int32_t __pyx_t_1;
@@ -25526,15 +27518,15 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_se
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2768);
- __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.isize = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2795);
+ __pyx_t_1 = __Pyx_PyInt_from_py_int32_t(__pyx_v_isize); if (unlikely((__pyx_t_1 == (int32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->_delegate->core.isize = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.tlen.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.tlen.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25542,7 +27534,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2771
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2798
* property is_paired:
* """true if read is paired in sequencing"""
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0 # <<<<<<<<<<<<<<
@@ -25550,8 +27553,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(PyObject *__pyx_v_se
* if val: self._delegate.core.flag |= BAM_FPAIRED
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25559,10 +27561,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2771);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2798);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(((((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(((__pyx_v_self->_delegate->core.flag & 1) != 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25572,7 +27574,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_paired.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25581,7 +27583,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *
return __pyx_r;
}
-/* "csamtools.pyx":2772
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2799
* """true if read is paired in sequencing"""
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -25589,8 +27602,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(PyObject *
* else: self._delegate.core.flag &= ~BAM_FPAIRED
*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_paired_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -25598,38 +27610,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2772);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2799);
- /* "csamtools.pyx":2773
+ /* "pysam/csamtools.pyx":2800
* def __get__(self): return (self._delegate.core.flag & BAM_FPAIRED) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPAIRED # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FPAIRED
* property is_proper_pair:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2800; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2774
+ /* "pysam/csamtools.pyx":2801
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPAIRED
* else: self._delegate.core.flag &= ~BAM_FPAIRED # <<<<<<<<<<<<<<
* property is_proper_pair:
* """true if read is mapped in a proper pair"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_paired.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_paired.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25637,7 +27649,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2777
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2804
* property is_proper_pair:
* """true if read is mapped in a proper pair"""
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0 # <<<<<<<<<<<<<<
@@ -25645,8 +27668,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(PyObject *__pyx
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25655,16 +27677,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyOb
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2777);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2804);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25675,7 +27696,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyOb
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_proper_pair.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25684,7 +27705,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyOb
return __pyx_r;
}
-/* "csamtools.pyx":2778
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2805
* """true if read is mapped in a proper pair"""
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -25692,8 +27724,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(PyOb
* else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
*/
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_14is_proper_pair_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -25701,38 +27732,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2778);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2805);
- /* "csamtools.pyx":2779
+ /* "pysam/csamtools.pyx":2806
* def __get__(self): return (self.flag & BAM_FPROPER_PAIR) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR
* property is_unmapped:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 2);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 2);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2780
+ /* "pysam/csamtools.pyx":2807
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FPROPER_PAIR
* else: self._delegate.core.flag &= ~BAM_FPROPER_PAIR # <<<<<<<<<<<<<<
* property is_unmapped:
* """true if read itself is unmapped"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~2));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~2));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_proper_pair.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_proper_pair.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25740,7 +27771,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":2783
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2810
* property is_unmapped:
* """true if read itself is unmapped"""
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0 # <<<<<<<<<<<<<<
@@ -25748,8 +27790,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(PyObject
* if val: self._delegate.core.flag |= BAM_FUNMAP
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25758,16 +27799,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObjec
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2783);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2810);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25778,7 +27818,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObjec
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25787,7 +27827,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObjec
return __pyx_r;
}
-/* "csamtools.pyx":2784
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2811
* """true if read itself is unmapped"""
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -25795,8 +27846,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(PyObjec
* else: self._delegate.core.flag &= ~BAM_FUNMAP
*/
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_11is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -25804,38 +27854,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2784);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2811);
- /* "csamtools.pyx":2785
+ /* "pysam/csamtools.pyx":2812
* def __get__(self): return (self.flag & BAM_FUNMAP) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FUNMAP # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FUNMAP
* property mate_is_unmapped:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 4);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 4);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2786
+ /* "pysam/csamtools.pyx":2813
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FUNMAP
* else: self._delegate.core.flag &= ~BAM_FUNMAP # <<<<<<<<<<<<<<
* property mate_is_unmapped:
* """true if the mate is unmapped"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~4));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~4));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25843,7 +27893,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":2789
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2816
* property mate_is_unmapped:
* """true if the mate is unmapped"""
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0 # <<<<<<<<<<<<<<
@@ -25851,8 +27912,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(PyObject *__
* if val: self._delegate.core.flag |= BAM_FMUNMAP
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25861,16 +27921,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(Py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2789);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2816);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_8); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25881,7 +27940,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(Py
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_unmapped.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25890,7 +27949,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(Py
return __pyx_r;
}
-/* "csamtools.pyx":2790
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2817
* """true if the mate is unmapped"""
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -25898,8 +27968,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(Py
* else: self._delegate.core.flag &= ~BAM_FMUNMAP
*/
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -25907,38 +27976,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObjec
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2790);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2817);
- /* "csamtools.pyx":2791
+ /* "pysam/csamtools.pyx":2818
* def __get__(self): return (self.flag & BAM_FMUNMAP) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMUNMAP # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FMUNMAP
* property is_reverse:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 8);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 8);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2792
+ /* "pysam/csamtools.pyx":2819
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMUNMAP
* else: self._delegate.core.flag &= ~BAM_FMUNMAP # <<<<<<<<<<<<<<
* property is_reverse:
* """true if read is mapped to reverse strand"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~8));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~8));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_unmapped.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -25946,7 +28015,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObjec
return __pyx_r;
}
-/* "csamtools.pyx":2795
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2822
* property is_reverse:
* """true if read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0 # <<<<<<<<<<<<<<
@@ -25954,8 +28034,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(PyObjec
* if val: self._delegate.core.flag |= BAM_FREVERSE
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -25964,16 +28043,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2795);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2822);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -25984,7 +28062,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -25993,7 +28071,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":2796
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2823
* """true if read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26001,8 +28090,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(PyObject
* else: self._delegate.core.flag &= ~BAM_FREVERSE
*/
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_10is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26010,38 +28098,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2796);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2823);
- /* "csamtools.pyx":2797
+ /* "pysam/csamtools.pyx":2824
* def __get__(self): return (self.flag & BAM_FREVERSE) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREVERSE # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FREVERSE
* property mate_is_reverse:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 16);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 16);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2798
+ /* "pysam/csamtools.pyx":2825
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREVERSE
* else: self._delegate.core.flag &= ~BAM_FREVERSE # <<<<<<<<<<<<<<
* property mate_is_reverse:
* """true is read is mapped to reverse strand"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~16));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~16));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26049,7 +28137,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":2801
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2828
* property mate_is_reverse:
* """true is read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0 # <<<<<<<<<<<<<<
@@ -26057,8 +28156,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(PyObject *__p
* if val: self._delegate.core.flag |= BAM_FMREVERSE
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26067,16 +28165,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyO
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2801);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2828);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_32); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26087,7 +28184,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyO
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_reverse.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -26096,7 +28193,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyO
return __pyx_r;
}
-/* "csamtools.pyx":2802
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2829
* """true is read is mapped to reverse strand"""
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26104,8 +28212,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(PyO
* else: self._delegate.core.flag &= ~BAM_FMREVERSE
*/
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26113,38 +28220,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2802);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2829);
- /* "csamtools.pyx":2803
+ /* "pysam/csamtools.pyx":2830
* def __get__(self): return (self.flag & BAM_FMREVERSE) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMREVERSE # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FMREVERSE
* property is_read1:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 32);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 32);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2804
+ /* "pysam/csamtools.pyx":2831
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FMREVERSE
* else: self._delegate.core.flag &= ~BAM_FMREVERSE # <<<<<<<<<<<<<<
* property is_read1:
* """true if this is read1"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~32));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~32));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.mate_is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.mate_is_reverse.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26152,7 +28259,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":2807
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2834
* property is_read1:
* """true if this is read1"""
* def __get__(self): return (self.flag & BAM_FREAD1) != 0 # <<<<<<<<<<<<<<
@@ -26160,8 +28278,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(PyObject
* if val: self._delegate.core.flag |= BAM_FREAD1
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26170,16 +28287,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2807);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2834);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_64); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_64); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26190,7 +28306,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *_
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read1.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -26199,7 +28315,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *_
return __pyx_r;
}
-/* "csamtools.pyx":2808
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2835
* """true if this is read1"""
* def __get__(self): return (self.flag & BAM_FREAD1) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26207,8 +28334,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(PyObject *_
* else: self._delegate.core.flag &= ~BAM_FREAD1
*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read1_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26216,38 +28342,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2808);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2835);
- /* "csamtools.pyx":2809
+ /* "pysam/csamtools.pyx":2836
* def __get__(self): return (self.flag & BAM_FREAD1) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD1 # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FREAD1
* property is_read2:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 64);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 64);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2810
+ /* "pysam/csamtools.pyx":2837
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD1
* else: self._delegate.core.flag &= ~BAM_FREAD1 # <<<<<<<<<<<<<<
* property is_read2:
* """true if this is read2"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~64));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~64));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read1.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read1.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26255,7 +28381,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":2813
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2840
* property is_read2:
* """true if this is read2"""
* def __get__(self): return (self.flag & BAM_FREAD2) != 0 # <<<<<<<<<<<<<<
@@ -26263,8 +28400,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(PyObject *__pyx_
* if val: self._delegate.core.flag |= BAM_FREAD2
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26273,16 +28409,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2813);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2840);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_128); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_128); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26293,7 +28428,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *_
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read2.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -26302,7 +28437,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *_
return __pyx_r;
}
-/* "csamtools.pyx":2814
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2841
* """true if this is read2"""
* def __get__(self): return (self.flag & BAM_FREAD2) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26310,8 +28456,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(PyObject *_
* else: self._delegate.core.flag &= ~BAM_FREAD2
*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_8is_read2_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26319,38 +28464,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2814);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2841);
- /* "csamtools.pyx":2815
+ /* "pysam/csamtools.pyx":2842
* def __get__(self): return (self.flag & BAM_FREAD2) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD2 # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FREAD2
* property is_secondary:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 128);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 128);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2816
+ /* "pysam/csamtools.pyx":2843
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FREAD2
* else: self._delegate.core.flag &= ~BAM_FREAD2 # <<<<<<<<<<<<<<
* property is_secondary:
* """true if not primary alignment"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~128));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~128));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_read2.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_read2.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26358,7 +28503,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":2819
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2846
* property is_secondary:
* """true if not primary alignment"""
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0 # <<<<<<<<<<<<<<
@@ -26366,8 +28522,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(PyObject *__pyx_
* if val: self._delegate.core.flag |= BAM_FSECONDARY
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26376,16 +28531,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2819);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2846);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_256); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_256); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26396,7 +28550,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObje
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_secondary.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -26405,7 +28559,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObje
return __pyx_r;
}
-/* "csamtools.pyx":2820
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2847
* """true if not primary alignment"""
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26413,8 +28578,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(PyObje
* else: self._delegate.core.flag &= ~BAM_FSECONDARY
*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_secondary_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26422,38 +28586,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2820);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2847);
- /* "csamtools.pyx":2821
+ /* "pysam/csamtools.pyx":2848
* def __get__(self): return (self.flag & BAM_FSECONDARY) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FSECONDARY # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FSECONDARY
* property is_qcfail:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2848; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 256);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 256);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2822
+ /* "pysam/csamtools.pyx":2849
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FSECONDARY
* else: self._delegate.core.flag &= ~BAM_FSECONDARY # <<<<<<<<<<<<<<
* property is_qcfail:
* """true if QC failure"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~256));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~256));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_secondary.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_secondary.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26461,7 +28625,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *_
return __pyx_r;
}
-/* "csamtools.pyx":2825
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2852
* property is_qcfail:
* """true if QC failure"""
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0 # <<<<<<<<<<<<<<
@@ -26469,8 +28644,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(PyObject *_
* if val: self._delegate.core.flag |= BAM_FQCFAIL
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26479,16 +28653,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2825);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2852);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_512); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_512); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26499,7 +28672,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_qcfail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -26508,7 +28681,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *
return __pyx_r;
}
-/* "csamtools.pyx":2826
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2853
* """true if QC failure"""
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26516,8 +28700,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(PyObject *
* else: self._delegate.core.flag &= ~BAM_FQCFAIL
*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26525,38 +28708,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2826);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2853);
- /* "csamtools.pyx":2827
+ /* "pysam/csamtools.pyx":2854
* def __get__(self): return (self.flag & BAM_FQCFAIL) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FQCFAIL # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FQCFAIL
* property is_duplicate:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 512);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 512);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2828
+ /* "pysam/csamtools.pyx":2855
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FQCFAIL
* else: self._delegate.core.flag &= ~BAM_FQCFAIL # <<<<<<<<<<<<<<
* property is_duplicate:
* """true if optical or PCR duplicate"""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~512));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~512));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_qcfail.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_qcfail.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26564,7 +28747,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":2831
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2858
* property is_duplicate:
* """true if optical or PCR duplicate"""
* def __get__(self): return (self.flag & BAM_FDUP) != 0 # <<<<<<<<<<<<<<
@@ -26572,8 +28766,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(PyObject *__pyx
* if val: self._delegate.core.flag |= BAM_FDUP
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -26582,16 +28775,15 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2831);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2858);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__flag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_1024); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_And(__pyx_t_1, __pyx_int_1024); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -26602,7 +28794,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObje
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_duplicate.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -26611,7 +28803,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObje
return __pyx_r;
}
-/* "csamtools.pyx":2832
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_val));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2859
* """true if optical or PCR duplicate"""
* def __get__(self): return (self.flag & BAM_FDUP) != 0
* def __set__(self,val): # <<<<<<<<<<<<<<
@@ -26619,8 +28822,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(PyObje
* else: self._delegate.core.flag &= ~BAM_FDUP
*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val); /*proto*/
-static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_val) {
+static int __pyx_pf_5pysam_9csamtools_11AlignedRead_12is_duplicate_2__set__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_val) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -26628,38 +28830,38 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 2832);
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 2859);
- /* "csamtools.pyx":2833
+ /* "pysam/csamtools.pyx":2860
* def __get__(self): return (self.flag & BAM_FDUP) != 0
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FDUP # <<<<<<<<<<<<<<
* else: self._delegate.core.flag &= ~BAM_FDUP
* property positions:
*/
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_val); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag | 1024);
- goto __pyx_L5;
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag | 1024);
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":2834
+ /* "pysam/csamtools.pyx":2861
* def __set__(self,val):
* if val: self._delegate.core.flag |= BAM_FDUP
* else: self._delegate.core.flag &= ~BAM_FDUP # <<<<<<<<<<<<<<
* property positions:
* """a list of reference positions that this read aligns to."""
*/
- ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag = (((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate->core.flag & (~1024));
+ __pyx_v_self->_delegate->core.flag = (__pyx_v_self->_delegate->core.flag & (~1024));
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.is_duplicate.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.is_duplicate.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -26667,7 +28869,18 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *_
return __pyx_r;
}
-/* "csamtools.pyx":2837
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2864
* property positions:
* """a list of reference positions that this read aligns to."""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -26675,8 +28888,7 @@ static int __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(PyObject *_
* cdef int op
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_9positions___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
uint32_t __pyx_v_k;
uint32_t __pyx_v_i;
uint32_t __pyx_v_pos;
@@ -26687,69 +28899,73 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
PyObject *__pyx_v_l = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- uint32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ int32_t __pyx_t_4;
uint32_t __pyx_t_5;
- int __pyx_t_6;
+ PyObject *__pyx_t_6 = NULL;
+ uint32_t __pyx_t_7;
+ int __pyx_t_8;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2837);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2864);
- /* "csamtools.pyx":2843
+ /* "pysam/csamtools.pyx":2870
* cdef bam1_t * src
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return []
*
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2844
+ /* "pysam/csamtools.pyx":2871
*
* src = self._delegate
* if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
*
* result = []
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2844; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2846
+ /* "pysam/csamtools.pyx":2873
* if src.core.n_cigar == 0: return []
*
* result = [] # <<<<<<<<<<<<<<
* pos = src.core.pos
* cigar_p = bam1_cigar(src)
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_result = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_result = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2847
+ /* "pysam/csamtools.pyx":2874
*
* result = []
* pos = src.core.pos # <<<<<<<<<<<<<<
* cigar_p = bam1_cigar(src)
*
*/
- __pyx_v_pos = __pyx_v_src->core.pos;
+ __pyx_t_4 = __pyx_v_src->core.pos;
+ __pyx_v_pos = __pyx_t_4;
- /* "csamtools.pyx":2848
+ /* "pysam/csamtools.pyx":2875
* result = []
* pos = src.core.pos
* cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
@@ -26758,17 +28974,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2850
+ /* "pysam/csamtools.pyx":2877
* cigar_p = bam1_cigar(src)
*
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_3 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
+ __pyx_t_5 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
- /* "csamtools.pyx":2851
+ /* "pysam/csamtools.pyx":2878
*
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -26777,65 +28993,62 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "csamtools.pyx":2852
+ /* "pysam/csamtools.pyx":2879
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l:
*/
- __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_l = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2853
+ /* "pysam/csamtools.pyx":2880
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* if op == BAM_CMATCH: # <<<<<<<<<<<<<<
* for i from pos <= i < pos + l:
* result.append( i )
*/
- __pyx_t_1 = (__pyx_v_op == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_op == 0);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2854
+ /* "pysam/csamtools.pyx":2881
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( i )
*
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
- /* "csamtools.pyx":2855
+ /* "pysam/csamtools.pyx":2882
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l:
* result.append( i ) # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyList_Append(__pyx_v_result, __pyx_t_4); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_8 = PyList_Append(__pyx_v_result, __pyx_t_6); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
}
- goto __pyx_L8;
+ goto __pyx_L6;
}
- __pyx_L8:;
+ __pyx_L6:;
- /* "csamtools.pyx":2857
+ /* "pysam/csamtools.pyx":2884
* result.append( i )
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
@@ -26847,26 +29060,26 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
case 2:
case 3:
- /* "csamtools.pyx":2858
+ /* "pysam/csamtools.pyx":2885
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
* pos += l # <<<<<<<<<<<<<<
*
* return result
*/
- __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_2); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_pos = __pyx_t_5;
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_3); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_v_pos = __pyx_t_7;
break;
}
}
- /* "csamtools.pyx":2860
+ /* "pysam/csamtools.pyx":2887
* pos += l
*
* return result # <<<<<<<<<<<<<<
@@ -26881,9 +29094,9 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.AlignedRead.positions.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_6);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.positions.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
@@ -26894,7 +29107,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
return __pyx_r;
}
-/* "csamtools.pyx":2867
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2894
* Unaligned position are marked by None.
* """
* def __get__(self): # <<<<<<<<<<<<<<
@@ -26902,8 +29126,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_9positions___get__(PyObject *
* cdef int op
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_13aligned_pairs___get__(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
uint32_t __pyx_v_k;
uint32_t __pyx_v_i;
uint32_t __pyx_v_pos;
@@ -26915,70 +29138,74 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
PyObject *__pyx_v_l = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- uint32_t __pyx_t_3;
- PyObject *__pyx_t_4 = NULL;
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ int32_t __pyx_t_4;
uint32_t __pyx_t_5;
PyObject *__pyx_t_6 = NULL;
- int __pyx_t_7;
+ uint32_t __pyx_t_7;
+ PyObject *__pyx_t_8 = NULL;
+ int __pyx_t_9;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 2867);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2894);
- /* "csamtools.pyx":2873
+ /* "pysam/csamtools.pyx":2900
* cdef bam1_t * src
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return []
*
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2874
+ /* "pysam/csamtools.pyx":2901
*
* src = self._delegate
* if src.core.n_cigar == 0: return [] # <<<<<<<<<<<<<<
*
* result = []
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_r = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2876
+ /* "pysam/csamtools.pyx":2903
* if src.core.n_cigar == 0: return []
*
* result = [] # <<<<<<<<<<<<<<
* pos = src.core.pos
* qpos = 0
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_v_result = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_result = ((PyObject*)__pyx_t_3);
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2877
+ /* "pysam/csamtools.pyx":2904
*
* result = []
* pos = src.core.pos # <<<<<<<<<<<<<<
* qpos = 0
* cigar_p = bam1_cigar(src)
*/
- __pyx_v_pos = __pyx_v_src->core.pos;
+ __pyx_t_4 = __pyx_v_src->core.pos;
+ __pyx_v_pos = __pyx_t_4;
- /* "csamtools.pyx":2878
+ /* "pysam/csamtools.pyx":2905
* result = []
* pos = src.core.pos
* qpos = 0 # <<<<<<<<<<<<<<
@@ -26987,7 +29214,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
*/
__pyx_v_qpos = 0;
- /* "csamtools.pyx":2879
+ /* "pysam/csamtools.pyx":2906
* pos = src.core.pos
* qpos = 0
* cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
@@ -26996,17 +29223,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2881
+ /* "pysam/csamtools.pyx":2908
* cigar_p = bam1_cigar(src)
*
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_3 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_3; __pyx_v_k++) {
+ __pyx_t_5 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_5; __pyx_v_k++) {
- /* "csamtools.pyx":2882
+ /* "pysam/csamtools.pyx":2909
*
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -27015,20 +29242,20 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "csamtools.pyx":2883
+ /* "pysam/csamtools.pyx":2910
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH:
*/
- __pyx_t_2 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_l = __pyx_t_3;
+ __pyx_t_3 = 0;
- /* "csamtools.pyx":2896
+ /* "pysam/csamtools.pyx":2923
* qpos += 1
*
* elif op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
@@ -27037,7 +29264,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
*/
switch (__pyx_v_op) {
- /* "csamtools.pyx":2885
+ /* "pysam/csamtools.pyx":2912
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
* if op == BAM_CMATCH: # <<<<<<<<<<<<<<
@@ -27046,48 +29273,45 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
*/
case 0:
- /* "csamtools.pyx":2886
+ /* "pysam/csamtools.pyx":2913
*
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( (qpos, i) )
* qpos += 1
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_4); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2913; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
- /* "csamtools.pyx":2887
+ /* "pysam/csamtools.pyx":2914
* if op == BAM_CMATCH:
* for i from pos <= i < pos + l:
* result.append( (qpos, i) ) # <<<<<<<<<<<<<<
* qpos += 1
* pos += l
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_4 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_4 = 0;
- __pyx_t_2 = 0;
- __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_6)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2914; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2914; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2914; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __pyx_t_6 = 0;
+ __pyx_t_3 = 0;
+ __pyx_t_9 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_8)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2914; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- /* "csamtools.pyx":2888
+ /* "pysam/csamtools.pyx":2915
* for i from pos <= i < pos + l:
* result.append( (qpos, i) )
* qpos += 1 # <<<<<<<<<<<<<<
@@ -27097,24 +29321,24 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
__pyx_v_qpos = (__pyx_v_qpos + 1);
}
- /* "csamtools.pyx":2889
+ /* "pysam/csamtools.pyx":2916
* result.append( (qpos, i) )
* qpos += 1
* pos += l # <<<<<<<<<<<<<<
*
* elif op == BAM_CINS:
*/
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_t_6, __pyx_v_l); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_2); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_pos = __pyx_t_5;
+ __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_t_8, __pyx_v_l); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_3); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2916; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_v_pos = __pyx_t_7;
break;
- /* "csamtools.pyx":2891
+ /* "pysam/csamtools.pyx":2918
* pos += l
*
* elif op == BAM_CINS: # <<<<<<<<<<<<<<
@@ -27123,46 +29347,43 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
*/
case 1:
- /* "csamtools.pyx":2892
+ /* "pysam/csamtools.pyx":2919
*
* elif op == BAM_CINS:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( (qpos, None) )
* qpos += 1
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_8 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
- /* "csamtools.pyx":2893
+ /* "pysam/csamtools.pyx":2920
* elif op == BAM_CINS:
* for i from pos <= i < pos + l:
* result.append( (qpos, None) ) # <<<<<<<<<<<<<<
* qpos += 1
*
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
+ __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_qpos); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
__Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_t_2, 1, Py_None);
+ PyTuple_SET_ITEM(__pyx_t_3, 1, Py_None);
__Pyx_GIVEREF(Py_None);
- __pyx_t_6 = 0;
- __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_9 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_3)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "csamtools.pyx":2894
+ /* "pysam/csamtools.pyx":2921
* for i from pos <= i < pos + l:
* result.append( (qpos, None) )
* qpos += 1 # <<<<<<<<<<<<<<
@@ -27173,7 +29394,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
}
break;
- /* "csamtools.pyx":2896
+ /* "pysam/csamtools.pyx":2923
* qpos += 1
*
* elif op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
@@ -27183,66 +29404,63 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
case 2:
case 3:
- /* "csamtools.pyx":2897
+ /* "pysam/csamtools.pyx":2924
*
* elif op == BAM_CDEL or op == BAM_CREF_SKIP:
* for i from pos <= i < pos + l: # <<<<<<<<<<<<<<
* result.append( (None, i) )
* pos += l
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyNumber_Add(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_5; __pyx_v_i++) {
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_8 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ for (__pyx_v_i = __pyx_v_pos; __pyx_v_i < __pyx_t_7; __pyx_v_i++) {
- /* "csamtools.pyx":2898
+ /* "pysam/csamtools.pyx":2925
* elif op == BAM_CDEL or op == BAM_CREF_SKIP:
* for i from pos <= i < pos + l:
* result.append( (None, i) ) # <<<<<<<<<<<<<<
* pos += l
*
*/
- if (unlikely(((PyObject *)__pyx_v_result) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_i); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_t_2, 0, Py_None);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, Py_None);
__Pyx_GIVEREF(Py_None);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_6 = 0;
- __pyx_t_7 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2898; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_9 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_3)); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
}
- /* "csamtools.pyx":2899
+ /* "pysam/csamtools.pyx":2926
* for i from pos <= i < pos + l:
* result.append( (None, i) )
* pos += l # <<<<<<<<<<<<<<
*
* return result
*/
- __pyx_t_2 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyNumber_InPlaceAdd(__pyx_t_2, __pyx_v_l); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_6); if (unlikely((__pyx_t_5 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_v_pos = __pyx_t_5;
+ __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_8 = PyNumber_InPlaceAdd(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_7 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_8); if (unlikely((__pyx_t_7 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_pos = __pyx_t_7;
break;
}
}
- /* "csamtools.pyx":2901
+ /* "pysam/csamtools.pyx":2928
* pos += l
*
* return result # <<<<<<<<<<<<<<
@@ -27257,10 +29475,10 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_6);
- __Pyx_AddTraceback("csamtools.AlignedRead.aligned_pairs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.aligned_pairs.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_result);
@@ -27271,71 +29489,40 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(PyObj
return __pyx_r;
}
-/* "csamtools.pyx":2904
- *
- *
- * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
- * """return number of aligned bases of read overlapping the interval *start* and *end*
- * on the reference sequence.
- */
-
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_5overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11AlignedRead_10overlap[] = "AlignedRead.overlap(self, uint32_t start, uint32_t end)\nreturn number of aligned bases of read overlapping the interval *start* and *end*\n on the reference sequence.\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
uint32_t __pyx_v_start;
uint32_t __pyx_v_end;
- uint32_t __pyx_v_k;
- uint32_t __pyx_v_pos;
- uint32_t __pyx_v_overlap;
- int __pyx_v_op;
- int __pyx_v_o;
- uint32_t *__pyx_v_cigar_p;
- bam1_t *__pyx_v_src;
- PyObject *__pyx_v_l = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- uint32_t __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
- uint32_t __pyx_t_4;
- PyObject *__pyx_t_5 = NULL;
- PyObject *__pyx_t_6 = NULL;
- PyObject *__pyx_t_7 = NULL;
- uint32_t __pyx_t_8;
- uint32_t __pyx_t_9;
- int __pyx_t_10;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("overlap");
- __Pyx_TraceCall("overlap", __pyx_f[0], 2904);
+ __Pyx_RefNannySetupContext("overlap (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__start,&__pyx_n_s__end,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "overlap") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -27343,19 +29530,61 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
}
- __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(values[0]); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(values[1]); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_start = __Pyx_PyInt_from_py_uint32_t(values[0]); if (unlikely((__pyx_v_start == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_end = __Pyx_PyInt_from_py_uint32_t(values[1]); if (unlikely((__pyx_v_end == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2904; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2931; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), __pyx_v_start, __pyx_v_end);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2931
+ *
+ *
+ * def overlap( self, uint32_t start, uint32_t end ): # <<<<<<<<<<<<<<
+ * """return number of aligned bases of read overlapping the interval *start* and *end*
+ * on the reference sequence.
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_10overlap(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, uint32_t __pyx_v_start, uint32_t __pyx_v_end) {
+ uint32_t __pyx_v_k;
+ uint32_t __pyx_v_pos;
+ uint32_t __pyx_v_overlap;
+ int __pyx_v_op;
+ int __pyx_v_o;
+ uint32_t *__pyx_v_cigar_p;
+ bam1_t *__pyx_v_src;
+ PyObject *__pyx_v_l = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ bam1_t *__pyx_t_1;
+ int __pyx_t_2;
+ int32_t __pyx_t_3;
+ uint32_t __pyx_t_4;
+ PyObject *__pyx_t_5 = NULL;
+ uint32_t __pyx_t_6;
+ PyObject *__pyx_t_7 = NULL;
+ PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
+ uint32_t __pyx_t_10;
+ uint32_t __pyx_t_11;
+ int __pyx_t_12;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("overlap", 0);
+ __Pyx_TraceCall("overlap", __pyx_f[0], 2931);
- /* "csamtools.pyx":2913
+ /* "pysam/csamtools.pyx":2940
* cdef bam1_t * src
*
* overlap = 0 # <<<<<<<<<<<<<<
@@ -27364,42 +29593,44 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
*/
__pyx_v_overlap = 0;
- /* "csamtools.pyx":2915
+ /* "pysam/csamtools.pyx":2942
* overlap = 0
*
* src = self._delegate # <<<<<<<<<<<<<<
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos
*/
- __pyx_v_src = ((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate;
+ __pyx_t_1 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_1;
- /* "csamtools.pyx":2916
+ /* "pysam/csamtools.pyx":2943
*
* src = self._delegate
* if src.core.n_cigar == 0: return 0 # <<<<<<<<<<<<<<
* pos = src.core.pos
* o = 0
*/
- __pyx_t_1 = (__pyx_v_src->core.n_cigar == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_src->core.n_cigar == 0);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(__pyx_int_0);
__pyx_r = __pyx_int_0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":2917
+ /* "pysam/csamtools.pyx":2944
* src = self._delegate
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos # <<<<<<<<<<<<<<
* o = 0
*
*/
- __pyx_v_pos = __pyx_v_src->core.pos;
+ __pyx_t_3 = __pyx_v_src->core.pos;
+ __pyx_v_pos = __pyx_t_3;
- /* "csamtools.pyx":2918
+ /* "pysam/csamtools.pyx":2945
* if src.core.n_cigar == 0: return 0
* pos = src.core.pos
* o = 0 # <<<<<<<<<<<<<<
@@ -27408,7 +29639,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
*/
__pyx_v_o = 0;
- /* "csamtools.pyx":2920
+ /* "pysam/csamtools.pyx":2947
* o = 0
*
* cigar_p = bam1_cigar(src) # <<<<<<<<<<<<<<
@@ -27417,17 +29648,17 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "csamtools.pyx":2921
+ /* "pysam/csamtools.pyx":2948
*
* cigar_p = bam1_cigar(src)
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*/
- __pyx_t_2 = __pyx_v_src->core.n_cigar;
- for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_2; __pyx_v_k++) {
+ __pyx_t_4 = __pyx_v_src->core.n_cigar;
+ for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "csamtools.pyx":2922
+ /* "pysam/csamtools.pyx":2949
* cigar_p = bam1_cigar(src)
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -27436,94 +29667,93 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "csamtools.pyx":2923
+ /* "pysam/csamtools.pyx":2950
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK
* l = cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH:
*/
- __pyx_t_3 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_5 = PyInt_FromLong(((__pyx_v_cigar_p[__pyx_v_k]) >> 4)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_l = __pyx_t_5;
+ __pyx_t_5 = 0;
- /* "csamtools.pyx":2925
+ /* "pysam/csamtools.pyx":2952
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
*
* if op == BAM_CMATCH: # <<<<<<<<<<<<<<
* o = min( pos + l, end) - max( pos, start )
* if o > 0: overlap += o
*/
- __pyx_t_1 = (__pyx_v_op == 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_op == 0);
+ if (__pyx_t_2) {
- /* "csamtools.pyx":2926
+ /* "pysam/csamtools.pyx":2953
*
* if op == BAM_CMATCH:
* o = min( pos + l, end) - max( pos, start ) # <<<<<<<<<<<<<<
* if o > 0: overlap += o
*
*/
- __pyx_t_4 = __pyx_v_end;
- __pyx_t_3 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __pyx_v_end;
+ __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_6 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_LT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_5, __pyx_v_l); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (__pyx_t_1) {
- __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_3 = __pyx_t_7;
- __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
+ __pyx_t_8 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_t_7, Py_LT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ if (__pyx_t_2) {
+ __pyx_t_9 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_6); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_5 = __pyx_t_9;
+ __pyx_t_9 = 0;
} else {
- __Pyx_INCREF(__pyx_t_5);
- __pyx_t_3 = __pyx_t_5;
+ __Pyx_INCREF(__pyx_t_7);
+ __pyx_t_5 = __pyx_t_7;
}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __pyx_v_start;
- __pyx_t_8 = __pyx_v_pos;
- if ((__pyx_t_4 > __pyx_t_8)) {
- __pyx_t_9 = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_6 = __pyx_v_start;
+ __pyx_t_10 = __pyx_v_pos;
+ if ((__pyx_t_6 > __pyx_t_10)) {
+ __pyx_t_11 = __pyx_t_6;
} else {
- __pyx_t_9 = __pyx_t_8;
+ __pyx_t_11 = __pyx_t_10;
}
- __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_9); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyNumber_Subtract(__pyx_t_3, __pyx_t_5); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_t_11); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_9 = PyNumber_Subtract(__pyx_t_5, __pyx_t_7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_10 = __Pyx_PyInt_AsInt(__pyx_t_7); if (unlikely((__pyx_t_10 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_v_o = __pyx_t_10;
+ __pyx_t_12 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_12 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_v_o = __pyx_t_12;
- /* "csamtools.pyx":2927
+ /* "pysam/csamtools.pyx":2954
* if op == BAM_CMATCH:
* o = min( pos + l, end) - max( pos, start )
* if o > 0: overlap += o # <<<<<<<<<<<<<<
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
*/
- __pyx_t_1 = (__pyx_v_o > 0);
- if (__pyx_t_1) {
+ __pyx_t_2 = (__pyx_v_o > 0);
+ if (__pyx_t_2) {
__pyx_v_overlap = (__pyx_v_overlap + __pyx_v_o);
- goto __pyx_L10;
+ goto __pyx_L7;
}
- __pyx_L10:;
- goto __pyx_L9;
+ __pyx_L7:;
+ goto __pyx_L6;
}
- __pyx_L9:;
+ __pyx_L6:;
- /* "csamtools.pyx":2929
+ /* "pysam/csamtools.pyx":2956
* if o > 0: overlap += o
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP: # <<<<<<<<<<<<<<
@@ -27535,26 +29765,26 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
case 2:
case 3:
- /* "csamtools.pyx":2930
+ /* "pysam/csamtools.pyx":2957
*
* if op == BAM_CMATCH or op == BAM_CDEL or op == BAM_CREF_SKIP:
* pos += l # <<<<<<<<<<<<<<
*
* return overlap
*/
- __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_pos); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_t_9, __pyx_v_l); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_7, __pyx_v_l); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_11 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_7); if (unlikely((__pyx_t_11 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_9 = __Pyx_PyInt_from_py_uint32_t(__pyx_t_5); if (unlikely((__pyx_t_9 == (uint32_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_v_pos = __pyx_t_9;
+ __pyx_v_pos = __pyx_t_11;
break;
}
}
- /* "csamtools.pyx":2932
+ /* "pysam/csamtools.pyx":2959
* pos += l
*
* return overlap # <<<<<<<<<<<<<<
@@ -27562,20 +29792,20 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
* def opt(self, tag):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_overlap); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_r = __pyx_t_5;
- __pyx_t_5 = 0;
+ __pyx_t_7 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_overlap); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_r = __pyx_t_7;
+ __pyx_t_7 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_AddTraceback("csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.overlap", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_l);
@@ -27585,7 +29815,19 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":2934
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11AlignedRead_12opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("opt (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self), ((PyObject *)__pyx_v_tag));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2961
* return overlap
*
* def opt(self, tag): # <<<<<<<<<<<<<<
@@ -27593,14 +29835,12 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_5overlap(PyObject *__pyx_v_se
* #see bam_aux.c: bam_aux_get() and bam_aux2i() etc
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_6opt[] = "AlignedRead.opt(self, tag)\nretrieves optional data given a two-letter *tag*";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self, PyObject *__pyx_v_tag) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_12opt(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self, PyObject *__pyx_v_tag) {
uint8_t *__pyx_v_v;
- int __pyx_v_nvalues;
+ CYTHON_UNUSED int __pyx_v_nvalues;
PyObject *__pyx_v_btag = NULL;
PyObject *__pyx_v_auxtype = NULL;
- PyObject *__pyx_v_bytesize = NULL;
+ CYTHON_UNUSED PyObject *__pyx_v_bytesize = NULL;
PyObject *__pyx_v_values = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
@@ -27621,32 +29861,32 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("opt");
- __Pyx_TraceCall("opt", __pyx_f[0], 2934);
+ __Pyx_RefNannySetupContext("opt", 0);
+ __Pyx_TraceCall("opt", __pyx_f[0], 2961);
- /* "csamtools.pyx":2939
+ /* "pysam/csamtools.pyx":2966
* cdef uint8_t * v
* cdef int nvalues
* btag = _force_bytes(tag) # <<<<<<<<<<<<<<
* v = bam_aux_get(self._delegate, btag)
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
*/
- __pyx_t_1 = ((PyObject *)__pyx_f_9csamtools__force_bytes(__pyx_v_tag)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_bytes(__pyx_v_tag)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_btag = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":2940
+ /* "pysam/csamtools.pyx":2967
* cdef int nvalues
* btag = _force_bytes(tag)
* v = bam_aux_get(self._delegate, btag) # <<<<<<<<<<<<<<
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
* auxtype = chr(v[0])
*/
- __pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_btag)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_v = bam_aux_get(((struct __pyx_obj_9csamtools_AlignedRead *)__pyx_v_self)->_delegate, __pyx_t_2);
+ __pyx_t_2 = PyBytes_AsString(((PyObject *)__pyx_v_btag)); if (unlikely((!__pyx_t_2) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_v = bam_aux_get(__pyx_v_self->_delegate, __pyx_t_2);
- /* "csamtools.pyx":2941
+ /* "pysam/csamtools.pyx":2968
* btag = _force_bytes(tag)
* v = bam_aux_get(self._delegate, btag)
* if v == NULL: raise KeyError( "tag '%s' not present" % tag ) # <<<<<<<<<<<<<<
@@ -27655,57 +29895,65 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
*/
__pyx_t_3 = (__pyx_v_v == NULL);
if (__pyx_t_3) {
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_148), __pyx_v_tag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_152), __pyx_v_tag); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":2942
+ /* "pysam/csamtools.pyx":2969
* v = bam_aux_get(self._delegate, btag)
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
* auxtype = chr(v[0]) # <<<<<<<<<<<<<<
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
* return <int>bam_aux2i(v)
*/
- __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint8_t((__pyx_v_v[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_chr, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_chr, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_v_auxtype = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":2943
+ /* "pysam/csamtools.pyx":2970
* if v == NULL: raise KeyError( "tag '%s' not present" % tag )
* auxtype = chr(v[0])
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S': # <<<<<<<<<<<<<<
* return <int>bam_aux2i(v)
* elif auxtype == 'i' or auxtype == 'I':
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__c), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__c), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_3) {
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__C), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__C), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_5) {
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__s), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__s), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_6) {
- __pyx_t_7 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__S), Py_EQ); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__S), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_8 = __pyx_t_7;
} else {
__pyx_t_8 = __pyx_t_6;
@@ -27720,7 +29968,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
}
if (__pyx_t_5) {
- /* "csamtools.pyx":2944
+ /* "pysam/csamtools.pyx":2971
* auxtype = chr(v[0])
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
* return <int>bam_aux2i(v) # <<<<<<<<<<<<<<
@@ -27728,31 +29976,35 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* return <int32_t>bam_aux2i(v)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- /* "csamtools.pyx":2945
+ /* "pysam/csamtools.pyx":2972
* if auxtype == 'c' or auxtype == 'C' or auxtype == 's' or auxtype == 'S':
* return <int>bam_aux2i(v)
* elif auxtype == 'i' or auxtype == 'I': # <<<<<<<<<<<<<<
* return <int32_t>bam_aux2i(v)
* elif auxtype == 'f' or auxtype == 'F':
*/
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__i), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__i), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_5) {
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__I), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__I), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_6 = __pyx_t_3;
} else {
__pyx_t_6 = __pyx_t_5;
}
if (__pyx_t_6) {
- /* "csamtools.pyx":2946
+ /* "pysam/csamtools.pyx":2973
* return <int>bam_aux2i(v)
* elif auxtype == 'i' or auxtype == 'I':
* return <int32_t>bam_aux2i(v) # <<<<<<<<<<<<<<
@@ -27760,31 +30012,35 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* return <float>bam_aux2f(v)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((int32_t)bam_aux2i(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- /* "csamtools.pyx":2947
+ /* "pysam/csamtools.pyx":2974
* elif auxtype == 'i' or auxtype == 'I':
* return <int32_t>bam_aux2i(v)
* elif auxtype == 'f' or auxtype == 'F': # <<<<<<<<<<<<<<
* return <float>bam_aux2f(v)
* elif auxtype == 'd' or auxtype == 'D':
*/
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__f), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__f), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2974; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2974; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_6) {
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__F), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__F), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2974; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2974; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __pyx_t_5;
} else {
__pyx_t_3 = __pyx_t_6;
}
if (__pyx_t_3) {
- /* "csamtools.pyx":2948
+ /* "pysam/csamtools.pyx":2975
* return <int32_t>bam_aux2i(v)
* elif auxtype == 'f' or auxtype == 'F':
* return <float>bam_aux2f(v) # <<<<<<<<<<<<<<
@@ -27792,31 +30048,35 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* return <double>bam_aux2d(v)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(((float)bam_aux2f(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- /* "csamtools.pyx":2949
+ /* "pysam/csamtools.pyx":2976
* elif auxtype == 'f' or auxtype == 'F':
* return <float>bam_aux2f(v)
* elif auxtype == 'd' or auxtype == 'D': # <<<<<<<<<<<<<<
* return <double>bam_aux2d(v)
* elif auxtype == 'A':
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__d), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__d), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_3) {
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__D), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__D), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_5 = __pyx_t_6;
} else {
__pyx_t_5 = __pyx_t_3;
}
if (__pyx_t_5) {
- /* "csamtools.pyx":2950
+ /* "pysam/csamtools.pyx":2977
* return <float>bam_aux2f(v)
* elif auxtype == 'd' or auxtype == 'D':
* return <double>bam_aux2d(v) # <<<<<<<<<<<<<<
@@ -27824,25 +30084,27 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* # there might a more efficient way
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyFloat_FromDouble(((double)bam_aux2d(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2977; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- /* "csamtools.pyx":2951
+ /* "pysam/csamtools.pyx":2978
* elif auxtype == 'd' or auxtype == 'D':
* return <double>bam_aux2d(v)
* elif auxtype == 'A': # <<<<<<<<<<<<<<
* # there might a more efficient way
* # to convert a char into a string
*/
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__A), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
- /* "csamtools.pyx":2954
+ /* "pysam/csamtools.pyx":2981
* # there might a more efficient way
* # to convert a char into a string
* return '%c' % <char>bam_aux2A(v) # <<<<<<<<<<<<<<
@@ -27850,28 +30112,30 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* return _charptr_to_str(<char*>bam_aux2Z(v))
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(((char)bam_aux2A(__pyx_v_v))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_137), __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_141), __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = ((PyObject *)__pyx_t_4);
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- /* "csamtools.pyx":2955
+ /* "pysam/csamtools.pyx":2982
* # to convert a char into a string
* return '%c' % <char>bam_aux2A(v)
* elif auxtype == 'Z': # <<<<<<<<<<<<<<
* return _charptr_to_str(<char*>bam_aux2Z(v))
* elif auxtype == 'B':
*/
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__Z), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__Z), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2982; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_5) {
- /* "csamtools.pyx":2956
+ /* "pysam/csamtools.pyx":2983
* return '%c' % <char>bam_aux2A(v)
* elif auxtype == 'Z':
* return _charptr_to_str(<char*>bam_aux2Z(v)) # <<<<<<<<<<<<<<
@@ -27879,50 +30143,53 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __pyx_f_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_v))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_5pysam_9csamtools__charptr_to_str(((char *)bam_aux2Z(__pyx_v_v))); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
- /* "csamtools.pyx":2957
+ /* "pysam/csamtools.pyx":2984
* elif auxtype == 'Z':
* return _charptr_to_str(<char*>bam_aux2Z(v))
* elif auxtype == 'B': # <<<<<<<<<<<<<<
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
* return values
*/
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__B), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_auxtype, ((PyObject *)__pyx_n_s__B), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_5) {
- /* "csamtools.pyx":2958
+ /* "pysam/csamtools.pyx":2985
* return _charptr_to_str(<char*>bam_aux2Z(v))
* elif auxtype == 'B':
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 ) # <<<<<<<<<<<<<<
* return values
* else:
*/
- __pyx_t_4 = __pyx_f_9csamtools_convertBinaryTagToList((__pyx_v_v + 1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __pyx_f_5pysam_9csamtools_convertBinaryTagToList((__pyx_v_v + 1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 3)) {
+ if (size > 3) __Pyx_RaiseTooManyValuesError(3);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 3)) {
- if (PyTuple_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 2);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 3)) {
- if (PyList_GET_SIZE(sequence) > 3) __Pyx_RaiseTooManyValuesError(3);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_9 = PyList_GET_ITEM(sequence, 1);
__pyx_t_10 = PyList_GET_ITEM(sequence, 2);
@@ -27930,30 +30197,40 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_9);
__Pyx_INCREF(__pyx_t_10);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_9 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_11 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_11)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L7_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L7_unpacking_failed;
+ index = 1; __pyx_t_9 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_9)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_9);
- index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L7_unpacking_failed;
+ index = 2; __pyx_t_10 = __pyx_t_12(__pyx_t_11); if (unlikely(!__pyx_t_10)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_11), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L8_unpacking_done;
- __pyx_L7_unpacking_failed:;
+ goto __pyx_L6_unpacking_done;
+ __pyx_L5_unpacking_failed:;
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L8_unpacking_done:;
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L6_unpacking_done:;
}
- __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyInt_AsInt(__pyx_t_9); if (unlikely((__pyx_t_13 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_bytesize = __pyx_t_1;
__pyx_t_1 = 0;
@@ -27961,7 +30238,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
__pyx_v_values = __pyx_t_10;
__pyx_t_10 = 0;
- /* "csamtools.pyx":2959
+ /* "pysam/csamtools.pyx":2986
* elif auxtype == 'B':
* bytesize, nvalues, values = convertBinaryTagToList( v + 1 )
* return values # <<<<<<<<<<<<<<
@@ -27972,32 +30249,32 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
__Pyx_INCREF(__pyx_v_values);
__pyx_r = __pyx_v_values;
goto __pyx_L0;
- goto __pyx_L6;
+ goto __pyx_L4;
}
/*else*/ {
- /* "csamtools.pyx":2961
+ /* "pysam/csamtools.pyx":2988
* return values
* else:
* raise ValueError("unknown auxilliary type '%s'" % auxtype) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_149), __pyx_v_auxtype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_153), __pyx_v_auxtype); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L6:;
+ __pyx_L4:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -28007,7 +30284,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_t_11);
- __Pyx_AddTraceback("csamtools.AlignedRead.opt", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.opt", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_btag);
@@ -28020,7 +30297,19 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "csamtools.pyx":2964
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_11AlignedRead_14fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
+static PyObject *__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("fancy_str (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":2991
*
*
* def fancy_str (self): # <<<<<<<<<<<<<<
@@ -28028,9 +30317,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_6opt(PyObject *__pyx_v_self,
* """
*/
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_11AlignedRead_7fancy_str[] = "AlignedRead.fancy_str(self)\nreturns list of fieldnames/values in pretty format for debugging\n ";
-static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_14fancy_str(struct __pyx_obj_5pysam_9csamtools_AlignedRead *__pyx_v_self) {
PyObject *__pyx_v_ret_string = NULL;
PyObject *__pyx_v_field_names = NULL;
PyObject *__pyx_v_fields_names_in_order = NULL;
@@ -28052,60 +30339,60 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("fancy_str");
- __Pyx_TraceCall("fancy_str", __pyx_f[0], 2964);
+ __Pyx_RefNannySetupContext("fancy_str", 0);
+ __Pyx_TraceCall("fancy_str", __pyx_f[0], 2991);
- /* "csamtools.pyx":2967
+ /* "pysam/csamtools.pyx":2994
* """returns list of fieldnames/values in pretty format for debugging
* """
* ret_string = [] # <<<<<<<<<<<<<<
* field_names = {
* "tid": "Contig index",
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_ret_string = __pyx_t_1;
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_ret_string = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":2968
+ /* "pysam/csamtools.pyx":2995
* """
* ret_string = []
* field_names = { # <<<<<<<<<<<<<<
* "tid": "Contig index",
* "pos": "Mapped position on contig",
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__tid), ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mtid), ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mpos), ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__isize), ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__flag), ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__n_cigar), ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__cigar), ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bin), ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qname), ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qname), ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qseq), ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qseq), ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bqual), ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_aux), ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__m_data), ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__data_len), ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_field_names = __pyx_t_1;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__tid), ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mtid), ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__mpos), ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__isize), ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__flag), ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__n_cigar), ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__cigar), ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bin), ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qname), ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qname), ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_qseq), ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__qseq), ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__bqual), ((PyObject *)__pyx_kp_s_168)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__l_aux), ((PyObject *)__pyx_kp_s_169)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__m_data), ((PyObject *)__pyx_kp_s_170)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__data_len), ((PyObject *)__pyx_kp_s_171)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_field_names = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":2988
+ /* "pysam/csamtools.pyx":3015
* "data_len": "Current data length",
* }
* fields_names_in_order = ["tid", "pos", "mtid", "mpos", "isize", "flag", # <<<<<<<<<<<<<<
* "n_cigar", "cigar", "qual", "bin", "l_qname", "qname",
* "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
*/
- __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyList_New(18); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3015; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__tid));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__tid));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__tid));
@@ -28160,83 +30447,81 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
__Pyx_INCREF(((PyObject *)__pyx_n_s__data_len));
PyList_SET_ITEM(__pyx_t_1, 17, ((PyObject *)__pyx_n_s__data_len));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__data_len));
- __pyx_v_fields_names_in_order = __pyx_t_1;
+ __pyx_v_fields_names_in_order = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":2992
+ /* "pysam/csamtools.pyx":3019
* "l_qseq", "qseq", "bqual", "l_aux", "m_data", "data_len"]
*
* for f in fields_names_in_order: # <<<<<<<<<<<<<<
* if not f in self.__dict__:
* continue
*/
- if (unlikely(((PyObject *)__pyx_v_fields_names_in_order) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = ((PyObject *)__pyx_v_fields_names_in_order); __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
for (;;) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_3 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_3); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_3 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
__Pyx_XDECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":2993
+ /* "pysam/csamtools.pyx":3020
*
* for f in fields_names_in_order:
* if not f in self.__dict__: # <<<<<<<<<<<<<<
* continue
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = ((PySequence_Contains(__pyx_t_3, __pyx_v_f))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2993; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_3, Py_EQ)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_5 = (!__pyx_t_4);
if (__pyx_t_5) {
- /* "csamtools.pyx":2994
+ /* "pysam/csamtools.pyx":3021
* for f in fields_names_in_order:
* if not f in self.__dict__:
* continue # <<<<<<<<<<<<<<
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*
*/
- goto __pyx_L5_continue;
- goto __pyx_L7;
+ goto __pyx_L3_continue;
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
- /* "csamtools.pyx":2995
+ /* "pysam/csamtools.pyx":3022
* if not f in self.__dict__:
* continue
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f))) # <<<<<<<<<<<<<<
*
* for f in self.__dict__:
*/
- if (unlikely(((PyObject *)__pyx_v_ret_string) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_field_names), __pyx_v_f); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_field_names), __pyx_v_f); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_kp_s_169), __pyx_v_f); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_kp_s_173), __pyx_v_f); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyNumber_Add(__pyx_t_6, ((PyObject *)__pyx_kp_s_170)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_6, ((PyObject *)__pyx_kp_s_174)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_9 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
@@ -28246,46 +30531,54 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
__pyx_t_3 = 0;
__pyx_t_7 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_168), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_172), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_9)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_L5_continue:;
+ __pyx_L3_continue:;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":2997
+ /* "pysam/csamtools.pyx":3024
* ret_string.append("%-30s %-10s= %s" % (field_names[f], "(" + f + ")", self.__getattribute__(f)))
*
* for f in self.__dict__: # <<<<<<<<<<<<<<
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_9 = __pyx_t_1; __Pyx_INCREF(__pyx_t_9); __pyx_t_2 = 0;
__pyx_t_11 = NULL;
} else {
- __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_11 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
for (;;) {
- if (PyList_CheckExact(__pyx_t_9)) {
+ if (!__pyx_t_11 && PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
- } else if (PyTuple_CheckExact(__pyx_t_9)) {
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_2); __Pyx_INCREF(__pyx_t_1); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_1 = __pyx_t_11(__pyx_t_9);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -28295,43 +30588,37 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":2998
+ /* "pysam/csamtools.pyx":3025
*
* for f in self.__dict__:
* if not f in field_names: # <<<<<<<<<<<<<<
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
* return ret_string
*/
- if (unlikely(((PyObject *)__pyx_v_field_names) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_5 = ((PyDict_Contains(((PyObject *)__pyx_v_field_names), __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2998; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_PyDict_Contains(__pyx_v_f, ((PyObject *)__pyx_v_field_names), Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (!__pyx_t_5);
if (__pyx_t_4) {
- /* "csamtools.pyx":2999
+ /* "pysam/csamtools.pyx":3026
* for f in self.__dict__:
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f))) # <<<<<<<<<<<<<<
* return ret_string
*
*/
- if (unlikely(((PyObject *)__pyx_v_ret_string) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s____getattribute__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3026; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3026; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3026; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3026; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
@@ -28341,18 +30628,18 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_168), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_172), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3026; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyList_Append(__pyx_v_ret_string, ((PyObject *)__pyx_t_7)); if (unlikely(__pyx_t_10 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3026; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- goto __pyx_L10;
+ goto __pyx_L8;
}
- __pyx_L10:;
+ __pyx_L8:;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "csamtools.pyx":3000
+ /* "pysam/csamtools.pyx":3027
* if not f in field_names:
* ret_string.append("%-30s %-10s= %s" % (f, "", self.__getattribute__(f)))
* return ret_string # <<<<<<<<<<<<<<
@@ -28373,7 +30660,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("csamtools.AlignedRead.fancy_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.AlignedRead.fancy_str", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_ret_string);
@@ -28386,7 +30673,21 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":3019
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3046
* will change.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
@@ -28394,8 +30695,7 @@ static PyObject *__pyx_pf_9csamtools_11AlignedRead_7fancy_str(PyObject *__pyx_v_
*
*/
-static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pf_5pysam_9csamtools_11PileupProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28403,30 +30703,27 @@ static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, Py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 3019);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3046);
- /* "csamtools.pyx":3020
+ /* "pysam/csamtools.pyx":3047
* '''
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
*
* def __str__(self):
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_TypeError, ((PyObject *)__pyx_k_tuple_172), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_TypeError, ((PyObject *)__pyx_k_tuple_176), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -28434,7 +30731,18 @@ static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":3022
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3049
* raise TypeError("This class cannot be instantiated from Python")
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -28442,8 +30750,7 @@ static int __pyx_pf_9csamtools_11PileupProxy___init__(PyObject *__pyx_v_self, Py
* "\n" +\
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28455,10 +30762,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_se
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 3022);
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 3049);
- /* "csamtools.pyx":3023
+ /* "pysam/csamtools.pyx":3050
*
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
@@ -28467,31 +30774,31 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_se
*/
__Pyx_XDECREF(__pyx_r);
- /* "csamtools.pyx":3024
+ /* "pysam/csamtools.pyx":3051
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" +\ # <<<<<<<<<<<<<<
* "\n".join( map(str, self.pileups) )
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":3023
+ /* "pysam/csamtools.pyx":3050
*
* def __str__(self):
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\ # <<<<<<<<<<<<<<
* "\n" +\
* "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__n); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_3);
@@ -28501,62 +30808,62 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_se
__pyx_t_2 = 0;
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3023; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3050; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "csamtools.pyx":3025
+ /* "pysam/csamtools.pyx":3052
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" +\
* "\n".join( map(str, self.pileups) ) # <<<<<<<<<<<<<<
*
* property tid:
*/
- __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_6), __pyx_n_s__join); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pileups); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3025; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3052; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_Add(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(__pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
@@ -28572,7 +30879,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_se
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.PileupProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -28581,7 +30888,18 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "csamtools.pyx":3029
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3056
* property tid:
* '''the chromosome ID as is defined in the header'''
* def __get__(self): return self.tid # <<<<<<<<<<<<<<
@@ -28589,8 +30907,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1__str__(PyObject *__pyx_v_se
* property n:
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3tid___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28598,10 +30915,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3029);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3056);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3056; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -28611,7 +30928,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -28620,7 +30937,18 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":3033
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3060
* property n:
* '''number of reads mapping to this column.'''
* def __get__(self): return self.n_pu # <<<<<<<<<<<<<<
@@ -28628,8 +30956,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3tid___get__(PyObject *__pyx_
*
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_1n___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28637,10 +30964,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3033);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3060);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->n_pu); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3060; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -28650,7 +30977,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.n.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.n.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -28659,7 +30986,18 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_
return __pyx_r;
}
-/* "csamtools.pyx":3034
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__set__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self), ((PyObject *)__pyx_v_n));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3061
* '''number of reads mapping to this column.'''
* def __get__(self): return self.n_pu
* def __set__(self, n): self.n_pu = n # <<<<<<<<<<<<<<
@@ -28667,8 +31005,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_1n___get__(PyObject *__pyx_v_
* property pos:
*/
-static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n); /*proto*/
-static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self, PyObject *__pyx_v_n) {
+static int __pyx_pf_5pysam_9csamtools_11PileupProxy_1n_2__set__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self, PyObject *__pyx_v_n) {
int __pyx_r;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -28676,15 +31013,15 @@ static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self,
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__set__");
- __Pyx_TraceCall("__set__", __pyx_f[0], 3034);
- __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_n); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu = __pyx_t_1;
+ __Pyx_RefNannySetupContext("__set__", 0);
+ __Pyx_TraceCall("__set__", __pyx_f[0], 3061);
+ __pyx_t_1 = __Pyx_PyInt_AsInt(__pyx_v_n); if (unlikely((__pyx_t_1 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3061; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->n_pu = __pyx_t_1;
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_AddTraceback("csamtools.PileupProxy.n.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.n.__set__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -28692,7 +31029,18 @@ static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "csamtools.pyx":3037
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3064
*
* property pos:
* def __get__(self): return self.pos # <<<<<<<<<<<<<<
@@ -28700,8 +31048,7 @@ static int __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(PyObject *__pyx_v_self,
* property pileups:
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_3pos___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28709,10 +31056,10 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3037);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3064);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3037; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3064; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -28722,7 +31069,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -28731,7 +31078,18 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":3041
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(((struct __pyx_obj_5pysam_9csamtools_PileupProxy *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3068
* property pileups:
* '''list of reads (:class:`pysam.PileupRead`) aligned to this column'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -28739,8 +31097,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_3pos___get__(PyObject *__pyx_
* pileups = []
*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_11PileupProxy_7pileups___get__(struct __pyx_obj_5pysam_9csamtools_PileupProxy *__pyx_v_self) {
int __pyx_v_x;
PyObject *__pyx_v_pileups = NULL;
PyObject *__pyx_r = NULL;
@@ -28753,74 +31110,71 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3041);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3068);
- /* "csamtools.pyx":3043
+ /* "pysam/csamtools.pyx":3070
* def __get__(self):
* cdef int x
* pileups = [] # <<<<<<<<<<<<<<
*
* if self.plp[0] == NULL:
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_pileups = __pyx_t_1;
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3070; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_v_pileups = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":3045
+ /* "pysam/csamtools.pyx":3072
* pileups = []
*
* if self.plp[0] == NULL: # <<<<<<<<<<<<<<
* raise ValueError("PileupProxy accessed after iterator finished")
*
*/
- __pyx_t_2 = ((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0]) == NULL);
+ __pyx_t_2 = ((__pyx_v_self->plp[0]) == NULL);
if (__pyx_t_2) {
- /* "csamtools.pyx":3046
+ /* "pysam/csamtools.pyx":3073
*
* if self.plp[0] == NULL:
* raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<<
*
* # warning: there could be problems if self.n and self.buf are
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_174), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_178), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L5;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
- /* "csamtools.pyx":3050
+ /* "pysam/csamtools.pyx":3077
* # warning: there could be problems if self.n and self.buf are
* # out of sync.
* for x from 0 <= x < self.n_pu: # <<<<<<<<<<<<<<
* pileups.append( makePileupRead( &(self.plp[0][x])) )
* return pileups
*/
- __pyx_t_3 = ((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->n_pu;
+ __pyx_t_3 = __pyx_v_self->n_pu;
for (__pyx_v_x = 0; __pyx_v_x < __pyx_t_3; __pyx_v_x++) {
- /* "csamtools.pyx":3051
+ /* "pysam/csamtools.pyx":3078
* # out of sync.
* for x from 0 <= x < self.n_pu:
* pileups.append( makePileupRead( &(self.plp[0][x])) ) # <<<<<<<<<<<<<<
* return pileups
*
*/
- if (unlikely(((PyObject *)__pyx_v_pileups) == Py_None)) {
- PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "append"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_1 = __pyx_f_9csamtools_makePileupRead((&((((struct __pyx_obj_9csamtools_PileupProxy *)__pyx_v_self)->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_makePileupRead((&((__pyx_v_self->plp[0])[__pyx_v_x]))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3051; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_Append(__pyx_v_pileups, __pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3078; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
}
- /* "csamtools.pyx":3052
+ /* "pysam/csamtools.pyx":3079
* for x from 0 <= x < self.n_pu:
* pileups.append( makePileupRead( &(self.plp[0][x])) )
* return pileups # <<<<<<<<<<<<<<
@@ -28836,7 +31190,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupProxy.pileups.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupProxy.pileups.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_pileups);
@@ -28846,7 +31200,21 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":3058
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
+ if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
+ if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead___init__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3085
* '''
*
* def __init__(self): # <<<<<<<<<<<<<<
@@ -28854,8 +31222,7 @@ static PyObject *__pyx_pf_9csamtools_11PileupProxy_7pileups___get__(PyObject *__
*
*/
-static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static int __pyx_pf_5pysam_9csamtools_10PileupRead___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
int __pyx_r;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28863,30 +31230,27 @@ static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyO
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 3058);
- if (unlikely(PyTuple_GET_SIZE(__pyx_args) > 0)) {
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 0, 0, PyTuple_GET_SIZE(__pyx_args)); return -1;}
- if (unlikely(__pyx_kwds) && unlikely(PyDict_Size(__pyx_kwds) > 0) && unlikely(!__Pyx_CheckKeywordStrings(__pyx_kwds, "__init__", 0))) return -1;
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3085);
- /* "csamtools.pyx":3059
+ /* "pysam/csamtools.pyx":3086
*
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
*
* def __str__(self):
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_TypeError, ((PyObject *)__pyx_k_tuple_175), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_TypeError, ((PyObject *)__pyx_k_tuple_179), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_TraceReturn(Py_None);
@@ -28894,7 +31258,18 @@ static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyO
return __pyx_r;
}
-/* "csamtools.pyx":3061
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_3__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3088
* raise TypeError("This class cannot be instantiated from Python")
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -28902,8 +31277,7 @@ static int __pyx_pf_9csamtools_10PileupRead___init__(PyObject *__pyx_v_self, PyO
*
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_2__str__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -28919,10 +31293,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_sel
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 3061);
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 3088);
- /* "csamtools.pyx":3062
+ /* "pysam/csamtools.pyx":3089
*
* def __str__(self):
* return "\t".join( map(str, (self.alignment, self.qpos, self.indel, self.level, self.is_del, self.is_head, self.is_tail ) ) ) # <<<<<<<<<<<<<<
@@ -28930,24 +31304,24 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_sel
* property alignment:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__alignment); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__qpos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__indel); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__level); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_del); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_head); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__is_tail); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(7); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
@@ -28969,23 +31343,23 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_sel
__pyx_t_6 = 0;
__pyx_t_7 = 0;
__pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_8, 1, ((PyObject *)__pyx_t_9));
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3062; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3089; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
@@ -29005,7 +31379,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_sel
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
- __Pyx_AddTraceback("csamtools.PileupRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29014,7 +31388,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":3066
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3093
* property alignment:
* """a :class:`pysam.AlignedRead` object of the aligned read"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29022,15 +31407,14 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_1__str__(PyObject *__pyx_v_sel
* property qpos:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_9alignment___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3066);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3093);
- /* "csamtools.pyx":3067
+ /* "pysam/csamtools.pyx":3094
* """a :class:`pysam.AlignedRead` object of the aligned read"""
* def __get__(self):
* return self._alignment # <<<<<<<<<<<<<<
@@ -29038,8 +31422,8 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *_
* """position of the read base at the pileup site, 0-based"""
*/
__Pyx_XDECREF(__pyx_r);
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment));
- __pyx_r = ((PyObject *)((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_alignment);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->_alignment));
+ __pyx_r = ((PyObject *)__pyx_v_self->_alignment);
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -29050,7 +31434,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *_
return __pyx_r;
}
-/* "csamtools.pyx":3070
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3097
* property qpos:
* """position of the read base at the pileup site, 0-based"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29058,8 +31453,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_9alignment___get__(PyObject *_
* property indel:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_4qpos___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29067,10 +31461,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3070);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3097);
- /* "csamtools.pyx":3071
+ /* "pysam/csamtools.pyx":3098
* """position of the read base at the pileup site, 0-based"""
* def __get__(self):
* return self._qpos # <<<<<<<<<<<<<<
@@ -29078,7 +31472,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_
* """indel length; 0 for no indel, positive for ins and negative for del"""
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3071; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_int32_t(__pyx_v_self->_qpos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29088,7 +31482,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.qpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.qpos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29097,7 +31491,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":3074
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3101
* property indel:
* """indel length; 0 for no indel, positive for ins and negative for del"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29105,8 +31510,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_4qpos___get__(PyObject *__pyx_
* property is_del:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5indel___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29114,10 +31518,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3074);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3101);
- /* "csamtools.pyx":3075
+ /* "pysam/csamtools.pyx":3102
* """indel length; 0 for no indel, positive for ins and negative for del"""
* def __get__(self):
* return self._indel # <<<<<<<<<<<<<<
@@ -29125,7 +31529,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx
* """1 iff the base on the padded read is a deletion"""
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3075; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_indel); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3102; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29135,7 +31539,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.indel.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.indel.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29144,7 +31548,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":3078
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3105
* property is_del:
* """1 iff the base on the padded read is a deletion"""
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29152,8 +31567,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5indel___get__(PyObject *__pyx
* property is_head:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_6is_del___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29161,10 +31575,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__py
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3078);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3105);
- /* "csamtools.pyx":3079
+ /* "pysam/csamtools.pyx":3106
* """1 iff the base on the padded read is a deletion"""
* def __get__(self):
* return self._is_del # <<<<<<<<<<<<<<
@@ -29172,7 +31586,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__py
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3079; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_del); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29182,7 +31596,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__py
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.is_del.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.is_del.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29191,7 +31605,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__py
return __pyx_r;
}
-/* "csamtools.pyx":3081
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3108
* return self._is_del
* property is_head:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29199,8 +31624,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_6is_del___get__(PyObject *__py
* property is_tail:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_head___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29208,10 +31632,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3081);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3108);
- /* "csamtools.pyx":3082
+ /* "pysam/csamtools.pyx":3109
* property is_head:
* def __get__(self):
* return self._is_head # <<<<<<<<<<<<<<
@@ -29219,7 +31643,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__p
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3082; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_head); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29229,7 +31653,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__p
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.is_head.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.is_head.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29238,7 +31662,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":3084
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3111
* return self._is_head
* property is_tail:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29246,8 +31681,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_head___get__(PyObject *__p
* property level:
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_7is_tail___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29255,10 +31689,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__p
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3084);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3111);
- /* "csamtools.pyx":3085
+ /* "pysam/csamtools.pyx":3112
* property is_tail:
* def __get__(self):
* return self._is_tail # <<<<<<<<<<<<<<
@@ -29266,7 +31700,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__p
* def __get__(self):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3085; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->_is_tail); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29276,7 +31710,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__p
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.is_tail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.is_tail.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29285,7 +31719,18 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__p
return __pyx_r;
}
-/* "csamtools.pyx":3087
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(((struct __pyx_obj_5pysam_9csamtools_PileupRead *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3114
* return self._is_tail
* property level:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -29293,8 +31738,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_7is_tail___get__(PyObject *__p
*
*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_10PileupRead_5level___get__(struct __pyx_obj_5pysam_9csamtools_PileupRead *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29302,10 +31746,10 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3087);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3114);
- /* "csamtools.pyx":3088
+ /* "pysam/csamtools.pyx":3115
* property level:
* def __get__(self):
* return self._level # <<<<<<<<<<<<<<
@@ -29313,7 +31757,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx
* class Outs:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_PileupRead *)__pyx_v_self)->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_level); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -29323,7 +31767,7 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.PileupRead.level.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.PileupRead.level.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29332,47 +31776,33 @@ static PyObject *__pyx_pf_9csamtools_10PileupRead_5level___get__(PyObject *__pyx
return __pyx_r;
}
-/* "csamtools.pyx":3092
- * class Outs:
- * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
- * def __init__(self, id = 1): # <<<<<<<<<<<<<<
- * self.streams = []
- * self.id = id
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs___init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pf_9csamtools_4Outs___init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs___init__)};
-static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_4Outs___init__[] = "Outs.__init__(self, id=1)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_1__init__ = {__Pyx_NAMESTR("__init__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_1__init__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs___init__)};
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_id = 0;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 3092);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__id,0};
PyObject* values[2] = {0,0};
- values[1] = ((PyObject *)__pyx_int_1);
+ values[1] = ((PyObject *)((PyObject *)__pyx_int_1));
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -29381,7 +31811,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObje
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -29396,39 +31826,62 @@ static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs___init__(__pyx_self, __pyx_v_self, __pyx_v_id);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3119
+ * class Outs:
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1): # <<<<<<<<<<<<<<
+ * self.streams = []
+ * self.id = id
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_id) {
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3119);
- /* "csamtools.pyx":3093
+ /* "pysam/csamtools.pyx":3120
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
* self.streams = [] # <<<<<<<<<<<<<<
* self.id = id
*
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__streams, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3093; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__streams, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":3094
+ /* "pysam/csamtools.pyx":3121
* def __init__(self, id = 1):
* self.streams = []
* self.id = id # <<<<<<<<<<<<<<
*
* def setdevice(self, filename):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__id, __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__id, __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -29437,59 +31890,41 @@ static PyObject *__pyx_pf_9csamtools_4Outs___init__(PyObject *__pyx_self, PyObje
return __pyx_r;
}
-/* "csamtools.pyx":3096
- * self.id = id
- *
- * def setdevice(self, filename): # <<<<<<<<<<<<<<
- * '''open an existing file, like "/dev/null"'''
- * fd = os.open(filename, os.O_WRONLY)
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_1setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_1setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pf_9csamtools_4Outs_1setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_1setdevice)};
-static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_4Outs_2setdevice[] = "Outs.setdevice(self, filename)\nopen an existing file, like \"/dev/null\"";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_3setdevice = {__Pyx_NAMESTR("setdevice"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_3setdevice, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_2setdevice)};
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_3setdevice(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- PyObject *__pyx_v_fd = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setdevice");
- __Pyx_TraceCall("setdevice", __pyx_f[0], 3096);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("setdevice (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setdevice") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -29502,60 +31937,86 @@ static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyOb
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setdevice", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_2setdevice(__pyx_self, __pyx_v_self, __pyx_v_filename);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3123
+ * self.id = id
+ *
+ * def setdevice(self, filename): # <<<<<<<<<<<<<<
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_2setdevice(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setdevice", 0);
+ __Pyx_TraceCall("setdevice", __pyx_f[0], 3123);
- /* "csamtools.pyx":3098
+ /* "pysam/csamtools.pyx":3125
* def setdevice(self, filename):
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY) # <<<<<<<<<<<<<<
* self.setfd(fd)
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3098; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_fd = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":3099
+ /* "pysam/csamtools.pyx":3126
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY)
* self.setfd(fd) # <<<<<<<<<<<<<<
*
* def setfile(self, filename):
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -29567,7 +32028,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyOb
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.setdevice", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_fd);
@@ -29577,60 +32038,41 @@ static PyObject *__pyx_pf_9csamtools_4Outs_1setdevice(PyObject *__pyx_self, PyOb
return __pyx_r;
}
-/* "csamtools.pyx":3101
- * self.setfd(fd)
- *
- * def setfile(self, filename): # <<<<<<<<<<<<<<
- * '''open a new file.'''
- * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_2setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_2setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pf_9csamtools_4Outs_2setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_2setfile)};
-static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_4Outs_4setfile[] = "Outs.setfile(self, filename)\nopen a new file.";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_5setfile = {__Pyx_NAMESTR("setfile"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_5setfile, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_4setfile)};
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_5setfile(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- PyObject *__pyx_v_fd = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfile");
- __Pyx_TraceCall("setfile", __pyx_f[0], 3101);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("setfile (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfile") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -29643,41 +32085,68 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfile", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_4setfile(__pyx_self, __pyx_v_self, __pyx_v_filename);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
- /* "csamtools.pyx":3103
+/* "pysam/csamtools.pyx":3128
+ * self.setfd(fd)
+ *
+ * def setfile(self, filename): # <<<<<<<<<<<<<<
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_4setfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename) {
+ PyObject *__pyx_v_fd = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfile", 0);
+ __Pyx_TraceCall("setfile", __pyx_f[0], 3128);
+
+ /* "pysam/csamtools.pyx":3130
* def setfile(self, filename):
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660); # <<<<<<<<<<<<<<
* self.setfd(fd)
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__open); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_WRONLY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_CREAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__O_CREAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Or(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Or(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
@@ -29687,28 +32156,28 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObje
PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_int_0660);
__Pyx_GIVEREF(__pyx_int_0660);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3103; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3130; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__pyx_v_fd = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":3104
+ /* "pysam/csamtools.pyx":3131
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
* self.setfd(fd) # <<<<<<<<<<<<<<
*
* def setfd(self, fd):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3104; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
@@ -29721,7 +32190,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObje
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.setfile", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_fd);
@@ -29731,59 +32200,41 @@ static PyObject *__pyx_pf_9csamtools_4Outs_2setfile(PyObject *__pyx_self, PyObje
return __pyx_r;
}
-/* "csamtools.pyx":3106
- * self.setfd(fd)
- *
- * def setfd(self, fd): # <<<<<<<<<<<<<<
- * ofd = os.dup(self.id) # Save old stream on new unit.
- * self.streams.append(ofd)
- */
-
-static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_3setfd[] = "Outs.setfd(self, fd)";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_3setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pf_9csamtools_4Outs_3setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_3setfd)};
-static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_4Outs_6setfd[] = "Outs.setfd(self, fd)";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_7setfd = {__Pyx_NAMESTR("setfd"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_7setfd, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_6setfd)};
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_7setfd(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_fd = 0;
- PyObject *__pyx_v_ofd = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("setfd");
- __Pyx_TraceCall("setfd", __pyx_f[0], 3106);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("setfd (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fd,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fd);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fd)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfd") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -29796,139 +32247,165 @@ static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfd", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_6setfd(__pyx_self, __pyx_v_self, __pyx_v_fd);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3133
+ * self.setfd(fd)
+ *
+ * def setfd(self, fd): # <<<<<<<<<<<<<<
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_6setfd(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fd) {
+ PyObject *__pyx_v_ofd = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_3 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("setfd", 0);
+ __Pyx_TraceCall("setfd", __pyx_f[0], 3133);
- /* "csamtools.pyx":3107
+ /* "pysam/csamtools.pyx":3134
*
* def setfd(self, fd):
* ofd = os.dup(self.id) # Save old stream on new unit. # <<<<<<<<<<<<<<
* self.streams.append(ofd)
* sys.stdout.flush() # Buffered data goes to old stream.
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3107; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_v_ofd = __pyx_t_1;
__pyx_t_1 = 0;
- /* "csamtools.pyx":3108
+ /* "pysam/csamtools.pyx":3135
* def setfd(self, fd):
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd) # <<<<<<<<<<<<<<
* sys.stdout.flush() # Buffered data goes to old stream.
* sys.stderr.flush() # Buffered data goes to old stream.
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_Append(__pyx_t_1, __pyx_v_ofd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_Append(__pyx_t_1, __pyx_v_ofd); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":3109
+ /* "pysam/csamtools.pyx":3136
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd)
* sys.stdout.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
* sys.stderr.flush() # Buffered data goes to old stream.
* os.dup2(fd, self.id) # Open unit 1 on new stream.
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3109; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3136; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3110
+ /* "pysam/csamtools.pyx":3137
* self.streams.append(ofd)
* sys.stdout.flush() # Buffered data goes to old stream.
* sys.stderr.flush() # Buffered data goes to old stream. # <<<<<<<<<<<<<<
* os.dup2(fd, self.id) # Open unit 1 on new stream.
* os.close(fd) # Close other unit (look out, caller.)
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stderr); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stderr); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3110; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":3111
+ /* "pysam/csamtools.pyx":3138
* sys.stdout.flush() # Buffered data goes to old stream.
* sys.stderr.flush() # Buffered data goes to old stream.
* os.dup2(fd, self.id) # Open unit 1 on new stream. # <<<<<<<<<<<<<<
* os.close(fd) # Close other unit (look out, caller.)
*
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__dup2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__dup2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3138; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":3112
+ /* "pysam/csamtools.pyx":3139
* sys.stderr.flush() # Buffered data goes to old stream.
* os.dup2(fd, self.id) # Open unit 1 on new stream.
* os.close(fd) # Close other unit (look out, caller.) # <<<<<<<<<<<<<<
*
* def restore(self):
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__close); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_fd);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_fd);
__Pyx_GIVEREF(__pyx_v_fd);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -29940,7 +32417,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.setfd", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_ofd);
@@ -29950,7 +32427,20 @@ static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject
return __pyx_r;
}
-/* "csamtools.pyx":3114
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_4Outs_8restore[] = "Outs.restore(self)\nrestore previous output stream";
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_4Outs_9restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pw_5pysam_9csamtools_4Outs_9restore, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_4Outs_8restore)};
+static PyObject *__pyx_pw_5pysam_9csamtools_4Outs_9restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("restore (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_4Outs_8restore(__pyx_self, ((PyObject *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3141
* os.close(fd) # Close other unit (look out, caller.)
*
* def restore(self): # <<<<<<<<<<<<<<
@@ -29958,10 +32448,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_3setfd(PyObject *__pyx_self, PyObject
* if self.streams:
*/
-static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObject *__pyx_v_self); /*proto*/
-static char __pyx_doc_9csamtools_4Outs_4restore[] = "Outs.restore(self)\nrestore previous output stream";
-static PyMethodDef __pyx_mdef_9csamtools_4Outs_4restore = {__Pyx_NAMESTR("restore"), (PyCFunction)__pyx_pf_9csamtools_4Outs_4restore, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_4Outs_4restore)};
-static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_4Outs_8restore(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -29973,138 +32460,137 @@ static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("restore");
- __Pyx_TraceCall("restore", __pyx_f[0], 3114);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("restore", 0);
+ __Pyx_TraceCall("restore", __pyx_f[0], 3141);
- /* "csamtools.pyx":3116
+ /* "pysam/csamtools.pyx":3143
* def restore(self):
* '''restore previous output stream'''
* if self.streams: # <<<<<<<<<<<<<<
* # the following was not sufficient, hence flush both stderr and stdout
* # os.fsync( self.id )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- /* "csamtools.pyx":3119
+ /* "pysam/csamtools.pyx":3146
* # the following was not sufficient, hence flush both stderr and stdout
* # os.fsync( self.id )
* sys.stdout.flush() # <<<<<<<<<<<<<<
* sys.stderr.flush()
* os.dup2(self.streams[-1], self.id)
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stdout); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__stdout); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__flush); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":3120
+ /* "pysam/csamtools.pyx":3147
* # os.fsync( self.id )
* sys.stdout.flush()
* sys.stderr.flush() # <<<<<<<<<<<<<<
* os.dup2(self.streams[-1], self.id)
* os.close(self.streams[-1])
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stderr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stderr); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__flush); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3121
+ /* "pysam/csamtools.pyx":3148
* sys.stdout.flush()
* sys.stderr.flush()
* os.dup2(self.streams[-1], self.id) # <<<<<<<<<<<<<<
* os.close(self.streams[-1])
* del self.streams[-1]
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__dup2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_5));
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_4 = 0;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3122
+ /* "pysam/csamtools.pyx":3149
* sys.stderr.flush()
* os.dup2(self.streams[-1], self.id)
* os.close(self.streams[-1]) # <<<<<<<<<<<<<<
* del self.streams[-1]
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__close); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_t_1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3122; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3149; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":3123
+ /* "pysam/csamtools.pyx":3150
* os.dup2(self.streams[-1], self.id)
* os.close(self.streams[-1])
* del self.streams[-1] # <<<<<<<<<<<<<<
*
* def _samtools_dispatch( method,
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__streams); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_DelItemInt(__pyx_t_3, -1, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_DelItemInt(__pyx_t_3, -1, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -30113,7 +32599,7 @@ static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObje
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_5);
- __Pyx_AddTraceback("csamtools.Outs.restore", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.Outs.restore", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -30122,70 +32608,22 @@ static PyObject *__pyx_pf_9csamtools_4Outs_4restore(PyObject *__pyx_self, PyObje
return __pyx_r;
}
-/* "csamtools.pyx":3125
- * del self.streams[-1]
- *
- * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
- * args = (),
- * catch_stdout = True ):
- */
-
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static char __pyx_doc_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout to capture it \n from samtools. If for some reason stdout disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n\n .. note::\n This method captures stdout and stderr us [...]
-static PyMethodDef __pyx_mdef_9csamtools__samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pf_9csamtools__samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools__samtools_dispatch)};
-static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_9csamtools__samtools_dispatch[] = "_samtools_dispatch(method, args=(), catch_stdout=True)\ncall ``method`` in samtools providing arguments in args.\n \n .. note:: \n This method redirects stdout to capture it \n from samtools. If for some reason stdout disappears\n the reason might be in this method.\n\n .. note::\n The current implementation might only work on linux.\n\n .. note::\n This method captures stdout and st [...]
+static PyMethodDef __pyx_mdef_5pysam_9csamtools_1_samtools_dispatch = {__Pyx_NAMESTR("_samtools_dispatch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_1_samtools_dispatch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools__samtools_dispatch)};
+static PyObject *__pyx_pw_5pysam_9csamtools_1_samtools_dispatch(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_method = 0;
PyObject *__pyx_v_args = 0;
PyObject *__pyx_v_catch_stdout = 0;
- PyObject *__pyx_v_stderr_h = NULL;
- PyObject *__pyx_v_stderr_f = NULL;
- PyObject *__pyx_v_stdout_h = NULL;
- PyObject *__pyx_v_stdout_f = NULL;
- PyObject *__pyx_v_stdout_save = NULL;
- char **__pyx_v_cargs;
- int __pyx_v_i;
- int __pyx_v_n;
- int __pyx_v_retval;
- PyObject *__pyx_v_inf = NULL;
- PyObject *__pyx_v_out_stdout = NULL;
- PyObject *__pyx_v_out_stderr = NULL;
- PyObject *__pyx_v_a = NULL;
- PyObject *__pyx_r = NULL;
+ PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
- PyObject *__pyx_t_3 = NULL;
- PyObject *__pyx_t_4 = NULL;
- int __pyx_t_5;
- PyObject *__pyx_t_6 = NULL;
- PyObject *(*__pyx_t_7)(PyObject *);
- int __pyx_t_8;
- PyObject *__pyx_t_9 = NULL;
- PyObject *__pyx_t_10 = NULL;
- PyObject *__pyx_t_11 = NULL;
- Py_ssize_t __pyx_t_12;
- PyObject *(*__pyx_t_13)(PyObject *);
- char *__pyx_t_14;
- PyObject *__pyx_t_15 = NULL;
- PyObject *__pyx_t_16 = NULL;
- PyObject *__pyx_t_17 = NULL;
- PyObject *__pyx_t_18 = NULL;
- PyObject *__pyx_t_19 = NULL;
- PyObject *__pyx_t_20 = NULL;
- PyObject *__pyx_t_21 = NULL;
- PyObject *__pyx_t_22 = NULL;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("_samtools_dispatch");
- __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3125);
- __pyx_self = __pyx_self;
+ __Pyx_RefNannySetupContext("_samtools_dispatch (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__method,&__pyx_n_s__args,&__pyx_n_s__catch_stdout,0};
PyObject* values[3] = {0,0,0};
- /* "csamtools.pyx":3126
+ /* "pysam/csamtools.pyx":3153
*
* def _samtools_dispatch( method,
* args = (), # <<<<<<<<<<<<<<
@@ -30193,10 +32631,11 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
* '''call ``method`` in samtools providing arguments in args.
*/
values[1] = ((PyObject *)__pyx_empty_tuple);
- values[2] = __pyx_k_176;
+ values[2] = __pyx_k_180;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2);
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
@@ -30204,10 +32643,9 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__method)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -30221,7 +32659,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_samtools_dispatch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -30238,232 +32676,309 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_samtools_dispatch", 0, 1, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return NULL;
__pyx_L4_argument_unpacking_done:;
+ __pyx_r = __pyx_pf_5pysam_9csamtools__samtools_dispatch(__pyx_self, __pyx_v_method, __pyx_v_args, __pyx_v_catch_stdout);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3152
+ * del self.streams[-1]
+ *
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
+ * args = (),
+ * catch_stdout = True ):
+ */
+
+static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_method, PyObject *__pyx_v_args, PyObject *__pyx_v_catch_stdout) {
+ PyObject *__pyx_v_stderr_h = NULL;
+ PyObject *__pyx_v_stderr_f = NULL;
+ PyObject *__pyx_v_stdout_h = NULL;
+ PyObject *__pyx_v_stdout_f = NULL;
+ PyObject *__pyx_v_stdout_save = NULL;
+ char **__pyx_v_cargs;
+ int __pyx_v_i;
+ int __pyx_v_n;
+ int __pyx_v_retval;
+ PyObject *__pyx_v_inf = NULL;
+ PyObject *__pyx_v_out_stdout = NULL;
+ PyObject *__pyx_v_out_stderr = NULL;
+ PyObject *__pyx_v_a = NULL;
+ PyObject *__pyx_r = NULL;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
+ PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_4 = NULL;
+ int __pyx_t_5;
+ PyObject *__pyx_t_6 = NULL;
+ PyObject *(*__pyx_t_7)(PyObject *);
+ int __pyx_t_8;
+ PyObject *__pyx_t_9 = NULL;
+ PyObject *__pyx_t_10 = NULL;
+ PyObject *__pyx_t_11 = NULL;
+ Py_ssize_t __pyx_t_12;
+ PyObject *(*__pyx_t_13)(PyObject *);
+ char *__pyx_t_14;
+ PyObject *__pyx_t_15 = NULL;
+ PyObject *__pyx_t_16 = NULL;
+ PyObject *__pyx_t_17 = NULL;
+ PyObject *__pyx_t_18 = NULL;
+ PyObject *__pyx_t_19 = NULL;
+ PyObject *__pyx_t_20 = NULL;
+ PyObject *__pyx_t_21 = NULL;
+ PyObject *__pyx_t_22 = NULL;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("_samtools_dispatch", 0);
+ __Pyx_TraceCall("_samtools_dispatch", __pyx_f[0], 3152);
__Pyx_INCREF(__pyx_v_method);
__Pyx_INCREF(__pyx_v_args);
__Pyx_INCREF(__pyx_v_catch_stdout);
- /* "csamtools.pyx":3151
+ /* "pysam/csamtools.pyx":3178
*
* # some special cases
* if method == "index": # <<<<<<<<<<<<<<
* if not os.path.exists( args[0] ):
* raise IOError( "No such file or directory: '%s'" % args[0] )
*/
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_method, ((PyObject *)__pyx_n_s__index), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3151; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_method, ((PyObject *)__pyx_n_s__index), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
- /* "csamtools.pyx":3152
+ /* "pysam/csamtools.pyx":3179
* # some special cases
* if method == "index":
* if not os.path.exists( args[0] ): # <<<<<<<<<<<<<<
* raise IOError( "No such file or directory: '%s'" % args[0] )
*
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = (!__pyx_t_1);
+ __pyx_t_5 = (!__pyx_t_2);
if (__pyx_t_5) {
- /* "csamtools.pyx":3153
+ /* "pysam/csamtools.pyx":3180
* if method == "index":
* if not os.path.exists( args[0] ):
* raise IOError( "No such file or directory: '%s'" % args[0] ) # <<<<<<<<<<<<<<
*
* # redirect stderr and stdout to file
*/
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_177), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_181), __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L7;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L4;
}
- __pyx_L7:;
- goto __pyx_L6;
+ __pyx_L4:;
+ goto __pyx_L3;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":3156
+ /* "pysam/csamtools.pyx":3183
*
* # redirect stderr and stdout to file
* stderr_h, stderr_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
* pysam_set_stderr( stderr_h )
*
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_3 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_2 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_3);
- __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_1);
+ #else
+ __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
+ index = 0; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
- index = 1; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L8_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ index = 1; __pyx_t_1 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_1)) goto __pyx_L5_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L9_unpacking_done;
- __pyx_L8_unpacking_failed:;
+ goto __pyx_L6_unpacking_done;
+ __pyx_L5_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L9_unpacking_done:;
+ __pyx_t_7 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L6_unpacking_done:;
}
__pyx_v_stderr_h = __pyx_t_3;
__pyx_t_3 = 0;
- __pyx_v_stderr_f = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_stderr_f = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "csamtools.pyx":3157
+ /* "pysam/csamtools.pyx":3184
* # redirect stderr and stdout to file
* stderr_h, stderr_f = tempfile.mkstemp()
* pysam_set_stderr( stderr_h ) # <<<<<<<<<<<<<<
*
* if catch_stdout:
*/
- __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_v_stderr_h); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyInt_AsInt(__pyx_v_stderr_h); if (unlikely((__pyx_t_8 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
pysam_set_stderr(__pyx_t_8);
- /* "csamtools.pyx":3159
+ /* "pysam/csamtools.pyx":3186
* pysam_set_stderr( stderr_h )
*
* if catch_stdout: # <<<<<<<<<<<<<<
* stdout_h, stdout_f = tempfile.mkstemp()
* try:
*/
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "csamtools.pyx":3160
+ /* "pysam/csamtools.pyx":3187
*
* if catch_stdout:
* stdout_h, stdout_f = tempfile.mkstemp() # <<<<<<<<<<<<<<
* try:
* stdout_save = Outs( sys.stdout.fileno() )
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__tempfile); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__mkstemp); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_2 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_3 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_3);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_7 = Py_TYPE(__pyx_t_6)->tp_iternext;
- index = 0; __pyx_t_2 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_2)) goto __pyx_L11_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L11_unpacking_failed;
+ index = 0; __pyx_t_1 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_1)) goto __pyx_L8_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_1);
+ index = 1; __pyx_t_3 = __pyx_t_7(__pyx_t_6); if (unlikely(!__pyx_t_3)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_7(__pyx_t_6), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = NULL;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L12_unpacking_done;
- __pyx_L11_unpacking_failed:;
+ goto __pyx_L9_unpacking_done;
+ __pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3160; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_L12_unpacking_done:;
+ __pyx_t_7 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_L9_unpacking_done:;
}
- __pyx_v_stdout_h = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_stdout_h = __pyx_t_1;
+ __pyx_t_1 = 0;
__pyx_v_stdout_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":3161
+ /* "pysam/csamtools.pyx":3188
* if catch_stdout:
* stdout_h, stdout_f = tempfile.mkstemp()
* try: # <<<<<<<<<<<<<<
@@ -30477,69 +32992,69 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
- /* "csamtools.pyx":3162
+ /* "pysam/csamtools.pyx":3189
* stdout_h, stdout_f = tempfile.mkstemp()
* try:
* stdout_save = Outs( sys.stdout.fileno() ) # <<<<<<<<<<<<<<
* stdout_save.setfd( stdout_h )
* except AttributeError:
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__Outs); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__stdout); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fileno); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3162; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3189; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_v_stdout_save = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_stdout_save = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "csamtools.pyx":3163
+ /* "pysam/csamtools.pyx":3190
* try:
* stdout_save = Outs( sys.stdout.fileno() )
* stdout_save.setfd( stdout_h ) # <<<<<<<<<<<<<<
* except AttributeError:
* # stdout has already been redirected
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__setfd); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3190; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3190; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_stdout_h);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_h);
__Pyx_GIVEREF(__pyx_v_stdout_h);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3163; __pyx_clineno = __LINE__; goto __pyx_L13_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3190; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L20_try_end;
- __pyx_L13_error:;
+ goto __pyx_L17_try_end;
+ __pyx_L10_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":3164
+ /* "pysam/csamtools.pyx":3191
* stdout_save = Outs( sys.stdout.fileno() )
* stdout_save.setfd( stdout_h )
* except AttributeError: # <<<<<<<<<<<<<<
@@ -30548,152 +33063,162 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_AttributeError);
if (__pyx_t_8) {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3164; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3191; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":3166
+ /* "pysam/csamtools.pyx":3193
* except AttributeError:
* # stdout has already been redirected
* catch_stdout = False # <<<<<<<<<<<<<<
*
* # patch for `samtools view`
*/
- __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3166; __pyx_clineno = __LINE__; goto __pyx_L15_except_error;}
+ __pyx_t_6 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3193; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_v_catch_stdout);
__pyx_v_catch_stdout = __pyx_t_6;
__pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L14_exception_handled;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L11_exception_handled;
}
- __pyx_L15_except_error:;
+ __pyx_L12_except_error:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
goto __pyx_L1_error;
- __pyx_L14_exception_handled:;
+ __pyx_L11_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
- __pyx_L20_try_end:;
+ __pyx_L17_try_end:;
}
- /* "csamtools.pyx":3171
+ /* "pysam/csamtools.pyx":3198
* # samtools `view` closes stdout, from which I can not
* # recover. Thus redirect output to file with -o option.
* if method == "view": # <<<<<<<<<<<<<<
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
* args = ( "-o", stdout_f ) + args
*/
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_method, ((PyObject *)__pyx_n_s__view), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3171; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_method, ((PyObject *)__pyx_n_s__view), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
- /* "csamtools.pyx":3172
+ /* "pysam/csamtools.pyx":3199
* # recover. Thus redirect output to file with -o option.
* if method == "view":
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
* args = ( "-o", stdout_f ) + args
*
*/
- __pyx_t_5 = ((PySequence_Contains(__pyx_v_args, ((PyObject *)__pyx_kp_s_178)))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_kp_s_182), __pyx_v_args, Py_EQ)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_180), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_Raise(__pyx_t_2, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- goto __pyx_L24;
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_184), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L21;
}
- __pyx_L24:;
+ __pyx_L21:;
- /* "csamtools.pyx":3173
+ /* "pysam/csamtools.pyx":3200
* if method == "view":
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view")
* args = ( "-o", stdout_f ) + args # <<<<<<<<<<<<<<
*
* # do the function call to samtools
*/
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_178));
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_178));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_178));
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(((PyObject *)__pyx_kp_s_182));
+ PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_182));
+ __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_182));
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_2), __pyx_v_args); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_1), __pyx_v_args); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_v_args);
__pyx_v_args = __pyx_t_3;
__pyx_t_3 = 0;
- goto __pyx_L23;
+ goto __pyx_L20;
}
- __pyx_L23:;
- goto __pyx_L10;
+ __pyx_L20:;
+ goto __pyx_L7;
}
- __pyx_L10:;
+ __pyx_L7:;
- /* "csamtools.pyx":3179
+ /* "pysam/csamtools.pyx":3206
* cdef int i, n, retval
*
* n = len(args) # <<<<<<<<<<<<<<
* method = _force_cmdline_bytes(method)
* args = [ _force_cmdline_bytes(a) for a in args ]
*/
- __pyx_t_12 = PyObject_Length(__pyx_v_args); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Length(__pyx_v_args); if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_n = __pyx_t_12;
- /* "csamtools.pyx":3180
+ /* "pysam/csamtools.pyx":3207
*
* n = len(args)
* method = _force_cmdline_bytes(method) # <<<<<<<<<<<<<<
* args = [ _force_cmdline_bytes(a) for a in args ]
*
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_9csamtools__force_cmdline_bytes(__pyx_v_method)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_cmdline_bytes(__pyx_v_method)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_v_method);
__pyx_v_method = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":3181
+ /* "pysam/csamtools.pyx":3208
* n = len(args)
* method = _force_cmdline_bytes(method)
* args = [ _force_cmdline_bytes(a) for a in args ] # <<<<<<<<<<<<<<
*
* # allocate two more for first (dummy) argument (contains command)
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
if (PyList_CheckExact(__pyx_v_args) || PyTuple_CheckExact(__pyx_v_args)) {
- __pyx_t_2 = __pyx_v_args; __Pyx_INCREF(__pyx_t_2); __pyx_t_12 = 0;
+ __pyx_t_1 = __pyx_v_args; __Pyx_INCREF(__pyx_t_1); __pyx_t_12 = 0;
__pyx_t_13 = NULL;
} else {
- __pyx_t_12 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_13 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_12 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_args); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_13 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
- if (PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
- } else if (PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++;
+ if (!__pyx_t_13 && PyList_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_12 >= PyList_GET_SIZE(__pyx_t_1)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_13 && PyTuple_CheckExact(__pyx_t_1)) {
+ if (__pyx_t_12 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_12); __Pyx_INCREF(__pyx_t_4); __pyx_t_12++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_12); __pyx_t_12++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_4 = __pyx_t_13(__pyx_t_2);
+ __pyx_t_4 = __pyx_t_13(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -30702,18 +33227,20 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
__Pyx_XDECREF(__pyx_v_a);
__pyx_v_a = __pyx_t_4;
__pyx_t_4 = 0;
- __pyx_t_4 = ((PyObject *)__pyx_f_9csamtools__force_cmdline_bytes(__pyx_v_a)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = ((PyObject *)__pyx_f_5pysam_9csamtools__force_cmdline_bytes(__pyx_v_a)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (unlikely(PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_3, (PyObject*)__pyx_t_4))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_3));
- __Pyx_DECREF(__pyx_v_args);
- __pyx_v_args = ((PyObject *)__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = ((PyObject *)__pyx_t_3);
+ __Pyx_INCREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_v_args);
+ __pyx_v_args = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "csamtools.pyx":3184
+ /* "pysam/csamtools.pyx":3211
*
* # allocate two more for first (dummy) argument (contains command)
* cargs = <char**>calloc( n+2, sizeof( char *) ) # <<<<<<<<<<<<<<
@@ -30722,7 +33249,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
__pyx_v_cargs = ((char **)calloc((__pyx_v_n + 2), (sizeof(char *))));
- /* "csamtools.pyx":3185
+ /* "pysam/csamtools.pyx":3212
* # allocate two more for first (dummy) argument (contains command)
* cargs = <char**>calloc( n+2, sizeof( char *) )
* cargs[0] = "samtools" # <<<<<<<<<<<<<<
@@ -30731,17 +33258,17 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
(__pyx_v_cargs[0]) = __pyx_k__samtools;
- /* "csamtools.pyx":3186
+ /* "pysam/csamtools.pyx":3213
* cargs = <char**>calloc( n+2, sizeof( char *) )
* cargs[0] = "samtools"
* cargs[1] = method # <<<<<<<<<<<<<<
* for i from 0 <= i < n: cargs[i+2] = args[i]
*
*/
- __pyx_t_14 = PyBytes_AsString(__pyx_v_method); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyBytes_AsString(__pyx_v_method); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
(__pyx_v_cargs[1]) = __pyx_t_14;
- /* "csamtools.pyx":3187
+ /* "pysam/csamtools.pyx":3214
* cargs[0] = "samtools"
* cargs[1] = method
* for i from 0 <= i < n: cargs[i+2] = args[i] # <<<<<<<<<<<<<<
@@ -30750,14 +33277,14 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
__pyx_t_8 = __pyx_v_n;
for (__pyx_v_i = 0; __pyx_v_i < __pyx_t_8; __pyx_v_i++) {
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_14 = PyBytes_AsString(__pyx_t_3); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_args, __pyx_v_i, sizeof(int), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_14 = PyBytes_AsString(__pyx_t_1); if (unlikely((!__pyx_t_14) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
(__pyx_v_cargs[(__pyx_v_i + 2)]) = __pyx_t_14;
}
- /* "csamtools.pyx":3189
+ /* "pysam/csamtools.pyx":3216
* for i from 0 <= i < n: cargs[i+2] = args[i]
*
* retval = pysam_dispatch(n+2, cargs) # <<<<<<<<<<<<<<
@@ -30766,7 +33293,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
__pyx_v_retval = pysam_dispatch((__pyx_v_n + 2), __pyx_v_cargs);
- /* "csamtools.pyx":3190
+ /* "pysam/csamtools.pyx":3217
*
* retval = pysam_dispatch(n+2, cargs)
* free( cargs ) # <<<<<<<<<<<<<<
@@ -30775,31 +33302,32 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
free(__pyx_v_cargs);
- /* "csamtools.pyx":3194
+ /* "pysam/csamtools.pyx":3221
* # restore stdout/stderr. This will also flush, so
* # needs to be before reading back the file contents
* if catch_stdout: # <<<<<<<<<<<<<<
* stdout_save.restore()
* try:
*/
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_v_catch_stdout); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_3 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":3195
+ /* "pysam/csamtools.pyx":3222
* # needs to be before reading back the file contents
* if catch_stdout:
* stdout_save.restore() # <<<<<<<<<<<<<<
* try:
* with open( stdout_f, "r") as inf:
*/
+ if (unlikely(!__pyx_v_stdout_save)) { __Pyx_RaiseUnboundLocalError("stdout_save"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_stdout_save, __pyx_n_s__restore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":3196
+ /* "pysam/csamtools.pyx":3223
* if catch_stdout:
* stdout_save.restore()
* try: # <<<<<<<<<<<<<<
@@ -30813,7 +33341,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
__Pyx_XGOTREF(__pyx_t_9);
/*try:*/ {
- /* "csamtools.pyx":3197
+ /* "pysam/csamtools.pyx":3224
* stdout_save.restore()
* try:
* with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
@@ -30821,25 +33349,26 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
* except UnicodeDecodeError:
*/
/*with:*/ {
- if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;} }__pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ if (unlikely(!__pyx_v_stdout_f)) { __Pyx_RaiseUnboundLocalError("stdout_f"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L27_error;} }
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_3 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s____enter__); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L38_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L38_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____enter__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L35_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
@@ -30847,35 +33376,36 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_18);
/*try:*/ {
- __pyx_v_inf = __pyx_t_3;
- __pyx_t_3 = 0;
+ __Pyx_INCREF(__pyx_t_4);
+ __pyx_v_inf = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":3198
+ /* "pysam/csamtools.pyx":3225
* try:
* with open( stdout_f, "r") as inf:
* out_stdout = inf.readlines() # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf:
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L44_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3198; __pyx_clineno = __LINE__; goto __pyx_L44_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_v_out_stdout = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3225; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3225; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_out_stdout = __pyx_t_1;
+ __pyx_t_1 = 0;
}
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- goto __pyx_L51_try_end;
- __pyx_L44_error:;
+ goto __pyx_L48_try_end;
+ __pyx_L41_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3197
+ /* "pysam/csamtools.pyx":3224
* stdout_save.restore()
* try:
* with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
@@ -30883,89 +33413,89 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
* except UnicodeDecodeError:
*/
/*except:*/ {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_3, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_INCREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_INCREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
__pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
__Pyx_GOTREF(__pyx_t_19);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
- __pyx_t_1 = (!__pyx_t_5);
- if (__pyx_t_1) {
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_3);
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ __pyx_t_2 = (!__pyx_t_5);
+ if (__pyx_t_2) {
+ __Pyx_GIVEREF(__pyx_t_1);
__Pyx_GIVEREF(__pyx_t_4);
- __Pyx_ErrRestore(__pyx_t_2, __pyx_t_3, __pyx_t_4);
- __pyx_t_2 = 0; __pyx_t_3 = 0; __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L46_except_error;}
- goto __pyx_L54;
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_ErrRestore(__pyx_t_1, __pyx_t_4, __pyx_t_3);
+ __pyx_t_1 = 0; __pyx_t_4 = 0; __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L43_except_error;}
+ goto __pyx_L52;
}
- __pyx_L54:;
+ __pyx_L52:;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L45_exception_handled;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L42_exception_handled;
}
- __pyx_L46_except_error:;
+ __pyx_L43_except_error:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- goto __pyx_L30_error;
- __pyx_L45_exception_handled:;
+ goto __pyx_L27_error;
+ __pyx_L42_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- __pyx_L51_try_end:;
+ __pyx_L48_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
- __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_181, NULL);
+ __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_185, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
__Pyx_GOTREF(__pyx_t_18);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_18);
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L30_error;}
+ if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L27_error;}
}
}
- goto __pyx_L55;
- __pyx_L38_error:;
+ goto __pyx_L53;
+ __pyx_L35_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L30_error;
- __pyx_L55:;
+ goto __pyx_L27_error;
+ __pyx_L53:;
}
}
__Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- goto __pyx_L37_try_end;
- __pyx_L30_error:;
+ goto __pyx_L34_try_end;
+ __pyx_L27_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "csamtools.pyx":3199
+ /* "pysam/csamtools.pyx":3226
* with open( stdout_f, "r") as inf:
* out_stdout = inf.readlines()
* except UnicodeDecodeError: # <<<<<<<<<<<<<<
@@ -30974,13 +33504,13 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
__pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
if (__pyx_t_8) {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_3, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
- __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":3200
+ /* "pysam/csamtools.pyx":3227
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
@@ -30988,25 +33518,25 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
* out_stdout = inf.read()
*/
/*with:*/ {
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_stdout_f);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
__Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
+ __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L58_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
- __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L58_error;}
- __Pyx_GOTREF(__pyx_t_20);
+ __pyx_t_21 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_21);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
/*try:*/ {
{
__Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
@@ -31014,35 +33544,37 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
__Pyx_XGOTREF(__pyx_t_17);
__Pyx_XGOTREF(__pyx_t_16);
/*try:*/ {
+ __Pyx_INCREF(__pyx_t_21);
__Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_20;
- __pyx_t_20 = 0;
+ __pyx_v_inf = __pyx_t_21;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- /* "csamtools.pyx":3202
+ /* "pysam/csamtools.pyx":3229
* with open( stdout_f, "rb") as inf:
* # read binary output
* out_stdout = inf.read() # <<<<<<<<<<<<<<
* os.remove( stdout_f )
* else:
*/
- __pyx_t_20 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L64_error;}
+ __pyx_t_21 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3229; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3229; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
__Pyx_GOTREF(__pyx_t_20);
- __pyx_t_6 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3202; __pyx_clineno = __LINE__; goto __pyx_L64_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
__Pyx_XDECREF(__pyx_v_out_stdout);
- __pyx_v_out_stdout = __pyx_t_6;
- __pyx_t_6 = 0;
+ __pyx_v_out_stdout = __pyx_t_20;
+ __pyx_t_20 = 0;
}
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
- goto __pyx_L71_try_end;
- __pyx_L64_error:;
- __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ goto __pyx_L69_try_end;
+ __pyx_L62_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
- /* "csamtools.pyx":3200
+ /* "pysam/csamtools.pyx":3227
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
@@ -31050,137 +33582,137 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
* out_stdout = inf.read()
*/
/*except:*/ {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_20, &__pyx_t_21) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_20, &__pyx_t_21, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
__Pyx_GOTREF(__pyx_t_20);
__Pyx_GOTREF(__pyx_t_21);
- __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_22));
- __Pyx_INCREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_INCREF(__pyx_t_20);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_20);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_20);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_INCREF(__pyx_t_21);
- PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_21);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_21);
__Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_INCREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
+ __Pyx_GIVEREF(__pyx_t_6);
__pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
__Pyx_GOTREF(__pyx_t_19);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_19);
__Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
- __pyx_t_5 = (!__pyx_t_1);
+ if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ __pyx_t_5 = (!__pyx_t_2);
if (__pyx_t_5) {
- __Pyx_GIVEREF(__pyx_t_6);
__Pyx_GIVEREF(__pyx_t_20);
__Pyx_GIVEREF(__pyx_t_21);
- __Pyx_ErrRestore(__pyx_t_6, __pyx_t_20, __pyx_t_21);
- __pyx_t_6 = 0; __pyx_t_20 = 0; __pyx_t_21 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L66_except_error;}
- goto __pyx_L74;
+ __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_ErrRestore(__pyx_t_20, __pyx_t_21, __pyx_t_6);
+ __pyx_t_20 = 0; __pyx_t_21 = 0; __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
+ goto __pyx_L73;
}
- __pyx_L74:;
+ __pyx_L73:;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- goto __pyx_L65_exception_handled;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L63_exception_handled;
}
- __pyx_L66_except_error:;
+ __pyx_L64_except_error:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- goto __pyx_L32_except_error;
- __pyx_L65_exception_handled:;
+ goto __pyx_L29_except_error;
+ __pyx_L63_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_18);
__Pyx_XGIVEREF(__pyx_t_17);
__Pyx_XGIVEREF(__pyx_t_16);
__Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- __pyx_L71_try_end:;
+ __pyx_L69_try_end:;
}
}
/*finally:*/ {
if (__pyx_t_15) {
- __pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_182, NULL);
+ __pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_186, NULL);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L32_except_error;}
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
}
}
- goto __pyx_L75;
- __pyx_L58_error:;
+ goto __pyx_L74;
+ __pyx_L56_error:;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L32_except_error;
- __pyx_L75:;
+ goto __pyx_L29_except_error;
+ __pyx_L74:;
}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L31_exception_handled;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L28_exception_handled;
}
- __pyx_L32_except_error:;
+ __pyx_L29_except_error:;
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
goto __pyx_L1_error;
- __pyx_L31_exception_handled:;
+ __pyx_L28_exception_handled:;
__Pyx_XGIVEREF(__pyx_t_11);
__Pyx_XGIVEREF(__pyx_t_10);
__Pyx_XGIVEREF(__pyx_t_9);
__Pyx_ExceptionReset(__pyx_t_11, __pyx_t_10, __pyx_t_9);
- __pyx_L37_try_end:;
+ __pyx_L34_try_end:;
}
- /* "csamtools.pyx":3203
+ /* "pysam/csamtools.pyx":3230
* # read binary output
* out_stdout = inf.read()
* os.remove( stdout_f ) # <<<<<<<<<<<<<<
* else:
* out_stdout = []
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__remove); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_stdout_f);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stdout_f);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_stdout_f);
__Pyx_GIVEREF(__pyx_v_stdout_f);
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3230; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L29;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L26;
}
/*else*/ {
- /* "csamtools.pyx":3205
+ /* "pysam/csamtools.pyx":3232
* os.remove( stdout_f )
* else:
* out_stdout = [] # <<<<<<<<<<<<<<
*
* # get error messages
*/
- __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_v_out_stdout = ((PyObject *)__pyx_t_4);
- __pyx_t_4 = 0;
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3232; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_v_out_stdout = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
}
- __pyx_L29:;
+ __pyx_L26:;
- /* "csamtools.pyx":3208
+ /* "pysam/csamtools.pyx":3235
*
* # get error messages
* pysam_unset_stderr() # <<<<<<<<<<<<<<
@@ -31189,430 +33721,476 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*/
pysam_unset_stderr();
- /* "csamtools.pyx":3209
+ /* "pysam/csamtools.pyx":3236
* # get error messages
* pysam_unset_stderr()
* try: # <<<<<<<<<<<<<<
* with open( stderr_f, "r") as inf:
* out_stderr = inf.readlines()
*/
- {
- __Pyx_ExceptionSave(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11);
- __Pyx_XGOTREF(__pyx_t_9);
- __Pyx_XGOTREF(__pyx_t_10);
- __Pyx_XGOTREF(__pyx_t_11);
- /*try:*/ {
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_9, &__pyx_t_10, &__pyx_t_11);
+ __Pyx_XGOTREF(__pyx_t_9);
+ __Pyx_XGOTREF(__pyx_t_10);
+ __Pyx_XGOTREF(__pyx_t_11);
+ /*try:*/ {
- /* "csamtools.pyx":3210
+ /* "pysam/csamtools.pyx":3237
* pysam_unset_stderr()
* try:
* with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
*/
- /*with:*/ {
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_stderr_f);
- __Pyx_GIVEREF(__pyx_v_stderr_f);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __pyx_t_2 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s____enter__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L84_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L84_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /*try:*/ {
- {
- __Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
- __Pyx_XGOTREF(__pyx_t_16);
- __Pyx_XGOTREF(__pyx_t_17);
- __Pyx_XGOTREF(__pyx_t_18);
- /*try:*/ {
- __Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_2;
- __pyx_t_2 = 0;
+ /*with:*/ {
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L78_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(__pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stderr_f);
+ __Pyx_GIVEREF(__pyx_v_stderr_f);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
+ PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L78_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L78_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s____enter__); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L86_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L86_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_16, &__pyx_t_17, &__pyx_t_18);
+ __Pyx_XGOTREF(__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_17);
+ __Pyx_XGOTREF(__pyx_t_18);
+ /*try:*/ {
+ __Pyx_INCREF(__pyx_t_4);
+ __Pyx_XDECREF(__pyx_v_inf);
+ __pyx_v_inf = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":3211
+ /* "pysam/csamtools.pyx":3238
* try:
* with open( stderr_f, "r") as inf:
* out_stderr = inf.readlines() # <<<<<<<<<<<<<<
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L90_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3211; __pyx_clineno = __LINE__; goto __pyx_L90_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_v_out_stderr = __pyx_t_4;
- __pyx_t_4 = 0;
- }
- __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
- __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
- __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- goto __pyx_L97_try_end;
- __pyx_L90_error:;
- __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
- __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
-
- /* "csamtools.pyx":3210
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3238; __pyx_clineno = __LINE__; goto __pyx_L92_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3238; __pyx_clineno = __LINE__; goto __pyx_L92_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_v_out_stderr = __pyx_t_1;
+ __pyx_t_1 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
+ __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
+ goto __pyx_L99_try_end;
+ __pyx_L92_error:;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+
+ /* "pysam/csamtools.pyx":3237
* pysam_unset_stderr()
* try:
* with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
*/
- /*except:*/ {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_4, &__pyx_t_2, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_21 = PyTuple_New(3); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_21));
- __Pyx_INCREF(__pyx_t_4);
- PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
- __Pyx_INCREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_21, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_21, 2, __pyx_t_3);
- __Pyx_GIVEREF(__pyx_t_3);
- __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_21, NULL);
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
- __Pyx_GOTREF(__pyx_t_19);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
- __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
- __pyx_t_1 = (!__pyx_t_5);
- if (__pyx_t_1) {
+ /*except:*/ {
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_4, &__pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L94_except_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L94_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- __Pyx_ErrRestore(__pyx_t_4, __pyx_t_2, __pyx_t_3);
- __pyx_t_4 = 0; __pyx_t_2 = 0; __pyx_t_3 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L92_except_error;}
- goto __pyx_L100;
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_6, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L94_except_error;}
+ __Pyx_GOTREF(__pyx_t_19);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L94_except_error;}
+ __pyx_t_2 = (!__pyx_t_5);
+ if (__pyx_t_2) {
+ __Pyx_GIVEREF(__pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_4);
+ __Pyx_GIVEREF(__pyx_t_3);
+ __Pyx_ErrRestore(__pyx_t_1, __pyx_t_4, __pyx_t_3);
+ __pyx_t_1 = 0; __pyx_t_4 = 0; __pyx_t_3 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L94_except_error;}
+ goto __pyx_L103;
+ }
+ __pyx_L103:;
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L93_exception_handled;
}
- __pyx_L100:;
- __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- goto __pyx_L91_exception_handled;
+ __pyx_L94_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
+ goto __pyx_L78_error;
+ __pyx_L93_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
+ __pyx_L99_try_end:;
}
- __pyx_L92_except_error:;
- __Pyx_XGIVEREF(__pyx_t_16);
- __Pyx_XGIVEREF(__pyx_t_17);
- __Pyx_XGIVEREF(__pyx_t_18);
- __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- goto __pyx_L76_error;
- __pyx_L91_exception_handled:;
- __Pyx_XGIVEREF(__pyx_t_16);
- __Pyx_XGIVEREF(__pyx_t_17);
- __Pyx_XGIVEREF(__pyx_t_18);
- __Pyx_ExceptionReset(__pyx_t_16, __pyx_t_17, __pyx_t_18);
- __pyx_L97_try_end:;
}
- }
- /*finally:*/ {
- if (__pyx_t_15) {
- __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_183, NULL);
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
- __Pyx_GOTREF(__pyx_t_18);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_18);
- __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L76_error;}
+ /*finally:*/ {
+ if (__pyx_t_15) {
+ __pyx_t_18 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_187, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L78_error;}
+ __Pyx_GOTREF(__pyx_t_18);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_18);
+ __Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
+ if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L78_error;}
+ }
}
+ goto __pyx_L104;
+ __pyx_L86_error:;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L78_error;
+ __pyx_L104:;
}
- goto __pyx_L101;
- __pyx_L84_error:;
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L76_error;
- __pyx_L101:;
}
- }
- /*else:*/ {
+ /*else:*/ {
- /* "csamtools.pyx":3218
- * os.remove( stderr_f )
+ /* "pysam/csamtools.pyx":3244
+ * out_stderr = inf.read()
* else:
* out_stderr = [] # <<<<<<<<<<<<<<
- *
- * return retval, out_stderr, out_stdout
+ * finally:
+ * os.remove( stderr_f )
*/
- __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3218; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_XDECREF(__pyx_v_out_stderr);
- __pyx_v_out_stderr = ((PyObject *)__pyx_t_3);
- __pyx_t_3 = 0;
- }
- __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
- goto __pyx_L83_try_end;
- __pyx_L76_error:;
- __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
- __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
-
- /* "csamtools.pyx":3212
+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_v_out_stderr);
+ __pyx_v_out_stderr = ((PyObject *)__pyx_t_3);
+ __pyx_t_3 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_XDECREF(__pyx_t_11); __pyx_t_11 = 0;
+ goto __pyx_L85_try_end;
+ __pyx_L78_error:;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+
+ /* "pysam/csamtools.pyx":3239
* with open( stderr_f, "r") as inf:
* out_stderr = inf.readlines()
* except UnicodeDecodeError: # <<<<<<<<<<<<<<
* with open( stderr_f, "rb") as inf:
* # read binary output
*/
- __pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
- if (__pyx_t_8) {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3212; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_t_4);
+ __pyx_t_8 = PyErr_ExceptionMatches(__pyx_builtin_UnicodeDecodeError);
+ if (__pyx_t_8) {
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_4, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3239; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":3213
+ /* "pysam/csamtools.pyx":3240
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
* # read binary output
* out_stderr = inf.read()
*/
- /*with:*/ {
- __pyx_t_21 = PyTuple_New(2); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_21));
- __Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_21, 0, __pyx_v_stderr_f);
- __Pyx_GIVEREF(__pyx_v_stderr_f);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
- PyTuple_SET_ITEM(__pyx_t_21, 1, ((PyObject *)__pyx_n_s__rb));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
- __pyx_t_20 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_21), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(((PyObject *)__pyx_t_21)); __pyx_t_21 = 0;
- __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_15);
- __pyx_t_21 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____enter__); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
- __pyx_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L104_error;}
- __Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- /*try:*/ {
- {
- __Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
- __Pyx_XGOTREF(__pyx_t_18);
- __Pyx_XGOTREF(__pyx_t_17);
- __Pyx_XGOTREF(__pyx_t_16);
- /*try:*/ {
- __Pyx_XDECREF(__pyx_v_inf);
- __pyx_v_inf = __pyx_t_20;
- __pyx_t_20 = 0;
-
- /* "csamtools.pyx":3215
+ /*with:*/ {
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __Pyx_INCREF(__pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
+ __Pyx_GIVEREF(__pyx_v_stderr_f);
+ __Pyx_INCREF(((PyObject *)__pyx_n_s__rb));
+ PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
+ __pyx_t_21 = PyObject_Call(__pyx_builtin_open, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ __Pyx_GOTREF(__pyx_t_15);
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_21, __pyx_n_s____enter__); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L107_error;}
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_20 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L107_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ /*try:*/ {
+ {
+ __Pyx_ExceptionSave(&__pyx_t_18, &__pyx_t_17, &__pyx_t_16);
+ __Pyx_XGOTREF(__pyx_t_18);
+ __Pyx_XGOTREF(__pyx_t_17);
+ __Pyx_XGOTREF(__pyx_t_16);
+ /*try:*/ {
+ __Pyx_INCREF(__pyx_t_20);
+ __Pyx_XDECREF(__pyx_v_inf);
+ __pyx_v_inf = __pyx_t_20;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+
+ /* "pysam/csamtools.pyx":3242
* with open( stderr_f, "rb") as inf:
* # read binary output
* out_stderr = inf.read() # <<<<<<<<<<<<<<
- * os.remove( stderr_f )
* else:
+ * out_stderr = []
*/
- __pyx_t_20 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3215; __pyx_clineno = __LINE__; goto __pyx_L110_error;}
- __Pyx_GOTREF(__pyx_t_20);
- __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3215; __pyx_clineno = __LINE__; goto __pyx_L110_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
- __Pyx_XDECREF(__pyx_v_out_stderr);
- __pyx_v_out_stderr = __pyx_t_21;
- __pyx_t_21 = 0;
- }
- __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
- __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
- __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
- goto __pyx_L117_try_end;
- __pyx_L110_error:;
- __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
- __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
-
- /* "csamtools.pyx":3213
+ __pyx_t_20 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3242; __pyx_clineno = __LINE__; goto __pyx_L113_error;}
+ __Pyx_GOTREF(__pyx_t_20);
+ __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3242; __pyx_clineno = __LINE__; goto __pyx_L113_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_v_out_stderr);
+ __pyx_v_out_stderr = __pyx_t_21;
+ __pyx_t_21 = 0;
+ }
+ __Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
+ __Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
+ __Pyx_XDECREF(__pyx_t_16); __pyx_t_16 = 0;
+ goto __pyx_L120_try_end;
+ __pyx_L113_error:;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+
+ /* "pysam/csamtools.pyx":3240
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
* # read binary output
* out_stderr = inf.read()
*/
- /*except:*/ {
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_21, &__pyx_t_20, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_GOTREF(__pyx_t_20);
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_22));
- __Pyx_INCREF(__pyx_t_21);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_21);
- __Pyx_GIVEREF(__pyx_t_21);
- __Pyx_INCREF(__pyx_t_20);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_20);
- __Pyx_GIVEREF(__pyx_t_20);
- __Pyx_INCREF(__pyx_t_6);
- PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
- __Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __Pyx_GOTREF(__pyx_t_19);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_19);
- __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
- if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- __pyx_t_5 = (!__pyx_t_1);
- if (__pyx_t_5) {
+ /*except:*/ {
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ if (__Pyx_GetException(&__pyx_t_21, &__pyx_t_20, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L115_except_error;}
+ __Pyx_GOTREF(__pyx_t_21);
+ __Pyx_GOTREF(__pyx_t_20);
+ __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L115_except_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_INCREF(__pyx_t_21);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_21);
__Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_INCREF(__pyx_t_20);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_20);
__Pyx_GIVEREF(__pyx_t_20);
+ __Pyx_INCREF(__pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- __Pyx_ErrRestore(__pyx_t_21, __pyx_t_20, __pyx_t_6);
- __pyx_t_21 = 0; __pyx_t_20 = 0; __pyx_t_6 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L112_except_error;}
- goto __pyx_L120;
+ __pyx_t_19 = PyObject_Call(__pyx_t_15, __pyx_t_22, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_19)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L115_except_error;}
+ __Pyx_GOTREF(__pyx_t_19);
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_19);
+ __Pyx_DECREF(__pyx_t_19); __pyx_t_19 = 0;
+ if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L115_except_error;}
+ __pyx_t_5 = (!__pyx_t_2);
+ if (__pyx_t_5) {
+ __Pyx_GIVEREF(__pyx_t_21);
+ __Pyx_GIVEREF(__pyx_t_20);
+ __Pyx_GIVEREF(__pyx_t_6);
+ __Pyx_ErrRestore(__pyx_t_21, __pyx_t_20, __pyx_t_6);
+ __pyx_t_21 = 0; __pyx_t_20 = 0; __pyx_t_6 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L115_except_error;}
+ goto __pyx_L124;
+ }
+ __pyx_L124:;
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
+ goto __pyx_L114_exception_handled;
}
- __pyx_L120:;
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- goto __pyx_L111_exception_handled;
+ __pyx_L115_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
+ goto __pyx_L80_except_error;
+ __pyx_L114_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_18);
+ __Pyx_XGIVEREF(__pyx_t_17);
+ __Pyx_XGIVEREF(__pyx_t_16);
+ __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
+ __pyx_L120_try_end:;
}
- __pyx_L112_except_error:;
- __Pyx_XGIVEREF(__pyx_t_18);
- __Pyx_XGIVEREF(__pyx_t_17);
- __Pyx_XGIVEREF(__pyx_t_16);
- __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- goto __pyx_L78_except_error;
- __pyx_L111_exception_handled:;
- __Pyx_XGIVEREF(__pyx_t_18);
- __Pyx_XGIVEREF(__pyx_t_17);
- __Pyx_XGIVEREF(__pyx_t_16);
- __Pyx_ExceptionReset(__pyx_t_18, __pyx_t_17, __pyx_t_16);
- __pyx_L117_try_end:;
}
- }
- /*finally:*/ {
- if (__pyx_t_15) {
- __pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_184, NULL);
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_16);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
- __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
+ /*finally:*/ {
+ if (__pyx_t_15) {
+ __pyx_t_16 = PyObject_Call(__pyx_t_15, __pyx_k_tuple_188, NULL);
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ __Pyx_GOTREF(__pyx_t_16);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_16);
+ __Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
+ if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L80_except_error;}
+ }
}
+ goto __pyx_L125;
+ __pyx_L107_error:;
+ __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
+ goto __pyx_L80_except_error;
+ __pyx_L125:;
}
- goto __pyx_L121;
- __pyx_L104_error:;
- __Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- goto __pyx_L78_except_error;
- __pyx_L121:;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ goto __pyx_L79_exception_handled;
}
+ __pyx_L80_except_error:;
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
+ goto __pyx_L76;
+ __pyx_L79_exception_handled:;
+ __Pyx_XGIVEREF(__pyx_t_9);
+ __Pyx_XGIVEREF(__pyx_t_10);
+ __Pyx_XGIVEREF(__pyx_t_11);
+ __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
+ __pyx_L85_try_end:;
+ }
+ }
- /* "csamtools.pyx":3216
- * # read binary output
- * out_stderr = inf.read()
- * os.remove( stderr_f ) # <<<<<<<<<<<<<<
- * else:
+ /* "pysam/csamtools.pyx":3246
* out_stderr = []
+ * finally:
+ * os.remove( stderr_f ) # <<<<<<<<<<<<<<
+ *
+ * return retval, out_stderr, out_stdout
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_6);
- __pyx_t_20 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__remove); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_20);
- __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __Pyx_INCREF(__pyx_v_stderr_f);
- PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stderr_f);
- __Pyx_GIVEREF(__pyx_v_stderr_f);
- __pyx_t_21 = PyObject_Call(__pyx_t_20, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3216; __pyx_clineno = __LINE__; goto __pyx_L78_except_error;}
- __Pyx_GOTREF(__pyx_t_21);
- __Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- goto __pyx_L77_exception_handled;
+ /*finally:*/ {
+ int __pyx_why;
+ PyObject *__pyx_exc_type, *__pyx_exc_value, *__pyx_exc_tb;
+ int __pyx_exc_lineno;
+ __pyx_exc_type = 0; __pyx_exc_value = 0; __pyx_exc_tb = 0; __pyx_exc_lineno = 0;
+ __pyx_why = 0; goto __pyx_L77;
+ __pyx_L76: {
+ __pyx_why = 4;
+ __Pyx_XDECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_t_21); __pyx_t_21 = 0;
+ __Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
+ __Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
+ __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_ErrFetch(&__pyx_exc_type, &__pyx_exc_value, &__pyx_exc_tb);
+ __pyx_exc_lineno = __pyx_lineno;
+ goto __pyx_L77;
+ }
+ __pyx_L77:;
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3246; __pyx_clineno = __LINE__; goto __pyx_L126_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3246; __pyx_clineno = __LINE__; goto __pyx_L126_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3246; __pyx_clineno = __LINE__; goto __pyx_L126_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_INCREF(__pyx_v_stderr_f);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_stderr_f);
+ __Pyx_GIVEREF(__pyx_v_stderr_f);
+ __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3246; __pyx_clineno = __LINE__; goto __pyx_L126_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ goto __pyx_L127;
+ __pyx_L126_error:;
+ if (__pyx_why == 4) {
+ Py_XDECREF(__pyx_exc_type);
+ Py_XDECREF(__pyx_exc_value);
+ Py_XDECREF(__pyx_exc_tb);
}
- __pyx_L78_except_error:;
- __Pyx_XGIVEREF(__pyx_t_9);
- __Pyx_XGIVEREF(__pyx_t_10);
- __Pyx_XGIVEREF(__pyx_t_11);
- __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
goto __pyx_L1_error;
- __pyx_L77_exception_handled:;
- __Pyx_XGIVEREF(__pyx_t_9);
- __Pyx_XGIVEREF(__pyx_t_10);
- __Pyx_XGIVEREF(__pyx_t_11);
- __Pyx_ExceptionReset(__pyx_t_9, __pyx_t_10, __pyx_t_11);
- __pyx_L83_try_end:;
+ __pyx_L127:;
+ switch (__pyx_why) {
+ case 4: {
+ __Pyx_ErrRestore(__pyx_exc_type, __pyx_exc_value, __pyx_exc_tb);
+ __pyx_lineno = __pyx_exc_lineno;
+ __pyx_exc_type = 0;
+ __pyx_exc_value = 0;
+ __pyx_exc_tb = 0;
+ goto __pyx_L1_error;
+ }
+ }
}
- /* "csamtools.pyx":3220
- * out_stderr = []
+ /* "pysam/csamtools.pyx":3248
+ * os.remove( stderr_f )
*
* return retval, out_stderr, out_stdout # <<<<<<<<<<<<<<
*
* cdef class SNPCall:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }__pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3220; __pyx_clineno = __LINE_ [...]
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_4);
- __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_3 = PyInt_FromLong(__pyx_v_retval); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ if (unlikely(!__pyx_v_out_stderr)) { __Pyx_RaiseUnboundLocalError("out_stderr"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (unlikely(!__pyx_v_out_stdout)) { __Pyx_RaiseUnboundLocalError("out_stdout"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
+ __Pyx_GIVEREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_out_stderr);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_out_stderr);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_out_stderr);
__Pyx_GIVEREF(__pyx_v_out_stderr);
__Pyx_INCREF(__pyx_v_out_stdout);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_out_stdout);
+ PyTuple_SET_ITEM(__pyx_t_1, 2, __pyx_v_out_stdout);
__Pyx_GIVEREF(__pyx_v_out_stdout);
- __pyx_t_4 = 0;
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_3 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
goto __pyx_L0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_20);
__Pyx_XDECREF(__pyx_t_21);
__Pyx_XDECREF(__pyx_t_22);
- __Pyx_AddTraceback("csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_stderr_h);
@@ -31633,7 +34211,18 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
return __pyx_r;
}
-/* "csamtools.pyx":3235
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3263
* property tid:
* '''the chromosome ID as is defined in the header'''
* def __get__(self): # <<<<<<<<<<<<<<
@@ -31641,8 +34230,7 @@ static PyObject *__pyx_pf_9csamtools__samtools_dispatch(PyObject *__pyx_self, Py
*
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3tid___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31650,10 +34238,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_sel
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3235);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3263);
- /* "csamtools.pyx":3236
+ /* "pysam/csamtools.pyx":3264
* '''the chromosome ID as is defined in the header'''
* def __get__(self):
* return self._tid # <<<<<<<<<<<<<<
@@ -31661,7 +34249,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_sel
* property pos:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_tid); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31671,7 +34259,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_sel
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.tid.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31680,7 +34268,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":3240
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3268
* property pos:
* '''nucleotide position of SNP.'''
* def __get__(self): return self._pos # <<<<<<<<<<<<<<
@@ -31688,8 +34287,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3tid___get__(PyObject *__pyx_v_sel
* property reference_base:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_3pos___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31697,10 +34295,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_sel
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3240);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3268);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31710,7 +34308,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_sel
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.pos.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31719,7 +34317,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":3244
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3272
* property reference_base:
* '''reference base at pos. ``N`` if no reference sequence supplied.'''
* def __get__(self): return from_string_and_size( &self._reference_base, 1 ) # <<<<<<<<<<<<<<
@@ -31727,8 +34336,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_3pos___get__(PyObject *__pyx_v_sel
* property genotype:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_14reference_base___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31736,10 +34344,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3244);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3272);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_from_string_and_size((&__pyx_v_self->_reference_base), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31749,7 +34357,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.reference_base.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.reference_base.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31758,7 +34366,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":3248
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3276
* property genotype:
* '''the genotype called.'''
* def __get__(self): return from_string_and_size( &self._genotype, 1 ) # <<<<<<<<<<<<<<
@@ -31766,8 +34385,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_14reference_base___get__(PyObject
* property consensus_quality:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8genotype___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31775,10 +34393,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3248);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3276);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __pyx_f_9csamtools_from_string_and_size((&((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_f_5pysam_9csamtools_from_string_and_size((&__pyx_v_self->_genotype), 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31788,7 +34406,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.genotype.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.genotype.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31797,7 +34415,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":3252
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3280
* property consensus_quality:
* '''the genotype quality (Phred-scaled).'''
* def __get__(self): return self._consensus_quality # <<<<<<<<<<<<<<
@@ -31805,8 +34434,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8genotype___get__(PyObject *__pyx_
* property snp_quality:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_17consensus_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31814,10 +34442,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObje
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3252);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3280);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_consensus_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3280; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31827,7 +34455,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObje
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.consensus_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.consensus_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31836,7 +34464,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObje
return __pyx_r;
}
-/* "csamtools.pyx":3256
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3284
* property snp_quality:
* '''the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.'''
* def __get__(self): return self._snp_quality # <<<<<<<<<<<<<<
@@ -31844,8 +34483,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(PyObje
* property mapping_quality:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_11snp_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31853,10 +34491,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3256);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3284);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_snp_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31866,7 +34504,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.snp_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.snp_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31875,7 +34513,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__
return __pyx_r;
}
-/* "csamtools.pyx":3260
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3288
* property mapping_quality:
* '''the root mean square (rms) of the mapping quality of all reads involved in the call.'''
* def __get__(self): return self._rms_mapping_quality # <<<<<<<<<<<<<<
@@ -31883,8 +34532,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(PyObject *__
* property coverage:
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_15mapping_quality___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31892,10 +34540,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3260);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3288);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_rms_mapping_quality); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3288; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31905,7 +34553,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.mapping_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.mapping_quality.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31914,7 +34562,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject
return __pyx_r;
}
-/* "csamtools.pyx":3264
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__get__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3292
* property coverage:
* '''coverage or read depth - the number of reads involved in the call.'''
* def __get__(self): return self._coverage # <<<<<<<<<<<<<<
@@ -31922,8 +34581,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(PyObject
* def __str__(self):
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall_8coverage___get__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31931,10 +34589,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__get__");
- __Pyx_TraceCall("__get__", __pyx_f[0], 3264);
+ __Pyx_RefNannySetupContext("__get__", 0);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 3292);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyInt_FromLong(((struct __pyx_obj_9csamtools_SNPCall *)__pyx_v_self)->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3264; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromLong(__pyx_v_self->_coverage); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -31944,7 +34602,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_AddTraceback("csamtools.SNPCall.coverage.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.coverage.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -31953,7 +34611,18 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_
return __pyx_r;
}
-/* "csamtools.pyx":3266
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_pw_5pysam_9csamtools_7SNPCall_1__str__(PyObject *__pyx_v_self) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__str__ (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_7SNPCall___str__(((struct __pyx_obj_5pysam_9csamtools_SNPCall *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3294
* def __get__(self): return self._coverage
*
* def __str__(self): # <<<<<<<<<<<<<<
@@ -31961,8 +34630,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall_8coverage___get__(PyObject *__pyx_
* return "\t".join( map(str, (
*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self); /*proto*/
-static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
+static PyObject *__pyx_pf_5pysam_9csamtools_7SNPCall___str__(struct __pyx_obj_5pysam_9csamtools_SNPCall *__pyx_v_self) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
@@ -31979,10 +34647,10 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__str__");
- __Pyx_TraceCall("__str__", __pyx_f[0], 3266);
+ __Pyx_RefNannySetupContext("__str__", 0);
+ __Pyx_TraceCall("__str__", __pyx_f[0], 3294);
- /* "csamtools.pyx":3268
+ /* "pysam/csamtools.pyx":3296
* def __str__(self):
*
* return "\t".join( map(str, ( # <<<<<<<<<<<<<<
@@ -31990,90 +34658,90 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
* self.pos,
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_5), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "csamtools.pyx":3269
+ /* "pysam/csamtools.pyx":3297
*
* return "\t".join( map(str, (
* self.tid, # <<<<<<<<<<<<<<
* self.pos,
* self.reference_base,
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- /* "csamtools.pyx":3270
+ /* "pysam/csamtools.pyx":3298
* return "\t".join( map(str, (
* self.tid,
* self.pos, # <<<<<<<<<<<<<<
* self.reference_base,
* self.genotype,
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__pos); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- /* "csamtools.pyx":3271
+ /* "pysam/csamtools.pyx":3299
* self.tid,
* self.pos,
* self.reference_base, # <<<<<<<<<<<<<<
* self.genotype,
* self.consensus_quality,
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3271; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__reference_base); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- /* "csamtools.pyx":3272
+ /* "pysam/csamtools.pyx":3300
* self.pos,
* self.reference_base,
* self.genotype, # <<<<<<<<<<<<<<
* self.consensus_quality,
* self.snp_quality,
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3272; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__genotype); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- /* "csamtools.pyx":3273
+ /* "pysam/csamtools.pyx":3301
* self.reference_base,
* self.genotype,
* self.consensus_quality, # <<<<<<<<<<<<<<
* self.snp_quality,
* self.mapping_quality,
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3273; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__consensus_quality); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "csamtools.pyx":3274
+ /* "pysam/csamtools.pyx":3302
* self.genotype,
* self.consensus_quality,
* self.snp_quality, # <<<<<<<<<<<<<<
* self.mapping_quality,
* self.coverage ) ) )
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3274; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__snp_quality); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "csamtools.pyx":3275
+ /* "pysam/csamtools.pyx":3303
* self.consensus_quality,
* self.snp_quality,
* self.mapping_quality, # <<<<<<<<<<<<<<
* self.coverage ) ) )
*
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3275; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__mapping_quality); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- /* "csamtools.pyx":3276
+ /* "pysam/csamtools.pyx":3304
* self.snp_quality,
* self.mapping_quality,
* self.coverage ) ) ) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3276; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__coverage); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_10));
+ __pyx_t_10 = PyTuple_New(8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3297; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_3);
@@ -32098,23 +34766,23 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
__pyx_t_7 = 0;
__pyx_t_8 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_9, 1, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3268; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
@@ -32135,7 +34803,7 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
__Pyx_XDECREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_t_10);
- __Pyx_AddTraceback("csamtools.SNPCall.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.SNPCall.__str__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -32144,47 +34812,30 @@ static PyObject *__pyx_pf_9csamtools_7SNPCall___str__(PyObject *__pyx_v_self) {
return __pyx_r;
}
-/* "csamtools.pyx":3786
- * """
- *
- * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
- * self.samfile = samfile
- *
- */
-
-static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
-static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
- struct __pyx_obj_9csamtools_Samfile *__pyx_v_samfile = 0;
+/* Python wrapper */
+static int __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static int __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile = 0;
int __pyx_v_reopen;
- PyObject *__pyx_v_mode = NULL;
- PyObject *__pyx_v_store = NULL;
int __pyx_r;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
- PyObject *__pyx_t_2 = NULL;
- char *__pyx_t_3;
- int __pyx_lineno = 0;
- const char *__pyx_filename = NULL;
- int __pyx_clineno = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
- __Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__init__");
- __Pyx_TraceCall("__init__", __pyx_f[0], 3786);
+ __Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__samfile,&__pyx_n_s__reopen,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
+ switch (pos_args) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
case 0: break;
default: goto __pyx_L5_argtuple_error;
}
kw_args = PyDict_Size(__pyx_kwds);
- switch (PyTuple_GET_SIZE(__pyx_args)) {
+ switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -32193,7 +34844,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, PyTuple_GET_SIZE(__pyx_args), "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3814; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -32203,24 +34854,56 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
default: goto __pyx_L5_argtuple_error;
}
}
- __pyx_v_samfile = ((struct __pyx_obj_9csamtools_Samfile *)values[0]);
+ __pyx_v_samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)values[0]);
if (values[1]) {
- __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_reopen = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_reopen == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3814; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
} else {
+
+ /* "pysam/csamtools.pyx":3814
+ * """
+ *
+ * def __init__(self, Samfile samfile, int reopen = True ): # <<<<<<<<<<<<<<
+ * self.samfile = samfile
+ *
+ */
__pyx_v_reopen = ((int)1);
}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3814; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
- __Pyx_AddTraceback("csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
return -1;
__pyx_L4_argument_unpacking_done:;
- if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_r = __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self), __pyx_v_samfile, __pyx_v_reopen);
+ goto __pyx_L0;
+ __pyx_L1_error:;
+ __pyx_r = -1;
+ __pyx_L0:;
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+static int __pyx_pf_5pysam_9csamtools_12IndexedReads___init__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, struct __pyx_obj_5pysam_9csamtools_Samfile *__pyx_v_samfile, int __pyx_v_reopen) {
+ PyObject *__pyx_v_mode = NULL;
+ PyObject *__pyx_v_store = NULL;
+ int __pyx_r;
+ __Pyx_RefNannyDeclarations
+ PyObject *__pyx_t_1 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ char *__pyx_t_3;
+ samfile_t *__pyx_t_4;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+ __Pyx_TraceDeclarations
+ __Pyx_RefNannySetupContext("__init__", 0);
+ __Pyx_TraceCall("__init__", __pyx_f[0], 3814);
- /* "csamtools.pyx":3787
+ /* "pysam/csamtools.pyx":3815
*
* def __init__(self, Samfile samfile, int reopen = True ):
* self.samfile = samfile # <<<<<<<<<<<<<<
@@ -32229,11 +34912,11 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
*/
__Pyx_INCREF(((PyObject *)__pyx_v_samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samfile));
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile);
- __Pyx_DECREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile = __pyx_v_samfile;
+ __Pyx_GOTREF(__pyx_v_self->samfile);
+ __Pyx_DECREF(((PyObject *)__pyx_v_self->samfile));
+ __pyx_v_self->samfile = __pyx_v_samfile;
- /* "csamtools.pyx":3789
+ /* "pysam/csamtools.pyx":3817
* self.samfile = samfile
*
* if samfile.isbam: mode = b"rb" # <<<<<<<<<<<<<<
@@ -32243,11 +34926,11 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
if (__pyx_v_samfile->isbam) {
__Pyx_INCREF(((PyObject *)__pyx_n_b__rb));
__pyx_v_mode = __pyx_n_b__rb;
- goto __pyx_L6;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":3790
+ /* "pysam/csamtools.pyx":3818
*
* if samfile.isbam: mode = b"rb"
* else: mode = b"r" # <<<<<<<<<<<<<<
@@ -32257,9 +34940,9 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
__Pyx_INCREF(((PyObject *)__pyx_n_b__r));
__pyx_v_mode = __pyx_n_b__r;
}
- __pyx_L6:;
+ __pyx_L3:;
- /* "csamtools.pyx":3794
+ /* "pysam/csamtools.pyx":3822
* # reopen the file - note that this makes the iterator
* # slow and causes pileup to slow down significantly.
* if reopen: # <<<<<<<<<<<<<<
@@ -32268,46 +34951,46 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
*/
if (__pyx_v_reopen) {
- /* "csamtools.pyx":3795
+ /* "pysam/csamtools.pyx":3823
* # slow and causes pileup to slow down significantly.
* if reopen:
* store = StderrStore() # <<<<<<<<<<<<<<
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStore); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_store = __pyx_t_2;
__pyx_t_2 = 0;
- /* "csamtools.pyx":3796
+ /* "pysam/csamtools.pyx":3824
* if reopen:
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL ) # <<<<<<<<<<<<<<
* store.release()
* assert self.fp != NULL
*/
- __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_mode)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_self->fp = samopen(__pyx_v_samfile->_filename, __pyx_t_3, NULL);
- /* "csamtools.pyx":3797
+ /* "pysam/csamtools.pyx":3825
* store = StderrStore()
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release() # <<<<<<<<<<<<<<
* assert self.fp != NULL
* self.owns_samfile = True
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3798
+ /* "pysam/csamtools.pyx":3826
* self.fp = samopen( samfile._filename, mode, NULL )
* store.release()
* assert self.fp != NULL # <<<<<<<<<<<<<<
@@ -32315,45 +34998,46 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
* else:
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- if (unlikely(!(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp != NULL))) {
+ if (unlikely(!(__pyx_v_self->fp != NULL))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "csamtools.pyx":3799
+ /* "pysam/csamtools.pyx":3827
* store.release()
* assert self.fp != NULL
* self.owns_samfile = True # <<<<<<<<<<<<<<
* else:
* self.fp = samfile.samfile
*/
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 1;
- goto __pyx_L7;
+ __pyx_v_self->owns_samfile = 1;
+ goto __pyx_L4;
}
/*else*/ {
- /* "csamtools.pyx":3801
+ /* "pysam/csamtools.pyx":3829
* self.owns_samfile = True
* else:
* self.fp = samfile.samfile # <<<<<<<<<<<<<<
* self.owns_samfile = False
*
*/
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp = __pyx_v_samfile->samfile;
+ __pyx_t_4 = __pyx_v_samfile->samfile;
+ __pyx_v_self->fp = __pyx_t_4;
- /* "csamtools.pyx":3802
+ /* "pysam/csamtools.pyx":3830
* else:
* self.fp = samfile.samfile
* self.owns_samfile = False # <<<<<<<<<<<<<<
*
* assert samfile.isbam, "can only IndexReads on bam files"
*/
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile = 0;
+ __pyx_v_self->owns_samfile = 0;
}
- __pyx_L7:;
+ __pyx_L4:;
- /* "csamtools.pyx":3804
+ /* "pysam/csamtools.pyx":3832
* self.owns_samfile = False
*
* assert samfile.isbam, "can only IndexReads on bam files" # <<<<<<<<<<<<<<
@@ -32362,8 +35046,8 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
if (unlikely(!__pyx_v_samfile->isbam)) {
- PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_185));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_189));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
@@ -32372,7 +35056,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IndexedReads.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = -1;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_mode);
@@ -32382,7 +35066,19 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
return __pyx_r;
}
-/* "csamtools.pyx":3806
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_12IndexedReads_2build[] = "IndexedReads.build(self)\nbuild index.";
+static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_3build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("build (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_12IndexedReads_2build(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3834
* assert samfile.isbam, "can only IndexReads on bam files"
*
* def build( self ): # <<<<<<<<<<<<<<
@@ -32390,9 +35086,7 @@ static int __pyx_pf_9csamtools_12IndexedReads___init__(PyObject *__pyx_v_self, P
*
*/
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused); /*proto*/
-static char __pyx_doc_9csamtools_12IndexedReads_1build[] = "IndexedReads.build(self)\nbuild index.";
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *unused) {
+static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_2build(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self) {
int __pyx_v_ret;
bam1_t *__pyx_v_b;
uint64_t __pyx_v_pos;
@@ -32407,37 +35101,37 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("build");
- __Pyx_TraceCall("build", __pyx_f[0], 3806);
+ __Pyx_RefNannySetupContext("build", 0);
+ __Pyx_TraceCall("build", __pyx_f[0], 3834);
- /* "csamtools.pyx":3809
+ /* "pysam/csamtools.pyx":3837
* '''build index.'''
*
* self.index = collections.defaultdict( list ) # <<<<<<<<<<<<<<
*
* # this method will start indexing from the current file position
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__collections); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__collections); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__defaultdict); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyList_Type))));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyList_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyList_Type))));
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_GIVEREF(__pyx_t_3);
- __Pyx_GOTREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
- __Pyx_DECREF(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index);
- ((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index = __pyx_t_3;
+ __Pyx_GOTREF(__pyx_v_self->index);
+ __Pyx_DECREF(__pyx_v_self->index);
+ __pyx_v_self->index = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":3813
+ /* "pysam/csamtools.pyx":3841
* # this method will start indexing from the current file position
* # if you decide
* cdef int ret = 1 # <<<<<<<<<<<<<<
@@ -32446,7 +35140,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
*/
__pyx_v_ret = 1;
- /* "csamtools.pyx":3814
+ /* "pysam/csamtools.pyx":3842
* # if you decide
* cdef int ret = 1
* cdef bam1_t * b = <bam1_t*> calloc(1, sizeof( bam1_t) ) # <<<<<<<<<<<<<<
@@ -32455,7 +35149,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
*/
__pyx_v_b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
- /* "csamtools.pyx":3818
+ /* "pysam/csamtools.pyx":3846
* cdef uint64_t pos
*
* while ret > 0: # <<<<<<<<<<<<<<
@@ -32466,25 +35160,25 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
__pyx_t_4 = (__pyx_v_ret > 0);
if (!__pyx_t_4) break;
- /* "csamtools.pyx":3819
+ /* "pysam/csamtools.pyx":3847
*
* while ret > 0:
* pos = bam_tell( self.fp.x.bam ) # <<<<<<<<<<<<<<
* ret = samread( self.fp, b)
* if ret > 0:
*/
- __pyx_v_pos = bam_tell(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp->x.bam);
+ __pyx_v_pos = bam_tell(__pyx_v_self->fp->x.bam);
- /* "csamtools.pyx":3820
+ /* "pysam/csamtools.pyx":3848
* while ret > 0:
* pos = bam_tell( self.fp.x.bam )
* ret = samread( self.fp, b) # <<<<<<<<<<<<<<
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b ))
*/
- __pyx_v_ret = samread(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp, __pyx_v_b);
+ __pyx_v_ret = samread(__pyx_v_self->fp, __pyx_v_b);
- /* "csamtools.pyx":3821
+ /* "pysam/csamtools.pyx":3849
* pos = bam_tell( self.fp.x.bam )
* ret = samread( self.fp, b)
* if ret > 0: # <<<<<<<<<<<<<<
@@ -32494,41 +35188,41 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
__pyx_t_4 = (__pyx_v_ret > 0);
if (__pyx_t_4) {
- /* "csamtools.pyx":3822
+ /* "pysam/csamtools.pyx":3850
* ret = samread( self.fp, b)
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b )) # <<<<<<<<<<<<<<
* self.index[qname].append( pos )
*
*/
- __pyx_t_3 = __pyx_f_9csamtools__charptr_to_str(bam1_qname(__pyx_v_b)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __pyx_f_5pysam_9csamtools__charptr_to_str(bam1_qname(__pyx_v_b)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_v_qname);
__pyx_v_qname = __pyx_t_3;
__pyx_t_3 = 0;
- /* "csamtools.pyx":3823
+ /* "pysam/csamtools.pyx":3851
* if ret > 0:
* qname = _charptr_to_str(bam1_qname( b ))
* self.index[qname].append( pos ) # <<<<<<<<<<<<<<
*
* bam_destroy1( b )
*/
- __pyx_t_3 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint64_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint64_t(__pyx_v_pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_Append(__pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Append(__pyx_t_3, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- goto __pyx_L7;
+ goto __pyx_L5;
}
- __pyx_L7:;
+ __pyx_L5:;
}
- /* "csamtools.pyx":3825
+ /* "pysam/csamtools.pyx":3853
* self.index[qname].append( pos )
*
* bam_destroy1( b ) # <<<<<<<<<<<<<<
@@ -32543,7 +35237,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
- __Pyx_AddTraceback("csamtools.IndexedReads.build", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IndexedReads.build", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XDECREF(__pyx_v_qname);
@@ -32553,7 +35247,19 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
return __pyx_r;
}
-/* "csamtools.pyx":3827
+/* Python wrapper */
+static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
+static char __pyx_doc_5pysam_9csamtools_12IndexedReads_4find[] = "IndexedReads.find(self, qname)";
+static PyObject *__pyx_pw_5pysam_9csamtools_12IndexedReads_5find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+ PyObject *__pyx_r = 0;
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("find (wrapper)", 0);
+ __pyx_r = __pyx_pf_5pysam_9csamtools_12IndexedReads_4find(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self), ((PyObject *)__pyx_v_qname));
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "pysam/csamtools.pyx":3855
* bam_destroy1( b )
*
* def find( self, qname ): # <<<<<<<<<<<<<<
@@ -32561,9 +35267,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_1build(PyObject *__pyx_v_sel
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
*/
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname); /*proto*/
-static char __pyx_doc_9csamtools_12IndexedReads_2find[] = "IndexedReads.find(self, qname)";
-static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self, PyObject *__pyx_v_qname) {
+static PyObject *__pyx_pf_5pysam_9csamtools_12IndexedReads_4find(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self, PyObject *__pyx_v_qname) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -32574,20 +35278,20 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("find");
- __Pyx_TraceCall("find", __pyx_f[0], 3827);
+ __Pyx_RefNannySetupContext("find", 0);
+ __Pyx_TraceCall("find", __pyx_f[0], 3855);
- /* "csamtools.pyx":3828
+ /* "pysam/csamtools.pyx":3856
*
* def find( self, qname ):
* if qname in self.index: # <<<<<<<<<<<<<<
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
* else:
*/
- __pyx_t_1 = ((PySequence_Contains(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_qname, __pyx_v_self->index, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
- /* "csamtools.pyx":3829
+ /* "pysam/csamtools.pyx":3857
* def find( self, qname ):
* if qname in self.index:
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False ) # <<<<<<<<<<<<<<
@@ -32595,55 +35299,55 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self
* raise KeyError( "read %s not found" % qname )
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyObject_GetItem(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_self->index, __pyx_v_qname); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __Pyx_INCREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
- __Pyx_GIVEREF(((PyObject *)((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->samfile));
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_INCREF(((PyObject *)__pyx_v_self->samfile));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_self->samfile));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_self->samfile));
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__reopen), __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyEval_CallObjectWithKeywords(((PyObject *)((PyObject*)__pyx_ptype_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3829; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_9csamtools_IteratorRowSelection)), ((PyObject *)__pyx_t_3), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
goto __pyx_L0;
- goto __pyx_L5;
+ goto __pyx_L3;
}
/*else*/ {
- /* "csamtools.pyx":3831
+ /* "pysam/csamtools.pyx":3859
* return IteratorRowSelection( self.samfile, self.index[qname], reopen = False )
* else:
* raise KeyError( "read %s not found" % qname ) # <<<<<<<<<<<<<<
*
* def __dealloc__(self):
*/
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_186), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_190), __pyx_v_qname); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_KeyError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_L5:;
+ __pyx_L3:;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -32651,7 +35355,7 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
- __Pyx_AddTraceback("csamtools.IndexedReads.find", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.csamtools.IndexedReads.find", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -32660,7 +35364,16 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self
return __pyx_r;
}
-/* "csamtools.pyx":3833
+/* Python wrapper */
+static void __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
+static void __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(PyObject *__pyx_v_self) {
+ __Pyx_RefNannyDeclarations
+ __Pyx_RefNannySetupContext("__dealloc__ (wrapper)", 0);
+ __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)__pyx_v_self));
+ __Pyx_RefNannyFinishContext();
+}
+
+/* "pysam/csamtools.pyx":3861
* raise KeyError( "read %s not found" % qname )
*
* def __dealloc__(self): # <<<<<<<<<<<<<<
@@ -32668,49 +35381,48 @@ static PyObject *__pyx_pf_9csamtools_12IndexedReads_2find(PyObject *__pyx_v_self
*
*/
-static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self); /*proto*/
-static void __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pf_5pysam_9csamtools_12IndexedReads_6__dealloc__(struct __pyx_obj_5pysam_9csamtools_IndexedReads *__pyx_v_self) {
__Pyx_RefNannyDeclarations
__Pyx_TraceDeclarations
- __Pyx_RefNannySetupContext("__dealloc__");
- __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3833);
+ __Pyx_RefNannySetupContext("__dealloc__", 0);
+ __Pyx_TraceCall("__dealloc__", __pyx_f[0], 3861);
- /* "csamtools.pyx":3834
+ /* "pysam/csamtools.pyx":3862
*
* def __dealloc__(self):
* if self.owns_samfile: samclose( self.fp ) # <<<<<<<<<<<<<<
*
* __all__ = ["Samfile",
*/
- if (((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->owns_samfile) {
- samclose(((struct __pyx_obj_9csamtools_IndexedReads *)__pyx_v_self)->fp);
- goto __pyx_L5;
+ if (__pyx_v_self->owns_samfile) {
+ samclose(__pyx_v_self->fp);
+ goto __pyx_L3;
}
- __pyx_L5:;
+ __pyx_L3:;
__Pyx_TraceReturn(Py_None);
__Pyx_RefNannyFinishContext();
}
-static struct __pyx_vtabstruct_9csamtools_Fastafile __pyx_vtable_9csamtools_Fastafile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile __pyx_vtable_5pysam_9csamtools_Fastafile;
-static PyObject *__pyx_tp_new_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_Fastafile *p;
+static PyObject *__pyx_tp_new_5pysam_9csamtools_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_Fastafile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_Fastafile *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_Fastafile;
- if (__pyx_pf_9csamtools_9Fastafile___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Fastafile;
+ if (__pyx_pw_5pysam_9csamtools_9Fastafile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_9csamtools_Fastafile(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_9Fastafile_5__dealloc__(o);
+ __pyx_pw_5pysam_9csamtools_9Fastafile_11__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -32718,20 +35430,20 @@ static void __pyx_tp_dealloc_9csamtools_Fastafile(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_9Fastafile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_9Fastafile_8filename___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_9Fastafile_filename(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_9Fastafile_8filename_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_Fastafile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_1_isOpen)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_3_open, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_3_open)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_4close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_4close)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_9Fastafile_6fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_9Fastafile_6fetch)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_Fastafile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_2_isOpen)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_7_open, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_6_open)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_9close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_8close)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_9Fastafile_13fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_9Fastafile_12fetch)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_Fastafile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Fastafile[] = {
+ {(char *)"filename", __pyx_getprop_5pysam_9csamtools_9Fastafile_filename, 0, __Pyx_DOCSTR(__pyx_k_191), 0},
{0, 0, 0, 0, 0}
};
@@ -32794,7 +35506,7 @@ static PyNumberMethods __pyx_tp_as_number_Fastafile = {
};
static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile_2__len__, /*sq_length*/
+ __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
0, /*sq_item*/
@@ -32807,7 +35519,7 @@ static PySequenceMethods __pyx_tp_as_sequence_Fastafile = {
};
static PyMappingMethods __pyx_tp_as_mapping_Fastafile = {
- __pyx_pf_9csamtools_9Fastafile_2__len__, /*mp_length*/
+ __pyx_pw_5pysam_9csamtools_9Fastafile_5__len__, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
@@ -32833,12 +35545,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Fastafile = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_Fastafile = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_Fastafile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Fastafile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Fastafile), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.Fastafile"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_Fastafile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Fastafile, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_Fastafile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -32865,9 +35577,9 @@ static PyTypeObject __pyx_type_9csamtools_Fastafile = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_Fastafile, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools_Fastafile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_Fastafile, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_Fastafile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -32875,7 +35587,7 @@ static PyTypeObject __pyx_type_9csamtools_Fastafile = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_Fastafile, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_Fastafile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -32889,18 +35601,18 @@ static PyTypeObject __pyx_type_9csamtools_Fastafile = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_AlignedRead(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_9csamtools_AlignedRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_11AlignedRead_1__dealloc__(o);
+ __pyx_pw_5pysam_9csamtools_11AlignedRead_3__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -32908,13 +35620,13 @@ static void __pyx_tp_dealloc_9csamtools_AlignedRead(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qname(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5qname___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5qname_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qname_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -32922,13 +35634,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_qname(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigar(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5cigar___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5cigar_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5cigar_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -32936,13 +35648,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_cigar(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_11cigarstring___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_11cigarstring_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_11cigarstring_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -32950,13 +35662,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_cigarstring(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_seq(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3seq___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3seq_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3seq_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -32964,13 +35676,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_seq(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qual(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4qual___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4qual_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qual_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -32978,33 +35690,33 @@ static int __pyx_setprop_9csamtools_11AlignedRead_qual(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_query(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5query___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_query(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5query_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qqual(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5qqual___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5qqual_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qstart(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_6qstart___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_6qstart_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qend(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4qend___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qend(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qend_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_qlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4qlen___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4qlen_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tags(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4tags___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4tags_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tags_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33012,13 +35724,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tags(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_flag(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4flag___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4flag_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4flag_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33026,13 +35738,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_flag(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rname(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5rname___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5rname_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rname_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33040,13 +35752,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_rname(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3tid___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3tid_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3tid_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33054,13 +35766,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tid(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3pos___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3pos_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3pos_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33068,13 +35780,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_pos(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_bin(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_3bin___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_3bin_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_3bin_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33082,25 +35794,25 @@ static int __pyx_setprop_9csamtools_11AlignedRead_bin(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4rlen___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4rlen_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aend(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4aend___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aend(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4aend_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_alen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4alen___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_alen(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4alen_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mapq(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mapq___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mapq_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mapq_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33108,13 +35820,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mapq(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mrnm(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mrnm___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mrnm_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mrnm_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33122,13 +35834,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mrnm(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_rnext(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5rnext___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5rnext_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5rnext_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33136,13 +35848,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_rnext(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mpos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4mpos___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4mpos_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4mpos_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33150,13 +35862,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mpos(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_pnext(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5pnext___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5pnext_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5pnext_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33164,13 +35876,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_pnext(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_isize(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_5isize___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_5isize_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_5isize_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33178,13 +35890,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_isize(PyObject *o, PyObject *v
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_tlen(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_4tlen___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_4tlen_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_4tlen_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33192,13 +35904,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_tlen(PyObject *o, PyObject *v,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_paired(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_paired___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_paired_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_paired_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33206,13 +35918,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_paired(PyObject *o, PyObjec
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_14is_proper_pair_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_14is_proper_pair_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33220,13 +35932,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair(PyObject *o, Py
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_11is_unmapped_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_11is_unmapped_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33234,13 +35946,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_unmapped(PyObject *o, PyObj
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_16mate_is_unmapped_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_16mate_is_unmapped_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33248,13 +35960,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped(PyObject *o,
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_10is_reverse___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_10is_reverse_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_10is_reverse_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33262,13 +35974,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_reverse(PyObject *o, PyObje
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_15mate_is_reverse_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_15mate_is_reverse_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33276,13 +35988,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse(PyObject *o, P
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read1(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read1___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read1_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read1_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33290,13 +36002,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_read1(PyObject *o, PyObject
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_read2(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read2___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_8is_read2_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_8is_read2_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33304,13 +36016,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_read2(PyObject *o, PyObject
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_secondary___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_secondary_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_secondary_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33318,13 +36030,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_secondary(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_9is_qcfail_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_9is_qcfail_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33332,13 +36044,13 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_qcfail(PyObject *o, PyObjec
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11AlignedRead_12is_duplicate_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_12is_duplicate_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33346,62 +36058,62 @@ static int __pyx_setprop_9csamtools_11AlignedRead_is_duplicate(PyObject *o, PyOb
}
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_positions(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_9positions___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_positions(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11AlignedRead_13aligned_pairs___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_13aligned_pairs_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_AlignedRead[] = {
- {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_3compare, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_3compare)},
- {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_5overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_5overlap)},
- {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_6opt, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_6opt)},
- {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pf_9csamtools_11AlignedRead_7fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_11AlignedRead_7fancy_str)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_AlignedRead[] = {
+ {__Pyx_NAMESTR("compare"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_7compare, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_6compare)},
+ {__Pyx_NAMESTR("overlap"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_11overlap, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_10overlap)},
+ {__Pyx_NAMESTR("opt"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_13opt, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_12opt)},
+ {__Pyx_NAMESTR("fancy_str"), (PyCFunction)__pyx_pw_5pysam_9csamtools_11AlignedRead_15fancy_str, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_11AlignedRead_14fancy_str)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_AlignedRead[] = {
- {(char *)"qname", __pyx_getprop_9csamtools_11AlignedRead_qname, __pyx_setprop_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_188), 0},
- {(char *)"cigar", __pyx_getprop_9csamtools_11AlignedRead_cigar, __pyx_setprop_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_189), 0},
- {(char *)"cigarstring", __pyx_getprop_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_190), 0},
- {(char *)"seq", __pyx_getprop_9csamtools_11AlignedRead_seq, __pyx_setprop_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_191), 0},
- {(char *)"qual", __pyx_getprop_9csamtools_11AlignedRead_qual, __pyx_setprop_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_192), 0},
- {(char *)"query", __pyx_getprop_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_193), 0},
- {(char *)"qqual", __pyx_getprop_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_194), 0},
- {(char *)"qstart", __pyx_getprop_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_195), 0},
- {(char *)"qend", __pyx_getprop_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_196), 0},
- {(char *)"qlen", __pyx_getprop_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
- {(char *)"tags", __pyx_getprop_9csamtools_11AlignedRead_tags, __pyx_setprop_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_198), 0},
- {(char *)"flag", __pyx_getprop_9csamtools_11AlignedRead_flag, __pyx_setprop_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_199), 0},
- {(char *)"rname", __pyx_getprop_9csamtools_11AlignedRead_rname, __pyx_setprop_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_200), 0},
- {(char *)"tid", __pyx_getprop_9csamtools_11AlignedRead_tid, __pyx_setprop_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_201), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_11AlignedRead_pos, __pyx_setprop_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_202), 0},
- {(char *)"bin", __pyx_getprop_9csamtools_11AlignedRead_bin, __pyx_setprop_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_203), 0},
- {(char *)"rlen", __pyx_getprop_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_204), 0},
- {(char *)"aend", __pyx_getprop_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_205), 0},
- {(char *)"alen", __pyx_getprop_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_206), 0},
- {(char *)"mapq", __pyx_getprop_9csamtools_11AlignedRead_mapq, __pyx_setprop_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_207), 0},
- {(char *)"mrnm", __pyx_getprop_9csamtools_11AlignedRead_mrnm, __pyx_setprop_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_208), 0},
- {(char *)"rnext", __pyx_getprop_9csamtools_11AlignedRead_rnext, __pyx_setprop_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_209), 0},
- {(char *)"mpos", __pyx_getprop_9csamtools_11AlignedRead_mpos, __pyx_setprop_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_210), 0},
- {(char *)"pnext", __pyx_getprop_9csamtools_11AlignedRead_pnext, __pyx_setprop_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_211), 0},
- {(char *)"isize", __pyx_getprop_9csamtools_11AlignedRead_isize, __pyx_setprop_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_212), 0},
- {(char *)"tlen", __pyx_getprop_9csamtools_11AlignedRead_tlen, __pyx_setprop_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_213), 0},
- {(char *)"is_paired", __pyx_getprop_9csamtools_11AlignedRead_is_paired, __pyx_setprop_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_214), 0},
- {(char *)"is_proper_pair", __pyx_getprop_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_215), 0},
- {(char *)"is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_216), 0},
- {(char *)"mate_is_unmapped", __pyx_getprop_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_217), 0},
- {(char *)"is_reverse", __pyx_getprop_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_218), 0},
- {(char *)"mate_is_reverse", __pyx_getprop_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_219), 0},
- {(char *)"is_read1", __pyx_getprop_9csamtools_11AlignedRead_is_read1, __pyx_setprop_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_220), 0},
- {(char *)"is_read2", __pyx_getprop_9csamtools_11AlignedRead_is_read2, __pyx_setprop_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_221), 0},
- {(char *)"is_secondary", __pyx_getprop_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_222), 0},
- {(char *)"is_qcfail", __pyx_getprop_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_223), 0},
- {(char *)"is_duplicate", __pyx_getprop_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_224), 0},
- {(char *)"positions", __pyx_getprop_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_225), 0},
- {(char *)"aligned_pairs", __pyx_getprop_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_226), 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_AlignedRead[] = {
+ {(char *)"qname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_qname, __Pyx_DOCSTR(__pyx_k_192), 0},
+ {(char *)"cigar", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigar, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigar, __Pyx_DOCSTR(__pyx_k_193), 0},
+ {(char *)"cigarstring", __pyx_getprop_5pysam_9csamtools_11AlignedRead_cigarstring, __pyx_setprop_5pysam_9csamtools_11AlignedRead_cigarstring, __Pyx_DOCSTR(__pyx_k_194), 0},
+ {(char *)"seq", __pyx_getprop_5pysam_9csamtools_11AlignedRead_seq, __pyx_setprop_5pysam_9csamtools_11AlignedRead_seq, __Pyx_DOCSTR(__pyx_k_195), 0},
+ {(char *)"qual", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qual, __pyx_setprop_5pysam_9csamtools_11AlignedRead_qual, __Pyx_DOCSTR(__pyx_k_196), 0},
+ {(char *)"query", __pyx_getprop_5pysam_9csamtools_11AlignedRead_query, 0, __Pyx_DOCSTR(__pyx_k_197), 0},
+ {(char *)"qqual", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qqual, 0, __Pyx_DOCSTR(__pyx_k_198), 0},
+ {(char *)"qstart", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qstart, 0, __Pyx_DOCSTR(__pyx_k_199), 0},
+ {(char *)"qend", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qend, 0, __Pyx_DOCSTR(__pyx_k_200), 0},
+ {(char *)"qlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_qlen, 0, __Pyx_DOCSTR(__pyx_k_201), 0},
+ {(char *)"tags", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tags, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tags, __Pyx_DOCSTR(__pyx_k_202), 0},
+ {(char *)"flag", __pyx_getprop_5pysam_9csamtools_11AlignedRead_flag, __pyx_setprop_5pysam_9csamtools_11AlignedRead_flag, __Pyx_DOCSTR(__pyx_k_203), 0},
+ {(char *)"rname", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rname, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rname, __Pyx_DOCSTR(__pyx_k_204), 0},
+ {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tid, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tid, __Pyx_DOCSTR(__pyx_k_205), 0},
+ {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pos, __Pyx_DOCSTR(__pyx_k_206), 0},
+ {(char *)"bin", __pyx_getprop_5pysam_9csamtools_11AlignedRead_bin, __pyx_setprop_5pysam_9csamtools_11AlignedRead_bin, __Pyx_DOCSTR(__pyx_k_207), 0},
+ {(char *)"rlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rlen, 0, __Pyx_DOCSTR(__pyx_k_208), 0},
+ {(char *)"aend", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aend, 0, __Pyx_DOCSTR(__pyx_k_209), 0},
+ {(char *)"alen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_alen, 0, __Pyx_DOCSTR(__pyx_k_210), 0},
+ {(char *)"mapq", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mapq, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mapq, __Pyx_DOCSTR(__pyx_k_211), 0},
+ {(char *)"mrnm", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mrnm, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mrnm, __Pyx_DOCSTR(__pyx_k_212), 0},
+ {(char *)"rnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_rnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_rnext, __Pyx_DOCSTR(__pyx_k_213), 0},
+ {(char *)"mpos", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mpos, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mpos, __Pyx_DOCSTR(__pyx_k_214), 0},
+ {(char *)"pnext", __pyx_getprop_5pysam_9csamtools_11AlignedRead_pnext, __pyx_setprop_5pysam_9csamtools_11AlignedRead_pnext, __Pyx_DOCSTR(__pyx_k_215), 0},
+ {(char *)"isize", __pyx_getprop_5pysam_9csamtools_11AlignedRead_isize, __pyx_setprop_5pysam_9csamtools_11AlignedRead_isize, __Pyx_DOCSTR(__pyx_k_216), 0},
+ {(char *)"tlen", __pyx_getprop_5pysam_9csamtools_11AlignedRead_tlen, __pyx_setprop_5pysam_9csamtools_11AlignedRead_tlen, __Pyx_DOCSTR(__pyx_k_217), 0},
+ {(char *)"is_paired", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_paired, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_paired, __Pyx_DOCSTR(__pyx_k_218), 0},
+ {(char *)"is_proper_pair", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_proper_pair, __Pyx_DOCSTR(__pyx_k_219), 0},
+ {(char *)"is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_unmapped, __Pyx_DOCSTR(__pyx_k_220), 0},
+ {(char *)"mate_is_unmapped", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_unmapped, __Pyx_DOCSTR(__pyx_k_221), 0},
+ {(char *)"is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_reverse, __Pyx_DOCSTR(__pyx_k_222), 0},
+ {(char *)"mate_is_reverse", __pyx_getprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __pyx_setprop_5pysam_9csamtools_11AlignedRead_mate_is_reverse, __Pyx_DOCSTR(__pyx_k_223), 0},
+ {(char *)"is_read1", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read1, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read1, __Pyx_DOCSTR(__pyx_k_224), 0},
+ {(char *)"is_read2", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_read2, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_read2, __Pyx_DOCSTR(__pyx_k_225), 0},
+ {(char *)"is_secondary", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_secondary, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_secondary, __Pyx_DOCSTR(__pyx_k_226), 0},
+ {(char *)"is_qcfail", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_qcfail, __Pyx_DOCSTR(__pyx_k_227), 0},
+ {(char *)"is_duplicate", __pyx_getprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __pyx_setprop_5pysam_9csamtools_11AlignedRead_is_duplicate, __Pyx_DOCSTR(__pyx_k_228), 0},
+ {(char *)"positions", __pyx_getprop_5pysam_9csamtools_11AlignedRead_positions, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
+ {(char *)"aligned_pairs", __pyx_getprop_5pysam_9csamtools_11AlignedRead_aligned_pairs, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
{0, 0, 0, 0, 0}
};
@@ -33503,12 +36215,12 @@ static PyBufferProcs __pyx_tp_as_buffer_AlignedRead = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_AlignedRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.AlignedRead"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_AlignedRead), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.AlignedRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_AlignedRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_AlignedRead, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_AlignedRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -33521,9 +36233,9 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
&__pyx_tp_as_number_AlignedRead, /*tp_as_number*/
&__pyx_tp_as_sequence_AlignedRead, /*tp_as_sequence*/
&__pyx_tp_as_mapping_AlignedRead, /*tp_as_mapping*/
- __pyx_pf_9csamtools_11AlignedRead_4__hash__, /*tp_hash*/
+ __pyx_pw_5pysam_9csamtools_11AlignedRead_9__hash__, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_11AlignedRead_2__str__, /*tp_str*/
+ __pyx_pw_5pysam_9csamtools_11AlignedRead_5__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_AlignedRead, /*tp_as_buffer*/
@@ -33535,17 +36247,17 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_AlignedRead, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools_AlignedRead, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_AlignedRead, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_AlignedRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_11AlignedRead___init__, /*tp_init*/
+ __pyx_pw_5pysam_9csamtools_11AlignedRead_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_AlignedRead, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_AlignedRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -33558,26 +36270,26 @@ static PyTypeObject __pyx_type_9csamtools_AlignedRead = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_Samfile __pyx_vtable_9csamtools_Samfile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile __pyx_vtable_5pysam_9csamtools_Samfile;
-static PyObject *__pyx_tp_new_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_Samfile *p;
+static PyObject *__pyx_tp_new_5pysam_9csamtools_Samfile(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_Samfile *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_Samfile *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_Samfile;
- if (__pyx_pf_9csamtools_7Samfile___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_Samfile;
+ if (__pyx_pw_5pysam_9csamtools_7Samfile_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_9csamtools_Samfile(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_7Samfile_15__dealloc__(o);
+ __pyx_pw_5pysam_9csamtools_7Samfile_31__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -33585,70 +36297,70 @@ static void __pyx_tp_dealloc_9csamtools_Samfile(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_filename(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_8filename___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_8filename_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_nreferences(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_11nreferences___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_nreferences(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_11nreferences_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_references(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_10references___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_references(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_10references_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_lengths(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_7lengths___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_lengths(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_7lengths_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_mapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_6mapped___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_mapped(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_6mapped_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_unmapped(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_8unmapped___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_unmapped(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_8unmapped_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_text(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_4text___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_text(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_4text_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_7Samfile_header(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7Samfile_6header___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_7Samfile_header(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7Samfile_6header_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_Samfile[] = {
- {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_1_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_1_isOpen)},
- {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_2_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_2_hasIndex)},
- {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_3_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_3_open)},
- {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_4gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_4gettid)},
- {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_5getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_5getrname)},
- {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_6_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_6_parseRegion)},
- {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_7reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_7reset)},
- {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_8seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_8seek)},
- {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_9tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_9tell)},
- {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_10fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_10fetch)},
- {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_11mate, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_11mate)},
- {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_12count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_12count)},
- {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_13pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_13pileup)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_14close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_14close)},
- {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_16write, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_16write)},
- {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_17__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_17__enter__)},
- {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_18__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_18__exit__)},
- {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_19_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_19_buildLine)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_7Samfile_21__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_7Samfile_21__next__)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_Samfile[] = {
+ {__Pyx_NAMESTR("_isOpen"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_3_isOpen, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_2_isOpen)},
+ {__Pyx_NAMESTR("_hasIndex"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_5_hasIndex, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_4_hasIndex)},
+ {__Pyx_NAMESTR("_open"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_7_open, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_6_open)},
+ {__Pyx_NAMESTR("gettid"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_9gettid, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_8gettid)},
+ {__Pyx_NAMESTR("getrname"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_11getrname, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_10getrname)},
+ {__Pyx_NAMESTR("_parseRegion"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_13_parseRegion, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_12_parseRegion)},
+ {__Pyx_NAMESTR("reset"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_15reset, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_14reset)},
+ {__Pyx_NAMESTR("seek"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_17seek, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_16seek)},
+ {__Pyx_NAMESTR("tell"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_19tell, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_18tell)},
+ {__Pyx_NAMESTR("fetch"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_21fetch, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_20fetch)},
+ {__Pyx_NAMESTR("mate"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_23mate, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_22mate)},
+ {__Pyx_NAMESTR("count"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_25count, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_24count)},
+ {__Pyx_NAMESTR("pileup"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_27pileup, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_26pileup)},
+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_29close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_28close)},
+ {__Pyx_NAMESTR("write"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_33write, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_32write)},
+ {__Pyx_NAMESTR("__enter__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_35__enter__, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_34__enter__)},
+ {__Pyx_NAMESTR("__exit__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_37__exit__, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_36__exit__)},
+ {__Pyx_NAMESTR("_buildLine"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_39_buildLine, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_38_buildLine)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_7Samfile_43__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_7Samfile_42__next__)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_Samfile[] = {
- {(char *)"filename", __pyx_getprop_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_187), 0},
- {(char *)"nreferences", __pyx_getprop_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_227), 0},
- {(char *)"references", __pyx_getprop_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_228), 0},
- {(char *)"lengths", __pyx_getprop_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_229), 0},
- {(char *)"mapped", __pyx_getprop_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_230), 0},
- {(char *)"unmapped", __pyx_getprop_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
- {(char *)"text", __pyx_getprop_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
- {(char *)"header", __pyx_getprop_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_Samfile[] = {
+ {(char *)"filename", __pyx_getprop_5pysam_9csamtools_7Samfile_filename, 0, __Pyx_DOCSTR(__pyx_k_191), 0},
+ {(char *)"nreferences", __pyx_getprop_5pysam_9csamtools_7Samfile_nreferences, 0, __Pyx_DOCSTR(__pyx_k_231), 0},
+ {(char *)"references", __pyx_getprop_5pysam_9csamtools_7Samfile_references, 0, __Pyx_DOCSTR(__pyx_k_232), 0},
+ {(char *)"lengths", __pyx_getprop_5pysam_9csamtools_7Samfile_lengths, 0, __Pyx_DOCSTR(__pyx_k_233), 0},
+ {(char *)"mapped", __pyx_getprop_5pysam_9csamtools_7Samfile_mapped, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
+ {(char *)"unmapped", __pyx_getprop_5pysam_9csamtools_7Samfile_unmapped, 0, __Pyx_DOCSTR(__pyx_k_235), 0},
+ {(char *)"text", __pyx_getprop_5pysam_9csamtools_7Samfile_text, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
+ {(char *)"header", __pyx_getprop_5pysam_9csamtools_7Samfile_header, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
{0, 0, 0, 0, 0}
};
@@ -33750,12 +36462,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Samfile = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_Samfile = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_Samfile = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.Samfile"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_Samfile), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.Samfile"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_Samfile), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_Samfile, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_Samfile, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -33780,11 +36492,11 @@ static PyTypeObject __pyx_type_9csamtools_Samfile = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_7Samfile_20__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_7Samfile_21__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_Samfile, /*tp_methods*/
+ __pyx_pw_5pysam_9csamtools_7Samfile_41__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_9csamtools_7Samfile_43__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_Samfile, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_Samfile, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_Samfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -33792,7 +36504,7 @@ static PyTypeObject __pyx_type_9csamtools_Samfile = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_Samfile, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_Samfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -33806,27 +36518,27 @@ static PyTypeObject __pyx_type_9csamtools_Samfile = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_PileupProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupProxy(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_9csamtools_PileupProxy(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_3tid___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_tid(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11PileupProxy_3tid_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_n(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_1n___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_1__get__(o);
}
-static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, void *x) {
+static int __pyx_setprop_5pysam_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
if (v) {
- return __pyx_pf_9csamtools_11PileupProxy_1n_1__set__(o, v);
+ return __pyx_pw_5pysam_9csamtools_11PileupProxy_1n_3__set__(o, v);
}
else {
PyErr_SetString(PyExc_NotImplementedError, "__del__");
@@ -33834,23 +36546,23 @@ static int __pyx_setprop_9csamtools_11PileupProxy_n(PyObject *o, PyObject *v, vo
}
}
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_3pos___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11PileupProxy_3pos_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_11PileupProxy_pileups(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_11PileupProxy_7pileups___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11PileupProxy_7pileups_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_PileupProxy[] = {
+static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupProxy[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_PileupProxy[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
- {(char *)"n", __pyx_getprop_9csamtools_11PileupProxy_n, __pyx_setprop_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_235), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_11PileupProxy_pos, 0, 0, 0},
- {(char *)"pileups", __pyx_getprop_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_236), 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupProxy[] = {
+ {(char *)"tid", __pyx_getprop_5pysam_9csamtools_11PileupProxy_tid, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
+ {(char *)"n", __pyx_getprop_5pysam_9csamtools_11PileupProxy_n, __pyx_setprop_5pysam_9csamtools_11PileupProxy_n, __Pyx_DOCSTR(__pyx_k_239), 0},
+ {(char *)"pos", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pos, 0, 0, 0},
+ {(char *)"pileups", __pyx_getprop_5pysam_9csamtools_11PileupProxy_pileups, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
{0, 0, 0, 0, 0}
};
@@ -33952,12 +36664,12 @@ static PyBufferProcs __pyx_tp_as_buffer_PileupProxy = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_PileupProxy = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.PileupProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_PileupProxy), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.PileupProxy"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_PileupProxy), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_PileupProxy, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_PileupProxy, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -33972,7 +36684,7 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
&__pyx_tp_as_mapping_PileupProxy, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_11PileupProxy_1__str__, /*tp_str*/
+ __pyx_pw_5pysam_9csamtools_11PileupProxy_3__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_PileupProxy, /*tp_as_buffer*/
@@ -33984,17 +36696,17 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_PileupProxy, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools_PileupProxy, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_PileupProxy, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_PileupProxy, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_11PileupProxy___init__, /*tp_init*/
+ __pyx_pw_5pysam_9csamtools_11PileupProxy_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_PileupProxy, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_PileupProxy, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -34008,79 +36720,81 @@ static PyTypeObject __pyx_type_9csamtools_PileupProxy = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_PileupRead(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_PileupRead *p;
+static PyObject *__pyx_tp_new_5pysam_9csamtools_PileupRead(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_PileupRead *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_PileupRead *)o);
- p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ p = ((struct __pyx_obj_5pysam_9csamtools_PileupRead *)o);
+ p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
- Py_XDECREF(((PyObject *)p->_alignment));
+static void __pyx_tp_dealloc_5pysam_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->_alignment);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_9csamtools_PileupRead(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+ struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
if (p->_alignment) {
e = (*v)(((PyObject*)p->_alignment), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_PileupRead(PyObject *o) {
- struct __pyx_obj_9csamtools_PileupRead *p = (struct __pyx_obj_9csamtools_PileupRead *)o;
+static int __pyx_tp_clear_5pysam_9csamtools_PileupRead(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_PileupRead *p = (struct __pyx_obj_5pysam_9csamtools_PileupRead *)o;
PyObject* tmp;
tmp = ((PyObject*)p->_alignment);
- p->_alignment = ((struct __pyx_obj_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
+ p->_alignment = ((struct __pyx_obj_5pysam_9csamtools_AlignedRead *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_alignment(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_9alignment___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_alignment(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_9alignment_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_qpos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_4qpos___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_qpos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_4qpos_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_indel(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_5indel___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_indel(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_5indel_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_del(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_6is_del___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_del(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_6is_del_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_head(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_7is_head___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_head(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_head_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_is_tail(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_7is_tail___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_7is_tail_1__get__(o);
}
-static PyObject *__pyx_getprop_9csamtools_10PileupRead_level(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_10PileupRead_5level___get__(o);
+static PyObject *__pyx_getprop_5pysam_9csamtools_10PileupRead_level(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_10PileupRead_5level_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools_PileupRead[] = {
+static PyMethodDef __pyx_methods_5pysam_9csamtools_PileupRead[] = {
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_PileupRead[] = {
- {(char *)"alignment", __pyx_getprop_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_237), 0},
- {(char *)"qpos", __pyx_getprop_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
- {(char *)"indel", __pyx_getprop_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_239), 0},
- {(char *)"is_del", __pyx_getprop_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_240), 0},
- {(char *)"is_head", __pyx_getprop_9csamtools_10PileupRead_is_head, 0, 0, 0},
- {(char *)"is_tail", __pyx_getprop_9csamtools_10PileupRead_is_tail, 0, 0, 0},
- {(char *)"level", __pyx_getprop_9csamtools_10PileupRead_level, 0, 0, 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_PileupRead[] = {
+ {(char *)"alignment", __pyx_getprop_5pysam_9csamtools_10PileupRead_alignment, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
+ {(char *)"qpos", __pyx_getprop_5pysam_9csamtools_10PileupRead_qpos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
+ {(char *)"indel", __pyx_getprop_5pysam_9csamtools_10PileupRead_indel, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
+ {(char *)"is_del", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_del, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
+ {(char *)"is_head", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_head, 0, 0, 0},
+ {(char *)"is_tail", __pyx_getprop_5pysam_9csamtools_10PileupRead_is_tail, 0, 0, 0},
+ {(char *)"level", __pyx_getprop_5pysam_9csamtools_10PileupRead_level, 0, 0, 0},
{0, 0, 0, 0, 0}
};
@@ -34142,387 +36856,7 @@ static PyNumberMethods __pyx_tp_as_number_PileupRead = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_PileupRead = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_9csamtools_PileupRead = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.PileupRead"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_PileupRead), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_PileupRead, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_PileupRead, /*tp_as_number*/
- &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pf_9csamtools_10PileupRead_1__str__, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_PileupRead, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_PileupRead, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_PileupRead, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_9csamtools_PileupRead, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_10PileupRead___init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_PileupRead, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-
-static PyObject *__pyx_tp_new_9csamtools_IteratorRow(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = (*t->tp_alloc)(t, 0);
- if (!o) return 0;
- return o;
-}
-
-static void __pyx_tp_dealloc_9csamtools_IteratorRow(PyObject *o) {
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IteratorRow[] = {
- {0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IteratorRow = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRow = {
- 0, /*sq_length*/
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- 0, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = {
- 0, /*mp_length*/
- 0, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
-};
-
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getreadbuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getwritebuffer*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getsegcount*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*bf_getcharbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_getbuffer*/
- #endif
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*bf_releasebuffer*/
- #endif
-};
-
-static PyTypeObject __pyx_type_9csamtools_IteratorRow = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRow"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRow), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRow, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRow, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference [...]
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRow, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRow, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
-};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowRegion __pyx_vtable_9csamtools_IteratorRowRegion;
-
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
- if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowRegion;
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_17IteratorRowRegion___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
- return o;
-}
-
-static void __pyx_tp_dealloc_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_17IteratorRowRegion_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_XDECREF(((PyObject *)p->samfile));
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
-}
-
-static int __pyx_tp_traverse_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
- }
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_9csamtools_IteratorRowRegion(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_9csamtools_IteratorRowRegion *)o;
- PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_17IteratorRowRegion_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_17IteratorRowRegion_2__next__)},
- {0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
- 0, /*nb_add*/
- 0, /*nb_subtract*/
- 0, /*nb_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_divide*/
- #endif
- 0, /*nb_remainder*/
- 0, /*nb_divmod*/
- 0, /*nb_power*/
- 0, /*nb_negative*/
- 0, /*nb_positive*/
- 0, /*nb_absolute*/
- 0, /*nb_nonzero*/
- 0, /*nb_invert*/
- 0, /*nb_lshift*/
- 0, /*nb_rshift*/
- 0, /*nb_and*/
- 0, /*nb_xor*/
- 0, /*nb_or*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_coerce*/
- #endif
- 0, /*nb_int*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_long*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*nb_float*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_oct*/
- #endif
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_hex*/
- #endif
- 0, /*nb_inplace_add*/
- 0, /*nb_inplace_subtract*/
- 0, /*nb_inplace_multiply*/
- #if PY_MAJOR_VERSION < 3
- 0, /*nb_inplace_divide*/
- #endif
- 0, /*nb_inplace_remainder*/
- 0, /*nb_inplace_power*/
- 0, /*nb_inplace_lshift*/
- 0, /*nb_inplace_rshift*/
- 0, /*nb_inplace_and*/
- 0, /*nb_inplace_xor*/
- 0, /*nb_inplace_or*/
- 0, /*nb_floor_divide*/
- 0, /*nb_true_divide*/
- 0, /*nb_inplace_floor_divide*/
- 0, /*nb_inplace_true_divide*/
- #if PY_VERSION_HEX >= 0x02050000
- 0, /*nb_index*/
- #endif
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
+static PySequenceMethods __pyx_tp_as_sequence_PileupRead = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -34535,13 +36869,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
+static PyMappingMethods __pyx_tp_as_mapping_PileupRead = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
+static PyBufferProcs __pyx_tp_as_buffer_PileupRead = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -34562,12 +36896,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_PileupRead = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.PileupRead"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_PileupRead), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowRegion, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_PileupRead, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -34577,34 +36911,34 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/
+ &__pyx_tp_as_number_PileupRead, /*tp_as_number*/
+ &__pyx_tp_as_sequence_PileupRead, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_PileupRead, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pw_5pysam_9csamtools_10PileupRead_3__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_PileupRead, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each [...]
- __pyx_tp_traverse_9csamtools_IteratorRowRegion, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowRegion, /*tp_clear*/
+ __Pyx_DOCSTR("PileupRead()\nA read aligned to a column.\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools_PileupRead, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_PileupRead, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_17IteratorRowRegion_1__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_17IteratorRowRegion_2__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowRegion, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_PileupRead, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_PileupRead, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pw_5pysam_9csamtools_10PileupRead_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowRegion, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_PileupRead, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -34617,39 +36951,22 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowRegion = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowAll __pyx_vtable_9csamtools_IteratorRowAll;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAll *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRow(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAll *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowAll;
- if (__pyx_pf_9csamtools_14IteratorRowAll___cinit__(o, a, k) < 0) {
- Py_DECREF(o); o = 0;
- }
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAll(PyObject *o) {
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_14IteratorRowAll_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(PyObject *o) {
+ (*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAll[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_14IteratorRowAll_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorRowAll_2__next__)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRow[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRow = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -34707,7 +37024,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRow = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -34720,13 +37037,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRow = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRow = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -34747,12 +37064,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAll"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorRow"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRow), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAll, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -34762,24 +37079,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRow, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRow, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRow, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorRow, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("abstract base class for iterators over mapped reads.\n\n Various iterators implement different behaviours for wrapping around\n contig boundaries. Examples include:\n\n :class:`pysam.IteratorRowRegion`\n iterate within a single contig and a defined region.\n\n :class:`pysam.IteratorRowAll`\n iterate until EOF. This iterator will also include unmapped reads.\n\n :class:`pysam.IteratorRowAllRefs`\n iterate over all reads in all reference [...]
0, /*tp_traverse*/
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorRowAll_1__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_14IteratorRowAll_2__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAll, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorRow, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -34789,7 +37106,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAll, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorRow, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -34802,64 +37119,64 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAll = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion __pyx_vtable_5pysam_9csamtools_IteratorRowRegion;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p;
+ PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_18IteratorRowAllRefs___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->rowiter));
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
+ PyObject_GC_UnTrack(o);
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->samfile);
+ PyObject_GC_Track(o);
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
- }
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
+ e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion)); if (e) return e;
if (p->samfile) {
e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
- if (p->rowiter) {
- e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
- }
return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowAllRefs(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_9csamtools_IteratorRowAllRefs *)o;
+static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)o;
PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
+ if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion);
tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->rowiter);
- p->rowiter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowAllRefs[] = {
- {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_1nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_1nextiter)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -34917,7 +37234,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowRegion = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -34930,13 +37247,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -34957,12 +37274,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorRowRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowRegion, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -34972,24 +37289,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowRegion, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowRegion, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowRegion, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorRowRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowAllRefs, /*tp_clear*/
+ __Pyx_DOCSTR("*(Samfile samfile, int tid, int beg, int end, int reopen = True )*\n\n iterate over mapped reads in a region.\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n\n The samtools iterators assume that the file\n position between iterations do not change.\n As a consequence, no two iterators can work\n on the same file. To permit this, each [...]
+ __pyx_tp_traverse_5pysam_9csamtools_IteratorRowRegion, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IteratorRowRegion, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs_2__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_18IteratorRowAllRefs_3__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowAllRefs, /*tp_methods*/
+ __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_9csamtools_17IteratorRowRegion_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorRowRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -34999,7 +37316,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowAllRefs, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorRowRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -35012,66 +37329,247 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowAllRefs = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorRowSelection __pyx_vtable_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll __pyx_vtable_5pysam_9csamtools_IteratorRowAll;
-static PyObject *__pyx_tp_new_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorRow(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAll(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *p;
+ PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorRowSelection *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorRowSelection;
- p->positions = Py_None; Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_20IteratorRowSelection___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
+ if (__pyx_pw_5pysam_9csamtools_14IteratorRowAll_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_20IteratorRowSelection_3__dealloc__(o);
+ __pyx_pw_5pysam_9csamtools_14IteratorRowAll_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(p->positions);
- __pyx_tp_dealloc_9csamtools_IteratorRow(o);
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+}
+
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAll[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__)},
+ {0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAll = {
+ 0, /*nb_add*/
+ 0, /*nb_subtract*/
+ 0, /*nb_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_divide*/
+ #endif
+ 0, /*nb_remainder*/
+ 0, /*nb_divmod*/
+ 0, /*nb_power*/
+ 0, /*nb_negative*/
+ 0, /*nb_positive*/
+ 0, /*nb_absolute*/
+ 0, /*nb_nonzero*/
+ 0, /*nb_invert*/
+ 0, /*nb_lshift*/
+ 0, /*nb_rshift*/
+ 0, /*nb_and*/
+ 0, /*nb_xor*/
+ 0, /*nb_or*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_coerce*/
+ #endif
+ 0, /*nb_int*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_long*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*nb_float*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_oct*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_hex*/
+ #endif
+ 0, /*nb_inplace_add*/
+ 0, /*nb_inplace_subtract*/
+ 0, /*nb_inplace_multiply*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*nb_inplace_divide*/
+ #endif
+ 0, /*nb_inplace_remainder*/
+ 0, /*nb_inplace_power*/
+ 0, /*nb_inplace_lshift*/
+ 0, /*nb_inplace_rshift*/
+ 0, /*nb_inplace_and*/
+ 0, /*nb_inplace_xor*/
+ 0, /*nb_inplace_or*/
+ 0, /*nb_floor_divide*/
+ 0, /*nb_true_divide*/
+ 0, /*nb_inplace_floor_divide*/
+ 0, /*nb_inplace_true_divide*/
+ #if PY_VERSION_HEX >= 0x02050000
+ 0, /*nb_index*/
+ #endif
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAll = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ 0, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAll = {
+ 0, /*mp_length*/
+ 0, /*mp_subscript*/
+ 0, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAll = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_getbuffer*/
+ #endif
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*bf_releasebuffer*/
+ #endif
+};
+
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("pysam.csamtools.IteratorRowAll"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAll, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ &__pyx_tp_as_number_IteratorRowAll, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAll, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAll, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_IteratorRowAll, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("*(Samfile samfile, int reopen = True)*\n\n iterate over all reads in *samfile*\n\n By default, the file is re-openend to avoid conflicts between\n multiple iterators working on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ __pyx_pw_5pysam_9csamtools_14IteratorRowAll_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_9csamtools_14IteratorRowAll_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorRowAll, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorRowAll, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ #if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p;
+ PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
+ if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
}
-static int __pyx_tp_traverse_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
+static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->samfile);
+ Py_CLEAR(p->rowiter);
+ PyObject_GC_Track(o);
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
+}
+
+static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_traverse) {
- e = __pyx_ptype_9csamtools_IteratorRow->tp_traverse(o, v, a); if (e) return e;
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
+ e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs)); if (e) return e;
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
}
- if (p->positions) {
- e = (*v)(p->positions, a); if (e) return e;
+ if (p->rowiter) {
+ e = (*v)(((PyObject*)p->rowiter), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorRowSelection(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_9csamtools_IteratorRowSelection *)o;
+static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs *)o;
PyObject* tmp;
- if (__pyx_ptype_9csamtools_IteratorRow->tp_clear) {
- __pyx_ptype_9csamtools_IteratorRow->tp_clear(o);
- }
- tmp = ((PyObject*)p->positions);
- p->positions = Py_None; Py_INCREF(Py_None);
+ if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs);
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->rowiter);
+ p->rowiter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorRowSelection[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorRowSelection_2__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorRowSelection_2__next__)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs[] = {
+ {__Pyx_NAMESTR("nextiter"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_3nextiter, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_2nextiter)},
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -35129,7 +37627,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowAllRefs = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -35142,13 +37640,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -35169,12 +37667,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorRowSelection"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorRowSelection), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorRowAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorRowSelection, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowAllRefs, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -35184,24 +37682,24 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowAllRefs, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowAllRefs, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowAllRefs, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorRowAllRefs, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorRowSelection, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorRowSelection, /*tp_clear*/
+ __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_20IteratorRowSelection_1__iter__, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorRowSelection_2__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorRowSelection, /*tp_methods*/
+ __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_5__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_9csamtools_18IteratorRowAllRefs_7__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorRowAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -35211,7 +37709,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorRowSelection, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorRowAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -35224,94 +37722,64 @@ static PyTypeObject __pyx_type_9csamtools_IteratorRowSelection = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumn __pyx_vtable_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection __pyx_vtable_5pysam_9csamtools_IteratorRowSelection;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumn *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorRowSelection(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p;
+ PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorRow(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumn *)o);
- p->__pyx_vtab = __pyx_vtabptr_9csamtools_IteratorColumn;
- p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
- p->stepper = Py_None; Py_INCREF(Py_None);
- if (__pyx_pf_9csamtools_14IteratorColumn___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+ p->positions = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
+static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pf_9csamtools_14IteratorColumn_4__dealloc__(o);
+ __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->iter));
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(((PyObject *)p->fastafile));
- Py_XDECREF(p->stepper);
- (*Py_TYPE(o)->tp_free)(o);
+ Py_CLEAR(p->positions);
+ PyObject_GC_Track(o);
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRow(o);
}
-static int __pyx_tp_traverse_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
- if (p->iter) {
- e = (*v)(((PyObject*)p->iter), a); if (e) return e;
- }
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- if (p->fastafile) {
- e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
- }
- if (p->stepper) {
- e = (*v)(p->stepper, a); if (e) return e;
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
+ e = ((likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) ? ((__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse) ? __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection)); if (e) return e;
+ if (p->positions) {
+ e = (*v)(p->positions, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_9csamtools_IteratorColumn(PyObject *o) {
- struct __pyx_obj_9csamtools_IteratorColumn *p = (struct __pyx_obj_9csamtools_IteratorColumn *)o;
+static int __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *p = (struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *)o;
PyObject* tmp;
- tmp = ((PyObject*)p->iter);
- p->iter = ((struct __pyx_obj_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->fastafile);
- p->fastafile = ((struct __pyx_obj_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->stepper);
- p->stepper = Py_None; Py_INCREF(Py_None);
+ if (likely(__pyx_ptype_5pysam_9csamtools_IteratorRow)) { if (__pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear) __pyx_ptype_5pysam_9csamtools_IteratorRow->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection);
+ tmp = ((PyObject*)p->positions);
+ p->positions = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyObject *__pyx_getprop_9csamtools_14IteratorColumn_seq_len(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_14IteratorColumn_7seq_len___get__(o);
-}
-
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumn[] = {
- {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_2addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_2addReference)},
- {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pf_9csamtools_14IteratorColumn_3hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_14IteratorColumn_3hasReference)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorRowSelection[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_IteratorColumn[] = {
- {(char *)"seq_len", __pyx_getprop_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_241), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
+static PyNumberMethods __pyx_tp_as_number_IteratorRowSelection = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -35369,7 +37837,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorRowSelection = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -35382,13 +37850,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorRowSelection = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorRowSelection = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -35409,12 +37877,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumn"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumn), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorRowSelection"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorRowSelection, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -35424,26 +37892,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorRowSelection, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorRowSelection, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorRowSelection, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorRowSelection, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n\n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will conta [...]
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pf_9csamtools_14IteratorColumn_1__iter__, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumn, /*tp_methods*/
+ __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_9csamtools_20IteratorRowSelection_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorRowSelection, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_IteratorColumn, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -35451,7 +37919,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumn, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorRowSelection, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -35464,26 +37932,96 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumn = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnRegion __pyx_vtable_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_vtable_5pysam_9csamtools_IteratorColumn;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumnRegion *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumn(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumnRegion *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnRegion;
- if (__pyx_pf_9csamtools_20IteratorColumnRegion___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+ p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ p->stepper = Py_None; Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnRegion[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_20IteratorColumnRegion_1__next__)},
+static void __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+ PyObject_GC_UnTrack(o);
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_5pysam_9csamtools_14IteratorColumn_9__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->iter);
+ Py_CLEAR(p->samfile);
+ Py_CLEAR(p->fastafile);
+ Py_CLEAR(p->stepper);
+ PyObject_GC_Track(o);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+ if (p->iter) {
+ e = (*v)(((PyObject*)p->iter), a); if (e) return e;
+ }
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->fastafile) {
+ e = (*v)(((PyObject*)p->fastafile), a); if (e) return e;
+ }
+ if (p->stepper) {
+ e = (*v)(p->stepper, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_5pysam_9csamtools_IteratorColumn(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumn *p = (struct __pyx_obj_5pysam_9csamtools_IteratorColumn *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->iter);
+ p->iter = ((struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->fastafile);
+ p->fastafile = ((struct __pyx_obj_5pysam_9csamtools_Fastafile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->stepper);
+ p->stepper = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_14IteratorColumn_7seq_len_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumn[] = {
+ {__Pyx_NAMESTR("addReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_5addReference, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_4addReference)},
+ {__Pyx_NAMESTR("hasReference"), (PyCFunction)__pyx_pw_5pysam_9csamtools_14IteratorColumn_7hasReference, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_14IteratorColumn_6hasReference)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_IteratorColumn[] = {
+ {(char *)"seq_len", __pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_IteratorColumn = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -35541,7 +38079,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumn = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -35554,13 +38092,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumn = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumn = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -35581,12 +38119,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumn = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnRegion"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorColumn"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumn), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -35596,26 +38134,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumn, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumn, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumn, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorColumn, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ __Pyx_DOCSTR("abstract base class for iterators over columns.\n\n IteratorColumn objects wrap the pileup functionality of samtools.\n\n For reasons of efficiency, the iterator points to the current\n pileup buffer. The pileup buffer is updated at every iteration.\n This might cause some unexpected behavious. For example,\n consider the conversion to a list::\n\n f = Samfile(\"file.bam\", \"rb\")\n result = list( f.pileup() )\n\n Here, ``result`` will conta [...]
+ __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- 0, /*tp_iter*/
- __pyx_pf_9csamtools_20IteratorColumnRegion_1__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnRegion, /*tp_methods*/
+ __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorColumn, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_IteratorColumn, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -35623,7 +38161,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnRegion, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorColumn, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -35636,26 +38174,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnRegion = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_9csamtools_IteratorColumnAllRefs __pyx_vtable_9csamtools_IteratorColumnAllRefs;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion;
-static PyObject *__pyx_tp_new_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IteratorColumnAllRefs *p;
- PyObject *o = __pyx_tp_new_9csamtools_IteratorColumn(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *p;
+ PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IteratorColumnAllRefs *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_9csamtools_IteratorColumn*)__pyx_vtabptr_9csamtools_IteratorColumnAllRefs;
- if (__pyx_pf_9csamtools_21IteratorColumnAllRefs___cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
+ if (__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IteratorColumnAllRefs[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnRegion[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnRegion = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -35713,7 +38251,7 @@ static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnRegion = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -35726,13 +38264,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnRegion = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnRegion = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -35753,12 +38291,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnRegion = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IteratorColumnAllRefs"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorColumnRegion"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IteratorColumn, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -35768,24 +38306,28 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/
- &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumnRegion, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumnRegion, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumnRegion, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorColumnRegion, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IteratorColumn, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IteratorColumn, /*tp_clear*/
+ __Pyx_DOCSTR("iterates over a region only.\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ #else
0, /*tp_iter*/
- __pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__, /*tp_iternext*/
- __pyx_methods_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
+ #endif
+ __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_3__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorColumnRegion, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -35795,7 +38337,7 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IteratorColumnAllRefs, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorColumnRegion, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -35808,64 +38350,26 @@ static PyTypeObject __pyx_type_9csamtools_IteratorColumnAllRefs = {
0, /*tp_version_tag*/
#endif
};
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
-static PyObject *__pyx_tp_new_9csamtools_IndexedReads(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools_IndexedReads *p;
- PyObject *o = (*t->tp_alloc)(t, 0);
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *p;
+ PyObject *o = __pyx_tp_new_5pysam_9csamtools_IteratorColumn(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools_IndexedReads *)o);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- p->index = Py_None; Py_INCREF(Py_None);
- return o;
-}
-
-static void __pyx_tp_dealloc_9csamtools_IndexedReads(PyObject *o) {
- struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
- {
- PyObject *etype, *eval, *etb;
- PyErr_Fetch(&etype, &eval, &etb);
- ++Py_REFCNT(o);
- __pyx_pf_9csamtools_12IndexedReads_3__dealloc__(o);
- if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_XDECREF(((PyObject *)p->samfile));
- Py_XDECREF(p->index);
- (*Py_TYPE(o)->tp_free)(o);
-}
-
-static int __pyx_tp_traverse_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
- if (p->samfile) {
- e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
- }
- if (p->index) {
- e = (*v)(p->index, a); if (e) return e;
+ p = ((struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn*)__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
+ if (__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_1__cinit__(o, a, k) < 0) {
+ Py_DECREF(o); o = 0;
}
- return 0;
-}
-
-static int __pyx_tp_clear_9csamtools_IndexedReads(PyObject *o) {
- struct __pyx_obj_9csamtools_IndexedReads *p = (struct __pyx_obj_9csamtools_IndexedReads *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->samfile);
- p->samfile = ((struct __pyx_obj_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->index);
- p->index = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+ return o;
}
-static PyMethodDef __pyx_methods_9csamtools_IndexedReads[] = {
- {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_1build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_1build)},
- {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pf_9csamtools_12IndexedReads_2find, METH_O, __Pyx_DOCSTR(__pyx_doc_9csamtools_12IndexedReads_2find)},
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__)},
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number_IndexedReads = {
+static PyNumberMethods __pyx_tp_as_number_IteratorColumnAllRefs = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -35923,7 +38427,7 @@ static PyNumberMethods __pyx_tp_as_number_IndexedReads = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_IndexedReads = {
+static PySequenceMethods __pyx_tp_as_sequence_IteratorColumnAllRefs = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -35936,13 +38440,13 @@ static PySequenceMethods __pyx_tp_as_sequence_IndexedReads = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_IndexedReads = {
+static PyMappingMethods __pyx_tp_as_mapping_IteratorColumnAllRefs = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = {
+static PyBufferProcs __pyx_tp_as_buffer_IteratorColumnAllRefs = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -35963,12 +38467,12 @@ static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.IndexedReads"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_IndexedReads), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IteratorColumnAllRefs"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_IndexedReads, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IteratorColumn, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -35978,24 +38482,28 @@ static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_IndexedReads, /*tp_as_number*/
- &__pyx_tp_as_sequence_IndexedReads, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_IndexedReads, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IteratorColumnAllRefs, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IteratorColumnAllRefs, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IteratorColumnAllRefs, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/
+ &__pyx_tp_as_buffer_IteratorColumnAllRefs, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
- __pyx_tp_traverse_9csamtools_IndexedReads, /*tp_traverse*/
- __pyx_tp_clear_9csamtools_IndexedReads, /*tp_clear*/
+ __Pyx_DOCSTR("iterates over all columns by chaining iterators over each reference\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools_IteratorColumn, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IteratorColumn, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
+ #if CYTHON_COMPILING_IN_PYPY
+ __pyx_pw_5pysam_9csamtools_14IteratorColumn_3__iter__, /*tp_iter*/
+ #else
0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_methods_9csamtools_IndexedReads, /*tp_methods*/
+ #endif
+ __pyx_pw_5pysam_9csamtools_21IteratorColumnAllRefs_3__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -36003,9 +38511,9 @@ static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pf_9csamtools_12IndexedReads___init__, /*tp_init*/
+ 0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_IndexedReads, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IteratorColumnAllRefs, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36019,65 +38527,65 @@ static PyTypeObject __pyx_type_9csamtools_IndexedReads = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools_SNPCall(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_9csamtools_IndexedReads(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools_IndexedReads *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
+ p = ((struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ p->index = Py_None; Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_9csamtools_SNPCall(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+ PyObject_GC_UnTrack(o);
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_pw_5pysam_9csamtools_12IndexedReads_7__dealloc__(o);
+ if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->samfile);
+ Py_CLEAR(p->index);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_tid(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_3tid___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_pos(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_3pos___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_reference_base(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_14reference_base___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_genotype(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8genotype___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_consensus_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_17consensus_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_snp_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_11snp_quality___get__(o);
-}
-
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_mapping_quality(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_15mapping_quality___get__(o);
+static int __pyx_tp_traverse_5pysam_9csamtools_IndexedReads(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+ if (p->samfile) {
+ e = (*v)(((PyObject*)p->samfile), a); if (e) return e;
+ }
+ if (p->index) {
+ e = (*v)(p->index, a); if (e) return e;
+ }
+ return 0;
}
-static PyObject *__pyx_getprop_9csamtools_7SNPCall_coverage(PyObject *o, void *x) {
- return __pyx_pf_9csamtools_7SNPCall_8coverage___get__(o);
+static int __pyx_tp_clear_5pysam_9csamtools_IndexedReads(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools_IndexedReads *p = (struct __pyx_obj_5pysam_9csamtools_IndexedReads *)o;
+ PyObject* tmp;
+ tmp = ((PyObject*)p->samfile);
+ p->samfile = ((struct __pyx_obj_5pysam_9csamtools_Samfile *)Py_None); Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->index);
+ p->index = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
}
-static PyMethodDef __pyx_methods_9csamtools_SNPCall[] = {
+static PyMethodDef __pyx_methods_5pysam_9csamtools_IndexedReads[] = {
+ {__Pyx_NAMESTR("build"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_3build, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_2build)},
+ {__Pyx_NAMESTR("find"), (PyCFunction)__pyx_pw_5pysam_9csamtools_12IndexedReads_5find, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_9csamtools_12IndexedReads_4find)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_9csamtools_SNPCall[] = {
- {(char *)"tid", __pyx_getprop_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_234), 0},
- {(char *)"pos", __pyx_getprop_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_242), 0},
- {(char *)"reference_base", __pyx_getprop_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_243), 0},
- {(char *)"genotype", __pyx_getprop_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_244), 0},
- {(char *)"consensus_quality", __pyx_getprop_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
- {(char *)"snp_quality", __pyx_getprop_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
- {(char *)"mapping_quality", __pyx_getprop_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
- {(char *)"coverage", __pyx_getprop_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PyNumberMethods __pyx_tp_as_number_SNPCall = {
+static PyNumberMethods __pyx_tp_as_number_IndexedReads = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -36135,7 +38643,7 @@ static PyNumberMethods __pyx_tp_as_number_SNPCall = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
+static PySequenceMethods __pyx_tp_as_sequence_IndexedReads = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -36148,13 +38656,13 @@ static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping_SNPCall = {
+static PyMappingMethods __pyx_tp_as_mapping_IndexedReads = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
+static PyBufferProcs __pyx_tp_as_buffer_IndexedReads = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -36175,12 +38683,12 @@ static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools_SNPCall = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_IndexedReads = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.SNPCall"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools_SNPCall), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.IndexedReads"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_IndexedReads), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools_SNPCall, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_IndexedReads, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36190,34 +38698,34 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number_SNPCall, /*tp_as_number*/
- &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
+ &__pyx_tp_as_number_IndexedReads, /*tp_as_number*/
+ &__pyx_tp_as_sequence_IndexedReads, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_IndexedReads, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- __pyx_pf_9csamtools_7SNPCall___str__, /*tp_str*/
+ 0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
- __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
- 0, /*tp_traverse*/
- 0, /*tp_clear*/
+ &__pyx_tp_as_buffer_IndexedReads, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ __Pyx_DOCSTR("IndexedReads(Samfile samfile, int reopen=True)\nindex a bamfile by read.\n\n The index is kept in memory.\n\n By default, the file is re-openend to avoid conflicts if\n multiple operators work on the same file. Set *reopen* = False\n to not re-open *samfile*.\n "), /*tp_doc*/
+ __pyx_tp_traverse_5pysam_9csamtools_IndexedReads, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools_IndexedReads, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools_SNPCall, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools_IndexedReads, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_9csamtools_SNPCall, /*tp_getset*/
+ 0, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- 0, /*tp_init*/
+ __pyx_pw_5pysam_9csamtools_12IndexedReads_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools_SNPCall, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_IndexedReads, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36231,63 +38739,65 @@ static PyTypeObject __pyx_type_9csamtools_SNPCall = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools___pyx_Generator(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_Generator_object *p;
+static PyObject *__pyx_tp_new_5pysam_9csamtools_SNPCall(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_Generator_object *)o);
- p->exc_type = 0;
- p->exc_value = 0;
- p->exc_traceback = 0;
return o;
}
-static void __pyx_tp_dealloc_9csamtools___pyx_Generator(PyObject *o) {
- struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
- Py_XDECREF(p->exc_type);
- Py_XDECREF(p->exc_value);
- Py_XDECREF(p->exc_traceback);
+static void __pyx_tp_dealloc_5pysam_9csamtools_SNPCall(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools___pyx_Generator(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
- if (p->exc_type) {
- e = (*v)(p->exc_type, a); if (e) return e;
- }
- if (p->exc_value) {
- e = (*v)(p->exc_value, a); if (e) return e;
- }
- if (p->exc_traceback) {
- e = (*v)(p->exc_traceback, a); if (e) return e;
- }
- return 0;
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_tid(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_3tid_1__get__(o);
}
-static int __pyx_tp_clear_9csamtools___pyx_Generator(PyObject *o) {
- struct __pyx_Generator_object *p = (struct __pyx_Generator_object *)o;
- PyObject* tmp;
- tmp = ((PyObject*)p->exc_type);
- p->exc_type = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->exc_value);
- p->exc_value = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->exc_traceback);
- p->exc_traceback = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_pos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_3pos_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_14reference_base_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_genotype(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_8genotype_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_consensus_quality(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_17consensus_quality_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_11snp_quality_1__get__(o);
}
-static PyMethodDef __pyx_methods_9csamtools___pyx_Generator[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction)__Pyx_Generator_Send, METH_O, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("close"), (PyCFunction)__Pyx_Generator_Close, METH_NOARGS, __Pyx_DOCSTR(0)},
- {__Pyx_NAMESTR("throw"), (PyCFunction)__Pyx_Generator_Throw, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(0)},
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_15mapping_quality_1__get__(o);
+}
+
+static PyObject *__pyx_getprop_5pysam_9csamtools_7SNPCall_coverage(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_7SNPCall_8coverage_1__get__(o);
+}
+
+static PyMethodDef __pyx_methods_5pysam_9csamtools_SNPCall[] = {
{0, 0, 0, 0}
};
-static PyNumberMethods __pyx_tp_as_number___pyx_Generator = {
+static struct PyGetSetDef __pyx_getsets_5pysam_9csamtools_SNPCall[] = {
+ {(char *)"tid", __pyx_getprop_5pysam_9csamtools_7SNPCall_tid, 0, __Pyx_DOCSTR(__pyx_k_238), 0},
+ {(char *)"pos", __pyx_getprop_5pysam_9csamtools_7SNPCall_pos, 0, __Pyx_DOCSTR(__pyx_k_246), 0},
+ {(char *)"reference_base", __pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_247), 0},
+ {(char *)"genotype", __pyx_getprop_5pysam_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_248), 0},
+ {(char *)"consensus_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_consensus_quality, 0, __Pyx_DOCSTR(__pyx_k_249), 0},
+ {(char *)"snp_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_250), 0},
+ {(char *)"mapping_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_251), 0},
+ {(char *)"coverage", __pyx_getprop_5pysam_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_252), 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PyNumberMethods __pyx_tp_as_number_SNPCall = {
0, /*nb_add*/
0, /*nb_subtract*/
0, /*nb_multiply*/
@@ -36345,7 +38855,7 @@ static PyNumberMethods __pyx_tp_as_number___pyx_Generator = {
#endif
};
-static PySequenceMethods __pyx_tp_as_sequence___pyx_Generator = {
+static PySequenceMethods __pyx_tp_as_sequence_SNPCall = {
0, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
@@ -36358,13 +38868,13 @@ static PySequenceMethods __pyx_tp_as_sequence___pyx_Generator = {
0, /*sq_inplace_repeat*/
};
-static PyMappingMethods __pyx_tp_as_mapping___pyx_Generator = {
+static PyMappingMethods __pyx_tp_as_mapping_SNPCall = {
0, /*mp_length*/
0, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
-static PyBufferProcs __pyx_tp_as_buffer___pyx_Generator = {
+static PyBufferProcs __pyx_tp_as_buffer_SNPCall = {
#if PY_MAJOR_VERSION < 3
0, /*bf_getreadbuffer*/
#endif
@@ -36385,12 +38895,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_Generator = {
#endif
};
-static PyTypeObject __pyx_Generator_type = {
+static PyTypeObject __pyx_type_5pysam_9csamtools_SNPCall = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.__pyx_Generator"), /*tp_name*/
- sizeof(struct __pyx_Generator_object), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.SNPCall"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools_SNPCall), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools___pyx_Generator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools_SNPCall, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36400,26 +38910,26 @@ static PyTypeObject __pyx_Generator_type = {
0, /*reserved*/
#endif
0, /*tp_repr*/
- &__pyx_tp_as_number___pyx_Generator, /*tp_as_number*/
- &__pyx_tp_as_sequence___pyx_Generator, /*tp_as_sequence*/
- &__pyx_tp_as_mapping___pyx_Generator, /*tp_as_mapping*/
+ &__pyx_tp_as_number_SNPCall, /*tp_as_number*/
+ &__pyx_tp_as_sequence_SNPCall, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_SNPCall, /*tp_as_mapping*/
0, /*tp_hash*/
0, /*tp_call*/
- 0, /*tp_str*/
+ __pyx_pw_5pysam_9csamtools_7SNPCall_1__str__, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
- &__pyx_tp_as_buffer___pyx_Generator, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- 0, /*tp_doc*/
- __pyx_tp_traverse_9csamtools___pyx_Generator, /*tp_traverse*/
- __pyx_tp_clear_9csamtools___pyx_Generator, /*tp_clear*/
+ &__pyx_tp_as_buffer_SNPCall, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ __Pyx_DOCSTR("the results of a SNP call."), /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- PyObject_SelfIter, /*tp_iter*/
- __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_methods_9csamtools___pyx_Generator, /*tp_methods*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_5pysam_9csamtools_SNPCall, /*tp_methods*/
0, /*tp_members*/
- 0, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_SNPCall, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
@@ -36427,7 +38937,7 @@ static PyTypeObject __pyx_Generator_type = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools___pyx_Generator, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_SNPCall, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36441,11 +38951,11 @@ static PyTypeObject __pyx_Generator_type = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p;
- PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o);
+ p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o);
p->__pyx_v_x = 0;
p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
@@ -36453,19 +38963,20 @@ static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct__genexpr(PyTypeObjec
return o;
}
-static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
- struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
- Py_XDECREF(p->__pyx_v_x);
- Py_XDECREF(p->__pyx_v_y);
- Py_XDECREF(p->__pyx_t_0);
- Py_XDECREF(p->__pyx_t_1);
- __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
+static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_x);
+ Py_CLEAR(p->__pyx_v_y);
+ Py_CLEAR(p->__pyx_t_0);
+ Py_CLEAR(p->__pyx_t_1);
+ PyObject_GC_Track(o);
+ (*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
- e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e;
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
@@ -36481,10 +38992,9 @@ static int __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr(PyObject *o,
return 0;
}
-static int __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
- struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr *)o;
+static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr *)o;
PyObject* tmp;
- __pyx_tp_clear_9csamtools___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -36500,7 +39010,7 @@ static int __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct__genexpr[] = {
+static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr[] = {
{0, 0, 0, 0}
};
@@ -36602,12 +39112,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__genexpr = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct__genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36628,13 +39138,13 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
&__pyx_tp_as_buffer___pyx_scope_struct__genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
- __pyx_tp_clear_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -36644,7 +39154,7 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct__genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36658,11 +39168,11 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct__genexpr = {
#endif
};
-static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p;
- PyObject *o = __pyx_tp_new_9csamtools___pyx_Generator(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p;
+ PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o);
+ p = ((struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o);
p->__pyx_v_x = 0;
p->__pyx_v_y = 0;
p->__pyx_t_0 = 0;
@@ -36670,19 +39180,20 @@ static PyObject *__pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr(PyTypeObje
return o;
}
-static void __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
- Py_XDECREF(p->__pyx_v_x);
- Py_XDECREF(p->__pyx_v_y);
- Py_XDECREF(p->__pyx_t_0);
- Py_XDECREF(p->__pyx_t_1);
- __pyx_tp_dealloc_9csamtools___pyx_Generator(o);
+static void __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_x);
+ Py_CLEAR(p->__pyx_v_y);
+ Py_CLEAR(p->__pyx_t_0);
+ Py_CLEAR(p->__pyx_t_1);
+ PyObject_GC_Track(o);
+ (*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
- e = __pyx_tp_traverse_9csamtools___pyx_Generator(o, v, a); if (e) return e;
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
if (p->__pyx_v_x) {
e = (*v)(p->__pyx_v_x, a); if (e) return e;
}
@@ -36698,10 +39209,9 @@ static int __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o
return 0;
}
-static int __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr *)o;
+static int __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr *)o;
PyObject* tmp;
- __pyx_tp_clear_9csamtools___pyx_Generator(o);
tmp = ((PyObject*)p->__pyx_v_x);
p->__pyx_v_x = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -36717,7 +39227,7 @@ static int __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr[] = {
+static PyMethodDef __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr[] = {
{0, 0, 0, 0}
};
@@ -36819,12 +39329,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
+static PyTypeObject __pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.csamtools.__pyx_scope_struct_1_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -36845,13 +39355,13 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
&__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
- __pyx_tp_clear_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ __pyx_methods_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -36861,7 +39371,7 @@ static PyTypeObject __pyx_type_9csamtools___pyx_scope_struct_1_genexpr = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools___pyx_scope_struct_1_genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -36881,7 +39391,11 @@ static PyMethodDef __pyx_methods[] = {
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
+ #if PY_VERSION_HEX < 0x03020000
+ { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
+ #else
PyModuleDef_HEAD_INIT,
+ #endif
__Pyx_NAMESTR("csamtools"),
0, /* m_doc */
-1, /* m_size */
@@ -36896,36 +39410,33 @@ static struct PyModuleDef __pyx_moduledef = {
static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_u_1, __pyx_k_1, sizeof(__pyx_k_1), 0, 1, 0, 0},
{&__pyx_kp_s_10, __pyx_k_10, sizeof(__pyx_k_10), 0, 0, 1, 0},
- {&__pyx_kp_s_100, __pyx_k_100, sizeof(__pyx_k_100), 0, 0, 1, 0},
{&__pyx_kp_s_102, __pyx_k_102, sizeof(__pyx_k_102), 0, 0, 1, 0},
{&__pyx_kp_s_104, __pyx_k_104, sizeof(__pyx_k_104), 0, 0, 1, 0},
- {&__pyx_kp_s_105, __pyx_k_105, sizeof(__pyx_k_105), 0, 0, 1, 0},
+ {&__pyx_kp_s_106, __pyx_k_106, sizeof(__pyx_k_106), 0, 0, 1, 0},
{&__pyx_kp_s_107, __pyx_k_107, sizeof(__pyx_k_107), 0, 0, 1, 0},
{&__pyx_kp_s_108, __pyx_k_108, sizeof(__pyx_k_108), 0, 0, 1, 0},
- {&__pyx_kp_s_109, __pyx_k_109, sizeof(__pyx_k_109), 0, 0, 1, 0},
- {&__pyx_kp_s_110, __pyx_k_110, sizeof(__pyx_k_110), 0, 0, 1, 0},
{&__pyx_kp_s_111, __pyx_k_111, sizeof(__pyx_k_111), 0, 0, 1, 0},
+ {&__pyx_kp_s_112, __pyx_k_112, sizeof(__pyx_k_112), 0, 0, 1, 0},
{&__pyx_kp_s_113, __pyx_k_113, sizeof(__pyx_k_113), 0, 0, 1, 0},
- {&__pyx_kp_s_116, __pyx_k_116, sizeof(__pyx_k_116), 0, 0, 1, 0},
- {&__pyx_kp_s_119, __pyx_k_119, sizeof(__pyx_k_119), 0, 0, 1, 0},
- {&__pyx_kp_s_125, __pyx_k_125, sizeof(__pyx_k_125), 0, 0, 1, 0},
- {&__pyx_kp_s_126, __pyx_k_126, sizeof(__pyx_k_126), 0, 0, 1, 0},
- {&__pyx_kp_s_127, __pyx_k_127, sizeof(__pyx_k_127), 0, 0, 1, 0},
+ {&__pyx_kp_s_114, __pyx_k_114, sizeof(__pyx_k_114), 0, 0, 1, 0},
+ {&__pyx_kp_s_115, __pyx_k_115, sizeof(__pyx_k_115), 0, 0, 1, 0},
+ {&__pyx_kp_s_117, __pyx_k_117, sizeof(__pyx_k_117), 0, 0, 1, 0},
+ {&__pyx_kp_s_120, __pyx_k_120, sizeof(__pyx_k_120), 0, 0, 1, 0},
+ {&__pyx_kp_s_123, __pyx_k_123, sizeof(__pyx_k_123), 0, 0, 1, 0},
{&__pyx_kp_s_129, __pyx_k_129, sizeof(__pyx_k_129), 0, 0, 1, 0},
{&__pyx_kp_s_13, __pyx_k_13, sizeof(__pyx_k_13), 0, 0, 1, 0},
- {&__pyx_kp_s_135, __pyx_k_135, sizeof(__pyx_k_135), 0, 0, 1, 0},
- {&__pyx_kp_s_136, __pyx_k_136, sizeof(__pyx_k_136), 0, 0, 1, 0},
- {&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0},
- {&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0},
+ {&__pyx_kp_s_130, __pyx_k_130, sizeof(__pyx_k_130), 0, 0, 1, 0},
+ {&__pyx_kp_s_131, __pyx_k_131, sizeof(__pyx_k_131), 0, 0, 1, 0},
+ {&__pyx_kp_s_133, __pyx_k_133, sizeof(__pyx_k_133), 0, 0, 1, 0},
+ {&__pyx_kp_s_139, __pyx_k_139, sizeof(__pyx_k_139), 0, 0, 1, 0},
{&__pyx_kp_s_140, __pyx_k_140, sizeof(__pyx_k_140), 0, 0, 1, 0},
{&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0},
+ {&__pyx_kp_s_142, __pyx_k_142, sizeof(__pyx_k_142), 0, 0, 1, 0},
+ {&__pyx_kp_s_144, __pyx_k_144, sizeof(__pyx_k_144), 0, 0, 1, 0},
{&__pyx_kp_s_145, __pyx_k_145, sizeof(__pyx_k_145), 0, 0, 1, 0},
- {&__pyx_n_s_147, __pyx_k_147, sizeof(__pyx_k_147), 0, 0, 1, 1},
- {&__pyx_kp_s_148, __pyx_k_148, sizeof(__pyx_k_148), 0, 0, 1, 0},
{&__pyx_kp_s_149, __pyx_k_149, sizeof(__pyx_k_149), 0, 0, 1, 0},
{&__pyx_kp_s_15, __pyx_k_15, sizeof(__pyx_k_15), 0, 0, 1, 0},
- {&__pyx_kp_s_150, __pyx_k_150, sizeof(__pyx_k_150), 0, 0, 1, 0},
- {&__pyx_kp_s_151, __pyx_k_151, sizeof(__pyx_k_151), 0, 0, 1, 0},
+ {&__pyx_n_s_151, __pyx_k_151, sizeof(__pyx_k_151), 0, 0, 1, 1},
{&__pyx_kp_s_152, __pyx_k_152, sizeof(__pyx_k_152), 0, 0, 1, 0},
{&__pyx_kp_s_153, __pyx_k_153, sizeof(__pyx_k_153), 0, 0, 1, 0},
{&__pyx_kp_s_154, __pyx_k_154, sizeof(__pyx_k_154), 0, 0, 1, 0},
@@ -36949,24 +39460,43 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_17, __pyx_k_17, sizeof(__pyx_k_17), 0, 0, 1, 0},
{&__pyx_kp_s_170, __pyx_k_170, sizeof(__pyx_k_170), 0, 0, 1, 0},
{&__pyx_kp_s_171, __pyx_k_171, sizeof(__pyx_k_171), 0, 0, 1, 0},
+ {&__pyx_kp_s_172, __pyx_k_172, sizeof(__pyx_k_172), 0, 0, 1, 0},
{&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0},
+ {&__pyx_kp_s_174, __pyx_k_174, sizeof(__pyx_k_174), 0, 0, 1, 0},
+ {&__pyx_kp_s_175, __pyx_k_175, sizeof(__pyx_k_175), 0, 0, 1, 0},
{&__pyx_kp_s_177, __pyx_k_177, sizeof(__pyx_k_177), 0, 0, 1, 0},
- {&__pyx_kp_s_178, __pyx_k_178, sizeof(__pyx_k_178), 0, 0, 1, 0},
- {&__pyx_kp_s_179, __pyx_k_179, sizeof(__pyx_k_179), 0, 0, 1, 0},
{&__pyx_kp_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 0},
- {&__pyx_kp_s_185, __pyx_k_185, sizeof(__pyx_k_185), 0, 0, 1, 0},
- {&__pyx_kp_s_186, __pyx_k_186, sizeof(__pyx_k_186), 0, 0, 1, 0},
+ {&__pyx_kp_s_181, __pyx_k_181, sizeof(__pyx_k_181), 0, 0, 1, 0},
+ {&__pyx_kp_s_182, __pyx_k_182, sizeof(__pyx_k_182), 0, 0, 1, 0},
+ {&__pyx_kp_s_183, __pyx_k_183, sizeof(__pyx_k_183), 0, 0, 1, 0},
+ {&__pyx_kp_s_189, __pyx_k_189, sizeof(__pyx_k_189), 0, 0, 1, 0},
{&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
+ {&__pyx_kp_s_190, __pyx_k_190, sizeof(__pyx_k_190), 0, 0, 1, 0},
{&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
- {&__pyx_n_s_249, __pyx_k_249, sizeof(__pyx_k_249), 0, 0, 1, 1},
- {&__pyx_kp_s_251, __pyx_k_251, sizeof(__pyx_k_251), 0, 0, 1, 0},
- {&__pyx_kp_s_254, __pyx_k_254, sizeof(__pyx_k_254), 0, 0, 1, 0},
+ {&__pyx_n_s_253, __pyx_k_253, sizeof(__pyx_k_253), 0, 0, 1, 1},
{&__pyx_kp_s_255, __pyx_k_255, sizeof(__pyx_k_255), 0, 0, 1, 0},
- {&__pyx_kp_s_256, __pyx_k_256, sizeof(__pyx_k_256), 0, 0, 1, 0},
- {&__pyx_kp_s_262, __pyx_k_262, sizeof(__pyx_k_262), 0, 0, 1, 0},
+ {&__pyx_kp_s_260, __pyx_k_260, sizeof(__pyx_k_260), 0, 0, 1, 0},
+ {&__pyx_n_s_261, __pyx_k_261, sizeof(__pyx_k_261), 0, 0, 1, 1},
+ {&__pyx_n_s_262, __pyx_k_262, sizeof(__pyx_k_262), 0, 0, 1, 1},
+ {&__pyx_kp_s_263, __pyx_k_263, sizeof(__pyx_k_263), 0, 0, 1, 0},
+ {&__pyx_n_s_266, __pyx_k_266, sizeof(__pyx_k_266), 0, 0, 1, 1},
+ {&__pyx_n_s_269, __pyx_k_269, sizeof(__pyx_k_269), 0, 0, 1, 1},
+ {&__pyx_n_s_272, __pyx_k_272, sizeof(__pyx_k_272), 0, 0, 1, 1},
+ {&__pyx_n_s_275, __pyx_k_275, sizeof(__pyx_k_275), 0, 0, 1, 1},
+ {&__pyx_kp_s_276, __pyx_k_276, sizeof(__pyx_k_276), 0, 0, 1, 0},
+ {&__pyx_n_s_279, __pyx_k_279, sizeof(__pyx_k_279), 0, 0, 1, 1},
+ {&__pyx_n_s_282, __pyx_k_282, sizeof(__pyx_k_282), 0, 0, 1, 1},
+ {&__pyx_n_s_285, __pyx_k_285, sizeof(__pyx_k_285), 0, 0, 1, 1},
+ {&__pyx_kp_s_286, __pyx_k_286, sizeof(__pyx_k_286), 0, 0, 1, 0},
{&__pyx_kp_s_29, __pyx_k_29, sizeof(__pyx_k_29), 0, 0, 1, 0},
+ {&__pyx_n_s_295, __pyx_k_295, sizeof(__pyx_k_295), 0, 0, 1, 1},
+ {&__pyx_n_s_298, __pyx_k_298, sizeof(__pyx_k_298), 0, 0, 1, 1},
{&__pyx_kp_u_3, __pyx_k_3, sizeof(__pyx_k_3), 0, 1, 0, 0},
{&__pyx_kp_s_30, __pyx_k_30, sizeof(__pyx_k_30), 0, 0, 1, 0},
+ {&__pyx_n_s_301, __pyx_k_301, sizeof(__pyx_k_301), 0, 0, 1, 1},
+ {&__pyx_n_s_304, __pyx_k_304, sizeof(__pyx_k_304), 0, 0, 1, 1},
+ {&__pyx_n_s_307, __pyx_k_307, sizeof(__pyx_k_307), 0, 0, 1, 1},
+ {&__pyx_kp_s_308, __pyx_k_308, sizeof(__pyx_k_308), 0, 0, 1, 0},
{&__pyx_kp_s_31, __pyx_k_31, sizeof(__pyx_k_31), 0, 0, 1, 0},
{&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
{&__pyx_kp_s_33, __pyx_k_33, sizeof(__pyx_k_33), 0, 0, 1, 0},
@@ -36999,7 +39529,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_85, __pyx_k_85, sizeof(__pyx_k_85), 0, 0, 1, 0},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_kp_s_92, __pyx_k_92, sizeof(__pyx_k_92), 0, 0, 1, 0},
- {&__pyx_kp_s_95, __pyx_k_95, sizeof(__pyx_k_95), 0, 0, 1, 0},
+ {&__pyx_kp_s_94, __pyx_k_94, sizeof(__pyx_k_94), 0, 0, 1, 0},
+ {&__pyx_kp_s_97, __pyx_k_97, sizeof(__pyx_k_97), 0, 0, 1, 0},
{&__pyx_kp_s__2scB, __pyx_k__2scB, sizeof(__pyx_k__2scB), 0, 0, 1, 0},
{&__pyx_kp_s__2scH, __pyx_k__2scH, sizeof(__pyx_k__2scH), 0, 0, 1, 0},
{&__pyx_kp_s__2scI, __pyx_k__2scI, sizeof(__pyx_k__2scI), 0, 0, 1, 0},
@@ -37093,6 +39624,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s___open, __pyx_k___open, sizeof(__pyx_k___open), 0, 0, 1, 1},
{&__pyx_n_s___parseRegion, __pyx_k___parseRegion, sizeof(__pyx_k___parseRegion), 0, 0, 1, 1},
{&__pyx_n_s___samtools_dispatch, __pyx_k___samtools_dispatch, sizeof(__pyx_k___samtools_dispatch), 0, 0, 1, 1},
+ {&__pyx_n_s__a, __pyx_k__a, sizeof(__pyx_k__a), 0, 0, 1, 1},
{&__pyx_n_s__add_sq_text, __pyx_k__add_sq_text, sizeof(__pyx_k__add_sq_text), 0, 0, 1, 1},
{&__pyx_n_s__alignment, __pyx_k__alignment, sizeof(__pyx_k__alignment), 0, 0, 1, 1},
{&__pyx_n_s__all, __pyx_k__all, sizeof(__pyx_k__all), 0, 0, 1, 1},
@@ -37105,6 +39637,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__c, __pyx_k__c, sizeof(__pyx_k__c), 0, 0, 1, 1},
{&__pyx_n_s__calcsize, __pyx_k__calcsize, sizeof(__pyx_k__calcsize), 0, 0, 1, 1},
{&__pyx_n_s__callback, __pyx_k__callback, sizeof(__pyx_k__callback), 0, 0, 1, 1},
+ {&__pyx_n_s__cargs, __pyx_k__cargs, sizeof(__pyx_k__cargs), 0, 0, 1, 1},
{&__pyx_n_s__catch_stdout, __pyx_k__catch_stdout, sizeof(__pyx_k__catch_stdout), 0, 0, 1, 1},
{&__pyx_n_s__check_header, __pyx_k__check_header, sizeof(__pyx_k__check_header), 0, 0, 1, 1},
{&__pyx_n_s__check_sq, __pyx_k__check_sq, sizeof(__pyx_k__check_sq), 0, 0, 1, 1},
@@ -37115,7 +39648,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__compile, __pyx_k__compile, sizeof(__pyx_k__compile), 0, 0, 1, 1},
{&__pyx_n_s__consensus_quality, __pyx_k__consensus_quality, sizeof(__pyx_k__consensus_quality), 0, 0, 1, 1},
{&__pyx_n_s__coverage, __pyx_k__coverage, sizeof(__pyx_k__coverage), 0, 0, 1, 1},
- {&__pyx_n_s__csamtools, __pyx_k__csamtools, sizeof(__pyx_k__csamtools), 0, 0, 1, 1},
{&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1},
{&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1},
{&__pyx_n_s__data_len, __pyx_k__data_len, sizeof(__pyx_k__data_len), 0, 0, 1, 1},
@@ -37148,6 +39680,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1},
{&__pyx_n_s__indel, __pyx_k__indel, sizeof(__pyx_k__indel), 0, 0, 1, 1},
{&__pyx_n_s__index, __pyx_k__index, sizeof(__pyx_k__index), 0, 0, 1, 1},
+ {&__pyx_n_s__inf, __pyx_k__inf, sizeof(__pyx_k__inf), 0, 0, 1, 1},
{&__pyx_n_s__is_del, __pyx_k__is_del, sizeof(__pyx_k__is_del), 0, 0, 1, 1},
{&__pyx_n_s__is_head, __pyx_k__is_head, sizeof(__pyx_k__is_head), 0, 0, 1, 1},
{&__pyx_n_s__is_tail, __pyx_k__is_tail, sizeof(__pyx_k__is_tail), 0, 0, 1, 1},
@@ -37181,10 +39714,13 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__nextiter, __pyx_k__nextiter, sizeof(__pyx_k__nextiter), 0, 0, 1, 1},
{&__pyx_n_s__nreferences, __pyx_k__nreferences, sizeof(__pyx_k__nreferences), 0, 0, 1, 1},
{&__pyx_n_s__object, __pyx_k__object, sizeof(__pyx_k__object), 0, 0, 1, 1},
+ {&__pyx_n_s__ofd, __pyx_k__ofd, sizeof(__pyx_k__ofd), 0, 0, 1, 1},
{&__pyx_n_s__offset, __pyx_k__offset, sizeof(__pyx_k__offset), 0, 0, 1, 1},
{&__pyx_n_s__open, __pyx_k__open, sizeof(__pyx_k__open), 0, 0, 1, 1},
{&__pyx_n_s__ord, __pyx_k__ord, sizeof(__pyx_k__ord), 0, 0, 1, 1},
{&__pyx_n_s__os, __pyx_k__os, sizeof(__pyx_k__os), 0, 0, 1, 1},
+ {&__pyx_n_s__out_stderr, __pyx_k__out_stderr, sizeof(__pyx_k__out_stderr), 0, 0, 1, 1},
+ {&__pyx_n_s__out_stdout, __pyx_k__out_stdout, sizeof(__pyx_k__out_stdout), 0, 0, 1, 1},
{&__pyx_n_s__pack_into, __pyx_k__pack_into, sizeof(__pyx_k__pack_into), 0, 0, 1, 1},
{&__pyx_n_s__path, __pyx_k__path, sizeof(__pyx_k__path), 0, 0, 1, 1},
{&__pyx_n_s__pileups, __pyx_k__pileups, sizeof(__pyx_k__pileups), 0, 0, 1, 1},
@@ -37217,6 +39753,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__remove, __pyx_k__remove, sizeof(__pyx_k__remove), 0, 0, 1, 1},
{&__pyx_n_s__reopen, __pyx_k__reopen, sizeof(__pyx_k__reopen), 0, 0, 1, 1},
{&__pyx_n_s__restore, __pyx_k__restore, sizeof(__pyx_k__restore), 0, 0, 1, 1},
+ {&__pyx_n_s__retval, __pyx_k__retval, sizeof(__pyx_k__retval), 0, 0, 1, 1},
{&__pyx_n_s__rlen, __pyx_k__rlen, sizeof(__pyx_k__rlen), 0, 0, 1, 1},
{&__pyx_n_s__rname, __pyx_k__rname, sizeof(__pyx_k__rname), 0, 0, 1, 1},
{&__pyx_n_s__s, __pyx_k__s, sizeof(__pyx_k__s), 0, 0, 1, 1},
@@ -37234,7 +39771,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1},
{&__pyx_n_s__startswith, __pyx_k__startswith, sizeof(__pyx_k__startswith), 0, 0, 1, 1},
{&__pyx_n_s__stderr, __pyx_k__stderr, sizeof(__pyx_k__stderr), 0, 0, 1, 1},
+ {&__pyx_n_s__stderr_f, __pyx_k__stderr_f, sizeof(__pyx_k__stderr_f), 0, 0, 1, 1},
+ {&__pyx_n_s__stderr_h, __pyx_k__stderr_h, sizeof(__pyx_k__stderr_h), 0, 0, 1, 1},
{&__pyx_n_s__stdout, __pyx_k__stdout, sizeof(__pyx_k__stdout), 0, 0, 1, 1},
+ {&__pyx_n_s__stdout_f, __pyx_k__stdout_f, sizeof(__pyx_k__stdout_f), 0, 0, 1, 1},
+ {&__pyx_n_s__stdout_h, __pyx_k__stdout_h, sizeof(__pyx_k__stdout_h), 0, 0, 1, 1},
+ {&__pyx_n_s__stdout_save, __pyx_k__stdout_save, sizeof(__pyx_k__stdout_save), 0, 0, 1, 1},
{&__pyx_n_s__stepper, __pyx_k__stepper, sizeof(__pyx_k__stepper), 0, 0, 1, 1},
{&__pyx_n_s__streams, __pyx_k__streams, sizeof(__pyx_k__streams), 0, 0, 1, 1},
{&__pyx_n_s__strip, __pyx_k__strip, sizeof(__pyx_k__strip), 0, 0, 1, 1},
@@ -37271,19 +39813,19 @@ static int __Pyx_InitCachedBuiltins(void) {
__pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_IOError = __Pyx_GetName(__pyx_b, __pyx_n_s__IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1305; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_sorted = __Pyx_GetName(__pyx_b, __pyx_n_s__sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_min = __Pyx_GetName(__pyx_b, __pyx_n_s__min); if (!__pyx_builtin_min) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_max = __Pyx_GetName(__pyx_b, __pyx_n_s__max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_chr = __Pyx_GetName(__pyx_b, __pyx_n_s__chr); if (!__pyx_builtin_chr) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_UnicodeDecodeError = __Pyx_GetName(__pyx_b, __pyx_n_s__UnicodeDecodeError); if (!__pyx_builtin_UnicodeDecodeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OverflowError = __Pyx_GetName(__pyx_b, __pyx_n_s__OverflowError); if (!__pyx_builtin_OverflowError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_OSError = __Pyx_GetName(__pyx_b, __pyx_n_s__OSError); if (!__pyx_builtin_OSError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_AttributeError = __Pyx_GetName(__pyx_b, __pyx_n_s__AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_sorted = __Pyx_GetName(__pyx_b, __pyx_n_s__sorted); if (!__pyx_builtin_sorted) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_min = __Pyx_GetName(__pyx_b, __pyx_n_s__min); if (!__pyx_builtin_min) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_max = __Pyx_GetName(__pyx_b, __pyx_n_s__max); if (!__pyx_builtin_max) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_chr = __Pyx_GetName(__pyx_b, __pyx_n_s__chr); if (!__pyx_builtin_chr) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_open = __Pyx_GetName(__pyx_b, __pyx_n_s__open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_UnicodeDecodeError = __Pyx_GetName(__pyx_b, __pyx_n_s__UnicodeDecodeError); if (!__pyx_builtin_UnicodeDecodeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -37291,1269 +39833,1102 @@ static int __Pyx_InitCachedBuiltins(void) {
static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
- __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants");
+ __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "csamtools.pyx":64
+ /* "pysam/csamtools.pyx":64
* return s
* elif PyUnicode_Check(s):
* return s.encode('ascii') # <<<<<<<<<<<<<<
* else:
* raise TypeError, u"Argument must be string, bytes or unicode."
*/
- __pyx_k_tuple_2 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_2));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_2, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __pyx_k_tuple_2 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_2);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
- /* "csamtools.pyx":84
+ /* "pysam/csamtools.pyx":84
* return s
* elif PyBytes_Check(s):
* return s.decode('ascii') # <<<<<<<<<<<<<<
* else:
* # assume unicode
*/
- __pyx_k_tuple_4 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_4));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __pyx_k_tuple_4 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_4);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
- /* "csamtools.pyx":398
+ /* "pysam/csamtools.pyx":398
* def __len__(self):
* if self.fastafile == NULL:
* raise ValueError( "calling len() on closed file" ) # <<<<<<<<<<<<<<
*
* return faidx_fetch_nseq(self.fastafile)
*/
- __pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_8));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
+ __pyx_k_tuple_8 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_8);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_8));
- /* "csamtools.pyx":431
+ /* "pysam/csamtools.pyx":431
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self._filename
*
*/
- __pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_11));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_11 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_11);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
- /* "csamtools.pyx":456
+ /* "pysam/csamtools.pyx":456
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* cdef int length
*/
- __pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_12));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_12 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_12);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
- /* "csamtools.pyx":462
+ /* "pysam/csamtools.pyx":462
*
* if not region:
* if reference is None: raise ValueError( 'no sequence/region supplied.' ) # <<<<<<<<<<<<<<
* if start is None: start = 0
* if end is None: end = max_pos -1
*/
- __pyx_k_tuple_14 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_14));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_13));
- PyTuple_SET_ITEM(__pyx_k_tuple_14, 0, ((PyObject *)__pyx_kp_s_13));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_13));
+ __pyx_k_tuple_14 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_13)); if (unlikely(!__pyx_k_tuple_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 462; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_14);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
- /* "csamtools.pyx":481
+ /* "pysam/csamtools.pyx":481
* region = "%s:%i-%i" % (reference, start+1, end)
* if PY_MAJOR_VERSION >= 3:
* region = region.encode('ascii') # <<<<<<<<<<<<<<
* seq = fai_fetch( self.fastafile,
* region,
*/
- __pyx_k_tuple_20 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_20));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_20, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __pyx_k_tuple_20 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_20);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
- /* "csamtools.pyx":663
+ /* "pysam/csamtools.pyx":663
* if self._filename != NULL: free(self._filename )
* filename = _my_encodeFilename(filename)
* cdef bytes bmode = mode.encode('ascii') # <<<<<<<<<<<<<<
* #cdef char* cfilename
* #cfilename = filename.encode(_FILENAME_ENCODING)
*/
- __pyx_k_tuple_25 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_25));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_25, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
+ __pyx_k_tuple_25 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_25)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_25);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_25));
- /* "csamtools.pyx":790
+ /* "pysam/csamtools.pyx":791
* returns -1 if reference is not known.
* '''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* reference = _force_bytes(reference)
* return pysam_reference2tid( self.samfile.header, reference )
*/
- __pyx_k_tuple_39 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_39));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_39, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_39 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_39)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_39);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_39));
- /* "csamtools.pyx":797
+ /* "pysam/csamtools.pyx":798
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_k_tuple_40 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_40));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_40, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_40 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_40)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_40);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_40));
- /* "csamtools.pyx":805
+ /* "pysam/csamtools.pyx":806
* '''
* convert numerical :term:`tid` into :term:`reference` name.'''
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not 0 <= tid < self.samfile.header.n_targets:
* raise ValueError( "tid %i out of range 0<=tid<%i" % (tid, self.samfile.header.n_targets ) )
*/
- __pyx_k_tuple_42 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_42));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_42, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_42 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_42);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
- /* "csamtools.pyx":855
+ /* "pysam/csamtools.pyx":856
* if len(parts) >= 3: rend = int(parts[2])
*
* if not reference: return 0, 0, 0, 0 # <<<<<<<<<<<<<<
*
* rtid = self.gettid( reference )
*/
- __pyx_k_tuple_44 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_44));
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_k_tuple_44, 1, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_k_tuple_44, 2, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
- __Pyx_INCREF(__pyx_int_0);
- PyTuple_SET_ITEM(__pyx_k_tuple_44, 3, __pyx_int_0);
- __Pyx_GIVEREF(__pyx_int_0);
+ __pyx_k_tuple_44 = PyTuple_Pack(4, __pyx_int_0, __pyx_int_0, __pyx_int_0, __pyx_int_0); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_44);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
- /* "csamtools.pyx":875
+ /* "pysam/csamtools.pyx":876
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
*/
- __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_47));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_47 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_47);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
- /* "csamtools.pyx":877
+ /* "pysam/csamtools.pyx":878
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
* if self.isstream:
* raise OSError("seek no available in streams")
*/
- __pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_49));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
- PyTuple_SET_ITEM(__pyx_k_tuple_49, 0, ((PyObject *)__pyx_kp_s_48));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
+ __pyx_k_tuple_49 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_48)); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_49);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
- /* "csamtools.pyx":879
+ /* "pysam/csamtools.pyx":880
* raise NotImplementedError("seek only available in bam files")
* if self.isstream:
* raise OSError("seek no available in streams") # <<<<<<<<<<<<<<
*
* return bam_seek( self.samfile.x.bam, offset, where )
*/
- __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_51));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_50));
- PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_50));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_50));
+ __pyx_k_tuple_51 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_50)); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_51);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
- /* "csamtools.pyx":888
+ /* "pysam/csamtools.pyx":889
* '''
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files")
*/
- __pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_52));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_52 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_52);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
- /* "csamtools.pyx":890
+ /* "pysam/csamtools.pyx":891
* raise ValueError( "I/O operation on closed file" )
* if not self.isbam:
* raise NotImplementedError("seek only available in bam files") # <<<<<<<<<<<<<<
*
* return bam_tell( self.samfile.x.bam )
*/
- __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_53));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_48));
- PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_48));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_48));
+ __pyx_k_tuple_53 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_48)); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_53);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
- /* "csamtools.pyx":925
+ /* "pysam/csamtools.pyx":926
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_55));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_55 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_55);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
- /* "csamtools.pyx":934
+ /* "pysam/csamtools.pyx":935
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_k_tuple_57 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_57));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
- PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, ((PyObject *)__pyx_kp_s_56));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
+ __pyx_k_tuple_57 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 935; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_57);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
- /* "csamtools.pyx":937
+ /* "pysam/csamtools.pyx":938
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
* return bam_fetch(self.samfile.x.bam,
*/
- __pyx_k_tuple_59 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_59));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
- PyTuple_SET_ITEM(__pyx_k_tuple_59, 0, ((PyObject *)__pyx_kp_s_58));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
+ __pyx_k_tuple_59 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_58)); if (unlikely(!__pyx_k_tuple_59)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_59);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_59));
- /* "csamtools.pyx":938
+ /* "pysam/csamtools.pyx":939
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* return bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_k_tuple_61 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_61));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
- PyTuple_SET_ITEM(__pyx_k_tuple_61, 0, ((PyObject *)__pyx_kp_s_60));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
+ __pyx_k_tuple_61 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_60)); if (unlikely(!__pyx_k_tuple_61)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_61);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_61));
- /* "csamtools.pyx":957
+ /* "pysam/csamtools.pyx":959
* else:
* if has_coord:
* raise ValueError ("fetching by region is not available for sam files" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_k_tuple_63 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_63));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_62));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_kp_s_62));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_62));
+ __pyx_k_tuple_63 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_62)); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_63);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
- /* "csamtools.pyx":960
+ /* "pysam/csamtools.pyx":962
*
* if callback:
* raise NotImplementedError( "callback not implemented yet" ) # <<<<<<<<<<<<<<
*
* if self.samfile.header == NULL:
*/
- __pyx_k_tuple_65 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_65));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_64));
- PyTuple_SET_ITEM(__pyx_k_tuple_65, 0, ((PyObject *)__pyx_kp_s_64));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_64));
+ __pyx_k_tuple_65 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_64)); if (unlikely(!__pyx_k_tuple_65)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_65);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_65));
- /* "csamtools.pyx":963
+ /* "pysam/csamtools.pyx":965
*
* if self.samfile.header == NULL:
* raise ValueError( "fetch called for samfile without header") # <<<<<<<<<<<<<<
*
* # check if targets are defined
*/
- __pyx_k_tuple_67 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 963; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_67));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 0, ((PyObject *)__pyx_kp_s_66));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
+ __pyx_k_tuple_67 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_66)); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 965; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_67);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67));
- /* "csamtools.pyx":968
+ /* "pysam/csamtools.pyx":970
* # give warning, sam_read1 segfaults
* if self.samfile.header.n_targets == 0:
* warnings.warn( "fetch called for samfile without header") # <<<<<<<<<<<<<<
*
* return IteratorRowAll( self, reopen=reopen )
*/
- __pyx_k_tuple_68 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_68));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_66));
- PyTuple_SET_ITEM(__pyx_k_tuple_68, 0, ((PyObject *)__pyx_kp_s_66));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_66));
+ __pyx_k_tuple_68 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_66)); if (unlikely(!__pyx_k_tuple_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_68);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_68));
- /* "csamtools.pyx":1009
+ /* "pysam/csamtools.pyx":1011
*
* if mate_data.mate == NULL:
* raise ValueError( "mate not found" ) # <<<<<<<<<<<<<<
*
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
*/
- __pyx_k_tuple_72 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_72));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_71));
- PyTuple_SET_ITEM(__pyx_k_tuple_72, 0, ((PyObject *)__pyx_kp_s_71));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_71));
+ __pyx_k_tuple_72 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_71)); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_72);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
- /* "csamtools.pyx":1034
+ /* "pysam/csamtools.pyx":1036
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_k_tuple_74 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1034; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_74));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_74, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_74 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_74);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_74));
- /* "csamtools.pyx":1043
+ /* "pysam/csamtools.pyx":1045
* if self.isbam:
* if not until_eof and not self._hasIndex() and not self.isremote:
* raise ValueError( "fetch called on bamfile without index" ) # <<<<<<<<<<<<<<
*
* if not region:
*/
- __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1043; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_75));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
- PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_kp_s_56));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_56));
+ __pyx_k_tuple_75 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_56)); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1045; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_75);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
- /* "csamtools.pyx":1046
+ /* "pysam/csamtools.pyx":1048
*
* if not region:
* raise ValueError( "counting functionality requires a region/reference" ) # <<<<<<<<<<<<<<
* if not self._hasIndex(): raise ValueError( "no index available for fetch" )
* bam_fetch(self.samfile.x.bam,
*/
- __pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_77));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
- PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_kp_s_76));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
+ __pyx_k_tuple_77 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_76)); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1048; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_77);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
- /* "csamtools.pyx":1047
+ /* "pysam/csamtools.pyx":1049
* if not region:
* raise ValueError( "counting functionality requires a region/reference" )
* if not self._hasIndex(): raise ValueError( "no index available for fetch" ) # <<<<<<<<<<<<<<
* bam_fetch(self.samfile.x.bam,
* self.index,
*/
- __pyx_k_tuple_78 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_78));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
- PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_kp_s_60));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
+ __pyx_k_tuple_78 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_60)); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1049; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_78);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
- /* "csamtools.pyx":1057
+ /* "pysam/csamtools.pyx":1059
* return counter
* else:
* raise ValueError ("count for a region is not available for sam files" ) # <<<<<<<<<<<<<<
*
* def pileup( self,
*/
- __pyx_k_tuple_80 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_80));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_79));
- PyTuple_SET_ITEM(__pyx_k_tuple_80, 0, ((PyObject *)__pyx_kp_s_79));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_79));
+ __pyx_k_tuple_80 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_79)); if (unlikely(!__pyx_k_tuple_80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_80);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
- /* "csamtools.pyx":1116
+ /* "pysam/csamtools.pyx":1118
*
* if not self._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* has_coord, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_k_tuple_81 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_81));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_81, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_81 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1118; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_81);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_81));
- /* "csamtools.pyx":1121
+ /* "pysam/csamtools.pyx":1123
*
* if self.isbam:
* if not self._hasIndex(): raise ValueError( "no index available for pileup" ) # <<<<<<<<<<<<<<
*
* if callback:
*/
- __pyx_k_tuple_83 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1121; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_83));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_82));
- PyTuple_SET_ITEM(__pyx_k_tuple_83, 0, ((PyObject *)__pyx_kp_s_82));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_82));
+ __pyx_k_tuple_83 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_82)); if (unlikely(!__pyx_k_tuple_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_83);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83));
- /* "csamtools.pyx":1124
+ /* "pysam/csamtools.pyx":1126
*
* if callback:
* if not has_coord: raise ValueError( "callback functionality requires a region/reference" ) # <<<<<<<<<<<<<<
*
* buf = bam_plbuf_init( <bam_pileup_f>pileup_callback, <void*>callback )
*/
- __pyx_k_tuple_84 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_84));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_58));
- PyTuple_SET_ITEM(__pyx_k_tuple_84, 0, ((PyObject *)__pyx_kp_s_58));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_58));
+ __pyx_k_tuple_84 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_58)); if (unlikely(!__pyx_k_tuple_84)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_84);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_84));
- /* "csamtools.pyx":1145
+ /* "pysam/csamtools.pyx":1147
*
* else:
* raise NotImplementedError( "pileup of samfiles not implemented yet" ) # <<<<<<<<<<<<<<
*
* def close( self ):
*/
- __pyx_k_tuple_86 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_86));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_85));
- PyTuple_SET_ITEM(__pyx_k_tuple_86, 0, ((PyObject *)__pyx_kp_s_85));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
+ __pyx_k_tuple_86 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_85)); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_86);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
- /* "csamtools.pyx":1189
+ /* "pysam/csamtools.pyx":1191
* '''number of :term:`filename` associated with this object.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self._filename
*
*/
- __pyx_k_tuple_87 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_87));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_87, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_87 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_87);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
- /* "csamtools.pyx":1195
+ /* "pysam/csamtools.pyx":1197
* '''number of :term:`reference` sequences in the file.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return self.samfile.header.n_targets
*
*/
- __pyx_k_tuple_88 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_88));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_88, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_88 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_88)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_88);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_88));
- /* "csamtools.pyx":1201
+ /* "pysam/csamtools.pyx":1203
* """tuple with the names of :term:`reference` sequences."""
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_k_tuple_89 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_89));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_89, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_89 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_89);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89));
- /* "csamtools.pyx":1212
+ /* "pysam/csamtools.pyx":1214
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* t = []
* for x from 0 <= x < self.samfile.header.n_targets:
*/
- __pyx_k_tuple_90 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_90)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_90));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_90, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_90 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_90)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_90);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_90));
- /* "csamtools.pyx":1222
+ /* "pysam/csamtools.pyx":1224
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
- *
+ * if self.index == NULL:
*/
- __pyx_k_tuple_91 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_91));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_91, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
+ __pyx_k_tuple_91 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_91)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_91);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_91));
- /* "csamtools.pyx":1223
+ /* "pysam/csamtools.pyx":1225
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" ) # <<<<<<<<<<<<<<
+ * if self.index == NULL:
+ * raise ValueError( "mapping information not recorded in index or index not available")
+ */
+ __pyx_k_tuple_93 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_92)); if (unlikely(!__pyx_k_tuple_93)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1225; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_93);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_93));
+
+ /* "pysam/csamtools.pyx":1227
+ * if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
+ * if self.index == NULL:
+ * raise ValueError( "mapping information not recorded in index or index not available") # <<<<<<<<<<<<<<
*
* cdef int tid
*/
- __pyx_k_tuple_93 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_93)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_93));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_92));
- PyTuple_SET_ITEM(__pyx_k_tuple_93, 0, ((PyObject *)__pyx_kp_s_92));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_92));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_93));
+ __pyx_k_tuple_95 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_94)); if (unlikely(!__pyx_k_tuple_95)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_95);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_95));
- /* "csamtools.pyx":1235
+ /* "pysam/csamtools.pyx":1239
* """
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" )
* cdef int tid
*/
- __pyx_k_tuple_94 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_94)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_94));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_94, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_94));
+ __pyx_k_tuple_96 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1239; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_96);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
- /* "csamtools.pyx":1236
+ /* "pysam/csamtools.pyx":1240
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam: raise AttributeError( "Samfile.unmapped only available in bam files" ) # <<<<<<<<<<<<<<
* cdef int tid
* cdef uint32_t total = 0
*/
- __pyx_k_tuple_96 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_96)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_96));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_95));
- PyTuple_SET_ITEM(__pyx_k_tuple_96, 0, ((PyObject *)__pyx_kp_s_95));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_95));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_96));
+ __pyx_k_tuple_98 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_97)); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_98);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
- /* "csamtools.pyx":1248
+ /* "pysam/csamtools.pyx":1252
* '''full contents of the :term:`sam file` header as a string.'''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* return from_string_and_size(self.samfile.header.text, self.samfile.header.l_text)
*
*/
- __pyx_k_tuple_97 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_97));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_97, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
+ __pyx_k_tuple_99 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_99);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
- /* "csamtools.pyx":1256
+ /* "pysam/csamtools.pyx":1260
* '''
* def __get__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* result = {}
*/
- __pyx_k_tuple_98 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_98));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_98, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
+ __pyx_k_tuple_100 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_100)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_100);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_100));
- /* "csamtools.pyx":1263
+ /* "pysam/csamtools.pyx":1267
* # convert to python string (note: call self.text to create 0-terminated string)
* t = self.text
* for line in t.split("\n"): # <<<<<<<<<<<<<<
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line
*/
- __pyx_k_tuple_99 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1263; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_99));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
- PyTuple_SET_ITEM(__pyx_k_tuple_99, 0, ((PyObject *)__pyx_kp_s_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
+ __pyx_k_tuple_101 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_k_tuple_101)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1267; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_101);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_101));
- /* "csamtools.pyx":1265
+ /* "pysam/csamtools.pyx":1269
* for line in t.split("\n"):
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line # <<<<<<<<<<<<<<
* fields = line[1:].split("\t")
* record = fields[0]
*/
- __pyx_k_tuple_101 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_101)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1265; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_101));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_100));
- PyTuple_SET_ITEM(__pyx_k_tuple_101, 0, ((PyObject *)__pyx_kp_s_100));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_100));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_101));
+ __pyx_k_tuple_103 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_102)); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1269; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_103);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
- /* "csamtools.pyx":1266
+ /* "pysam/csamtools.pyx":1270
* if not line.strip(): continue
* assert line.startswith("@"), "header line without '@': '%s'" % line
* fields = line[1:].split("\t") # <<<<<<<<<<<<<<
* record = fields[0]
* assert record in VALID_HEADER_TYPES, "header line with invalid type '%s': '%s'" % (record, line)
*/
- __pyx_k_tuple_103 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_103));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_5));
- PyTuple_SET_ITEM(__pyx_k_tuple_103, 0, ((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_5));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
+ __pyx_k_tuple_105 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_5)); if (unlikely(!__pyx_k_tuple_105)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1270; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_105);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_105));
- /* "csamtools.pyx":1279
- * x = {}
+ /* "pysam/csamtools.pyx":1283
* for field in fields[1:]:
+ * if ":" not in field:
+ * raise ValueError("malformatted header: no ':' in field" ) # <<<<<<<<<<<<<<
+ * key, value = field.split(":",1)
+ * # uppercase keys must be valid
+ */
+ __pyx_k_tuple_109 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_108)); if (unlikely(!__pyx_k_tuple_109)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_109);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109));
+
+ /* "pysam/csamtools.pyx":1284
+ * if ":" not in field:
+ * raise ValueError("malformatted header: no ':' in field" )
* key, value = field.split(":",1) # <<<<<<<<<<<<<<
* # uppercase keys must be valid
* # lowercase are permitted for user fields
*/
- __pyx_k_tuple_106 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_106)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_106));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_105));
- PyTuple_SET_ITEM(__pyx_k_tuple_106, 0, ((PyObject *)__pyx_kp_s_105));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_105));
- __Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_k_tuple_106, 1, __pyx_int_1);
- __Pyx_GIVEREF(__pyx_int_1);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_106));
+ __pyx_k_tuple_110 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_107), __pyx_int_1); if (unlikely(!__pyx_k_tuple_110)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_110);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110));
- /* "csamtools.pyx":1377
+ /* "pysam/csamtools.pyx":1382
* dest.text = <char*>calloc( len(text), sizeof(char))
* dest.l_text = len(text)
* cdef bytes btext = text.encode('ascii') # <<<<<<<<<<<<<<
* strncpy( dest.text, btext, dest.l_text )
*
*/
- __pyx_k_tuple_112 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_112));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_112, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112));
+ __pyx_k_tuple_116 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_116)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_116);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_116));
- /* "csamtools.pyx":1397
+ /* "pysam/csamtools.pyx":1402
* seqname, seqlen = seqs[x]
* dest.target_name[x] = <char*>calloc( len( seqname ) + 1, sizeof(char) )
* bseqname = seqname.encode('ascii') # <<<<<<<<<<<<<<
* strncpy( dest.target_name[x], bseqname, len(seqname) + 1 )
* dest.target_len[x] = seqlen
*/
- __pyx_k_tuple_114 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_114)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1397; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_114));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_114, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_114));
+ __pyx_k_tuple_118 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_118)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1402; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_118);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_118));
- /* "csamtools.pyx":1412
+ /* "pysam/csamtools.pyx":1417
* ###############################################################
* def __iter__(self):
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header")
*/
- __pyx_k_tuple_115 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_115)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_115));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_115, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_115));
+ __pyx_k_tuple_119 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_119)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_119);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_119));
- /* "csamtools.pyx":1414
+ /* "pysam/csamtools.pyx":1419
* if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
* if not self.isbam and self.samfile.header.n_targets == 0:
* raise NotImplementedError( "can not iterate over samfile without header") # <<<<<<<<<<<<<<
* return self
*
*/
- __pyx_k_tuple_117 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_117));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_116));
- PyTuple_SET_ITEM(__pyx_k_tuple_117, 0, ((PyObject *)__pyx_kp_s_116));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_116));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117));
+ __pyx_k_tuple_121 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_120)); if (unlikely(!__pyx_k_tuple_121)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_121);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_121));
- /* "csamtools.pyx":1484
+ /* "pysam/csamtools.pyx":1489
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* if not samfile._hasIndex():
*/
- __pyx_k_tuple_118 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_118)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_118));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_118, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_118));
+ __pyx_k_tuple_122 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_122);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
- /* "csamtools.pyx":1487
+ /* "pysam/csamtools.pyx":1492
*
* if not samfile._hasIndex():
* raise ValueError( "no index available for iteration" ) # <<<<<<<<<<<<<<
*
* # makes sure that samfile stays alive as long as the
*/
- __pyx_k_tuple_120 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_120));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_119));
- PyTuple_SET_ITEM(__pyx_k_tuple_120, 0, ((PyObject *)__pyx_kp_s_119));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_119));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_120));
+ __pyx_k_tuple_124 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_123)); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_124);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
- /* "csamtools.pyx":1553
+ /* "pysam/csamtools.pyx":1558
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* if samfile.isbam: mode = b"rb"
*/
- __pyx_k_tuple_121 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_121)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_121));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_121, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_121));
+ __pyx_k_tuple_125 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_125)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_125);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_125));
- /* "csamtools.pyx":1604
+ /* "pysam/csamtools.pyx":1609
* def __cinit__(self, Samfile samfile):
* assert samfile._isOpen()
* if not samfile._hasIndex(): raise ValueError("no index available for fetch") # <<<<<<<<<<<<<<
* self.samfile = samfile
* self.tid = -1
*/
- __pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_122));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_60));
- PyTuple_SET_ITEM(__pyx_k_tuple_122, 0, ((PyObject *)__pyx_kp_s_60));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_60));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
+ __pyx_k_tuple_126 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_60)); if (unlikely(!__pyx_k_tuple_126)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_126);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_126));
- /* "csamtools.pyx":1650
+ /* "pysam/csamtools.pyx":1655
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* if not samfile._isOpen():
*/
- __pyx_k_tuple_123 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_123)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_123));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_123, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_123));
+ __pyx_k_tuple_127 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_127)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_127);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_127));
- /* "csamtools.pyx":1653
+ /* "pysam/csamtools.pyx":1658
*
* if not samfile._isOpen():
* raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
*
* assert samfile.isbam, "can only use this iterator on bam files"
*/
- __pyx_k_tuple_124 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_124));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_10));
- PyTuple_SET_ITEM(__pyx_k_tuple_124, 0, ((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_10));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
+ __pyx_k_tuple_128 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_128)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_128);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_128));
- /* "csamtools.pyx":1954
+ /* "pysam/csamtools.pyx":1959
* self.cnext()
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
*
* if self.plp == NULL:
*/
- __pyx_k_tuple_130 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_130)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_130));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
- PyTuple_SET_ITEM(__pyx_k_tuple_130, 0, ((PyObject *)__pyx_kp_s_129));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_130));
+ __pyx_k_tuple_134 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_133)); if (unlikely(!__pyx_k_tuple_134)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_134);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_134));
- /* "csamtools.pyx":1990
+ /* "pysam/csamtools.pyx":1995
*
* if self.n_plp < 0:
* raise ValueError("error during iteration" ) # <<<<<<<<<<<<<<
*
* # return result, if within same reference
*/
- __pyx_k_tuple_131 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_131));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_129));
- PyTuple_SET_ITEM(__pyx_k_tuple_131, 0, ((PyObject *)__pyx_kp_s_129));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_129));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131));
+ __pyx_k_tuple_135 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_133)); if (unlikely(!__pyx_k_tuple_135)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_135);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_135));
- /* "csamtools.pyx":2153
+ /* "pysam/csamtools.pyx":2158
* qual = self.qual
* else:
* seq = self.seq.decode('ascii') # <<<<<<<<<<<<<<
* qual = self.qual.decode('ascii')
* return "\t".join(map(str, (self.qname,
*/
- __pyx_k_tuple_133 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_133));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_133, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_133));
+ __pyx_k_tuple_137 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_137)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_137);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_137));
- /* "csamtools.pyx":2154
+ /* "pysam/csamtools.pyx":2159
* else:
* seq = self.seq.decode('ascii')
* qual = self.qual.decode('ascii') # <<<<<<<<<<<<<<
* return "\t".join(map(str, (self.qname,
* self.flag,
*/
- __pyx_k_tuple_134 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_134)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_134));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_134, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_134));
+ __pyx_k_tuple_138 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_138)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_138);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_138));
- /* "csamtools.pyx":2563
+ /* "pysam/csamtools.pyx":2587
* for pytag, value in tags:
* if not type(pytag) is bytes:
* pytag = pytag.encode('ascii') # <<<<<<<<<<<<<<
* t = type(value)
*
*/
- __pyx_k_tuple_139 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_139));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_139, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_139));
+ __pyx_k_tuple_143 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_143)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_143);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_143));
- /* "csamtools.pyx":2591
+ /* "pysam/csamtools.pyx":2615
* datafmt = "2sccI%i%s" % (len(value), datafmt)
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* datatype.encode('ascii'),
* len(value)] + list(value) )
*/
- __pyx_k_tuple_142 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_142)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2591; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_142));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_142, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_142));
+ __pyx_k_tuple_146 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_146)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_146);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_146));
- /* "csamtools.pyx":2592
+ /* "pysam/csamtools.pyx":2616
* args.extend( [pytag[:2],
* pytype.encode('ascii'),
* datatype.encode('ascii'), # <<<<<<<<<<<<<<
* len(value)] + list(value) )
* fmts.append( datafmt )
*/
- __pyx_k_tuple_143 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_143)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2592; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_143));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_143, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_143));
+ __pyx_k_tuple_147 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_147)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_147);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_147));
- /* "csamtools.pyx":2615
+ /* "pysam/csamtools.pyx":2639
* # Note: hex strings (H) are not supported yet
* if t is not bytes:
* value = value.encode('ascii') # <<<<<<<<<<<<<<
* if len(value) == 1:
* fmt, pytype = "2scc", 'A'
*/
- __pyx_k_tuple_144 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_144)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_144));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_144, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_144));
+ __pyx_k_tuple_148 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_148)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_148);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_148));
- /* "csamtools.pyx":2622
+ /* "pysam/csamtools.pyx":2646
*
* args.extend( [pytag[:2],
* pytype.encode('ascii'), # <<<<<<<<<<<<<<
* value ] )
*
*/
- __pyx_k_tuple_146 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_146)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_146));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_146, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_146));
+ __pyx_k_tuple_150 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_150)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_150);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_150));
- /* "csamtools.pyx":3020
+ /* "pysam/csamtools.pyx":3047
* '''
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
*
* def __str__(self):
*/
- __pyx_k_tuple_172 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_172)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_172));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
- PyTuple_SET_ITEM(__pyx_k_tuple_172, 0, ((PyObject *)__pyx_kp_s_171));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_172));
+ __pyx_k_tuple_176 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_175)); if (unlikely(!__pyx_k_tuple_176)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3047; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_176);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_176));
- /* "csamtools.pyx":3046
+ /* "pysam/csamtools.pyx":3073
*
* if self.plp[0] == NULL:
* raise ValueError("PileupProxy accessed after iterator finished") # <<<<<<<<<<<<<<
*
* # warning: there could be problems if self.n and self.buf are
*/
- __pyx_k_tuple_174 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3046; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_174));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_173));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 0, ((PyObject *)__pyx_kp_s_173));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_173));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_174));
+ __pyx_k_tuple_178 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_177)); if (unlikely(!__pyx_k_tuple_178)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3073; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_178);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_178));
- /* "csamtools.pyx":3059
+ /* "pysam/csamtools.pyx":3086
*
* def __init__(self):
* raise TypeError("This class cannot be instantiated from Python") # <<<<<<<<<<<<<<
*
* def __str__(self):
*/
- __pyx_k_tuple_175 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3059; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_175));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_171));
- PyTuple_SET_ITEM(__pyx_k_tuple_175, 0, ((PyObject *)__pyx_kp_s_171));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_171));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_175));
+ __pyx_k_tuple_179 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_175)); if (unlikely(!__pyx_k_tuple_179)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_179);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_179));
- /* "csamtools.pyx":3172
+ /* "pysam/csamtools.pyx":3199
* # recover. Thus redirect output to file with -o option.
* if method == "view":
* if "-o" in args: raise ValueError("option -o is forbidden in samtools view") # <<<<<<<<<<<<<<
* args = ( "-o", stdout_f ) + args
*
*/
- __pyx_k_tuple_180 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_180));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_179));
- PyTuple_SET_ITEM(__pyx_k_tuple_180, 0, ((PyObject *)__pyx_kp_s_179));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_179));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_180));
+ __pyx_k_tuple_184 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_183)); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_184);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_184));
- /* "csamtools.pyx":3197
+ /* "pysam/csamtools.pyx":3224
* stdout_save.restore()
* try:
* with open( stdout_f, "r") as inf: # <<<<<<<<<<<<<<
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
*/
- __pyx_k_tuple_181 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3197; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_181));
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 0, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 1, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 2, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181));
-
- /* "csamtools.pyx":3200
+ __pyx_k_tuple_185 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_k_tuple_185)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_185);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_185));
+
+ /* "pysam/csamtools.pyx":3227
* out_stdout = inf.readlines()
* except UnicodeDecodeError:
* with open( stdout_f, "rb") as inf: # <<<<<<<<<<<<<<
* # read binary output
* out_stdout = inf.read()
*/
- __pyx_k_tuple_182 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_182));
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_182, 0, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_182, 1, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_182, 2, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_182));
-
- /* "csamtools.pyx":3210
+ __pyx_k_tuple_186 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_k_tuple_186)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3227; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_186);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_186));
+
+ /* "pysam/csamtools.pyx":3237
* pysam_unset_stderr()
* try:
* with open( stderr_f, "r") as inf: # <<<<<<<<<<<<<<
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
*/
- __pyx_k_tuple_183 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_183));
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 0, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 1, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 2, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_183));
-
- /* "csamtools.pyx":3213
+ __pyx_k_tuple_187 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_k_tuple_187)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_187);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_187));
+
+ /* "pysam/csamtools.pyx":3240
* out_stderr = inf.readlines()
* except UnicodeDecodeError:
* with open( stderr_f, "rb") as inf: # <<<<<<<<<<<<<<
* # read binary output
* out_stderr = inf.read()
*/
- __pyx_k_tuple_184 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_184));
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_184, 0, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_184, 1, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_INCREF(Py_None);
- PyTuple_SET_ITEM(__pyx_k_tuple_184, 2, Py_None);
- __Pyx_GIVEREF(Py_None);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_184));
+ __pyx_k_tuple_188 = PyTuple_Pack(3, Py_None, Py_None, Py_None); if (unlikely(!__pyx_k_tuple_188)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_188);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_188));
- /* "csamtools.pyx":143
+ /* "pysam/csamtools.pyx":143
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" ) # <<<<<<<<<<<<<<
*
* #####################################################################
*/
- __pyx_k_tuple_252 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_252));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_251));
- PyTuple_SET_ITEM(__pyx_k_tuple_252, 0, ((PyObject *)__pyx_kp_s_251));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_251));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_252));
+ __pyx_k_tuple_256 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_255)); if (unlikely(!__pyx_k_tuple_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_256);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_256));
+
+ /* "pysam/csamtools.pyx":260
+ * list of reads (:class:`pysam.PileupRead`) aligned to this column
+ * '''
+ * def __str__(self): # <<<<<<<<<<<<<<
+ * return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
+ * "\n" + "\n".join( map(str, self.pileups) )
+ */
+ __pyx_k_tuple_258 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_258);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
+ __pyx_k_codeobj_259 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_258, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s____str__, 260, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":308
+ * stderr is captured.
+ * '''
+ * def __init__(self): # <<<<<<<<<<<<<<
+ * return
+ * self.stderr_h, self.stderr_f = tempfile.mkstemp()
+ */
+ __pyx_k_tuple_264 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_264)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_264);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_264));
+ __pyx_k_codeobj_265 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_264, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s____init__, 308, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_265)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":314
+ * self.stderr_save.setfd( self.stderr_h )
+ *
+ * def readAndRelease( self ): # <<<<<<<<<<<<<<
+ * return []
+ * self.stderr_save.restore()
+ */
+ __pyx_k_tuple_267 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_267)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_267);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_267));
+ __pyx_k_codeobj_268 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_267, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__readAndRelease, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_268)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":323
+ * return lines
+ *
+ * def release(self): # <<<<<<<<<<<<<<
+ * return
+ * self.stderr_save.restore()
+ */
+ __pyx_k_tuple_270 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_270)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_270);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_270));
+ __pyx_k_codeobj_271 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_270, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__release, 323, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_271)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":354
+ /* "pysam/csamtools.pyx":329
+ * os.remove( self.stderr_f )
+ *
+ * def __del__(self): # <<<<<<<<<<<<<<
+ * self.release()
+ *
+ */
+ __pyx_k_tuple_273 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_273)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_273);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_273));
+ __pyx_k_codeobj_274 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_273, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s____del__, 329, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_274)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":334
+ * class StderrStoreWindows():
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass # <<<<<<<<<<<<<<
+ * def readAndRelease(self): return []
+ * def release(self): pass
+ */
+ __pyx_k_tuple_277 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_277)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_277);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_277));
+ __pyx_k_codeobj_278 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_277, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s____init__, 334, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_278)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":335
+ * '''does nothing. stderr can't be redirected on windows'''
+ * def __init__(self): pass
+ * def readAndRelease(self): return [] # <<<<<<<<<<<<<<
+ * def release(self): pass
+ *
+ */
+ __pyx_k_tuple_280 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_280)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_280);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_280));
+ __pyx_k_codeobj_281 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_280, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__readAndRelease, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_281)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":336
+ * def __init__(self): pass
+ * def readAndRelease(self): return []
+ * def release(self): pass # <<<<<<<<<<<<<<
+ *
+ * if platform.system()=='Windows':
+ */
+ __pyx_k_tuple_283 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_283)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_283);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_283));
+ __pyx_k_codeobj_284 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_283, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__release, 336, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_284)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":354
*
* # order of records within sam headers
* VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<<
*
* # type conversions within sam header records
*/
- __pyx_k_tuple_257 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_257));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__HD));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 0, ((PyObject *)__pyx_n_s__HD));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__HD));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__SQ));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 1, ((PyObject *)__pyx_n_s__SQ));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__SQ));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__RG));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 2, ((PyObject *)__pyx_n_s__RG));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__RG));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 3, ((PyObject *)__pyx_n_s__PG));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__CO));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 4, ((PyObject *)__pyx_n_s__CO));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__CO));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_257));
-
- /* "csamtools.pyx":364
+ __pyx_k_tuple_287 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_n_s__CO)); if (unlikely(!__pyx_k_tuple_287)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_287);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_287));
+
+ /* "pysam/csamtools.pyx":364
*
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
*/
- __pyx_k_tuple_258 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_258));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__VN));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__SO));
- PyTuple_SET_ITEM(__pyx_k_tuple_258, 1, ((PyObject *)__pyx_n_s__SO));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__SO));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__GO));
- PyTuple_SET_ITEM(__pyx_k_tuple_258, 2, ((PyObject *)__pyx_n_s__GO));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__GO));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
+ __pyx_k_tuple_288 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__VN), ((PyObject *)__pyx_n_s__SO), ((PyObject *)__pyx_n_s__GO)); if (unlikely(!__pyx_k_tuple_288)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_288);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_288));
- /* "csamtools.pyx":365
+ /* "pysam/csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*/
- __pyx_k_tuple_259 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_259));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__SN));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 0, ((PyObject *)__pyx_n_s__SN));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__SN));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__LN));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 1, ((PyObject *)__pyx_n_s__LN));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__LN));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__AS));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 2, ((PyObject *)__pyx_n_s__AS));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__AS));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__M5));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 3, ((PyObject *)__pyx_n_s__M5));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__M5));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__UR));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 4, ((PyObject *)__pyx_n_s__UR));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__UR));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__SP));
- PyTuple_SET_ITEM(__pyx_k_tuple_259, 5, ((PyObject *)__pyx_n_s__SP));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__SP));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_259));
-
- /* "csamtools.pyx":366
+ __pyx_k_tuple_289 = PyTuple_Pack(6, ((PyObject *)__pyx_n_s__SN), ((PyObject *)__pyx_n_s__LN), ((PyObject *)__pyx_n_s__AS), ((PyObject *)__pyx_n_s__M5), ((PyObject *)__pyx_n_s__UR), ((PyObject *)__pyx_n_s__SP)); if (unlikely(!__pyx_k_tuple_289)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_289);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_289));
+
+ /* "pysam/csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<<
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*
*/
- __pyx_k_tuple_260 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_260));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 0, ((PyObject *)__pyx_n_s__ID));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__SM));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 1, ((PyObject *)__pyx_n_s__SM));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__SM));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__LB));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 2, ((PyObject *)__pyx_n_s__LB));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__LB));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__DS));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 3, ((PyObject *)__pyx_n_s__DS));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__DS));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PU));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 4, ((PyObject *)__pyx_n_s__PU));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PU));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PI));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 5, ((PyObject *)__pyx_n_s__PI));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PI));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__CN));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 6, ((PyObject *)__pyx_n_s__CN));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__CN));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__DT));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 7, ((PyObject *)__pyx_n_s__DT));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__DT));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PL));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 8, ((PyObject *)__pyx_n_s__PL));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PL));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__FO));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 9, ((PyObject *)__pyx_n_s__FO));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__FO));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__KS));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 10, ((PyObject *)__pyx_n_s__KS));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__KS));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PG));
- PyTuple_SET_ITEM(__pyx_k_tuple_260, 11, ((PyObject *)__pyx_n_s__PG));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PG));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_260));
-
- /* "csamtools.pyx":367
+ __pyx_k_tuple_290 = PyTuple_Pack(12, ((PyObject *)__pyx_n_s__ID), ((PyObject *)__pyx_n_s__SM), ((PyObject *)__pyx_n_s__LB), ((PyObject *)__pyx_n_s__DS), ((PyObject *)__pyx_n_s__PU), ((PyObject *)__pyx_n_s__PI), ((PyObject *)__pyx_n_s__CN), ((PyObject *)__pyx_n_s__DT), ((PyObject *)__pyx_n_s__PL), ((PyObject *)__pyx_n_s__FO), ((PyObject *)__pyx_n_s__KS), ((PyObject *)__pyx_n_s__PG)); if (unlikely(!__pyx_k_tuple_290)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LI [...]
+ __Pyx_GOTREF(__pyx_k_tuple_290);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_290));
+
+ /* "pysam/csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<<
*
*
*/
- __pyx_k_tuple_261 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_261)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_k_tuple_261));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PN));
- PyTuple_SET_ITEM(__pyx_k_tuple_261, 0, ((PyObject *)__pyx_n_s__PN));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PN));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
- PyTuple_SET_ITEM(__pyx_k_tuple_261, 1, ((PyObject *)__pyx_n_s__ID));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ID));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__VN));
- PyTuple_SET_ITEM(__pyx_k_tuple_261, 2, ((PyObject *)__pyx_n_s__VN));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__VN));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__CL));
- PyTuple_SET_ITEM(__pyx_k_tuple_261, 3, ((PyObject *)__pyx_n_s__CL));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__CL));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__PP));
- PyTuple_SET_ITEM(__pyx_k_tuple_261, 4, ((PyObject *)__pyx_n_s__PP));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__PP));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_261));
+ __pyx_k_tuple_291 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__PN), ((PyObject *)__pyx_n_s__ID), ((PyObject *)__pyx_n_s__VN), ((PyObject *)__pyx_n_s__CL), ((PyObject *)__pyx_n_s__PP)); if (unlikely(!__pyx_k_tuple_291)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_291);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_291));
+
+ /* "pysam/csamtools.pyx":3119
+ * class Outs:
+ * '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
+ * def __init__(self, id = 1): # <<<<<<<<<<<<<<
+ * self.streams = []
+ * self.id = id
+ */
+ __pyx_k_tuple_292 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__id)); if (unlikely(!__pyx_k_tuple_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_292);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_292));
+ __pyx_k_codeobj_293 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_292, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s____init__, 3119, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_293)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_294 = PyTuple_Pack(1, ((PyObject *)__pyx_int_1)); if (unlikely(!__pyx_k_tuple_294)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_294);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_294));
+
+ /* "pysam/csamtools.pyx":3123
+ * self.id = id
+ *
+ * def setdevice(self, filename): # <<<<<<<<<<<<<<
+ * '''open an existing file, like "/dev/null"'''
+ * fd = os.open(filename, os.O_WRONLY)
+ */
+ __pyx_k_tuple_296 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filename), ((PyObject *)__pyx_n_s__fd)); if (unlikely(!__pyx_k_tuple_296)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_296);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_296));
+ __pyx_k_codeobj_297 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_296, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__setdevice, 3123, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_297)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":3128
+ * self.setfd(fd)
+ *
+ * def setfile(self, filename): # <<<<<<<<<<<<<<
+ * '''open a new file.'''
+ * fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
+ */
+ __pyx_k_tuple_299 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filename), ((PyObject *)__pyx_n_s__fd)); if (unlikely(!__pyx_k_tuple_299)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_299);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_299));
+ __pyx_k_codeobj_300 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_299, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__setfile, 3128, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_300)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":3133
+ * self.setfd(fd)
+ *
+ * def setfd(self, fd): # <<<<<<<<<<<<<<
+ * ofd = os.dup(self.id) # Save old stream on new unit.
+ * self.streams.append(ofd)
+ */
+ __pyx_k_tuple_302 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__fd), ((PyObject *)__pyx_n_s__ofd)); if (unlikely(!__pyx_k_tuple_302)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_302);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_302));
+ __pyx_k_codeobj_303 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_302, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__setfd, 3133, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_303)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":3141
+ * os.close(fd) # Close other unit (look out, caller.)
+ *
+ * def restore(self): # <<<<<<<<<<<<<<
+ * '''restore previous output stream'''
+ * if self.streams:
+ */
+ __pyx_k_tuple_305 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_305)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_305);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_305));
+ __pyx_k_codeobj_306 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_305, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s__restore, 3141, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_306)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":3152
+ * del self.streams[-1]
+ *
+ * def _samtools_dispatch( method, # <<<<<<<<<<<<<<
+ * args = (),
+ * catch_stdout = True ):
+ */
+ __pyx_k_tuple_309 = PyTuple_Pack(16, ((PyObject *)__pyx_n_s__method), ((PyObject *)__pyx_n_s__args), ((PyObject *)__pyx_n_s__catch_stdout), ((PyObject *)__pyx_n_s__stderr_h), ((PyObject *)__pyx_n_s__stderr_f), ((PyObject *)__pyx_n_s__stdout_h), ((PyObject *)__pyx_n_s__stdout_f), ((PyObject *)__pyx_n_s__stdout_save), ((PyObject *)__pyx_n_s__cargs), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__n), ((PyObject *)__pyx_n_s__retval), ((PyObject *)__pyx_n_s__inf), ((PyObject *)__pyx_n_ [...]
+ __Pyx_GOTREF(__pyx_k_tuple_309);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_309));
+ __pyx_k_codeobj_310 = (PyObject*)__Pyx_PyCode_New(3, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_309, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_260, __pyx_n_s___samtools_dispatch, 3152, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_310)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -38612,12 +40987,18 @@ PyMODINIT_FUNC PyInit_csamtools(void)
Py_FatalError("failed to import 'refnanny' module");
}
#endif
- __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)");
+ __Pyx_RefNannySetupContext("PyMODINIT_FUNC PyInit_csamtools(void)", 0);
if ( __Pyx_check_binary_version() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_tuple = PyTuple_New(0); if (unlikely(!__pyx_empty_tuple)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_empty_bytes = PyBytes_FromStringAndSize("", 0); if (unlikely(!__pyx_empty_bytes)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- #ifdef __pyx_binding_PyCFunctionType_USED
- if (__pyx_binding_PyCFunctionType_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #ifdef __Pyx_CyFunction_USED
+ if (__Pyx_CyFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ #ifdef __Pyx_FusedFunction_USED
+ if (__pyx_FusedFunction_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ #ifdef __Pyx_Generator_USED
+ if (__pyx_Generator_init() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#endif
/*--- Library function declarations ---*/
/*--- Threads initialization code ---*/
@@ -38628,20 +41009,27 @@ PyMODINIT_FUNC PyInit_csamtools(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("csamtools"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
+ if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION >= 3
+ {
+ PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!PyDict_GetItemString(modules, "pysam.csamtools")) {
+ if (unlikely(PyDict_SetItemString(modules, "pysam.csamtools", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ }
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_module_is_main_csamtools) {
+ if (__pyx_module_is_main_pysam__csamtools) {
if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
}
/*--- Builtin init code ---*/
@@ -38649,176 +41037,195 @@ PyMODINIT_FUNC PyInit_csamtools(void)
/*--- Constants init code ---*/
if (unlikely(__Pyx_InitCachedConstants() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Global init code ---*/
- __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- __pyx_vtabptr_9csamtools_Fastafile = &__pyx_vtable_9csamtools_Fastafile;
- __pyx_vtable_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_9csamtools_9Fastafile__fetch;
- if (PyType_Ready(&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Fastafile = &__pyx_type_9csamtools_Fastafile;
- if (PyType_Ready(&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_9csamtools_Fastafile = &__pyx_vtable_5pysam_9csamtools_Fastafile;
+ __pyx_vtable_5pysam_9csamtools_Fastafile._fetch = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *))__pyx_f_5pysam_9csamtools_9Fastafile__fetch;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastafile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastafile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_Fastafile = &__pyx_type_5pysam_9csamtools_Fastafile;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_11AlignedRead_2__str__.doc = __pyx_doc_9csamtools_11AlignedRead_2__str__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_11AlignedRead_2__str__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_AlignedRead = &__pyx_type_9csamtools_AlignedRead;
- __pyx_vtabptr_9csamtools_Samfile = &__pyx_vtable_9csamtools_Samfile;
- __pyx_vtable_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_9csamtools_Samfile *, PyObject *))__pyx_f_9csamtools_7Samfile__buildHeader;
- __pyx_vtable_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_getCurrent;
- __pyx_vtable_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_9csamtools_Samfile *))__pyx_f_9csamtools_7Samfile_cnext;
- __pyx_vtable_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_9csamtools_Samfile *, struct __pyx_obj_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_9csamtools_7Samfile_write;
- __pyx_vtable_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_9csamtools_Samfile *, int))__pyx_f_9csamtools_7Samfile__getrname;
- if (PyType_Ready(&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__.doc = __pyx_doc_5pysam_9csamtools_11AlignedRead_4__str__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_11AlignedRead_4__str__;
+ }
+ }
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2099; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_AlignedRead = &__pyx_type_5pysam_9csamtools_AlignedRead;
+ __pyx_vtabptr_5pysam_9csamtools_Samfile = &__pyx_vtable_5pysam_9csamtools_Samfile;
+ __pyx_vtable_5pysam_9csamtools_Samfile._buildHeader = (bam_header_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, PyObject *))__pyx_f_5pysam_9csamtools_7Samfile__buildHeader;
+ __pyx_vtable_5pysam_9csamtools_Samfile.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_getCurrent;
+ __pyx_vtable_5pysam_9csamtools_Samfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *))__pyx_f_5pysam_9csamtools_7Samfile_cnext;
+ __pyx_vtable_5pysam_9csamtools_Samfile.write = (int (*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, struct __pyx_obj_5pysam_9csamtools_AlignedRead *, int __pyx_skip_dispatch))__pyx_f_5pysam_9csamtools_7Samfile_write;
+ __pyx_vtable_5pysam_9csamtools_Samfile._getrname = (char *(*)(struct __pyx_obj_5pysam_9csamtools_Samfile *, int))__pyx_f_5pysam_9csamtools_7Samfile__getrname;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_7Samfile_21__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_7Samfile_21__next__.doc = __pyx_doc_9csamtools_7Samfile_21__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_7Samfile_21__next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_Samfile.tp_dict, __pyx_vtabptr_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_Samfile = &__pyx_type_9csamtools_Samfile;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupProxy = &__pyx_type_9csamtools_PileupProxy;
- if (PyType_Ready(&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_PileupRead = &__pyx_type_9csamtools_PileupRead;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRow = &__pyx_type_9csamtools_IteratorRow;
- __pyx_vtabptr_9csamtools_IteratorRowRegion = &__pyx_vtable_9csamtools_IteratorRowRegion;
- __pyx_vtable_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowRegion *))__pyx_f_9csamtools_17IteratorRowRegion_cnext;
- __pyx_type_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__.doc = __pyx_doc_5pysam_9csamtools_7Samfile_42__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_7Samfile_42__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Samfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_Samfile = &__pyx_type_5pysam_9csamtools_Samfile;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3029; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_PileupProxy = &__pyx_type_5pysam_9csamtools_PileupProxy;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3081; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "PileupRead", (PyObject *)&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3081; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_PileupRead = &__pyx_type_5pysam_9csamtools_PileupRead;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRow", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorRow = &__pyx_type_5pysam_9csamtools_IteratorRow;
+ __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion = &__pyx_vtable_5pysam_9csamtools_IteratorRowRegion;
+ __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_getCurrent;
+ __pyx_vtable_5pysam_9csamtools_IteratorRowRegion.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion *))__pyx_f_5pysam_9csamtools_17IteratorRowRegion_cnext;
+ __pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__.doc = __pyx_doc_9csamtools_17IteratorRowRegion_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_17IteratorRowRegion_2__next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowRegion = &__pyx_type_9csamtools_IteratorRowRegion;
- __pyx_vtabptr_9csamtools_IteratorRowAll = &__pyx_vtable_9csamtools_IteratorRowAll;
- __pyx_vtable_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowAll *))__pyx_f_9csamtools_14IteratorRowAll_cnext;
- __pyx_type_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__.doc = __pyx_doc_5pysam_9csamtools_17IteratorRowRegion_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_17IteratorRowRegion_4__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorRowRegion = &__pyx_type_5pysam_9csamtools_IteratorRowRegion;
+ __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll = &__pyx_vtable_5pysam_9csamtools_IteratorRowAll;
+ __pyx_vtable_5pysam_9csamtools_IteratorRowAll.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_getCurrent;
+ __pyx_vtable_5pysam_9csamtools_IteratorRowAll.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *))__pyx_f_5pysam_9csamtools_14IteratorRowAll_cnext;
+ __pyx_type_5pysam_9csamtools_IteratorRowAll.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__.doc = __pyx_doc_9csamtools_14IteratorRowAll_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_14IteratorRowAll_2__next__;
+ __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__.doc = __pyx_doc_5pysam_9csamtools_14IteratorRowAll_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_14IteratorRowAll_4__next__;
}
}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAll = &__pyx_type_9csamtools_IteratorRowAll;
- __pyx_type_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAll", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1545; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorRowAll = &__pyx_type_5pysam_9csamtools_IteratorRowAll;
+ __pyx_type_5pysam_9csamtools_IteratorRowAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__.doc = __pyx_doc_9csamtools_18IteratorRowAllRefs_3__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_18IteratorRowAllRefs_3__next__;
- }
- }
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowAllRefs = &__pyx_type_9csamtools_IteratorRowAllRefs;
- __pyx_vtabptr_9csamtools_IteratorRowSelection = &__pyx_vtable_9csamtools_IteratorRowSelection;
- __pyx_vtable_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_getCurrent;
- __pyx_vtable_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorRowSelection *))__pyx_f_9csamtools_20IteratorRowSelection_cnext;
- __pyx_type_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_9csamtools_IteratorRow;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__.doc = __pyx_doc_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_18IteratorRowAllRefs_6__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorRowAllRefs = &__pyx_type_5pysam_9csamtools_IteratorRowAllRefs;
+ __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection = &__pyx_vtable_5pysam_9csamtools_IteratorRowSelection;
+ __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.getCurrent = (bam1_t *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_getCurrent;
+ __pyx_vtable_5pysam_9csamtools_IteratorRowSelection.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *))__pyx_f_5pysam_9csamtools_20IteratorRowSelection_cnext;
+ __pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorRow;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__.doc = __pyx_doc_9csamtools_20IteratorRowSelection_2__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorRowSelection_2__next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorRowSelection = &__pyx_type_9csamtools_IteratorRowSelection;
- __pyx_vtabptr_9csamtools_IteratorColumn = &__pyx_vtable_9csamtools_IteratorColumn;
- __pyx_vtable_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_cnext;
- __pyx_vtable_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_9csamtools_IteratorColumn *))__pyx_f_9csamtools_14IteratorColumn_getSequence;
- __pyx_vtable_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_setMask;
- __pyx_vtable_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_9csamtools_14IteratorColumn_setupIteratorData;
- __pyx_vtable_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_9csamtools_14IteratorColumn_reset;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumn = &__pyx_type_9csamtools_IteratorColumn;
- __pyx_vtabptr_9csamtools_IteratorColumnRegion = &__pyx_vtable_9csamtools_IteratorColumnRegion;
- __pyx_vtable_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorRowSelection_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorRowSelection_4__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowSelection", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorRowSelection = &__pyx_type_5pysam_9csamtools_IteratorRowSelection;
+ __pyx_vtabptr_5pysam_9csamtools_IteratorColumn = &__pyx_vtable_5pysam_9csamtools_IteratorColumn;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumn.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_cnext;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumn.getSequence = (char *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *))__pyx_f_5pysam_9csamtools_14IteratorColumn_getSequence;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumn.setMask = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_setMask;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumn.setupIteratorData = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, int, int, int, struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData *__pyx_optional_args))__pyx_f_5pysam_9csamtools_14IteratorColumn_setupIteratorData;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumn.reset = (PyObject *(*)(struct __pyx_obj_5pysam_9csamtools_IteratorColumn *, PyObject *, PyObject *, PyObject *))__pyx_f_5pysam_9csamtools_14IteratorColumn_reset;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumn.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumn", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorColumn = &__pyx_type_5pysam_9csamtools_IteratorColumn;
+ __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion = &__pyx_vtable_5pysam_9csamtools_IteratorColumnRegion;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumnRegion.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+ __pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__.doc = __pyx_doc_9csamtools_20IteratorColumnRegion_1__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_20IteratorColumnRegion_1__next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumnRegion = &__pyx_type_9csamtools_IteratorColumnRegion;
- __pyx_vtabptr_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_9csamtools_IteratorColumnAllRefs;
- __pyx_vtable_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_9csamtools_IteratorColumn;
- __pyx_type_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_9csamtools_IteratorColumn;
- if (PyType_Ready(&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__.doc = __pyx_doc_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_20IteratorColumnRegion_2__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnRegion", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorColumnRegion = &__pyx_type_5pysam_9csamtools_IteratorColumnRegion;
+ __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs;
+ __pyx_vtable_5pysam_9csamtools_IteratorColumnAllRefs.__pyx_base = *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+ __pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_base = __pyx_ptype_5pysam_9csamtools_IteratorColumn;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__.doc = __pyx_doc_9csamtools_21IteratorColumnAllRefs_1__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_9csamtools_21IteratorColumnAllRefs_1__next__;
- }
- }
- if (__Pyx_SetVtable(__pyx_type_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IteratorColumnAllRefs = &__pyx_type_9csamtools_IteratorColumnAllRefs;
- if (PyType_Ready(&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_IndexedReads = &__pyx_type_9csamtools_IndexedReads;
- if (PyType_Ready(&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools_SNPCall = &__pyx_type_9csamtools_SNPCall;
- if (PyType_Ready(&__pyx_Generator_type) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools___pyx_Generator = &__pyx_Generator_type;
- __pyx_type_9csamtools___pyx_scope_struct__genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator;
- if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_9csamtools___pyx_scope_struct__genexpr;
- __pyx_type_9csamtools___pyx_scope_struct_1_genexpr.tp_base = __pyx_ptype_9csamtools___pyx_Generator;
- if (PyType_Ready(&__pyx_type_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_9csamtools___pyx_scope_struct_1_genexpr;
+ __pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__.doc = __pyx_doc_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorColumnAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IteratorColumnAllRefs = &__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "IndexedReads", (PyObject *)&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3804; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_IndexedReads = &__pyx_type_5pysam_9csamtools_IndexedReads;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "SNPCall", (PyObject *)&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_SNPCall = &__pyx_type_5pysam_9csamtools_SNPCall;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools___pyx_scope_struct__genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct__genexpr;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools___pyx_scope_struct_1_genexpr = &__pyx_type_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
/*--- Type import code ---*/
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
+ #if CYTHON_COMPILING_IN_PYPY
+ sizeof(PyTypeObject),
+ #else
+ sizeof(PyHeapTypeObject),
+ #endif
+ 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "csamtools.pyx":4
+ /* "pysam/csamtools.pyx":4
* # cython: profile=True
* # adds doc-strings for sphinx
* import tempfile # <<<<<<<<<<<<<<
@@ -38830,7 +41237,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tempfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":5
+ /* "pysam/csamtools.pyx":5
* # adds doc-strings for sphinx
* import tempfile
* import os # <<<<<<<<<<<<<<
@@ -38842,7 +41249,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__os, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 5; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":6
+ /* "pysam/csamtools.pyx":6
* import tempfile
* import os
* import sys # <<<<<<<<<<<<<<
@@ -38854,7 +41261,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__sys, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":7
+ /* "pysam/csamtools.pyx":7
* import os
* import sys
* import types # <<<<<<<<<<<<<<
@@ -38866,7 +41273,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__types, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":8
+ /* "pysam/csamtools.pyx":8
* import sys
* import types
* import itertools # <<<<<<<<<<<<<<
@@ -38878,7 +41285,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__itertools, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":9
+ /* "pysam/csamtools.pyx":9
* import types
* import itertools
* import struct # <<<<<<<<<<<<<<
@@ -38890,7 +41297,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__struct, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":10
+ /* "pysam/csamtools.pyx":10
* import itertools
* import struct
* import ctypes # <<<<<<<<<<<<<<
@@ -38902,7 +41309,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__ctypes, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 10; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":11
+ /* "pysam/csamtools.pyx":11
* import struct
* import ctypes
* import collections # <<<<<<<<<<<<<<
@@ -38914,7 +41321,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__collections, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 11; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":12
+ /* "pysam/csamtools.pyx":12
* import ctypes
* import collections
* import re # <<<<<<<<<<<<<<
@@ -38926,7 +41333,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__re, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":13
+ /* "pysam/csamtools.pyx":13
* import collections
* import re
* import platform # <<<<<<<<<<<<<<
@@ -38938,7 +41345,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__platform, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 13; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":14
+ /* "pysam/csamtools.pyx":14
* import re
* import platform
* import warnings # <<<<<<<<<<<<<<
@@ -38950,7 +41357,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__warnings, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":23
+ /* "pysam/csamtools.pyx":23
* ## Python 3 compatibility functions
* ########################################################################
* IS_PYTHON3 = PY_MAJOR_VERSION >= 3 # <<<<<<<<<<<<<<
@@ -38962,7 +41369,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__IS_PYTHON3, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":32
+ /* "pysam/csamtools.pyx":32
* # filename encoding (copied from lxml.etree.pyx)
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding() # <<<<<<<<<<<<<<
@@ -38971,30 +41378,30 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*/
__pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__sys); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s_249); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s_253); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
- __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "csamtools.pyx":33
+ /* "pysam/csamtools.pyx":33
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding()
* if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None:
*/
- __pyx_t_3 = (__pyx_v_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
+ __pyx_t_3 = (__pyx_v_5pysam_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "csamtools.pyx":34
+ /* "pysam/csamtools.pyx":34
* _FILENAME_ENCODING = sys.getfilesystemencoding()
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = sys.getdefaultencoding() # <<<<<<<<<<<<<<
@@ -39010,26 +41417,26 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyString_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected str, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 34; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(__pyx_t_1);
- __pyx_v_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
+ __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
goto __pyx_L2;
}
__pyx_L2:;
- /* "csamtools.pyx":35
+ /* "pysam/csamtools.pyx":35
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None: # <<<<<<<<<<<<<<
* _FILENAME_ENCODING = 'ascii'
*
*/
- __pyx_t_3 = (__pyx_v_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
+ __pyx_t_3 = (__pyx_v_5pysam_9csamtools__FILENAME_ENCODING == ((PyObject*)Py_None));
if (__pyx_t_3) {
- /* "csamtools.pyx":36
+ /* "pysam/csamtools.pyx":36
* _FILENAME_ENCODING = sys.getdefaultencoding()
* if _FILENAME_ENCODING is None:
* _FILENAME_ENCODING = 'ascii' # <<<<<<<<<<<<<<
@@ -39037,24 +41444,24 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* #cdef char* _C_FILENAME_ENCODING
*/
__Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- __Pyx_XGOTREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
- __Pyx_DECREF(((PyObject *)__pyx_v_9csamtools__FILENAME_ENCODING));
+ __Pyx_XGOTREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_9csamtools__FILENAME_ENCODING));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __pyx_v_9csamtools__FILENAME_ENCODING = __pyx_n_s__ascii;
+ __pyx_v_5pysam_9csamtools__FILENAME_ENCODING = __pyx_n_s__ascii;
goto __pyx_L3;
}
__pyx_L3:;
- /* "csamtools.pyx":138
+ /* "pysam/csamtools.pyx":138
* DEF BAM_CDIFF = 8
*
* cdef char* CODE2CIGAR= "MIDNSHP=X" # <<<<<<<<<<<<<<
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
*/
- __pyx_v_9csamtools_CODE2CIGAR = __pyx_k_250;
+ __pyx_v_5pysam_9csamtools_CODE2CIGAR = __pyx_k_254;
- /* "csamtools.pyx":139
+ /* "pysam/csamtools.pyx":139
*
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3: # <<<<<<<<<<<<<<
@@ -39067,17 +41474,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":140
+ /* "pysam/csamtools.pyx":140
* cdef char* CODE2CIGAR= "MIDNSHP=X"
* if IS_PYTHON3:
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
*/
- __pyx_t_1 = __pyx_pf_9csamtools_1genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_5pysam_9csamtools_2genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -39090,17 +41497,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
/*else*/ {
- /* "csamtools.pyx":142
+ /* "pysam/csamtools.pyx":142
* CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) ) # <<<<<<<<<<<<<<
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+ * CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" )
*
*/
- __pyx_t_1 = __pyx_pf_9csamtools_3genexpr(NULL, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_pf_5pysam_9csamtools_5genexpr(NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
@@ -39112,10 +41519,10 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
__pyx_L4:;
- /* "csamtools.pyx":143
+ /* "pysam/csamtools.pyx":143
* else:
* CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
- * CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" ) # <<<<<<<<<<<<<<
+ * CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" ) # <<<<<<<<<<<<<<
*
* #####################################################################
*/
@@ -39124,13 +41531,13 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_252), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_256), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__CIGAR_REGEX, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 143; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":147
+ /* "pysam/csamtools.pyx":147
* #####################################################################
* ## set pysam stderr to /dev/null
* pysam_unset_stderr() # <<<<<<<<<<<<<<
@@ -39139,25 +41546,25 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*/
pysam_unset_stderr();
- /* "csamtools.pyx":151
+ /* "pysam/csamtools.pyx":151
* #####################################################################
* # hard-coded constants
* cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN" # <<<<<<<<<<<<<<
* cdef int max_pos = 2 << 29
*
*/
- __pyx_v_9csamtools_bam_nt16_rev_table = __pyx_k_253;
+ __pyx_v_5pysam_9csamtools_bam_nt16_rev_table = __pyx_k_257;
- /* "csamtools.pyx":152
+ /* "pysam/csamtools.pyx":152
* # hard-coded constants
* cdef char * bam_nt16_rev_table = "=ACMGRSVTWYHKDBN"
* cdef int max_pos = 2 << 29 # <<<<<<<<<<<<<<
*
* #####################################################################
*/
- __pyx_v_9csamtools_max_pos = 1073741824;
+ __pyx_v_5pysam_9csamtools_max_pos = 1073741824;
- /* "csamtools.pyx":247
+ /* "pysam/csamtools.pyx":247
* (<object>f)(a)
*
* class PileupColumn(object): # <<<<<<<<<<<<<<
@@ -39167,19 +41574,19 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "csamtools.pyx":260
+ /* "pysam/csamtools.pyx":260
* list of reads (:class:`pysam.PileupRead`) aligned to this column
* '''
* def __str__(self): # <<<<<<<<<<<<<<
* return "\t".join( map(str, (self.tid, self.pos, self.n))) +\
* "\n" + "\n".join( map(str, self.pileups) )
*/
- __pyx_t_2 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_12PileupColumn___str__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_12PileupColumn_1__str__, 0, __pyx_n_s_261, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____str__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "csamtools.pyx":247
+ /* "pysam/csamtools.pyx":247
* (<object>f)(a)
*
* class PileupColumn(object): # <<<<<<<<<<<<<<
@@ -39187,19 +41594,19 @@ PyMODINIT_FUNC PyInit_csamtools(void)
* all the reads that map to a certain target base.
*/
__pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_builtin_object);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_builtin_object);
__Pyx_GIVEREF(__pyx_builtin_object);
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_254)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_263)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_t_1), __pyx_n_s__PileupColumn, __pyx_n_s__PileupColumn, __pyx_n_s_262); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PileupColumn, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":304
+ /* "pysam/csamtools.pyx":304
* return 0
*
* class StderrStore(): # <<<<<<<<<<<<<<
@@ -39209,69 +41616,69 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "csamtools.pyx":308
+ /* "pysam/csamtools.pyx":308
* stderr is captured.
* '''
* def __init__(self): # <<<<<<<<<<<<<<
* return
* self.stderr_h, self.stderr_f = tempfile.mkstemp()
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_1__init__, 0, __pyx_n_s_266, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_265)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 308; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":314
+ /* "pysam/csamtools.pyx":314
* self.stderr_save.setfd( self.stderr_h )
*
* def readAndRelease( self ): # <<<<<<<<<<<<<<
* return []
* self.stderr_save.restore()
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_3readAndRelease, 0, __pyx_n_s_269, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_268)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":323
+ /* "pysam/csamtools.pyx":323
* return lines
*
* def release(self): # <<<<<<<<<<<<<<
* return
* self.stderr_save.restore()
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_5release, 0, __pyx_n_s_272, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_271)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":329
+ /* "pysam/csamtools.pyx":329
* os.remove( self.stderr_f )
*
* def __del__(self): # <<<<<<<<<<<<<<
* self.release()
*
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_11StderrStore_3__del__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_11StderrStore_7__del__, 0, __pyx_n_s_275, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_274)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____del__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":304
+ /* "pysam/csamtools.pyx":304
* return 0
*
* class StderrStore(): # <<<<<<<<<<<<<<
* '''
* stderr is captured.
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_255)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_276)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStore, __pyx_n_s__StderrStore, __pyx_n_s_262); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":332
+ /* "pysam/csamtools.pyx":332
* self.release()
*
* class StderrStoreWindows(): # <<<<<<<<<<<<<<
@@ -39281,57 +41688,57 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- /* "csamtools.pyx":334
+ /* "pysam/csamtools.pyx":334
* class StderrStoreWindows():
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass # <<<<<<<<<<<<<<
* def readAndRelease(self): return []
* def release(self): pass
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_1__init__, 0, __pyx_n_s_279, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_278)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":335
+ /* "pysam/csamtools.pyx":335
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
* def readAndRelease(self): return [] # <<<<<<<<<<<<<<
* def release(self): pass
*
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_1readAndRelease, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_3readAndRelease, 0, __pyx_n_s_282, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_281)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__readAndRelease, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":336
+ /* "pysam/csamtools.pyx":336
* def __init__(self): pass
* def readAndRelease(self): return []
* def release(self): pass # <<<<<<<<<<<<<<
*
* if platform.system()=='Windows':
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_18StderrStoreWindows_2release, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_18StderrStoreWindows_5release, 0, __pyx_n_s_285, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_284)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__release, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":332
+ /* "pysam/csamtools.pyx":332
* self.release()
*
* class StderrStoreWindows(): # <<<<<<<<<<<<<<
* '''does nothing. stderr can't be redirected on windows'''
* def __init__(self): pass
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_256)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_286)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__StderrStoreWindows, __pyx_n_s__StderrStoreWindows, __pyx_n_s_262); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStoreWindows, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":338
+ /* "pysam/csamtools.pyx":338
* def release(self): pass
*
* if platform.system()=='Windows': # <<<<<<<<<<<<<<
@@ -39346,11 +41753,13 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Windows), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Windows), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_3) {
- /* "csamtools.pyx":339
+ /* "pysam/csamtools.pyx":339
*
* if platform.system()=='Windows':
* del StderrStore # <<<<<<<<<<<<<<
@@ -39359,446 +41768,447 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*/
if (__Pyx_DelAttrString(__pyx_m, "StderrStore") < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":340
+ /* "pysam/csamtools.pyx":340
* if platform.system()=='Windows':
* del StderrStore
* StderrStore = StderrStoreWindows # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStoreWindows); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__StderrStoreWindows); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__StderrStore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L5;
}
__pyx_L5:;
- /* "csamtools.pyx":347
+ /* "pysam/csamtools.pyx":347
* ######################################################################
* # valid types for sam headers
* VALID_HEADER_TYPES = { "HD" : dict, # <<<<<<<<<<<<<<
* "SQ" : list,
* "RG" : list,
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)(&PyDict_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__HD), ((PyObject *)((PyObject*)(&PyDict_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":348
+ /* "pysam/csamtools.pyx":348
* # valid types for sam headers
* VALID_HEADER_TYPES = { "HD" : dict,
* "SQ" : list, # <<<<<<<<<<<<<<
* "RG" : list,
* "PG" : list,
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":349
+ /* "pysam/csamtools.pyx":349
* VALID_HEADER_TYPES = { "HD" : dict,
* "SQ" : list,
* "RG" : list, # <<<<<<<<<<<<<<
* "PG" : list,
* "CO" : list }
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__RG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":350
+ /* "pysam/csamtools.pyx":350
* "SQ" : list,
* "RG" : list,
* "PG" : list, # <<<<<<<<<<<<<<
* "CO" : list }
*
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":351
+ /* "pysam/csamtools.pyx":351
* "RG" : list,
* "PG" : list,
* "CO" : list } # <<<<<<<<<<<<<<
*
* # order of records within sam headers
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CO), ((PyObject *)((PyObject*)(&PyList_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_TYPES, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "csamtools.pyx":354
+ /* "pysam/csamtools.pyx":354
*
* # order of records within sam headers
* VALID_HEADERS = ("HD", "SQ", "RG", "PG", "CO" ) # <<<<<<<<<<<<<<
*
* # type conversions within sam header records
*/
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_257)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADERS, ((PyObject *)__pyx_k_tuple_287)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":357
+ /* "pysam/csamtools.pyx":357
*
* # type conversions within sam header records
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str }, # <<<<<<<<<<<<<<
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__GO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":358
+ /* "pysam/csamtools.pyx":358
* # type conversions within sam header records
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str }, # <<<<<<<<<<<<<<
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)(&PyInt_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__LN), ((PyObject *)((PyObject*)(&PyInt_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__AS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__M5), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__UR), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":359
+ /* "pysam/csamtools.pyx":359
* VALID_HEADER_FIELDS = { "HD" : { "VN" : str, "SO" : str, "GO" : str },
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str, # <<<<<<<<<<<<<<
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
* "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "csamtools.pyx":360
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SM), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__LB), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__DS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PU), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PI), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/csamtools.pyx":360
* "SQ" : { "SN" : str, "LN" : int, "AS" : str, "M5" : str, "UR" : str, "SP" : str },
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,}, # <<<<<<<<<<<<<<
* "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, }
*
*/
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__DT), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__FO), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__KS), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "csamtools.pyx":361
+ /* "pysam/csamtools.pyx":361
* "RG" : { "ID" : str, "SM" : str, "LB" : str, "DS" : str, "PU" : str, "PI" : str,
* "CN" : str, "DT" : str, "PL" : str, "FO" : str, "KS" : str, "PG" : str,},
* "PG" : { "PN" : str, "ID" : str, "VN" : str, "CL" : str, "PP" : str }, } # <<<<<<<<<<<<<<
*
* # output order of fields within records
*/
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__ID), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__VN), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__CL), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PP), ((PyObject *)((PyObject*)(&PyString_Type)))) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_FIELDS, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "csamtools.pyx":364
+ /* "pysam/csamtools.pyx":364
*
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ), # <<<<<<<<<<<<<<
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_258)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__HD), ((PyObject *)__pyx_k_tuple_288)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":365
+ /* "pysam/csamtools.pyx":365
* # output order of fields within records
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ), # <<<<<<<<<<<<<<
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_259)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__SQ), ((PyObject *)__pyx_k_tuple_289)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":366
+ /* "pysam/csamtools.pyx":366
* VALID_HEADER_ORDER = { "HD" : ( "VN", "SO", "GO" ),
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ), # <<<<<<<<<<<<<<
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), }
*
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_260)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__RG), ((PyObject *)__pyx_k_tuple_290)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "csamtools.pyx":367
+ /* "pysam/csamtools.pyx":367
* "SQ" : ( "SN", "LN", "AS", "M5" , "UR" , "SP" ),
* "RG" : ( "ID", "SM", "LB", "DS" , "PU" , "PI" , "CN" , "DT", "PL", "FO", "KS", "PG" ),
* "PG" : ( "PN", "ID", "VN", "CL", "PP" ), } # <<<<<<<<<<<<<<
*
*
*/
- if (PyDict_SetItem(__pyx_t_1, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_261)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__PG), ((PyObject *)__pyx_k_tuple_291)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VALID_HEADER_ORDER, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "csamtools.pyx":619
+ /* "pysam/csamtools.pyx":619
* header = None,
* port = None,
* add_sq_text = True, # <<<<<<<<<<<<<<
* check_header = True,
* check_sq = True,
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_k_21 = __pyx_t_1;
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_k_21 = __pyx_t_4;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "csamtools.pyx":620
+ /* "pysam/csamtools.pyx":620
* port = None,
* add_sq_text = True,
* check_header = True, # <<<<<<<<<<<<<<
* check_sq = True,
* ):
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_k_22 = __pyx_t_1;
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_k_22 = __pyx_t_4;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "csamtools.pyx":621
+ /* "pysam/csamtools.pyx":621
* add_sq_text = True,
* check_header = True,
* check_sq = True, # <<<<<<<<<<<<<<
* ):
* '''open a sam/bam file.
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_k_23 = __pyx_t_1;
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_k_23 = __pyx_t_4;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "csamtools.pyx":900
+ /* "pysam/csamtools.pyx":901
* region = None,
* callback = None,
* until_eof = False ): # <<<<<<<<<<<<<<
* '''
* fetch aligned reads in a :term:`region` using 0-based indexing. The region is specified by
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_k_54 = __pyx_t_1;
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_k_54 = __pyx_t_4;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "csamtools.pyx":1020
+ /* "pysam/csamtools.pyx":1022
* end = None,
* region = None,
* until_eof = False ): # <<<<<<<<<<<<<<
* '''*(reference = None, start = None, end = None, region = None, callback = None, until_eof = False)*
*
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1020; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_k_73 = __pyx_t_1;
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_k_73 = __pyx_t_4;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "csamtools.pyx":1937
+ /* "pysam/csamtools.pyx":1942
* int tid = 0,
* int start = 0,
* int end = max_pos, # <<<<<<<<<<<<<<
* int truncate = False,
* **kwargs ):
*/
- __pyx_k_128 = __pyx_v_9csamtools_max_pos;
+ __pyx_k_132 = __pyx_v_5pysam_9csamtools_max_pos;
- /* "csamtools.pyx":3090
+ /* "pysam/csamtools.pyx":3117
* return self._level
*
* class Outs: # <<<<<<<<<<<<<<
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
- /* "csamtools.pyx":3092
+ /* "pysam/csamtools.pyx":3119
* class Outs:
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1): # <<<<<<<<<<<<<<
* self.streams = []
* self.id = id
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs___init__, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3092; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_1__init__, 0, __pyx_n_s_295, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_293)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_294));
+ if (PyObject_SetItem(__pyx_t_4, __pyx_n_s____init__, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3119; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3096
+ /* "pysam/csamtools.pyx":3123
* self.id = id
*
* def setdevice(self, filename): # <<<<<<<<<<<<<<
* '''open an existing file, like "/dev/null"'''
* fd = os.open(filename, os.O_WRONLY)
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_1setdevice, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setdevice, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3096; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_3setdevice, 0, __pyx_n_s_298, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_297)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__setdevice, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3101
+ /* "pysam/csamtools.pyx":3128
* self.setfd(fd)
*
* def setfile(self, filename): # <<<<<<<<<<<<<<
* '''open a new file.'''
* fd = os.open(filename, os.O_WRONLY|os.O_CREAT, 0660);
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_2setfile, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfile, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_5setfile, 0, __pyx_n_s_301, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_300)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__setfile, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3128; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3106
+ /* "pysam/csamtools.pyx":3133
* self.setfd(fd)
*
* def setfd(self, fd): # <<<<<<<<<<<<<<
* ofd = os.dup(self.id) # Save old stream on new unit.
* self.streams.append(ofd)
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_3setfd, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__setfd, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3106; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_7setfd, 0, __pyx_n_s_304, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_303)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__setfd, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3133; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3114
+ /* "pysam/csamtools.pyx":3141
* os.close(fd) # Close other unit (look out, caller.)
*
* def restore(self): # <<<<<<<<<<<<<<
* '''restore previous output stream'''
* if self.streams:
*/
- __pyx_t_4 = __pyx_binding_PyCFunctionType_NewEx(&__pyx_mdef_9csamtools_4Outs_4restore, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__restore, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3114; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_4Outs_9restore, 0, __pyx_n_s_307, NULL, __pyx_n_s_262, ((PyObject *)__pyx_k_codeobj_306)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_t_4, __pyx_n_s__restore, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "csamtools.pyx":3090
+ /* "pysam/csamtools.pyx":3117
* return self._level
*
* class Outs: # <<<<<<<<<<<<<<
* '''http://mail.python.org/pipermail/python-list/2000-June/038406.html'''
* def __init__(self, id = 1):
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_262)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s__Outs, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3090; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_4), "__doc__", ((PyObject *)__pyx_kp_s_308)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_4), __pyx_n_s__Outs, __pyx_n_s__Outs, __pyx_n_s_262); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__Outs, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "csamtools.pyx":3127
+ /* "pysam/csamtools.pyx":3154
* def _samtools_dispatch( method,
* args = (),
* catch_stdout = True ): # <<<<<<<<<<<<<<
* '''call ``method`` in samtools providing arguments in args.
*
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_k_176 = __pyx_t_1;
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ __pyx_k_180 = __pyx_t_4;
+ __Pyx_GIVEREF(__pyx_t_4);
+ __pyx_t_4 = 0;
- /* "csamtools.pyx":3125
+ /* "pysam/csamtools.pyx":3152
* del self.streams[-1]
*
* def _samtools_dispatch( method, # <<<<<<<<<<<<<<
* args = (),
* catch_stdout = True ):
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_9csamtools__samtools_dispatch, NULL, __pyx_n_s__csamtools); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = PyCFunction_NewEx(&__pyx_mdef_5pysam_9csamtools_1_samtools_dispatch, NULL, __pyx_n_s_262); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s___samtools_dispatch, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "csamtools.pyx":3836
+ /* "pysam/csamtools.pyx":3864
* if self.owns_samfile: samclose( self.fp )
*
* __all__ = ["Samfile", # <<<<<<<<<<<<<<
* "Fastafile",
* "IteratorRow",
*/
- __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
+ __pyx_t_4 = PyList_New(9); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Samfile));
- PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Samfile));
+ PyList_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_n_s__Samfile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Samfile));
__Pyx_INCREF(((PyObject *)__pyx_n_s__Fastafile));
- PyList_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__Fastafile));
+ PyList_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__Fastafile));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Fastafile));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorRow));
- PyList_SET_ITEM(__pyx_t_1, 2, ((PyObject *)__pyx_n_s__IteratorRow));
+ PyList_SET_ITEM(__pyx_t_4, 2, ((PyObject *)__pyx_n_s__IteratorRow));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorRow));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IteratorColumn));
- PyList_SET_ITEM(__pyx_t_1, 3, ((PyObject *)__pyx_n_s__IteratorColumn));
+ PyList_SET_ITEM(__pyx_t_4, 3, ((PyObject *)__pyx_n_s__IteratorColumn));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IteratorColumn));
__Pyx_INCREF(((PyObject *)__pyx_n_s__AlignedRead));
- PyList_SET_ITEM(__pyx_t_1, 4, ((PyObject *)__pyx_n_s__AlignedRead));
+ PyList_SET_ITEM(__pyx_t_4, 4, ((PyObject *)__pyx_n_s__AlignedRead));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__AlignedRead));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PileupColumn));
- PyList_SET_ITEM(__pyx_t_1, 5, ((PyObject *)__pyx_n_s__PileupColumn));
+ PyList_SET_ITEM(__pyx_t_4, 5, ((PyObject *)__pyx_n_s__PileupColumn));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupColumn));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PileupProxy));
- PyList_SET_ITEM(__pyx_t_1, 6, ((PyObject *)__pyx_n_s__PileupProxy));
+ PyList_SET_ITEM(__pyx_t_4, 6, ((PyObject *)__pyx_n_s__PileupProxy));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupProxy));
__Pyx_INCREF(((PyObject *)__pyx_n_s__PileupRead));
- PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__PileupRead));
+ PyList_SET_ITEM(__pyx_t_4, 7, ((PyObject *)__pyx_n_s__PileupRead));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__PileupRead));
__Pyx_INCREF(((PyObject *)__pyx_n_s__IndexedReads));
- PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__IndexedReads));
+ PyList_SET_ITEM(__pyx_t_4, 8, ((PyObject *)__pyx_n_s__IndexedReads));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__IndexedReads));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "csamtools.pyx":1
+ /* "pysam/csamtools.pyx":1
* # cython: embedsignature=True # <<<<<<<<<<<<<<
* # cython: profile=True
* # adds doc-strings for sphinx
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_4));
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_4)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_4);
if (__pyx_m) {
- __Pyx_AddTraceback("init csamtools", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init pysam.csamtools", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init csamtools");
+ PyErr_SetString(PyExc_ImportError, "init pysam.csamtools");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -39810,7 +42220,6 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
/* Runtime support code */
-
#if CYTHON_REFNANNY
static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
PyObject *m = NULL, *p = NULL;
@@ -39842,9 +42251,7 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
return result;
}
-
#if CYTHON_PROFILE
-
static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
PyFrameObject** frame,
const char *funcname,
@@ -39868,12 +42275,10 @@ static int __Pyx_TraceSetupAndCall(PyCodeObject** code,
}
return PyThreadState_GET()->c_profilefunc(PyThreadState_GET()->c_profileobj, *frame, PyTrace_CALL, NULL) == 0;
}
-
static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno) {
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
PyCodeObject *py_code = 0;
-
#if PY_MAJOR_VERSION < 3
py_funcname = PyString_FromString(funcname);
py_srcfile = PyString_FromString(srcfile);
@@ -39882,7 +42287,6 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha
py_srcfile = PyUnicode_FromString(srcfile);
#endif
if (!py_funcname | !py_srcfile) goto bad;
-
py_code = PyCode_New(
0, /*int argcount,*/
#if PY_MAJOR_VERSION >= 3
@@ -39902,20 +42306,43 @@ static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const cha
firstlineno, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
-
bad:
Py_XDECREF(py_srcfile);
Py_XDECREF(py_funcname);
-
return py_code;
}
-
#endif /* CYTHON_PROFILE */
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
+ Py_ssize_t length;
+ if (unlikely((start < 0) | (stop < 0))) {
+ length = strlen(cstring);
+ if (start < 0) {
+ start += length;
+ if (start < 0)
+ start = 0;
+ }
+ if (stop < 0)
+ stop += length;
+ }
+ length = stop - start;
+ if (unlikely(length <= 0))
+ return PyUnicode_FromUnicode(NULL, 0);
+ cstring += start;
+ if (decode_func) {
+ return decode_func(cstring, length, errors);
+ } else {
+ return PyUnicode_Decode(cstring, length, encoding, errors);
+ }
+}
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
-
tmp_type = tstate->curexc_type;
tmp_value = tstate->curexc_value;
tmp_tb = tstate->curexc_traceback;
@@ -39925,55 +42352,60 @@ static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyOb
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_Restore(type, value, tb);
+#endif
}
-
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->curexc_type;
*value = tstate->curexc_value;
*tb = tstate->curexc_traceback;
-
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(type, value, tb);
+#endif
}
-
#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- /* cause is unused */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- /* First, check the traceback argument, replacing None with NULL. */
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- /* Next, replace a missing value with None */
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- /* Raising an instance. The value should be a dummy. */
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- /* Normalize to raise <class>, <instance> */
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -39996,7 +42428,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
#endif
}
-
__Pyx_ErrRestore(type, value, tb);
return;
raise_error:
@@ -40005,10 +42436,9 @@ raise_error:
Py_XDECREF(tb);
return;
}
-
#else /* Python 3+ */
-
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -40018,7 +42448,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
if (value == Py_None)
value = 0;
-
if (PyExceptionInstance_Check(type)) {
if (value) {
PyErr_SetString(PyExc_TypeError,
@@ -40027,13 +42456,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
-
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -40050,14 +42502,9 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
-
PyErr_SetObject(type, value);
-
if (tb) {
PyThreadState *tstate = PyThreadState_GET();
PyObject* tmp_tb = tstate->curexc_traceback;
@@ -40067,8 +42514,8 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
Py_XDECREF(tmp_tb);
}
}
-
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
@@ -40092,13 +42539,17 @@ static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
{
PyObject* key = 0;
Py_ssize_t pos = 0;
+#if CPYTHON_COMPILING_IN_PYPY
+ if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
+ goto invalid_keyword;
+ return 1;
+#else
while (PyDict_Next(kwdict, &pos, &key, 0)) {
#if PY_MAJOR_VERSION < 3
if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key)))
#endif
- goto invalid_keyword_type;
+ if (unlikely(!PyUnicode_Check(key)))
+ goto invalid_keyword_type;
}
if ((!kw_allowed) && unlikely(key))
goto invalid_keyword;
@@ -40107,6 +42558,7 @@ invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
"%s() keywords must be strings", function_name);
return 0;
+#endif
invalid_keyword:
PyErr_Format(PyExc_TypeError,
#if PY_MAJOR_VERSION < 3
@@ -40128,7 +42580,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -40144,55 +42596,77 @@ static int __Pyx_ParseOptionalKeywords(
Py_ssize_t pos = 0;
PyObject*** name;
PyObject*** first_kw_arg = argnames + num_pos_args;
-
while (PyDict_Next(kwds, &pos, &key, &value)) {
name = first_kw_arg;
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_CheckExact(key)) && unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- /* unexpected keyword found */
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
}
}
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -40220,7 +42694,6 @@ static void __Pyx_RaiseArgtupleInvalid(
{
Py_ssize_t num_expected;
const char *more_or_less;
-
if (num_found < num_min) {
num_expected = num_min;
more_or_less = "at least";
@@ -40232,7 +42705,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -40259,6 +42732,7 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -40267,19 +42741,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -40287,10 +42769,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
@@ -40302,25 +42787,40 @@ bad:
return -1;
}
-
-
-static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
- index, (index == 1) ? "" : "s");
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
+ index, (index == 1) ? "" : "s");
}
-static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else if (PyErr_Occurred()) {
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
PyErr_Clear();
return 0;
@@ -40329,10 +42829,18 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
}
}
return 0;
+#endif
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ } else {
+ return __Pyx_IterFinish();
+ }
+ return 0;
}
static CYTHON_INLINE long __Pyx_div_long(long a, long b) {
@@ -40352,8 +42860,29 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
}
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_traverse != current_tp_traverse)
+ type = type->tp_base;
+ while (type && type->tp_traverse == current_tp_traverse)
+ type = type->tp_base;
+ if (type && type->tp_traverse)
+ return type->tp_traverse(obj, v, a);
+ return 0;
+}
+
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_clear != current_tp_clear)
+ type = type->tp_base;
+ while (type && type->tp_clear == current_tp_clear)
+ type = type->tp_base;
+ if (type && type->tp_clear)
+ type->tp_clear(obj);
+}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -40361,9 +42890,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
-
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -40375,18 +42907,23 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
- PyObject *py_import = 0;
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
PyObject *empty_dict = 0;
PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import = 0;
py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
if (!py_import)
goto bad;
+ #endif
if (from_list)
list = from_list;
else {
@@ -40403,12 +42940,42 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
goto bad;
#if PY_VERSION_HEX >= 0x02050000
{
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
+ #if PY_MAJOR_VERSION >= 3
+ if (level == -1) {
+ if (strchr(__Pyx_MODULE_NAME, '.')) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(1);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
+ if (!module) {
+ if (!PyErr_ExceptionMatches(PyExc_ImportError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ level = 0; /* try absolute import on failure */
+ }
+ #endif
+ if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
+ }
}
#else
if (level>0) {
@@ -40419,15 +42986,16 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
name, global_dict, empty_dict, list, NULL);
#endif
bad:
- Py_XDECREF(empty_list);
+ #if PY_VERSION_HEX < 0x03030000
Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
Py_XDECREF(empty_dict);
return module;
}
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
- /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -40452,14 +43020,13 @@ static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
}
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
- PyObject *modname) {
+ PyObject *qualname, PyObject *modname) {
PyObject *result;
PyObject *metaclass;
-
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
-
- /* Python2 __metaclass__ */
+ if (PyDict_SetItemString(dict, "__qualname__", qualname) < 0)
+ return NULL;
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -40471,105 +43038,559 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
return result;
}
-
-static PyObject *__pyx_binding_PyCFunctionType_NewEx(PyMethodDef *ml, PyObject *self, PyObject *module) {
- __pyx_binding_PyCFunctionType_object *op = PyObject_GC_New(__pyx_binding_PyCFunctionType_object, __pyx_binding_PyCFunctionType);
+static PyObject *
+__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
+{
+ if (unlikely(op->func_doc == NULL)) {
+ if (op->func.m_ml->ml_doc) {
+#if PY_MAJOR_VERSION >= 3
+ op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
+#else
+ op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
+#endif
+ if (unlikely(op->func_doc == NULL))
+ return NULL;
+ } else {
+ Py_INCREF(Py_None);
+ return Py_None;
+ }
+ }
+ Py_INCREF(op->func_doc);
+ return op->func_doc;
+}
+static int
+__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp = op->func_doc;
+ if (value == NULL)
+ value = Py_None; /* Mark as deleted */
+ Py_INCREF(value);
+ op->func_doc = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
+{
+ if (unlikely(op->func_name == NULL)) {
+#if PY_MAJOR_VERSION >= 3
+ op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
+#else
+ op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
+#endif
+ if (unlikely(op->func_name == NULL))
+ return NULL;
+ }
+ Py_INCREF(op->func_name);
+ return op->func_name;
+}
+static int
+__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+ if (unlikely(value == NULL || !PyUnicode_Check(value))) {
+#else
+ if (unlikely(value == NULL || !PyString_Check(value))) {
+#endif
+ PyErr_SetString(PyExc_TypeError,
+ "__name__ must be set to a string object");
+ return -1;
+ }
+ tmp = op->func_name;
+ Py_INCREF(value);
+ op->func_name = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
+{
+ Py_INCREF(op->func_qualname);
+ return op->func_qualname;
+}
+static int
+__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+ if (unlikely(value == NULL || !PyUnicode_Check(value))) {
+#else
+ if (unlikely(value == NULL || !PyString_Check(value))) {
+#endif
+ PyErr_SetString(PyExc_TypeError,
+ "__qualname__ must be set to a string object");
+ return -1;
+ }
+ tmp = op->func_qualname;
+ Py_INCREF(value);
+ op->func_qualname = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
+{
+ PyObject *self;
+ self = m->func_closure;
+ if (self == NULL)
+ self = Py_None;
+ Py_INCREF(self);
+ return self;
+}
+static PyObject *
+__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
+{
+ if (unlikely(op->func_dict == NULL)) {
+ op->func_dict = PyDict_New();
+ if (unlikely(op->func_dict == NULL))
+ return NULL;
+ }
+ Py_INCREF(op->func_dict);
+ return op->func_dict;
+}
+static int
+__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+ if (unlikely(value == NULL)) {
+ PyErr_SetString(PyExc_TypeError,
+ "function's dictionary may not be deleted");
+ return -1;
+ }
+ if (unlikely(!PyDict_Check(value))) {
+ PyErr_SetString(PyExc_TypeError,
+ "setting function's dictionary to a non-dict");
+ return -1;
+ }
+ tmp = op->func_dict;
+ Py_INCREF(value);
+ op->func_dict = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
+__Pyx_CyFunction_get_globals(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+ PyObject* dict = PyModule_GetDict(__pyx_m);
+ Py_XINCREF(dict);
+ return dict;
+}
+static PyObject *
+__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
+{
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+static PyObject *
+__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
+{
+ PyObject* result = (op->func_code) ? op->func_code : Py_None;
+ Py_INCREF(result);
+ return result;
+}
+static PyObject *
+__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
+{
+ if (op->defaults_tuple) {
+ Py_INCREF(op->defaults_tuple);
+ return op->defaults_tuple;
+ }
+ if (op->defaults_getter) {
+ PyObject *res = op->defaults_getter((PyObject *) op);
+ if (likely(res)) {
+ Py_INCREF(res);
+ op->defaults_tuple = res;
+ }
+ return res;
+ }
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+static PyGetSetDef __pyx_CyFunction_getsets[] = {
+ {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+ {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
+ {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
+ {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
+ {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+ {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
+ {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+ {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
+ {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+ {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
+ {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+ {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
+ {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+ {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
+#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
+#endif
+static PyMemberDef __pyx_CyFunction_members[] = {
+ {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
+ {0, 0, 0, 0, 0}
+};
+static PyObject *
+__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
+{
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_FromString(m->func.m_ml->ml_name);
+#else
+ return PyString_FromString(m->func.m_ml->ml_name);
+#endif
+}
+static PyMethodDef __pyx_CyFunction_methods[] = {
+ {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
+ {0, 0, 0, 0}
+};
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
+ PyObject *closure, PyObject *module, PyObject* code) {
+ __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
if (op == NULL)
return NULL;
+ op->flags = flags;
+ op->func_weakreflist = NULL;
op->func.m_ml = ml;
- Py_XINCREF(self);
- op->func.m_self = self;
+ op->func.m_self = (PyObject *) op;
+ Py_XINCREF(closure);
+ op->func_closure = closure;
Py_XINCREF(module);
op->func.m_module = module;
+ op->func_dict = NULL;
+ op->func_name = NULL;
+ Py_INCREF(qualname);
+ op->func_qualname = qualname;
+ op->func_doc = NULL;
+ op->func_classobj = NULL;
+ Py_XINCREF(code);
+ op->func_code = code;
+ op->defaults_pyobjects = 0;
+ op->defaults = NULL;
+ op->defaults_tuple = NULL;
+ op->defaults_getter = NULL;
PyObject_GC_Track(op);
- return (PyObject *)op;
+ return (PyObject *) op;
}
-
-static void __pyx_binding_PyCFunctionType_dealloc(__pyx_binding_PyCFunctionType_object *m) {
+static int
+__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
+{
+ Py_CLEAR(m->func_closure);
+ Py_CLEAR(m->func.m_module);
+ Py_CLEAR(m->func_dict);
+ Py_CLEAR(m->func_name);
+ Py_CLEAR(m->func_qualname);
+ Py_CLEAR(m->func_doc);
+ Py_CLEAR(m->func_code);
+ Py_CLEAR(m->func_classobj);
+ Py_CLEAR(m->defaults_tuple);
+ if (m->defaults) {
+ PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+ int i;
+ for (i = 0; i < m->defaults_pyobjects; i++)
+ Py_XDECREF(pydefaults[i]);
+ PyMem_Free(m->defaults);
+ m->defaults = NULL;
+ }
+ return 0;
+}
+static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
+{
PyObject_GC_UnTrack(m);
- Py_XDECREF(m->func.m_self);
- Py_XDECREF(m->func.m_module);
+ if (m->func_weakreflist != NULL)
+ PyObject_ClearWeakRefs((PyObject *) m);
+ __Pyx_CyFunction_clear(m);
PyObject_GC_Del(m);
}
-
-static PyObject *__pyx_binding_PyCFunctionType_descr_get(PyObject *func, PyObject *obj, PyObject *type) {
+static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
+{
+ Py_VISIT(m->func_closure);
+ Py_VISIT(m->func.m_module);
+ Py_VISIT(m->func_dict);
+ Py_VISIT(m->func_name);
+ Py_VISIT(m->func_qualname);
+ Py_VISIT(m->func_doc);
+ Py_VISIT(m->func_code);
+ Py_VISIT(m->func_classobj);
+ Py_VISIT(m->defaults_tuple);
+ if (m->defaults) {
+ PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
+ int i;
+ for (i = 0; i < m->defaults_pyobjects; i++)
+ Py_VISIT(pydefaults[i]);
+ }
+ return 0;
+}
+static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
+{
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
+ Py_INCREF(func);
+ return func;
+ }
+ if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
+ if (type == NULL)
+ type = (PyObject *)(Py_TYPE(obj));
+ return PyMethod_New(func,
+ type, (PyObject *)(Py_TYPE(type)));
+ }
if (obj == Py_None)
- obj = NULL;
+ obj = NULL;
return PyMethod_New(func, obj, type);
}
-
-static int __pyx_binding_PyCFunctionType_init(void) {
- __pyx_binding_PyCFunctionType_type = PyCFunction_Type;
- __pyx_binding_PyCFunctionType_type.tp_name = __Pyx_NAMESTR("cython_binding_builtin_function_or_method");
- __pyx_binding_PyCFunctionType_type.tp_dealloc = (destructor)__pyx_binding_PyCFunctionType_dealloc;
- __pyx_binding_PyCFunctionType_type.tp_descr_get = __pyx_binding_PyCFunctionType_descr_get;
- if (PyType_Ready(&__pyx_binding_PyCFunctionType_type) < 0) {
- return -1;
+static PyObject*
+__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
+{
+#if PY_MAJOR_VERSION >= 3
+ return PyUnicode_FromFormat("<cyfunction %U at %p>",
+ op->func_qualname, (void *)op);
+#else
+ return PyString_FromFormat("<cyfunction %s at %p>",
+ PyString_AsString(op->func_qualname), (void *)op);
+#endif
+}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyCFunctionObject* f = (PyCFunctionObject*)func;
+ PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+ PyObject *self = PyCFunction_GET_SELF(func);
+ Py_ssize_t size;
+ switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ case METH_VARARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ return (*meth)(self, arg);
+ break;
+ case METH_VARARGS | METH_KEYWORDS:
+ return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+ case METH_NOARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 0)
+ return (*meth)(self, NULL);
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes no arguments (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ case METH_O:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 1)
+ return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes exactly one argument (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ default:
+ PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+ "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+ "longer supported!");
+ return NULL;
}
- __pyx_binding_PyCFunctionType = &__pyx_binding_PyCFunctionType_type;
+ PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+ f->m_ml->ml_name);
+ return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ return PyCFunction_Call(func, arg, kw);
+}
+#endif
+static PyTypeObject __pyx_CyFunctionType_type = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
+ sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+#if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+#else
+ 0, /*reserved*/
+#endif
+ (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ __Pyx_CyFunction_Call, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
+ 0, /*tp_doc*/
+ (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
+ (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_CyFunction_methods, /*tp_methods*/
+ __pyx_CyFunction_members, /*tp_members*/
+ __pyx_CyFunction_getsets, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ __Pyx_CyFunction_descr_get, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ 0, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+#endif
+};
+static int __Pyx_CyFunction_init(void) {
+#if !CYTHON_COMPILING_IN_PYPY
+ __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
+ if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
+ return -1;
+ __pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
-
+}
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ m->defaults = PyMem_Malloc(size);
+ if (!m->defaults)
+ return PyErr_NoMemory();
+ memset(m->defaults, 0, sizeof(size));
+ m->defaults_pyobjects = pyobjects;
+ return m->defaults;
+}
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
+ __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
+ m->defaults_tuple = tuple;
+ Py_INCREF(tuple);
}
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyBytes_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
- else
- return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
- } else {
- int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
+static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
+ const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint64_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint64_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint64_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint64_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
+ uint64_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
}
- } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ #endif
+ return (uint64_t)-1;
}
}
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) { /* as done by PyObject_RichCompareBool(); also catches the (interned) empty string */
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyUnicode_AS_UNICODE(s1)[0] == PyUnicode_AS_UNICODE(s2)[0]);
- else
- return (PyUnicode_AS_UNICODE(s1)[0] != PyUnicode_AS_UNICODE(s2)[0]);
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
+static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
+ const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
+ const int is_unsigned = const_zero < neg_one;
+ if (sizeof(uint32_t) == sizeof(char)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
+ } else if (sizeof(uint32_t) == sizeof(short)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
+ } else if (sizeof(uint32_t) == sizeof(int)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
+ } else if (sizeof(uint32_t) == sizeof(long)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
+ } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
+ if (is_unsigned)
+ return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
+ else
+ return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
+ } else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
+ uint32_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_VERSION_HEX < 0x03000000
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
}
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+ #endif
+ return (uint32_t)-1;
}
}
@@ -40723,58 +43744,6 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
}
}
-static CYTHON_INLINE uint32_t __Pyx_PyInt_from_py_uint32_t(PyObject* x) {
- const uint32_t neg_one = (uint32_t)-1, const_zero = (uint32_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint32_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint32_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint32_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint32_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint32_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint32_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint32_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- uint32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (uint32_t)-1;
- }
-}
-
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
const int64_t neg_one = (int64_t)-1, const_zero = (int64_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -40800,58 +43769,6 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_int64_t(int64_t val) {
}
}
-static CYTHON_INLINE uint64_t __Pyx_PyInt_from_py_uint64_t(PyObject* x) {
- const uint64_t neg_one = (uint64_t)-1, const_zero = (uint64_t)0;
- const int is_unsigned = const_zero < neg_one;
- if (sizeof(uint64_t) == sizeof(char)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedChar(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedChar(x);
- } else if (sizeof(uint64_t) == sizeof(short)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedShort(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedShort(x);
- } else if (sizeof(uint64_t) == sizeof(int)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedInt(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedInt(x);
- } else if (sizeof(uint64_t) == sizeof(long)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLong(x);
- } else if (sizeof(uint64_t) == sizeof(PY_LONG_LONG)) {
- if (is_unsigned)
- return (uint64_t)__Pyx_PyInt_AsUnsignedLongLong(x);
- else
- return (uint64_t)__Pyx_PyInt_AsSignedLongLong(x);
- } else {
- uint64_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_VERSION_HEX < 0x03000000
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
- return (uint64_t)-1;
- }
-}
-
static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
const uint8_t neg_one = (uint8_t)-1, const_zero = (uint8_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -40881,6 +43798,10 @@ static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
else
return (uint8_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
uint8_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -40900,6 +43821,7 @@ static CYTHON_INLINE uint8_t __Pyx_PyInt_from_py_uint8_t(PyObject* x) {
if (likely(!ret))
return val;
}
+ #endif
return (uint8_t)-1;
}
}
@@ -40933,6 +43855,10 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
else
return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
int32_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -40952,6 +43878,7 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
if (likely(!ret))
return val;
}
+ #endif
return (int32_t)-1;
}
}
@@ -41383,129 +44310,526 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
-
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
-
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
-
+#else
+ PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
+ PyErr_SetExcInfo(*type, *value, *tb);
+#endif
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
}
-static CYTHON_INLINE void __Pyx_Generator_ExceptionClear(struct __pyx_Generator_object *self)
-{
- Py_XDECREF(self->exc_type);
- Py_XDECREF(self->exc_value);
- Py_XDECREF(self->exc_traceback);
-
+static PyObject *__Pyx_Generator_Next(PyObject *self);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
+static PyObject *__Pyx_Generator_Close(PyObject *self);
+static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
+static PyTypeObject *__pyx_GeneratorType = 0;
+#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
+#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
+ PyObject *et, *ev, *tb;
+ PyObject *value = NULL;
+ __Pyx_ErrFetch(&et, &ev, &tb);
+ if (!et) {
+ Py_XDECREF(tb);
+ Py_XDECREF(ev);
+ Py_INCREF(Py_None);
+ *pvalue = Py_None;
+ return 0;
+ }
+ if (unlikely(et != PyExc_StopIteration) &&
+ unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ if (likely(et == PyExc_StopIteration)) {
+ if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
+ if (!ev) {
+ Py_INCREF(Py_None);
+ ev = Py_None;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+ *pvalue = ev;
+ return 0;
+ }
+ }
+ PyErr_NormalizeException(&et, &ev, &tb);
+ if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+#if PY_VERSION_HEX >= 0x030300A0
+ value = ((PyStopIterationObject *)ev)->value;
+ Py_INCREF(value);
+ Py_DECREF(ev);
+#else
+ {
+ PyObject* args = PyObject_GetAttrString(ev, "args");
+ Py_DECREF(ev);
+ if (likely(args)) {
+ value = PyObject_GetItem(args, 0);
+ Py_DECREF(args);
+ }
+ if (unlikely(!value)) {
+ __Pyx_ErrRestore(NULL, NULL, NULL);
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+ }
+#endif
+ *pvalue = value;
+ return 0;
+}
+#endif
+static CYTHON_INLINE
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
+ PyObject *exc_type = self->exc_type;
+ PyObject *exc_value = self->exc_value;
+ PyObject *exc_traceback = self->exc_traceback;
self->exc_type = NULL;
self->exc_value = NULL;
self->exc_traceback = NULL;
+ Py_XDECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_traceback);
}
-
-static CYTHON_INLINE PyObject *__Pyx_Generator_SendEx(struct __pyx_Generator_object *self, PyObject *value)
-{
- PyObject *retval;
-
- if (self->is_running) {
+static CYTHON_INLINE
+int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
+ if (unlikely(gen->is_running)) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return NULL;
+ return 1;
}
-
- if (self->resume_label == 0) {
- if (value && value != Py_None) {
+ return 0;
+}
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
+ PyObject *retval;
+ assert(!self->is_running);
+ if (unlikely(self->resume_label == 0)) {
+ if (unlikely(value && value != Py_None)) {
PyErr_SetString(PyExc_TypeError,
"can't send non-None value to a "
"just-started generator");
return NULL;
}
}
-
- if (self->resume_label == -1) {
+ if (unlikely(self->resume_label == -1)) {
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
-
-
- if (value)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (value) {
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Generators always return to their most recent caller, not
+ * necessarily their creator. */
+ if (self->exc_traceback) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_XINCREF(tstate->frame);
+ assert(f->f_back == NULL);
+ f->f_back = tstate->frame;
+ }
+#endif
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+ } else {
__Pyx_Generator_ExceptionClear(self);
-
+ }
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
-
- if (retval)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (retval) {
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Don't keep the reference to f_back any longer than necessary. It
+ * may keep a chain of frames alive or it could create a reference
+ * cycle. */
+ if (self->exc_traceback) {
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_CLEAR(f->f_back);
+ }
+#endif
+ } else {
__Pyx_Generator_ExceptionClear(self);
-
+ }
return retval;
}
-
-static PyObject *__Pyx_Generator_Next(PyObject *self)
-{
- return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, Py_None);
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
+ PyObject *ret;
+ PyObject *val = NULL;
+ __Pyx_Generator_Undelegate(gen);
+ __Pyx_PyGen_FetchStopIterationValue(&val);
+ ret = __Pyx_Generator_SendEx(gen, val);
+ Py_XDECREF(val);
+ return ret;
+}
+static PyObject *__Pyx_Generator_Next(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ ret = Py_TYPE(yf)->tp_iternext(yf);
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, Py_None);
}
-
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
-{
- return __Pyx_Generator_SendEx((struct __pyx_Generator_object *) self, value);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Send(yf, value);
+ } else {
+ if (value == Py_None)
+ ret = PyIter_Next(yf);
+ else
+ ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
+ }
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, value);
}
-
-static PyObject *__Pyx_Generator_Close(PyObject *self)
-{
- struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
- PyObject *retval;
+static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
+ PyObject *retval = NULL;
+ int err = 0;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ retval = __Pyx_Generator_Close(yf);
+ if (!retval)
+ return -1;
+ } else {
+ PyObject *meth;
+ gen->is_running = 1;
+ meth = PyObject_GetAttrString(yf, "close");
+ if (unlikely(!meth)) {
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_WriteUnraisable(yf);
+ }
+ PyErr_Clear();
+ } else {
+ retval = PyObject_CallFunction(meth, NULL);
+ Py_DECREF(meth);
+ if (!retval)
+ err = -1;
+ }
+ gen->is_running = 0;
+ }
+ Py_XDECREF(retval);
+ return err;
+}
+static PyObject *__Pyx_Generator_Close(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject *retval, *raised_exception;
+ PyObject *yf = gen->yieldfrom;
+ int err = 0;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ Py_INCREF(yf);
+ err = __Pyx_Generator_CloseIter(gen, yf);
+ __Pyx_Generator_Undelegate(gen);
+ Py_DECREF(yf);
+ }
+ if (err == 0)
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(generator, NULL);
+ retval = __Pyx_Generator_SendEx(gen, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
-#if PY_VERSION_HEX < 0x02050000
- if (PyErr_ExceptionMatches(PyExc_StopIteration))
-#else
- if (PyErr_ExceptionMatches(PyExc_StopIteration)
- || PyErr_ExceptionMatches(PyExc_GeneratorExit))
+ raised_exception = PyErr_Occurred();
+ if (!raised_exception
+ || raised_exception == PyExc_StopIteration
+#if PY_VERSION_HEX >= 0x02050000
+ || raised_exception == PyExc_GeneratorExit
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
#endif
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- PyErr_Clear(); /* ignore these errors */
+ if (raised_exception) PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args, CYTHON_UNUSED PyObject *kwds)
-{
- struct __pyx_Generator_object *generator = (struct __pyx_Generator_object *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
-
+ PyObject *yf = gen->yieldfrom;
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ Py_INCREF(yf);
+#if PY_VERSION_HEX >= 0x02050000
+ if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
+ int err = __Pyx_Generator_CloseIter(gen, yf);
+ Py_DECREF(yf);
+ __Pyx_Generator_Undelegate(gen);
+ if (err < 0)
+ return __Pyx_Generator_SendEx(gen, NULL);
+ goto throw_here;
+ }
+#endif
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Throw(yf, args);
+ } else {
+ PyObject *meth = PyObject_GetAttrString(yf, "throw");
+ if (unlikely(!meth)) {
+ Py_DECREF(yf);
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ gen->is_running = 0;
+ return NULL;
+ }
+ PyErr_Clear();
+ __Pyx_Generator_Undelegate(gen);
+ gen->is_running = 0;
+ goto throw_here;
+ }
+ ret = PyObject_CallObject(meth, args);
+ Py_DECREF(meth);
+ }
+ gen->is_running = 0;
+ Py_DECREF(yf);
+ if (!ret) {
+ ret = __Pyx_Generator_FinishDelegation(gen);
+ }
+ return ret;
+ }
+throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(generator, NULL);
+ return __Pyx_Generator_SendEx(gen, NULL);
+}
+static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_VISIT(gen->closure);
+ Py_VISIT(gen->classobj);
+ Py_VISIT(gen->yieldfrom);
+ Py_VISIT(gen->exc_type);
+ Py_VISIT(gen->exc_value);
+ Py_VISIT(gen->exc_traceback);
+ return 0;
+}
+static int __Pyx_Generator_clear(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_CLEAR(gen->closure);
+ Py_CLEAR(gen->classobj);
+ Py_CLEAR(gen->yieldfrom);
+ Py_CLEAR(gen->exc_type);
+ Py_CLEAR(gen->exc_value);
+ Py_CLEAR(gen->exc_traceback);
+ return 0;
+}
+static void __Pyx_Generator_dealloc(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject_GC_UnTrack(gen);
+ if (gen->gi_weakreflist != NULL)
+ PyObject_ClearWeakRefs(self);
+ PyObject_GC_Track(self);
+ if (gen->resume_label > 0) {
+ Py_TYPE(gen)->tp_del(self);
+ if (self->ob_refcnt > 0)
+ return; /* resurrected. :( */
+ }
+ PyObject_GC_UnTrack(self);
+ __Pyx_Generator_clear(self);
+ PyObject_GC_Del(gen);
+}
+static void __Pyx_Generator_del(PyObject *self) {
+ PyObject *res;
+ PyObject *error_type, *error_value, *error_traceback;
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ if (gen->resume_label <= 0)
+ return ;
+ assert(self->ob_refcnt == 0);
+ self->ob_refcnt = 1;
+ __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
+ res = __Pyx_Generator_Close(self);
+ if (res == NULL)
+ PyErr_WriteUnraisable(self);
+ else
+ Py_DECREF(res);
+ __Pyx_ErrRestore(error_type, error_value, error_traceback);
+ /* Undo the temporary resurrection; can't use DECREF here, it would
+ * cause a recursive call.
+ */
+ assert(self->ob_refcnt > 0);
+ if (--self->ob_refcnt == 0)
+ return; /* this is the normal path out */
+ /* close() resurrected it! Make it look like the original Py_DECREF
+ * never happened.
+ */
+ {
+ Py_ssize_t refcnt = self->ob_refcnt;
+ _Py_NewReference(self);
+ self->ob_refcnt = refcnt;
+ }
+#if CYTHON_COMPILING_FOR_CPYTHON
+ assert(PyType_IS_GC(self->ob_type) &&
+ _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
+ /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
+ * we need to undo that. */
+ _Py_DEC_REFTOTAL;
+#endif
+ /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
+ * chain, so no more to do there.
+ * If COUNT_ALLOCS, the original decref bumped tp_frees, and
+ * _Py_NewReference bumped tp_allocs: both of those need to be
+ * undone.
+ */
+#ifdef COUNT_ALLOCS
+ --Py_TYPE(self)->tp_frees;
+ --Py_TYPE(self)->tp_allocs;
+#endif
+}
+static PyMemberDef __pyx_Generator_memberlist[] = {
+ {(char *) "gi_running",
+#if PY_VERSION_HEX >= 0x02060000
+ T_BOOL,
+#else
+ T_BYTE,
+#endif
+ offsetof(__pyx_GeneratorObject, is_running),
+ READONLY,
+ NULL},
+ {0, 0, 0, 0, 0}
+};
+static PyMethodDef __pyx_Generator_methods[] = {
+ {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
+ {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
+ {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
+ {0, 0, 0, 0}
+};
+static PyTypeObject __pyx_GeneratorType_type = {
+ PyVarObject_HEAD_INIT(0, 0)
+ __Pyx_NAMESTR("generator"), /*tp_name*/
+ sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+#if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+#else
+ 0, /*reserved*/
+#endif
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
+ 0, /*tp_doc*/
+ (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
+ 0, /*tp_iter*/
+ (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
+ __pyx_Generator_methods, /*tp_methods*/
+ __pyx_Generator_memberlist, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ 0, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ __Pyx_Generator_del, /*tp_del*/
+#if PY_VERSION_HEX >= 0x02060000
+ 0, /*tp_version_tag*/
+#endif
+};
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure) {
+ __pyx_GeneratorObject *gen =
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
+ if (gen == NULL)
+ return NULL;
+ gen->body = body;
+ gen->closure = closure;
+ Py_XINCREF(closure);
+ gen->is_running = 0;
+ gen->resume_label = 0;
+ gen->classobj = NULL;
+ gen->yieldfrom = NULL;
+ gen->exc_type = NULL;
+ gen->exc_value = NULL;
+ gen->exc_traceback = NULL;
+ gen->gi_weakreflist = NULL;
+ PyObject_GC_Track(gen);
+ return gen;
+}
+static int __pyx_Generator_init(void) {
+ __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
+ __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
+ if (PyType_Ready(&__pyx_GeneratorType_type)) {
+ return -1;
+ }
+ __pyx_GeneratorType = &__pyx_GeneratorType_type;
+ return 0;
}
-static void __Pyx_WriteUnraisable(const char *name, int clineno,
- int lineno, const char *filename) {
+static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
+ CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) {
PyObject *old_exc, *old_val, *old_tb;
PyObject *ctx;
__Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
@@ -41559,6 +44883,23 @@ bad:
return -1;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -41568,15 +44909,14 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
-
+ Py_ssize_t basicsize;
+#ifdef Py_LIMITED_API
+ PyObject *py_basicsize;
+#endif
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(class_name);
- #else
- py_name = PyUnicode_FromString(class_name);
- #endif
+ py_name = __Pyx_PyIdentifier_FromString(class_name);
if (!py_name)
goto bad;
result = PyObject_GetAttr(py_module, py_name);
@@ -41592,7 +44932,19 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && ((PyTypeObject *)result)->tp_basicsize > (Py_ssize_t)size) {
+#ifndef Py_LIMITED_API
+ basicsize = ((PyTypeObject *)result)->tp_basicsize;
+#else
+ py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
+ if (!py_basicsize)
+ goto bad;
+ basicsize = PyLong_AsSsize_t(py_basicsize);
+ Py_DECREF(py_basicsize);
+ py_basicsize = 0;
+ if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
+ goto bad;
+#endif
+ if (!strict && (size_t)basicsize > size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -41602,7 +44954,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if (((PyTypeObject *)result)->tp_basicsize != (Py_ssize_t)size) {
+ else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -41616,51 +44968,105 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
-
- #if PY_MAJOR_VERSION < 3
- py_name = PyString_FromString(name);
- #else
- py_name = PyUnicode_FromString(name);
- #endif
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
}
-#endif
#include "compile.h"
#include "frameobject.h"
#include "traceback.h"
-
-static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
- int __pyx_lineno, const char *__pyx_filename) {
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
PyObject *py_srcfile = 0;
PyObject *py_funcname = 0;
- PyObject *py_globals = 0;
- PyCodeObject *py_code = 0;
- PyFrameObject *py_frame = 0;
-
#if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(__pyx_filename);
+ py_srcfile = PyString_FromString(filename);
#else
- py_srcfile = PyUnicode_FromString(__pyx_filename);
+ py_srcfile = PyUnicode_FromString(filename);
#endif
if (!py_srcfile) goto bad;
- if (__pyx_clineno) {
+ if (c_line) {
#if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
#else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, __pyx_clineno);
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
#endif
}
else {
@@ -41671,28 +45077,45 @@ static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
#endif
}
if (!py_funcname) goto bad;
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_code = PyCode_New(
+ py_code = __Pyx_PyCode_New(
0, /*int argcount,*/
- #if PY_MAJOR_VERSION >= 3
0, /*int kwonlyargcount,*/
- #endif
0, /*int nlocals,*/
0, /*int stacksize,*/
0, /*int flags,*/
__pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
py_srcfile, /*PyObject *filename,*/
py_funcname, /*PyObject *name,*/
- __pyx_lineno, /*int firstlineno,*/
+ py_line, /*int firstlineno,*/
__pyx_empty_bytes /*PyObject *lnotab*/
);
- if (!py_code) goto bad;
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_globals = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_globals = PyModule_GetDict(__pyx_m);
+ if (!py_globals) goto bad;
py_frame = PyFrame_New(
PyThreadState_GET(), /*PyThreadState *tstate,*/
py_code, /*PyCodeObject *code,*/
@@ -41700,11 +45123,9 @@ static void __Pyx_AddTraceback(const char *funcname, int __pyx_clineno,
0 /*PyObject *locals*/
);
if (!py_frame) goto bad;
- py_frame->f_lineno = __pyx_lineno;
+ py_frame->f_lineno = py_line;
PyTraceBack_Here(py_frame);
bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
Py_XDECREF(py_code);
Py_XDECREF(py_frame);
}
@@ -41739,14 +45160,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-/* Type Conversion Functions */
-
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
else return PyObject_IsTrue(x);
}
-
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
@@ -41792,7 +45210,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
return res;
}
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject* x = PyNumber_Index(b);
@@ -41801,7 +45218,6 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
-
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
if (ival <= LONG_MAX)
@@ -41815,7 +45231,6 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
return PyInt_FromSize_t(ival);
#endif
}
-
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx
index e300c66..58fed03 100644
--- a/pysam/csamtools.pyx
+++ b/pysam/csamtools.pyx
@@ -140,7 +140,7 @@ if IS_PYTHON3:
CIGAR2CODE = dict( [y,x] for x,y in enumerate( CODE2CIGAR) )
else:
CIGAR2CODE = dict( [ord(y),x] for x,y in enumerate( CODE2CIGAR) )
-CIGAR_REGEX = re.compile( "([MIDNSHP=X])(\d+)" )
+CIGAR_REGEX = re.compile( "(\d+)([MIDNSHP=X])" )
#####################################################################
## set pysam stderr to /dev/null
@@ -766,7 +766,8 @@ cdef class Samfile:
if mode[0] == "r" and self.isbam:
if not self.isremote:
- if not os.path.exists(filename + b".bai"):
+ if not os.path.exists(filename + b".bai") \
+ and not os.path.exists( filename[:-4] + b".bai"):
self.index = NULL
else:
# returns NULL if there is no index or index could not be opened
@@ -945,7 +946,8 @@ cdef class Samfile:
fetch_callback )
else:
if has_coord:
- return IteratorRowRegion( self, rtid, rstart, rend, reopen=reopen )
+ return IteratorRowRegion( self, rtid, rstart, rend,
+ reopen=reopen )
else:
if until_eof:
return IteratorRowAll( self, reopen=reopen )
@@ -1221,6 +1223,8 @@ cdef class Samfile:
def __get__(self):
if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
if not self.isbam: raise AttributeError( "Samfile.mapped only available in bam files" )
+ if self.index == NULL:
+ raise ValueError( "mapping information not recorded in index or index not available")
cdef int tid
cdef uint32_t total = 0
@@ -1272,10 +1276,11 @@ cdef class Samfile:
if record not in result: result[record] = []
result[record].append( "\t".join( fields[1:] ) )
continue
-
# the following is clumsy as generators do not work?
x = {}
for field in fields[1:]:
+ if ":" not in field:
+ raise ValueError("malformatted header: no ':' in field" )
key, value = field.split(":",1)
# uppercase keys must be valid
# lowercase are permitted for user fields
@@ -1957,7 +1962,7 @@ cdef class IteratorColumnRegion(IteratorColumn):
raise StopIteration
if self.truncate:
- if self.start < self.pos: continue
+ if self.start > self.pos: continue
if self.pos >= self.end: raise StopIteration
return makePileupProxy( &self.plp,
@@ -2233,7 +2238,8 @@ cdef class AlignedRead:
property cigar:
"""the :term:`cigar` alignment (None if not present). The alignment
- is returned as a list of operations. The operations are:
+ is returned as a list of tuples of (operation, length).
+ The operations are:
+-----+--------------+-----+
|M |BAM_CMATCH |0 |
@@ -2255,6 +2261,13 @@ cdef class AlignedRead:
|X |BAM_CDIFF |8 |
+-----+--------------+-----+
+ .. note::
+ The output is a list of (operation, length) tuples, such as
+ ``[ (0, 30) ]``.
+ This is different from the SAM specification and the
+ the :meth:`cigarstring` property, which uses a
+ (length,operation order, for example: ``30M``.
+
"""
def __get__(self):
cdef uint32_t * cigar_p
@@ -2311,17 +2324,28 @@ cdef class AlignedRead:
property cigarstring:
'''the :term:`cigar` alignment as a string.
+ The cigar string is a string of alternating integers
+ and characters denoting the length and the type of
+ an operation.
+
+ .. note::
+ The order length,operation is specified in the
+ SAM format. It is different from the order of
+ the :meth:`cigar` property.
+
Returns the empty string if not present.
'''
def __get__(self):
c = self.cigar
if c == None: return ""
- else: return "".join([ "%c%i" % (CODE2CIGAR[x],y) for x,y in c])
+ # reverse order
+ else: return "".join([ "%i%c" % (y,CODE2CIGAR[x]) for x,y in c])
def __set__(self, cigar):
if cigar == None or len(cigar) == 0: self.cigar = []
parts = CIGAR_REGEX.findall( cigar )
- self.cigar = [ (CIGAR2CODE[ord(x)], int(y)) for x,y in parts ]
+ # reverse order
+ self.cigar = [ (CIGAR2CODE[ord(y)], int(x)) for x,y in parts ]
property seq:
"""read sequence bases, including :term:`soft clipped` bases (None if not present).
@@ -2649,7 +2673,10 @@ cdef class AlignedRead:
s = bam1_aux( src )
# check if there is direct path from buffer.raw to tmp
- temp = buffer.raw
+ p = buffer.raw
+ # create handle to make sure buffer stays alive long
+ # enough for memcpy, see issue 129
+ temp = p
memcpy( s, temp, total_size )
property flag:
@@ -3213,9 +3240,10 @@ def _samtools_dispatch( method,
with open( stderr_f, "rb") as inf:
# read binary output
out_stderr = inf.read()
- os.remove( stderr_f )
else:
out_stderr = []
+ finally:
+ os.remove( stderr_f )
return retval, out_stderr, out_stdout
diff --git a/pysam/ctabix.c b/pysam/ctabix.c
index 5846459..88603ad 100644
--- a/pysam/ctabix.c
+++ b/pysam/ctabix.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Tue Jan 15 06:50:01 2013 */
+/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,7 +11,6 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -23,22 +22,18 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
-
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,28 +41,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
-#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -75,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -89,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -101,11 +94,9 @@
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -115,31 +106,30 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
-
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
-
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -147,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -166,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -174,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -193,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -206,7 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -225,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -239,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -248,6 +228,7 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
@@ -281,6 +262,7 @@
#include "stdint.h"
#include "bgzf.h"
#include "tabix.h"
+#include "tabix_util.h"
#include "pythread.h"
#ifdef _OPENMP
#include <omp.h>
@@ -290,8 +272,6 @@
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-
-/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#define CYTHON_INLINE __inline__
@@ -303,8 +283,6 @@
#define CYTHON_INLINE
#endif
#endif
-
-/* unused attribute */
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -318,27 +296,25 @@
# define CYTHON_UNUSED
# endif
#endif
-
typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-/* Type Conversion Predeclarations */
-
#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
@@ -366,6 +342,7 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"ctabix.pyx",
"TabProxies.pxd",
+ "type.pxd",
"bool.pxd",
"complex.pxd",
};
@@ -374,19 +351,19 @@ static const char *__pyx_f[] = {
struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
struct __pyx_obj_5pysam_10TabProxies_BedProxy;
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_TabixIterator;
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
struct __pyx_obj_5pysam_6ctabix_Parser;
struct __pyx_obj_5pysam_6ctabix_asTuple;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
struct __pyx_obj_5pysam_6ctabix_Tabixfile;
-struct __pyx_obj_5pysam_6ctabix_asBed;
struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
+struct __pyx_obj_5pysam_6ctabix_asBed;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator;
struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
/* "TabProxies.pxd":41
* ctypedef int uint64_t
@@ -436,17 +413,27 @@ struct __pyx_obj_5pysam_10TabProxies_BedProxy {
};
-/* "pysam/ctabix.pxd":186
+/* "pysam/ctabix.pxd":190
* cdef tabix_t * tabixfile
*
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
+ *
*/
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
+struct __pyx_obj_5pysam_6ctabix_Parser {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
+};
+
+
+/* "pysam/ctabix.pxd":193
+ * pass
+ *
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
@@ -465,58 +452,73 @@ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
};
-/* "pysam/ctabix.pxd":182
- * cdef char * _filename
+/* "pysam/ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ *
+ * # pointer to tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
PyObject_HEAD
- ti_iter_t iterator;
tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
};
-/* "pysam/ctabix.pxd":210
- * cdef Parser parser
+/* "pysam/ctabix.pxd":196
+ * pass
*
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asGTF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+};
+
+
+/* "pysam/ctabix.pxd":218
+ * cdef __cnext__(self)
+ *
+ * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
* cdef FILE * infile
- * cdef char * buffer
+ * cdef Parser parser
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
FILE *infile;
- char *buffer;
- size_t size;
struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "pysam/ctabix.pxd":190
+/* "pysam/ctabix.pxd":186
* cdef tabix_t * tabixfile
*
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
- *
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_Parser {
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "pysam/ctabix.pxd":193
- * pass
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_asTuple {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
};
@@ -532,21 +534,6 @@ struct __pyx_obj_5pysam_6ctabix_asVCF {
};
-/* "pysam/ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
- *
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
- *
- * # pointer to tabixfile
- */
-struct __pyx_obj_5pysam_6ctabix_Tabixfile {
- PyObject_HEAD
- tabix_t *tabixfile;
- int isremote;
- char *_filename;
-};
-
-
/* "pysam/ctabix.pxd":199
* pass
*
@@ -559,29 +546,17 @@ struct __pyx_obj_5pysam_6ctabix_asBed {
};
-/* "pysam/ctabix.pxd":196
- * pass
- *
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asGTF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+/* "pysam/ctabix.pxd":182
+ * cdef char * _filename
*
- * cdef:
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
@@ -599,17 +574,19 @@ struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
};
-/* "pysam/ctabix.pxd":218
- * cdef __cnext__(self)
+/* "pysam/ctabix.pxd":210
+ * cdef Parser parser
*
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
* cdef FILE * infile
- * cdef Parser parser
+ * cdef char * buffer
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
FILE *infile;
+ char *buffer;
+ size_t size;
struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
@@ -661,20 +638,6 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-/* "pysam/ctabix.pyx":709
- * ## Iterators for parsing through unindexed files.
- * #########################################################
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
- *
- */
-
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
-};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
-
-
/* "TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
@@ -716,6 +679,20 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
+
+
+/* "pysam/ctabix.pyx":709
+ * ## Iterators for parsing through unindexed files.
+ * #########################################################
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -772,6 +749,11 @@ static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysa
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -799,42 +781,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -850,34 +837,39 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_GetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
return m->sq_item(o, i);
}
}
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
- if (unlikely(d == Py_None)) {
- __Pyx_RaiseNoneIndexingError();
- return NULL;
- }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -896,12 +888,12 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
- PyObject *modname); /*proto*/
+ PyObject *qualname, PyObject *modname); /*proto*/
#define __Pyx_CyFunction_USED 1
#include <structmember.h>
@@ -922,6 +914,7 @@ typedef struct {
PyObject *func_dict;
PyObject *func_weakreflist;
PyObject *func_name;
+ PyObject *func_qualname;
PyObject *func_doc;
PyObject *func_code;
PyObject *func_closure;
@@ -932,10 +925,10 @@ typedef struct {
PyObject *(*defaults_getter)(PyObject *);
} __pyx_CyFunctionObject;
static PyTypeObject *__pyx_CyFunctionType = 0;
-#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \
- __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code)
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *,
- PyMethodDef *ml, int flags,
+#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, code) \
+ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, code)
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
+ int flags, PyObject* qualname,
PyObject *self, PyObject *module,
PyObject* code);
static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
@@ -945,16 +938,6 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
PyObject *tuple);
static int __Pyx_CyFunction_init(void);
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
@@ -1001,10 +984,10 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
#endif
#endif
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
typedef struct {
@@ -1027,8 +1010,6 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from 'pysam' */
-
/* Module declarations from 'pysam.TabProxies' */
static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0;
static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0;
@@ -1050,6 +1031,8 @@ static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0;
/* Module declarations from 'cpython.list' */
+/* Module declarations from 'libc.string' */
+
/* Module declarations from 'libc.stdio' */
/* Module declarations from 'cpython.object' */
@@ -1060,7 +1043,10 @@ static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0;
/* Module declarations from 'cpython.iterator' */
+/* Module declarations from '__builtin__' */
+
/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
@@ -1221,8 +1207,12 @@ static char __pyx_k_61[] = "chromosome names";
static char __pyx_k_62[] = "getfilesystemencoding";
static char __pyx_k_65[] = "/home/andreas/devel/pysam/pysam/ctabix.pyx";
static char __pyx_k_66[] = "pysam.ctabix";
-static char __pyx_k_77[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
-static char __pyx_k_80[] = "tabix_inplace_iterator";
+static char __pyx_k_71[] = "tabix_generic_iterator.__init__";
+static char __pyx_k_74[] = "tabix_generic_iterator.__iter__";
+static char __pyx_k_77[] = "tabix_generic_iterator.__next__";
+static char __pyx_k_80[] = "tabix_generic_iterator.next";
+static char __pyx_k_81[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
+static char __pyx_k_84[] = "tabix_inplace_iterator";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__r[] = "r";
@@ -1354,8 +1344,12 @@ static PyObject *__pyx_n_s_62;
static PyObject *__pyx_kp_s_65;
static PyObject *__pyx_n_s_66;
static PyObject *__pyx_kp_s_7;
-static PyObject *__pyx_kp_s_77;
+static PyObject *__pyx_n_s_71;
+static PyObject *__pyx_n_s_74;
+static PyObject *__pyx_n_s_77;
static PyObject *__pyx_n_s_80;
+static PyObject *__pyx_kp_s_81;
+static PyObject *__pyx_n_s_84;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__KeyError;
@@ -1495,17 +1489,17 @@ static PyObject *__pyx_k_tuple_57;
static PyObject *__pyx_k_tuple_63;
static PyObject *__pyx_k_tuple_67;
static PyObject *__pyx_k_tuple_69;
-static PyObject *__pyx_k_tuple_71;
-static PyObject *__pyx_k_tuple_73;
+static PyObject *__pyx_k_tuple_72;
static PyObject *__pyx_k_tuple_75;
static PyObject *__pyx_k_tuple_78;
+static PyObject *__pyx_k_tuple_82;
static PyObject *__pyx_k_codeobj_64;
static PyObject *__pyx_k_codeobj_68;
static PyObject *__pyx_k_codeobj_70;
-static PyObject *__pyx_k_codeobj_72;
-static PyObject *__pyx_k_codeobj_74;
+static PyObject *__pyx_k_codeobj_73;
static PyObject *__pyx_k_codeobj_76;
static PyObject *__pyx_k_codeobj_79;
+static PyObject *__pyx_k_codeobj_83;
/* "pysam/ctabix.pyx":19
* from cpython.version cimport PY_MAJOR_VERSION
@@ -1560,7 +1554,7 @@ static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, si
* # filename encoding (copied from lxml.etree.pyx)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1957,7 +1951,7 @@ static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *__pyx_v_s) {
* cdef _force_str(object s):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, strlen(__pyx_v_s), NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, strlen(__pyx_v_s), NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -2109,7 +2103,6 @@ static int __pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self,
PyObject *__pyx_v_mode = 0;
PyObject *__pyx_v_args = 0;
PyObject *__pyx_v_kwargs = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
@@ -2127,6 +2120,7 @@ static int __pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self,
__pyx_v_args = __pyx_empty_tuple; __Pyx_INCREF(__pyx_empty_tuple);
}
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
PyObject* values[2] = {0,0};
values[1] = ((PyObject *)__pyx_n_s__r);
if (unlikely(__pyx_kwds)) {
@@ -2141,8 +2135,7 @@ static int __pyx_pw_5pysam_6ctabix_9Tabixfile_1__cinit__(PyObject *__pyx_v_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -2320,11 +2313,11 @@ static char __pyx_doc_5pysam_6ctabix_9Tabixfile_4_open[] = "Tabixfile._open(self
static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_filename = 0;
PyObject *__pyx_v_mode = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_open (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__mode,0};
PyObject* values[2] = {0,0};
values[1] = ((PyObject *)__pyx_n_s__r);
if (unlikely(__pyx_kwds)) {
@@ -2339,8 +2332,7 @@ static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_5_open(PyObject *__pyx_v_sel
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -2389,8 +2381,8 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
PyObject *__pyx_t_1 = NULL;
- int __pyx_t_2;
- PyObject *__pyx_t_3 = NULL;
+ PyObject *__pyx_t_2 = NULL;
+ int __pyx_t_3;
PyObject *__pyx_t_4 = NULL;
int __pyx_t_5;
char *__pyx_t_6;
@@ -2412,9 +2404,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
#ifndef CYTHON_WITHOUT_ASSERTIONS
__Pyx_INCREF(__pyx_v_mode);
__pyx_t_1 = __pyx_v_mode;
- __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (unlikely(!((int)__pyx_t_2))) {
+ if (unlikely(!((int)__pyx_t_3))) {
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_5), __pyx_v_mode); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_t_1));
@@ -2430,14 +2424,14 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* self.tabixfile = NULL
*
*/
- __pyx_t_2 = (__pyx_v_self->tabixfile != NULL);
- if (__pyx_t_2) {
+ __pyx_t_3 = (__pyx_v_self->tabixfile != NULL);
+ if (__pyx_t_3) {
__pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__close); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 108; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L3;
}
__pyx_L3:;
@@ -2458,10 +2452,10 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* self.isremote = filename.startswith( "http:") or filename.startswith( "ftp:" )
*
*/
- __pyx_t_3 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_v_filename_index = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_t_2 = PyNumber_Add(__pyx_v_filename, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 111; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_filename_index = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "pysam/ctabix.pyx":112
*
@@ -2470,27 +2464,27 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*
* # encode all the strings
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (!__pyx_t_2) {
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__pyx_t_3) {
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_filename, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = __pyx_t_4;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = __pyx_t_4;
__pyx_t_4 = 0;
} else {
- __pyx_t_3 = __pyx_t_1;
+ __pyx_t_2 = __pyx_t_1;
__pyx_t_1 = 0;
}
- __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_3); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __pyx_t_5 = __Pyx_PyInt_AsInt(__pyx_t_2); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_self->isremote = __pyx_t_5;
/* "pysam/ctabix.pyx":115
@@ -2500,11 +2494,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* filename_index = _my_encodeFilename(filename_index)
* cdef bytes bmode = mode.encode('ascii')
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_filename);
- __pyx_v_filename = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_filename = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "pysam/ctabix.pyx":116
* # encode all the strings
@@ -2513,11 +2507,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* cdef bytes bmode = mode.encode('ascii')
*
*/
- __pyx_t_3 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename_index)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = ((PyObject *)__pyx_f_5pysam_6ctabix__my_encodeFilename(__pyx_v_filename_index)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_filename_index);
- __pyx_v_filename_index = __pyx_t_3;
- __pyx_t_3 = 0;
+ __pyx_v_filename_index = __pyx_t_2;
+ __pyx_t_2 = 0;
/* "pysam/ctabix.pyx":117
* filename = _my_encodeFilename(filename)
@@ -2526,11 +2520,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*
* if self._filename != NULL: free(self._filename )
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_mode, __pyx_n_s__encode); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_k_tuple_11), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_mode, __pyx_n_s__encode); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_11), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!(likely(PyBytes_CheckExact(__pyx_t_1))||((__pyx_t_1) == Py_None)||(PyErr_Format(PyExc_TypeError, "Expected bytes, got %.200s", Py_TYPE(__pyx_t_1)->tp_name), 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_bmode = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
@@ -2542,8 +2536,8 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*
* self._filename = strdup(filename)
*/
- __pyx_t_2 = (__pyx_v_self->_filename != NULL);
- if (__pyx_t_2) {
+ __pyx_t_3 = (__pyx_v_self->_filename != NULL);
+ if (__pyx_t_3) {
free(__pyx_v_self->_filename);
goto __pyx_L4;
}
@@ -2568,9 +2562,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*/
__pyx_t_1 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__w), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__w), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 123; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__pyx_t_3) {
/* "pysam/ctabix.pyx":125
* if mode[0] == 'w':
@@ -2579,10 +2575,10 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*
* elif mode[0] == "r":
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_13), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_Raise(__pyx_t_1, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_13), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
}
@@ -2594,11 +2590,13 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* # open file for reading
*
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__r), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_mode, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__r), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__pyx_t_2) {
+ if (__pyx_t_3) {
/* "pysam/ctabix.pyx":130
* # open file for reading
@@ -2607,8 +2605,8 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* if not os.path.exists( filename ):
* raise IOError( "file `%s` not found" % filename)
*/
- __pyx_t_2 = (!__pyx_v_self->isremote);
- if (__pyx_t_2) {
+ __pyx_t_3 = (!__pyx_v_self->isremote);
+ if (__pyx_t_3) {
/* "pysam/ctabix.pyx":131
*
@@ -2619,24 +2617,24 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*/
__pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_filename);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_filename);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_7 = (!__pyx_t_2);
+ __pyx_t_7 = (!__pyx_t_3);
if (__pyx_t_7) {
/* "pysam/ctabix.pyx":132
@@ -2648,14 +2646,14 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*/
__pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_14), __pyx_v_filename); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_4));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2672,25 +2670,25 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*/
__pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__os); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__path); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__path); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__exists); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__exists); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_filename_index);
- PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_filename_index);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_filename_index);
__Pyx_GIVEREF(__pyx_v_filename_index);
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 134; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_2 = (!__pyx_t_7);
- if (__pyx_t_2) {
+ __pyx_t_3 = (!__pyx_t_7);
+ if (__pyx_t_3) {
/* "pysam/ctabix.pyx":135
*
@@ -2701,14 +2699,14 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*/
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_15), __pyx_v_filename_index); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 135; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2740,8 +2738,8 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
* raise IOError("could not open file `%s`" % filename )
*
*/
- __pyx_t_2 = (__pyx_v_self->tabixfile == NULL);
- if (__pyx_t_2) {
+ __pyx_t_3 = (__pyx_v_self->tabixfile == NULL);
+ if (__pyx_t_3) {
/* "pysam/ctabix.pyx":141
*
@@ -2752,14 +2750,14 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
*/
__pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_16), __pyx_v_filename); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1));
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -2771,7 +2769,7 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pys
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_1);
- __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_AddTraceback("pysam.ctabix.Tabixfile._open", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
@@ -2792,11 +2790,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_7_parseRegion(PyObject *__py
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_parseRegion (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[4] = {0,0,0,0};
/* "pysam/ctabix.pyx":144
@@ -2974,13 +2972,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_o
* region = "%s:%i-%i" % (reference, start+1, end)
* elif start == None and end != None:
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_1) {
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __pyx_t_3;
@@ -3025,13 +3021,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_o
* region = "%s:%i-%i" % (reference, 1, end)
* elif end == None and start != None:
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_3 = __pyx_t_1;
@@ -3074,13 +3068,11 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_o
* region = "%s:%i-%i" % (reference, start+1, max_pos-1)
* else:
*/
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_end, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_3) {
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_start, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 174; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_1 = __pyx_t_4;
@@ -3369,11 +3361,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_sel
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_parser = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__parser,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("fetch (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,&__pyx_n_s__parser,0};
PyObject* values[5] = {0,0,0,0,0};
/* "pysam/ctabix.pyx":191
@@ -3593,22 +3585,23 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pys
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 4)) {
+ if (size > 4) __Pyx_RaiseTooManyValuesError(4);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
- if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
- if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
@@ -3618,28 +3611,37 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pys
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ Py_ssize_t i;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ for (i=0; i < 4; i++) {
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(item);
+ *(temps[i]) = item;
+ }
+ #endif
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
__pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_1 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_1)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
- index = 1; __pyx_t_2 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_2)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
- index = 2; __pyx_t_6 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_6)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_6);
- index = 3; __pyx_t_7 = __pyx_t_9(__pyx_t_8); if (unlikely(!__pyx_t_7)) goto __pyx_L4_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_7);
+ for (index=0; index < 4; index++) {
+ PyObject* item = __pyx_t_9(__pyx_t_8); if (unlikely(!item)) goto __pyx_L4_unpacking_failed;
+ __Pyx_GOTREF(item);
+ *(temps[index]) = item;
+ }
if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = NULL;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L5_unpacking_done;
__pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_9 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
}
@@ -3660,8 +3662,7 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pys
* if region:
* return TabixIterator( self, rtid, rstart, rend )
*/
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_parser, Py_None, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_parser, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_4) {
@@ -4050,7 +4051,7 @@ static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(struct __py
*/
__pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_v_result = __pyx_t_1;
+ __pyx_v_result = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
/* "pysam/ctabix.pyx":259
@@ -4241,11 +4242,11 @@ static int __pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_
int __pyx_v_tid;
int __pyx_v_start;
int __pyx_v_end;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,0};
PyObject* values[4] = {0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -4261,24 +4262,20 @@ static int __pyx_pw_5pysam_6ctabix_13TabixIterator_1__cinit__(PyObject *__pyx_v_
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -4331,6 +4328,7 @@ static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5p
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ tabix_t *__pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -4364,7 +4362,8 @@ static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5p
*
* if tid < 0:
*/
- __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
+ __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
+ __pyx_v_self->tabixfile = __pyx_t_4;
/* "pysam/ctabix.pyx":293
* self.tabixfile = tabixfile.tabixfile
@@ -4492,7 +4491,9 @@ static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(struct __pyx_
/* Python wrapper */
static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_5pysam_6ctabix_13TabixIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__;
+#endif
static PyObject *__pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
@@ -4661,11 +4662,11 @@ static void __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_ob
static int __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -4678,8 +4679,7 @@ static int __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(PyObject *__
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
@@ -4724,6 +4724,7 @@ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ tabix_t *__pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -4757,7 +4758,8 @@ static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_
*
* self.iterator = ti_query(self.tabixfile, NULL, 0, 0)
*/
- __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
+ __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
+ __pyx_v_self->tabixfile = __pyx_t_4;
/* "pysam/ctabix.pyx":344
* self.tabixfile = tabixfile.tabixfile
@@ -4852,7 +4854,9 @@ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct
/* Python wrapper */
static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__;
+#endif
static PyObject *__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
@@ -4999,11 +5003,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_se
static PyObject *__pyx_pw_5pysam_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_buffer;
int __pyx_v_len;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5017,12 +5021,10 @@ static PyObject *__pyx_pw_5pysam_6ctabix_7asTuple_1__call__(PyObject *__pyx_v_se
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5123,11 +5125,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self
static PyObject *__pyx_pw_5pysam_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_buffer;
int __pyx_v_len;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5141,12 +5143,10 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asGTF_1__call__(PyObject *__pyx_v_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5247,11 +5247,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self
static PyObject *__pyx_pw_5pysam_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_buffer;
int __pyx_v_len;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5265,12 +5265,10 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asBed_1__call__(PyObject *__pyx_v_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5371,11 +5369,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self
static PyObject *__pyx_pw_5pysam_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_buffer;
int __pyx_v_len;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5389,12 +5387,10 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5asVCF_1__call__(PyObject *__pyx_v_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5498,11 +5494,11 @@ static int __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__
int __pyx_v_start;
int __pyx_v_end;
struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__parser,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__tabixfile,&__pyx_n_s__tid,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__parser,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5519,30 +5515,25 @@ static int __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(PyObject *__
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tabixfile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__tid)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser);
- if (likely(values[4])) kw_args--;
+ if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -5598,6 +5589,7 @@ static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_
PyObject *__pyx_t_1 = NULL;
PyObject *__pyx_t_2 = NULL;
int __pyx_t_3;
+ tabix_t *__pyx_t_4;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -5644,7 +5636,8 @@ static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_
*
* if tid < 0:
*/
- __pyx_v_self->tabixfile = __pyx_v_tabixfile->tabixfile;
+ __pyx_t_4 = __pyx_v_tabixfile->tabixfile;
+ __pyx_v_self->tabixfile = __pyx_t_4;
/* "pysam/ctabix.pyx":530
* self.tabixfile = tabixfile.tabixfile
@@ -5772,7 +5765,9 @@ static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct
/* Python wrapper */
static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self); /*proto*/
static char __pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__[] = "python version of next().\n\n pyrex uses this non-standard name instead of next()\n ";
+#if CYTHON_COMPILING_IN_CPYTHON
struct wrapperbase __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
+#endif
static PyObject *__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__(PyObject *__pyx_v_self) {
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
@@ -5950,12 +5945,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_1tabix_compress(PyObject *__pyx_self, P
PyObject *__pyx_v_filename_in = 0;
PyObject *__pyx_v_filename_out = 0;
PyObject *__pyx_v_force = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename_in,&__pyx_n_s__filename_out,&__pyx_n_s__force,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("tabix_compress (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename_in,&__pyx_n_s__filename_out,&__pyx_n_s__force,0};
PyObject* values[3] = {0,0,0};
values[2] = __pyx_k_30;
if (unlikely(__pyx_kwds)) {
@@ -5971,12 +5965,10 @@ static PyObject *__pyx_pw_5pysam_6ctabix_1tabix_compress(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_in);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_in)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_out);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename_out)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("tabix_compress", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -6375,12 +6367,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_3tabix_index(PyObject *__pyx_self, PyOb
PyObject *__pyx_v_preset = 0;
PyObject *__pyx_v_meta_char = 0;
PyObject *__pyx_v_zerobased = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("tabix_index (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0};
PyObject* values[8] = {0,0,0,0,0,0,0,0};
values[1] = __pyx_k_39;
@@ -6439,8 +6430,7 @@ static PyObject *__pyx_pw_5pysam_6ctabix_3tabix_index(PyObject *__pyx_self, PyOb
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -6616,23 +6606,19 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
* raise ValueError("neither preset nor seq_col,start_col and end_col given" )
*
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_preset, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_5) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (!__pyx_t_4) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (!__pyx_t_6) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_8 = __pyx_t_7;
@@ -6992,7 +6978,7 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
__Pyx_GIVEREF(__pyx_int_0);
if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__pileup), ((PyObject *)__pyx_t_3)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 669; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_v_preset2conf = __pyx_t_9;
+ __pyx_v_preset2conf = ((PyObject*)__pyx_t_9);
__pyx_t_9 = 0;
/* "pysam/ctabix.pyx":678
@@ -7127,8 +7113,7 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
* preset = 0
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_6) {
@@ -7223,12 +7208,18 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
*/
if ((likely(PyTuple_CheckExact(__pyx_v_conf_data))) || (PyList_CheckExact(__pyx_v_conf_data))) {
PyObject* sequence = __pyx_v_conf_data;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 6)) {
+ if (size > 6) __Pyx_RaiseTooManyValuesError(6);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 6)) {
- if (PyTuple_GET_SIZE(sequence) > 6) __Pyx_RaiseTooManyValuesError(6);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_14 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_15 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_9 = PyTuple_GET_ITEM(sequence, 2);
@@ -7236,11 +7227,6 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 4);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 5);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 6)) {
- if (PyList_GET_SIZE(sequence) > 6) __Pyx_RaiseTooManyValuesError(6);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_14 = PyList_GET_ITEM(sequence, 0);
__pyx_t_15 = PyList_GET_ITEM(sequence, 1);
__pyx_t_9 = PyList_GET_ITEM(sequence, 2);
@@ -7254,30 +7240,35 @@ static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_2);
- } else {
+ #else
+ Py_ssize_t i;
+ PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
+ for (i=0; i < 6; i++) {
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(item);
+ *(temps[i]) = item;
+ }
+ #endif
+ } else
+ {
Py_ssize_t index = -1;
+ PyObject** temps[6] = {&__pyx_t_14,&__pyx_t_15,&__pyx_t_9,&__pyx_t_3,&__pyx_t_1,&__pyx_t_2};
__pyx_t_16 = PyObject_GetIter(__pyx_v_conf_data); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
__pyx_t_17 = Py_TYPE(__pyx_t_16)->tp_iternext;
- index = 0; __pyx_t_14 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_14)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_14);
- index = 1; __pyx_t_15 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_15)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_15);
- index = 2; __pyx_t_9 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_9)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_9);
- index = 3; __pyx_t_3 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_3)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_3);
- index = 4; __pyx_t_1 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_1)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_1);
- index = 5; __pyx_t_2 = __pyx_t_17(__pyx_t_16); if (unlikely(!__pyx_t_2)) goto __pyx_L20_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_2);
+ for (index=0; index < 6; index++) {
+ PyObject* item = __pyx_t_17(__pyx_t_16); if (unlikely(!item)) goto __pyx_L20_unpacking_failed;
+ __Pyx_GOTREF(item);
+ *(temps[index]) = item;
+ }
if (__Pyx_IternextUnpackEndCheck(__pyx_t_17(__pyx_t_16), 6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_17 = NULL;
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
goto __pyx_L21_unpacking_done;
__pyx_L20_unpacking_failed:;
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
+ __pyx_t_17 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L21_unpacking_done:;
}
@@ -7363,11 +7354,11 @@ static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject
static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_infile = 0;
int __pyx_v_buffer_size;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__buffer_size,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__buffer_size,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -7381,8 +7372,7 @@ static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -7393,10 +7383,6 @@ static int __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(PyObject
if (unlikely(kw_args > 0)) {
if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
- if (values[1]) {
- } else {
- __pyx_v_buffer_size = ((int)65536);
- }
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
@@ -7587,14 +7573,15 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
char *__pyx_v_result;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- PyObject *__pyx_t_1 = NULL;
+ char *__pyx_t_1;
PyObject *__pyx_t_2 = NULL;
- int __pyx_t_3;
+ PyObject *__pyx_t_3 = NULL;
int __pyx_t_4;
int __pyx_t_5;
int __pyx_t_6;
- PyObject *__pyx_t_7 = NULL;
+ int __pyx_t_7;
PyObject *__pyx_t_8 = NULL;
+ PyObject *__pyx_t_9 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
@@ -7607,7 +7594,8 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
* r = self.Parser()
*
*/
- __pyx_v_b = __pyx_v_self->buffer;
+ __pyx_t_1 = __pyx_v_self->buffer;
+ __pyx_v_b = __pyx_t_1;
/* "pysam/ctabix.pyx":738
* cdef size_t nbytes
@@ -7616,13 +7604,13 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
* while not feof( self.infile ):
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__Parser); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_v_r = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_r = __pyx_t_3;
+ __pyx_t_3 = 0;
/* "pysam/ctabix.pyx":740
* r = self.Parser()
@@ -7632,8 +7620,8 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
*/
while (1) {
- __pyx_t_3 = (!feof(__pyx_v_self->infile));
- if (!__pyx_t_3) break;
+ __pyx_t_4 = (!feof(__pyx_v_self->infile));
+ if (!__pyx_t_4) break;
/* "pysam/ctabix.pyx":741
*
@@ -7651,8 +7639,8 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
* # skip comments
* if (b[0] == '#'): continue
*/
- __pyx_t_3 = (__pyx_v_nbytes == -1);
- if (__pyx_t_3) {
+ __pyx_t_4 = (__pyx_v_nbytes == -1);
+ if (__pyx_t_4) {
goto __pyx_L4_break;
goto __pyx_L5;
}
@@ -7665,8 +7653,8 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
* # skip empty lines
*/
- __pyx_t_3 = ((__pyx_v_b[0]) == '#');
- if (__pyx_t_3) {
+ __pyx_t_4 = ((__pyx_v_b[0]) == '#');
+ if (__pyx_t_4) {
goto __pyx_L3_continue;
goto __pyx_L6;
}
@@ -7679,20 +7667,20 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
* # make sure that entry is complete
*/
- __pyx_t_3 = ((__pyx_v_b[0]) == '\x00');
- if (!__pyx_t_3) {
- __pyx_t_4 = ((__pyx_v_b[0]) == '\n');
- if (!__pyx_t_4) {
- __pyx_t_5 = ((__pyx_v_b[0]) == '\r');
- __pyx_t_6 = __pyx_t_5;
+ __pyx_t_4 = ((__pyx_v_b[0]) == '\x00');
+ if (!__pyx_t_4) {
+ __pyx_t_5 = ((__pyx_v_b[0]) == '\n');
+ if (!__pyx_t_5) {
+ __pyx_t_6 = ((__pyx_v_b[0]) == '\r');
+ __pyx_t_7 = __pyx_t_6;
} else {
- __pyx_t_6 = __pyx_t_4;
+ __pyx_t_7 = __pyx_t_5;
}
- __pyx_t_4 = __pyx_t_6;
+ __pyx_t_5 = __pyx_t_7;
} else {
- __pyx_t_4 = __pyx_t_3;
+ __pyx_t_5 = __pyx_t_4;
}
- if (__pyx_t_4) {
+ if (__pyx_t_5) {
goto __pyx_L3_continue;
goto __pyx_L7;
}
@@ -7705,14 +7693,14 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
* result = b
* raise ValueError( "incomplete line at %s" % result )
*/
- __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n');
- if (__pyx_t_4) {
- __pyx_t_3 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r');
- __pyx_t_6 = __pyx_t_3;
+ __pyx_t_5 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\n');
+ if (__pyx_t_5) {
+ __pyx_t_4 = ((__pyx_v_b[(__pyx_v_nbytes - 1)]) != '\r');
+ __pyx_t_7 = __pyx_t_4;
} else {
- __pyx_t_6 = __pyx_t_4;
+ __pyx_t_7 = __pyx_t_5;
}
- if (__pyx_t_6) {
+ if (__pyx_t_7) {
/* "pysam/ctabix.pyx":753
* # make sure that entry is complete
@@ -7730,21 +7718,21 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
*
* # make sure that this goes fully through C
*/
- __pyx_t_2 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyBytes_FromString(__pyx_v_result); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_54), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __Pyx_Raise(__pyx_t_1, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_Raise(__pyx_t_2, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
{__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
@@ -7757,25 +7745,25 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
* return r
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__present); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_7 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__present); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyBytes_FromString(__pyx_v_b); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_3));
+ __pyx_t_8 = __Pyx_PyInt_FromSize_t(__pyx_v_nbytes); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_3));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_3));
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_3 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_7);
- __Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_2 = 0;
- __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
/* "pysam/ctabix.pyx":761
* # the wrong memory is freed
@@ -7805,10 +7793,10 @@ static PyObject *__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__(struc
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_XDECREF(__pyx_t_7);
+ __Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_8);
+ __Pyx_XDECREF(__pyx_t_9);
__Pyx_AddTraceback("pysam.ctabix.tabix_inplace_iterator.__cnext__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
@@ -7910,11 +7898,11 @@ static int __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__
static int __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_infile = 0;
struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -7928,12 +7916,10 @@ static int __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(PyObject *__
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -8405,12 +8391,11 @@ static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_1__init__(PyOb
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_infile = 0;
PyObject *__pyx_v_parser = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__infile,&__pyx_n_s__parser,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__infile,&__pyx_n_s__parser,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -8425,18 +8410,15 @@ static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_1__init__(PyOb
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("__init__", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -8550,7 +8532,6 @@ static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_3__iter__(PyOb
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__iter__ (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
@@ -8596,7 +8577,6 @@ static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_5__next__(PyOb
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__next__ (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
@@ -8904,7 +8884,6 @@ static PyObject *__pyx_pw_5pysam_6ctabix_22tabix_generic_iterator_7next(PyObject
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("next (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
@@ -8965,12 +8944,11 @@ static PyMethodDef __pyx_mdef_5pysam_6ctabix_5tabix_iterator = {__Pyx_NAMESTR("t
static PyObject *__pyx_pw_5pysam_6ctabix_5tabix_iterator(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_infile = 0;
PyObject *__pyx_v_parser = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("tabix_iterator (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__infile,&__pyx_n_s__parser,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -8984,12 +8962,10 @@ static PyObject *__pyx_pw_5pysam_6ctabix_5tabix_iterator(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__infile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__parser)) != 0)) kw_args--;
else {
__Pyx_RaiseArgtupleInvalid("tabix_iterator", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
@@ -9100,15 +9076,15 @@ static void __pyx_tp_dealloc_5pysam_6ctabix_Tabixfile(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_filename(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_filename(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_6ctabix_9Tabixfile_8filename_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_header(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_6ctabix_9Tabixfile_6header_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_6ctabix_9Tabixfile_contigs(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_6ctabix_9Tabixfile_7contigs_1__get__(o);
}
@@ -9644,7 +9620,7 @@ static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
@@ -10482,6 +10458,7 @@ static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t
static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -10491,7 +10468,8 @@ static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->parser));
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -10688,6 +10666,7 @@ static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator(PyTypeObject
static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) {
struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
@@ -10697,7 +10676,8 @@ static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o)
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->parser));
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -10894,7 +10874,9 @@ static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator(PyTypeObject *t
static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) {
struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
- Py_XDECREF(((PyObject *)p->parser));
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -11081,7 +11063,11 @@ static PyMethodDef __pyx_methods[] = {
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
+ #if PY_VERSION_HEX < 0x03020000
+ { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
+ #else
PyModuleDef_HEAD_INIT,
+ #endif
__Pyx_NAMESTR("ctabix"),
0, /* m_doc */
-1, /* m_size */
@@ -11128,8 +11114,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 0},
{&__pyx_n_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 1},
{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
- {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0},
+ {&__pyx_n_s_71, __pyx_k_71, sizeof(__pyx_k_71), 0, 0, 1, 1},
+ {&__pyx_n_s_74, __pyx_k_74, sizeof(__pyx_k_74), 0, 0, 1, 1},
+ {&__pyx_n_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 1},
{&__pyx_n_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 1},
+ {&__pyx_kp_s_81, __pyx_k_81, sizeof(__pyx_k_81), 0, 0, 1, 0},
+ {&__pyx_n_s_84, __pyx_k_84, sizeof(__pyx_k_84), 0, 0, 1, 1},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
{&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
@@ -11256,11 +11246,8 @@ static int __Pyx_InitCachedConstants(void) {
* else:
* raise TypeError, u"Argument must be string, bytes or unicode."
*/
- __pyx_k_tuple_2 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_2 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_2);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_2, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
/* "pysam/ctabix.pyx":78
@@ -11270,11 +11257,8 @@ static int __Pyx_InitCachedConstants(void) {
* else:
* # assume unicode
*/
- __pyx_k_tuple_4 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_4 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_4);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_4, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
/* "pysam/ctabix.pyx":112
@@ -11284,17 +11268,11 @@ static int __Pyx_InitCachedConstants(void) {
*
* # encode all the strings
*/
- __pyx_k_tuple_8 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_8 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_7)); if (unlikely(!__pyx_k_tuple_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_8);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_7));
- PyTuple_SET_ITEM(__pyx_k_tuple_8, 0, ((PyObject *)__pyx_kp_s_7));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_7));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_8));
- __pyx_k_tuple_10 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_10 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_9)); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 112; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_10);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
- PyTuple_SET_ITEM(__pyx_k_tuple_10, 0, ((PyObject *)__pyx_kp_s_9));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
/* "pysam/ctabix.pyx":117
@@ -11304,11 +11282,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* if self._filename != NULL: free(self._filename )
*/
- __pyx_k_tuple_11 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_11 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__ascii)); if (unlikely(!__pyx_k_tuple_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 117; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_11);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ascii));
- PyTuple_SET_ITEM(__pyx_k_tuple_11, 0, ((PyObject *)__pyx_n_s__ascii));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
/* "pysam/ctabix.pyx":125
@@ -11318,11 +11293,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* elif mode[0] == "r":
*/
- __pyx_k_tuple_13 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_13 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_12)); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_13);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_12));
- PyTuple_SET_ITEM(__pyx_k_tuple_13, 0, ((PyObject *)__pyx_kp_s_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_12));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
/* "pysam/ctabix.pyx":212
@@ -11332,11 +11304,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* region, rtid, rstart, rend = self._parseRegion( reference, start, end, region )
*/
- __pyx_k_tuple_23 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_23 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_22)); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_23);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_22));
- PyTuple_SET_ITEM(__pyx_k_tuple_23, 0, ((PyObject *)__pyx_kp_s_22));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_22));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
/* "pysam/ctabix.pyx":235
@@ -11346,11 +11315,8 @@ static int __Pyx_InitCachedConstants(void) {
* return self._filename
*
*/
- __pyx_k_tuple_24 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_24 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_22)); if (unlikely(!__pyx_k_tuple_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 235; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_24);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_22));
- PyTuple_SET_ITEM(__pyx_k_tuple_24, 0, ((PyObject *)__pyx_kp_s_22));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_22));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_24));
/* "pysam/ctabix.pyx":302
@@ -11360,11 +11326,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* def __iter__(self):
*/
- __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_26 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_25)); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_26);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_25));
- PyTuple_SET_ITEM(__pyx_k_tuple_26, 0, ((PyObject *)__pyx_kp_s_25));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
/* "pysam/ctabix.pyx":347
@@ -11374,11 +11337,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* def __iter__(self):
*/
- __pyx_k_tuple_28 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_28 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_27)); if (unlikely(!__pyx_k_tuple_28)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_28);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_27));
- PyTuple_SET_ITEM(__pyx_k_tuple_28, 0, ((PyObject *)__pyx_kp_s_27));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_27));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_28));
/* "pysam/ctabix.pyx":539
@@ -11388,11 +11348,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* def __iter__(self):
*/
- __pyx_k_tuple_29 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_29 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_25)); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_29);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_25));
- PyTuple_SET_ITEM(__pyx_k_tuple_29, 0, ((PyObject *)__pyx_kp_s_25));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29));
/* "pysam/ctabix.pyx":590
@@ -11402,11 +11359,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* fn = _force_bytes(filename_in)
*/
- __pyx_k_tuple_33 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_33 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_33);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_k_tuple_33, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33));
/* "pysam/ctabix.pyx":595
@@ -11416,11 +11370,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* buffer = malloc(WINDOW_SIZE)
*/
- __pyx_k_tuple_35 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_35 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_34)); if (unlikely(!__pyx_k_tuple_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_35);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_34));
- PyTuple_SET_ITEM(__pyx_k_tuple_35, 0, ((PyObject *)__pyx_kp_s_34));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_34));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35));
/* "pysam/ctabix.pyx":605
@@ -11430,11 +11381,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* free( buffer )
*/
- __pyx_k_tuple_37 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_37)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_37 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_36)); if (unlikely(!__pyx_k_tuple_37)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_37);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_36));
- PyTuple_SET_ITEM(__pyx_k_tuple_37, 0, ((PyObject *)__pyx_kp_s_36));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_36));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_37));
/* "pysam/ctabix.pyx":609
@@ -11444,11 +11392,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* def tabix_index( filename,
*/
- __pyx_k_tuple_38 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_38)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_38 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_36)); if (unlikely(!__pyx_k_tuple_38)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_38);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_36));
- PyTuple_SET_ITEM(__pyx_k_tuple_38, 0, ((PyObject *)__pyx_kp_s_36));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_36));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_38));
/* "pysam/ctabix.pyx":656
@@ -11458,11 +11403,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* if not filename.endswith(".gz"):
*/
- __pyx_k_tuple_44 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_44 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_43)); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_44);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_43));
- PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, ((PyObject *)__pyx_kp_s_43));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_43));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
/* "pysam/ctabix.pyx":658
@@ -11472,11 +11414,8 @@ static int __Pyx_InitCachedConstants(void) {
* tabix_compress( filename, filename + ".gz", force = force )
* os.unlink( filename )
*/
- __pyx_k_tuple_46 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_46 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_45)); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_46);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_45));
- PyTuple_SET_ITEM(__pyx_k_tuple_46, 0, ((PyObject *)__pyx_kp_s_45));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_45));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_46));
/* "pysam/ctabix.pyx":664
@@ -11486,11 +11425,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* # columns (1-based)
*/
- __pyx_k_tuple_48 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_48 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_47)); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_48);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_47));
- PyTuple_SET_ITEM(__pyx_k_tuple_48, 0, ((PyObject *)__pyx_kp_s_47));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_47));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48));
/* "pysam/ctabix.pyx":722
@@ -11500,11 +11436,8 @@ static int __Pyx_InitCachedConstants(void) {
* self.infile = fdopen( fd, 'r')
*
*/
- __pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_52 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_51)); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_52);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
- PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_51));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
/* "pysam/ctabix.pyx":725
@@ -11514,11 +11447,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* self.buffer = <char*>malloc( buffer_size )
*/
- __pyx_k_tuple_53 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_53 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_51)); if (unlikely(!__pyx_k_tuple_53)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_53);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
- PyTuple_SET_ITEM(__pyx_k_tuple_53, 0, ((PyObject *)__pyx_kp_s_51));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_53));
/* "pysam/ctabix.pyx":783
@@ -11528,11 +11458,8 @@ static int __Pyx_InitCachedConstants(void) {
* self.infile = fdopen( fd, 'r')
* if self.infile == NULL: raise ValueError( "I/O operation on closed file." )
*/
- __pyx_k_tuple_55 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_55 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_51)); if (unlikely(!__pyx_k_tuple_55)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_55);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
- PyTuple_SET_ITEM(__pyx_k_tuple_55, 0, ((PyObject *)__pyx_kp_s_51));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_55));
/* "pysam/ctabix.pyx":785
@@ -11542,11 +11469,8 @@ static int __Pyx_InitCachedConstants(void) {
* self.parser = parser
*
*/
- __pyx_k_tuple_56 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_56 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_51)); if (unlikely(!__pyx_k_tuple_56)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_56);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
- PyTuple_SET_ITEM(__pyx_k_tuple_56, 0, ((PyObject *)__pyx_kp_s_51));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_56));
/* "pysam/ctabix.pyx":839
@@ -11556,11 +11480,8 @@ static int __Pyx_InitCachedConstants(void) {
* self.parser = parser
*
*/
- __pyx_k_tuple_57 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_57 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_51)); if (unlikely(!__pyx_k_tuple_57)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_57);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_51));
- PyTuple_SET_ITEM(__pyx_k_tuple_57, 0, ((PyObject *)__pyx_kp_s_51));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_51));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_57));
/* "pysam/ctabix.pyx":564
@@ -11570,41 +11491,8 @@ static int __Pyx_InitCachedConstants(void) {
* filename_out,
* force = False ):
*/
- __pyx_k_tuple_63 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_63 = PyTuple_Pack(11, ((PyObject *)__pyx_n_s__filename_in), ((PyObject *)__pyx_n_s__filename_out), ((PyObject *)__pyx_n_s__force), ((PyObject *)__pyx_n_s__WINDOW_SIZE), ((PyObject *)__pyx_n_s__c), ((PyObject *)__pyx_n_s__r), ((PyObject *)__pyx_n_s__buffer), ((PyObject *)__pyx_n_s__fp), ((PyObject *)__pyx_n_s__fd_src), ((PyObject *)__pyx_n_s__O_RDONLY), ((PyObject *)__pyx_n_s__fn)); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_cl [...]
__Pyx_GOTREF(__pyx_k_tuple_63);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename_in));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_n_s__filename_in));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename_in));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename_out));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 1, ((PyObject *)__pyx_n_s__filename_out));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename_out));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__force));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 2, ((PyObject *)__pyx_n_s__force));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__force));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__WINDOW_SIZE));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 3, ((PyObject *)__pyx_n_s__WINDOW_SIZE));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__WINDOW_SIZE));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__c));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 4, ((PyObject *)__pyx_n_s__c));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__c));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 5, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__buffer));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 6, ((PyObject *)__pyx_n_s__buffer));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__buffer));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fp));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 7, ((PyObject *)__pyx_n_s__fp));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fp));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fd_src));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 8, ((PyObject *)__pyx_n_s__fd_src));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fd_src));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__O_RDONLY));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 9, ((PyObject *)__pyx_n_s__O_RDONLY));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__O_RDONLY));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fn));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 10, ((PyObject *)__pyx_n_s__fn));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fn));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
__pyx_k_codeobj_64 = (PyObject*)__Pyx_PyCode_New(3, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_compress, 564, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11615,44 +11503,8 @@ static int __Pyx_InitCachedConstants(void) {
* force = False,
* seq_col = None,
*/
- __pyx_k_tuple_67 = PyTuple_New(12); if (unlikely(!__pyx_k_tuple_67)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_67 = PyTuple_Pack(12, ((PyObject *)__pyx_n_s__filename), ((PyObject *)__pyx_n_s__force), ((PyObject *)__pyx_n_s__seq_col), ((PyObject *)__pyx_n_s__start_col), ((PyObject *)__pyx_n_s__end_col), ((PyObject *)__pyx_n_s__preset), ((PyObject *)__pyx_n_s__meta_char), ((PyObject *)__pyx_n_s__zerobased), ((PyObject *)__pyx_n_s__preset2conf), ((PyObject *)__pyx_n_s__conf_data), ((PyObject *)__pyx_n_s__conf), ((PyObject *)__pyx_n_s__fn)); if (unlikely(!__pyx_k_tuple_67)) {__pyx_fil [...]
__Pyx_GOTREF(__pyx_k_tuple_67);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 0, ((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__force));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 1, ((PyObject *)__pyx_n_s__force));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__force));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__seq_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 2, ((PyObject *)__pyx_n_s__seq_col));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__seq_col));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__start_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 3, ((PyObject *)__pyx_n_s__start_col));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start_col));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__end_col));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 4, ((PyObject *)__pyx_n_s__end_col));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end_col));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__preset));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 5, ((PyObject *)__pyx_n_s__preset));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__preset));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__meta_char));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 6, ((PyObject *)__pyx_n_s__meta_char));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__meta_char));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__zerobased));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 7, ((PyObject *)__pyx_n_s__zerobased));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__zerobased));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__preset2conf));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 8, ((PyObject *)__pyx_n_s__preset2conf));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__preset2conf));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__conf_data));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 9, ((PyObject *)__pyx_n_s__conf_data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__conf_data));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__conf));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 10, ((PyObject *)__pyx_n_s__conf));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__conf));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fn));
- PyTuple_SET_ITEM(__pyx_k_tuple_67, 11, ((PyObject *)__pyx_n_s__fn));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fn));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_67));
__pyx_k_codeobj_68 = (PyObject*)__Pyx_PyCode_New(8, 0, 12, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_index, 611, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11663,17 +11515,8 @@ static int __Pyx_InitCachedConstants(void) {
*
* self.infile = infile
*/
- __pyx_k_tuple_69 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_69 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__infile), ((PyObject *)__pyx_n_s__parser)); if (unlikely(!__pyx_k_tuple_69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_69);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_69, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__infile));
- PyTuple_SET_ITEM(__pyx_k_tuple_69, 1, ((PyObject *)__pyx_n_s__infile));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__infile));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__parser));
- PyTuple_SET_ITEM(__pyx_k_tuple_69, 2, ((PyObject *)__pyx_n_s__parser));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parser));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_69));
__pyx_k_codeobj_70 = (PyObject*)__Pyx_PyCode_New(3, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____init__, 836, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11684,13 +11527,10 @@ static int __Pyx_InitCachedConstants(void) {
* return self
*
*/
- __pyx_k_tuple_71 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_71);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_71, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_71));
- __pyx_k_codeobj_72 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_71, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____iter__, 842, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_72 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_72)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_72);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_72));
+ __pyx_k_codeobj_73 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____iter__, 842, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/ctabix.pyx":846
*
@@ -11699,28 +11539,10 @@ static int __Pyx_InitCachedConstants(void) {
*
* cdef char * b, * cpy
*/
- __pyx_k_tuple_73 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_73);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_73, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__b));
- PyTuple_SET_ITEM(__pyx_k_tuple_73, 1, ((PyObject *)__pyx_n_s__b));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__b));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__cpy));
- PyTuple_SET_ITEM(__pyx_k_tuple_73, 2, ((PyObject *)__pyx_n_s__cpy));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cpy));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__nbytes));
- PyTuple_SET_ITEM(__pyx_k_tuple_73, 3, ((PyObject *)__pyx_n_s__nbytes));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__nbytes));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_73, 4, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__s));
- PyTuple_SET_ITEM(__pyx_k_tuple_73, 5, ((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_73));
- __pyx_k_codeobj_74 = (PyObject*)__Pyx_PyCode_New(1, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_73, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____next__, 846, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_75 = PyTuple_Pack(6, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__b), ((PyObject *)__pyx_n_s__cpy), ((PyObject *)__pyx_n_s__nbytes), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__s)); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_75);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
+ __pyx_k_codeobj_76 = (PyObject*)__Pyx_PyCode_New(1, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s____next__, 846, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/ctabix.pyx":880
*
@@ -11729,13 +11551,10 @@ static int __Pyx_InitCachedConstants(void) {
* return self.__next__()
*
*/
- __pyx_k_tuple_75 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_75);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_75, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
- __pyx_k_codeobj_76 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__next, 880, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_78 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_78);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
+ __pyx_k_codeobj_79 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__next, 880, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/* "pysam/ctabix.pyx":883
* return self.__next__()
@@ -11744,16 +11563,10 @@ static int __Pyx_InitCachedConstants(void) {
* """return an iterator over all entries in a file."""
* return tabix_generic_iterator( infile, parser )
*/
- __pyx_k_tuple_78 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_78);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__infile));
- PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_n_s__infile));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__infile));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__parser));
- PyTuple_SET_ITEM(__pyx_k_tuple_78, 1, ((PyObject *)__pyx_n_s__parser));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__parser));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
- __pyx_k_codeobj_79 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_iterator, 883, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_82 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__infile), ((PyObject *)__pyx_n_s__parser)); if (unlikely(!__pyx_k_tuple_82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_82);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_82));
+ __pyx_k_codeobj_83 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_65, __pyx_n_s__tabix_iterator, 883, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -11823,16 +11636,23 @@ PyMODINIT_FUNC PyInit_ctabix(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
+ if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION >= 3
+ {
+ PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!PyDict_GetItemString(modules, "pysam.ctabix")) {
+ if (unlikely(PyDict_SetItemString(modules, "pysam.ctabix", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ }
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11852,6 +11672,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (__Pyx_SetAttrString(__pyx_m, "Tabixfile", (PyObject *)&__pyx_type_5pysam_6ctabix_Tabixfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_Tabixfile = &__pyx_type_5pysam_6ctabix_Tabixfile;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
@@ -11860,9 +11681,11 @@ PyMODINIT_FUNC PyInit_ctabix(void)
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_13TabixIterator_4__next__;
}
}
+ #endif
if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixIterator = &__pyx_type_5pysam_6ctabix_TabixIterator;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
@@ -11871,6 +11694,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixHeaderIterator_4__next__;
}
}
+ #endif
if (__Pyx_SetAttrString(__pyx_m, "TabixHeaderIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixHeaderIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = &__pyx_type_5pysam_6ctabix_TabixHeaderIterator;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_Parser) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11893,6 +11717,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_asVCF = &__pyx_type_5pysam_6ctabix_asVCF;
if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
@@ -11901,6 +11726,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
}
}
+ #endif
if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = &__pyx_type_5pysam_6ctabix_TabixIteratorParsed;
__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator;
@@ -11926,8 +11752,15 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__pyx_vtabptr_5pysam_10TabProxies_BedProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_10TabProxies_VCFProxy = __Pyx_ImportType("pysam.TabProxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_vtabptr_5pysam_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
+ #if CYTHON_COMPILING_IN_PYPY
+ sizeof(PyTypeObject),
+ #else
+ sizeof(PyHeapTypeObject),
+ #endif
+ 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
@@ -11937,7 +11770,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
* # from csamtools.pyx
* import tempfile, os, sys, types, itertools, struct, ctypes, gzip # <<<<<<<<<<<<<<
* import io
- * from pysam cimport TabProxies
+ * cimport TabProxies
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -11976,7 +11809,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
* # from csamtools.pyx
* import tempfile, os, sys, types, itertools, struct, ctypes, gzip
* import io # <<<<<<<<<<<<<<
- * from pysam cimport TabProxies
+ * cimport TabProxies
*
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__io), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -12159,7 +11992,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
*
* self.infile = infile
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_1__init__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_70)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_1__init__, 0, __pyx_n_s_71, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_70)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____init__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12171,7 +12004,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
* return self
*
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_3__iter__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_72)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_3__iter__, 0, __pyx_n_s_74, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_73)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____iter__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12183,7 +12016,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
*
* cdef char * b, * cpy
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_5__next__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_74)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_5__next__, 0, __pyx_n_s_77, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_76)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s____next__, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 846; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12195,7 +12028,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
* return self.__next__()
*
*/
- __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_7next, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_76)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_7next, 0, __pyx_n_s_80, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_79)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetItem(__pyx_t_1, __pyx_n_s__next, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12207,8 +12040,8 @@ PyMODINIT_FUNC PyInit_ctabix(void)
* '''iterate over ``infile``.
*
*/
- if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_77)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s_58, __pyx_n_s_66); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_81)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_CreateClass(((PyObject *)__pyx_empty_tuple), ((PyObject *)__pyx_t_1), __pyx_n_s_58, __pyx_n_s_58, __pyx_n_s_66); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
if (PyObject_SetAttr(__pyx_m, __pyx_n_s_58, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -12259,9 +12092,9 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__Pyx_INCREF(((PyObject *)__pyx_n_s__tabix_iterator));
PyList_SET_ITEM(__pyx_t_1, 7, ((PyObject *)__pyx_n_s__tabix_iterator));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__tabix_iterator));
- __Pyx_INCREF(((PyObject *)__pyx_n_s_80));
- PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_80));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s_80));
+ __Pyx_INCREF(((PyObject *)__pyx_n_s_84));
+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_84));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s_84));
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -12325,6 +12158,32 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
return result;
}
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
+ Py_ssize_t length;
+ if (unlikely((start < 0) | (stop < 0))) {
+ length = strlen(cstring);
+ if (start < 0) {
+ start += length;
+ if (start < 0)
+ start = 0;
+ }
+ if (stop < 0)
+ stop += length;
+ }
+ length = stop - start;
+ if (unlikely(length <= 0))
+ return PyUnicode_FromUnicode(NULL, 0);
+ cstring += start;
+ if (decode_func) {
+ return decode_func(cstring, length, errors);
+ } else {
+ return PyUnicode_Decode(cstring, length, encoding, errors);
+ }
+}
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
@@ -12360,33 +12219,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -12419,6 +12283,7 @@ raise_error:
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -12436,12 +12301,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -12458,9 +12347,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -12474,6 +12360,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
@@ -12487,7 +12374,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -12508,48 +12395,72 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
}
}
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -12588,22 +12499,54 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
-
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
+}
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
@@ -12611,13 +12554,8 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else if (PyErr_Occurred()) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
+ } else {
+ return __Pyx_IterFinish();
}
return 0;
}
@@ -12642,12 +12580,9 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
return 0;
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
-}
-
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -12656,19 +12591,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -12676,10 +12619,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
@@ -12692,6 +12638,7 @@ bad:
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -12699,8 +12646,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -12712,18 +12663,23 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
- PyObject *py_import = 0;
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
PyObject *empty_dict = 0;
PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import = 0;
py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
if (!py_import)
goto bad;
+ #endif
if (from_list)
list = from_list;
else {
@@ -12743,13 +12699,17 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
#if PY_MAJOR_VERSION >= 3
if (level == -1) {
if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(1);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
if (!module) {
if (!PyErr_ExceptionMatches(PyExc_ImportError))
goto bad;
@@ -12760,12 +12720,17 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
}
#endif
if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(level);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
}
}
#else
@@ -12777,15 +12742,16 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
name, global_dict, empty_dict, list, NULL);
#endif
bad:
- Py_XDECREF(empty_list);
+ #if PY_VERSION_HEX < 0x03030000
Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
Py_XDECREF(empty_dict);
return module;
}
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
- /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -12810,12 +12776,13 @@ static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
}
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
- PyObject *modname) {
+ PyObject *qualname, PyObject *modname) {
PyObject *result;
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
- /* Python2 __metaclass__ */
+ if (PyDict_SetItemString(dict, "__qualname__", qualname) < 0)
+ return NULL;
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -12830,16 +12797,19 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
static PyObject *
__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
{
- if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
+ if (unlikely(op->func_doc == NULL)) {
+ if (op->func.m_ml->ml_doc) {
#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
+ op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
+ op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
#endif
- }
- if (op->func_doc == 0) {
- Py_INCREF(Py_None);
- return Py_None;
+ if (unlikely(op->func_doc == NULL))
+ return NULL;
+ } else {
+ Py_INCREF(Py_None);
+ return Py_None;
+ }
}
Py_INCREF(op->func_doc);
return op->func_doc;
@@ -12849,22 +12819,23 @@ __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
{
PyObject *tmp = op->func_doc;
if (value == NULL)
- op->func_doc = Py_None; /* Mark as deleted */
- else
- op->func_doc = value;
- Py_INCREF(op->func_doc);
+ value = Py_None; /* Mark as deleted */
+ Py_INCREF(value);
+ op->func_doc = value;
Py_XDECREF(tmp);
return 0;
}
static PyObject *
__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
{
- if (op->func_name == NULL) {
+ if (unlikely(op->func_name == NULL)) {
#if PY_MAJOR_VERSION >= 3
op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
#else
op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
#endif
+ if (unlikely(op->func_name == NULL))
+ return NULL;
}
Py_INCREF(op->func_name);
return op->func_name;
@@ -12874,9 +12845,9 @@ __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
{
PyObject *tmp;
#if PY_MAJOR_VERSION >= 3
- if (value == NULL || !PyUnicode_Check(value)) {
+ if (unlikely(value == NULL || !PyUnicode_Check(value))) {
#else
- if (value == NULL || !PyString_Check(value)) {
+ if (unlikely(value == NULL || !PyString_Check(value))) {
#endif
PyErr_SetString(PyExc_TypeError,
"__name__ must be set to a string object");
@@ -12889,6 +12860,31 @@ __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
return 0;
}
static PyObject *
+__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
+{
+ Py_INCREF(op->func_qualname);
+ return op->func_qualname;
+}
+static int
+__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+ if (unlikely(value == NULL || !PyUnicode_Check(value))) {
+#else
+ if (unlikely(value == NULL || !PyString_Check(value))) {
+#endif
+ PyErr_SetString(PyExc_TypeError,
+ "__qualname__ must be set to a string object");
+ return -1;
+ }
+ tmp = op->func_qualname;
+ Py_INCREF(value);
+ op->func_qualname = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
{
PyObject *self;
@@ -12901,9 +12897,9 @@ __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure
static PyObject *
__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
{
- if (op->func_dict == NULL) {
+ if (unlikely(op->func_dict == NULL)) {
op->func_dict = PyDict_New();
- if (op->func_dict == NULL)
+ if (unlikely(op->func_dict == NULL))
return NULL;
}
Py_INCREF(op->func_dict);
@@ -12913,12 +12909,12 @@ static int
__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
{
PyObject *tmp;
- if (value == NULL) {
+ if (unlikely(value == NULL)) {
PyErr_SetString(PyExc_TypeError,
"function's dictionary may not be deleted");
return -1;
}
- if (!PyDict_Check(value)) {
+ if (unlikely(!PyDict_Check(value))) {
PyErr_SetString(PyExc_TypeError,
"setting function's dictionary to a non-dict");
return -1;
@@ -12958,7 +12954,7 @@ __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
}
if (op->defaults_getter) {
PyObject *res = op->defaults_getter((PyObject *) op);
- if (res) {
+ if (likely(res)) {
Py_INCREF(res);
op->defaults_tuple = res;
}
@@ -12972,6 +12968,7 @@ static PyGetSetDef __pyx_CyFunction_getsets[] = {
{(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
{(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
{(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
{(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
{(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
{(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
@@ -13005,7 +13002,7 @@ static PyMethodDef __pyx_CyFunction_methods[] = {
{__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
{0, 0, 0, 0}
};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
PyObject *closure, PyObject *module, PyObject* code) {
__pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
if (op == NULL)
@@ -13020,6 +13017,8 @@ static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int f
op->func.m_module = module;
op->func_dict = NULL;
op->func_name = NULL;
+ Py_INCREF(qualname);
+ op->func_qualname = qualname;
op->func_doc = NULL;
op->func_classobj = NULL;
Py_XINCREF(code);
@@ -13038,6 +13037,7 @@ __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
Py_CLEAR(m->func.m_module);
Py_CLEAR(m->func_dict);
Py_CLEAR(m->func_name);
+ Py_CLEAR(m->func_qualname);
Py_CLEAR(m->func_doc);
Py_CLEAR(m->func_code);
Py_CLEAR(m->func_classobj);
@@ -13066,6 +13066,7 @@ static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit,
Py_VISIT(m->func.m_module);
Py_VISIT(m->func_dict);
Py_VISIT(m->func_name);
+ Py_VISIT(m->func_qualname);
Py_VISIT(m->func_doc);
Py_VISIT(m->func_code);
Py_VISIT(m->func_classobj);
@@ -13098,15 +13099,64 @@ static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObj
static PyObject*
__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
{
- PyObject *func_name = __Pyx_CyFunction_get_name(op);
#if PY_MAJOR_VERSION >= 3
return PyUnicode_FromFormat("<cyfunction %U at %p>",
- func_name, (void *)op);
+ op->func_qualname, (void *)op);
#else
return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(func_name), (void *)op);
+ PyString_AsString(op->func_qualname), (void *)op);
#endif
}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyCFunctionObject* f = (PyCFunctionObject*)func;
+ PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+ PyObject *self = PyCFunction_GET_SELF(func);
+ Py_ssize_t size;
+ switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ case METH_VARARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ return (*meth)(self, arg);
+ break;
+ case METH_VARARGS | METH_KEYWORDS:
+ return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+ case METH_NOARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 0)
+ return (*meth)(self, NULL);
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes no arguments (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ case METH_O:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 1)
+ return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes exactly one argument (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ default:
+ PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+ "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+ "longer supported!");
+ return NULL;
+ }
+ PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+ f->m_ml->ml_name);
+ return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ return PyCFunction_Call(func, arg, kw);
+}
+#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -13126,7 +13176,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_PyCFunction_Call, /*tp_call*/
+ __Pyx_CyFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -13162,15 +13212,16 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void)
-{
+static int __Pyx_CyFunction_init(void) {
+#if !CYTHON_COMPILING_IN_PYPY
+ __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
-{
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults = PyMem_Malloc(size);
if (!m->defaults)
@@ -13179,85 +13230,12 @@ void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
-{
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults_tuple = tuple;
Py_INCREF(tuple);
}
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyBytes_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
- else
- return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
- } else {
- int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -13287,6 +13265,10 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
else
return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
int32_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -13306,6 +13288,7 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
if (likely(!ret))
return val;
}
+ #endif
return (int32_t)-1;
}
}
@@ -13746,6 +13729,23 @@ bad:
return -1;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -13755,6 +13755,10 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+ Py_ssize_t basicsize;
+#ifdef Py_LIMITED_API
+ PyObject *py_basicsize;
+#endif
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
@@ -13774,7 +13778,19 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+#ifndef Py_LIMITED_API
+ basicsize = ((PyTypeObject *)result)->tp_basicsize;
+#else
+ py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
+ if (!py_basicsize)
+ goto bad;
+ basicsize = PyLong_AsSsize_t(py_basicsize);
+ Py_DECREF(py_basicsize);
+ py_basicsize = 0;
+ if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
+ goto bad;
+#endif
+ if (!strict && (size_t)basicsize > size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -13784,7 +13800,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -13798,23 +13814,6 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
@@ -14026,15 +14025,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-
-/* Type Conversion Functions */
-
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
else return PyObject_IsTrue(x);
}
-
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
@@ -14080,7 +14075,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
return res;
}
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject* x = PyNumber_Index(b);
@@ -14089,7 +14083,6 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
-
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
if (ival <= LONG_MAX)
@@ -14103,7 +14096,6 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
return PyInt_FromSize_t(ival);
#endif
}
-
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
diff --git a/pysam/ctabix.pxd b/pysam/ctabix.pxd
index a140169..c10dc43 100644
--- a/pysam/ctabix.pxd
+++ b/pysam/ctabix.pxd
@@ -207,7 +207,7 @@ cdef class TabixIteratorParsed:
cdef tabix_t * tabixfile
cdef Parser parser
-ctypedef class tabix_inplace_iterator:
+cdef class tabix_inplace_iterator:
cdef FILE * infile
cdef char * buffer
cdef size_t size
@@ -215,8 +215,10 @@ ctypedef class tabix_inplace_iterator:
cdef __cnext__(self)
-ctypedef class tabix_copy_iterator:
+cdef class tabix_copy_iterator:
cdef FILE * infile
cdef Parser parser
cdef __cnext__(self)
+cdef extern from "tabix_util.h":
+ pass
diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx
index 67e8514..6a19541 100644
--- a/pysam/ctabix.pyx
+++ b/pysam/ctabix.pyx
@@ -5,7 +5,7 @@
# from csamtools.pyx
import tempfile, os, sys, types, itertools, struct, ctypes, gzip
import io
-from pysam cimport TabProxies
+cimport TabProxies
from cpython cimport PyErr_SetString, PyBytes_Check, \
PyUnicode_Check, PyBytes_FromStringAndSize, \
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index a4eb2db..8456837 100644
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Tue Jan 15 06:50:15 2013 */
+/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,7 +11,6 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -23,22 +22,18 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
-
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,28 +41,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
-#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -75,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -89,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -101,11 +94,9 @@
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -115,31 +106,30 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
-
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
-
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -147,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -166,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -174,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -193,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -206,7 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -225,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -239,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -248,6 +228,7 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
@@ -281,6 +262,7 @@
#include "unistd.h"
#include "bgzf.h"
#include "tabix.h"
+#include "tabix_util.h"
#ifdef _OPENMP
#include <omp.h>
#endif /* _OPENMP */
@@ -289,8 +271,6 @@
#define CYTHON_WITHOUT_ASSERTIONS
#endif
-
-/* inline attribute */
#ifndef CYTHON_INLINE
#if defined(__GNUC__)
#define CYTHON_INLINE __inline__
@@ -302,8 +282,6 @@
#define CYTHON_INLINE
#endif
#endif
-
-/* unused attribute */
#ifndef CYTHON_UNUSED
# if defined(__GNUC__)
# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
@@ -317,27 +295,25 @@
# define CYTHON_UNUSED
# endif
#endif
-
typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-/* Type Conversion Predeclarations */
-
#define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s)
#define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s))
-
#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
-
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+
#ifdef __GNUC__
/* Test for GCC > 2.95 */
#if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
@@ -369,27 +345,27 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data;
+struct __pyx_obj_5pysam_6ctabix_Parser;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_4cvcf_VCFRecord;
struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile;
struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_TabixIterator;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data;
struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse;
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
-struct __pyx_obj_5pysam_6ctabix_Parser;
-struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
-struct __pyx_obj_5pysam_6ctabix_Tabixfile;
-struct __pyx_obj_5pysam_6ctabix_asBed;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator;
+struct __pyx_obj_5pysam_6ctabix_asBed;
struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
-struct __pyx_obj_5pysam_4cvcf_VCFRecord;
-struct __pyx_obj_5pysam_6ctabix_asTuple;
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
struct __pyx_defaults;
typedef struct __pyx_defaults __pyx_defaults;
struct __pyx_defaults1;
@@ -417,16 +393,55 @@ struct __pyx_defaults4 {
PyObject *__pyx_arg_lineparse;
};
-/* "pysam/cvcf.pyx":647
- * return False
+/* "ctabix.pxd":190
+ * cdef tabix_t * tabixfile
+ *
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
*
- * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
- * cols = line.split('\t')
- * if len(cols) != len(self._samples)+9:
*/
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data {
+struct __pyx_obj_5pysam_6ctabix_Parser {
PyObject_HEAD
- PyObject *__pyx_v_alt;
+};
+
+
+/* "ctabix.pxd":193
+ * pass
+ *
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+};
+
+
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
+ *
+ * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
+ */
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
+ FILE *infile;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+};
+
+
+/* "pysam/cvcf.pyx":229
+ *
+ *
+ * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a VCF record.'''
+ * cdef vcffile
+ */
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+ PyObject *vcffile;
};
@@ -450,31 +465,18 @@ struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
};
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
+/* "pysam/cvcf.pyx":95
+ * ###########################################################################################################
*
- * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
- * pass
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
*
*/
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+struct __pyx_obj_5pysam_4cvcf_VCFRecord {
struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
-};
-
-
-/* "TabProxies.pxd":72
- * pass
- *
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_BedProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ PyObject *vcf;
char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
+ uint32_t pos;
};
@@ -492,6 +494,21 @@ struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
};
+/* "ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+ *
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ *
+ * # pointer to tabixfile
+ */
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
+ PyObject_HEAD
+ tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
+};
+
+
/* "ctabix.pxd":205
* pass
*
@@ -507,24 +524,23 @@ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
};
-/* "ctabix.pxd":182
- * cdef char * _filename
+/* "pysam/cvcf.pyx":650
+ * return False
*
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
+ * cols = line.split('\t')
+ * if len(cols) != len(self._samples)+9:
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
+ PyObject *__pyx_v_alt;
};
/* "ctabix.pxd":210
* cdef Parser parser
*
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
* cdef FILE * infile
* cdef char * buffer
*/
@@ -538,24 +554,7 @@ struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
};
-/* "pysam/cvcf.pyx":790
- * if alt:
- * for i in range(1,min(len(ref),min(map(len,alt)))):
- * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<<
- * break
- * ref, alt = ref[:-1], [allele[:-1] for allele in alt]
- */
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr {
- PyObject_HEAD
- struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope;
- PyObject *__pyx_v_allele;
- PyObject *__pyx_t_0;
- Py_ssize_t __pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
-};
-
-
-/* "pysam/cvcf.pyx":899
+/* "pysam/cvcf.pyx":902
* return line
*
* def _parse(self, line, stream): # <<<<<<<<<<<<<<
@@ -574,70 +573,74 @@ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse {
};
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "ctabix.pxd":202
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_6ctabix_asVCF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pxd":190
- * cdef tabix_t * tabixfile
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( self )
*
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_Parser {
- PyObject_HEAD
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
};
-/* "pysam/cvcf.pyx":226
+/* "TabProxies.pxd":72
+ * pass
*
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
- * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a VCF record.'''
- * cdef vcffile
+ * cdef:
*/
-struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
- PyObject *vcffile;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
};
-/* "ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
- * # pointer to tabixfile
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_Tabixfile {
- PyObject_HEAD
- tabix_t *tabixfile;
- int isremote;
- char *_filename;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
-/* "ctabix.pxd":199
- * pass
- *
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
- *
+/* "pysam/cvcf.pyx":793
+ * if alt:
+ * for i in range(1,min(len(ref),min(map(len,alt)))):
+ * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<<
+ * break
+ * ref, alt = ref[:-1], [allele[:-1] for allele in alt]
*/
-struct __pyx_obj_5pysam_6ctabix_asBed {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr {
+ PyObject_HEAD
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope;
+ PyObject *__pyx_v_allele;
+ PyObject *__pyx_t_0;
+ Py_ssize_t __pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
@@ -653,70 +656,43 @@ struct __pyx_obj_5pysam_6ctabix_asGTF {
};
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
-};
-
-
-/* "pysam/cvcf.pyx":94
- * ###########################################################################################################
- *
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
+/* "ctabix.pxd":182
+ * cdef char * _filename
*
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_4cvcf_VCFRecord {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- PyObject *vcf;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "ctabix.pxd":193
+/* "ctabix.pxd":199
* pass
*
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_asTuple {
+struct __pyx_obj_5pysam_6ctabix_asBed {
struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":60
+/* "TabProxies.pxd":83
* cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
-};
-
-
-/* "ctabix.pxd":202
- * pass
- *
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asVCF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
};
@@ -753,46 +729,18 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
+/* "TabProxies.pxd":72
+ * pass
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-
-
-/* "pysam/cvcf.pyx":94
- * ###########################################################################################################
- *
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
- *
- */
-
-struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
-};
-static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
-
-
-/* "ctabix.pxd":210
- * cdef Parser parser
- *
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
- */
-
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
-};
-static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
/* "TabProxies.pxd":60
@@ -813,7 +761,7 @@ static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysa
/* "ctabix.pxd":218
* cdef __cnext__(self)
*
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
* cdef FILE * infile
* cdef Parser parser
*/
@@ -824,18 +772,46 @@ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator {
static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
-/* "TabProxies.pxd":72
- * pass
+/* "pysam/cvcf.pyx":95
+ * ###########################################################################################################
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
+
+
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
+ *
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
+
+
+/* "ctabix.pxd":210
+ * cdef Parser parser
+ *
+ * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -912,42 +888,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -963,13 +944,22 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_GetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
return m->sq_item(o, i);
}
}
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
@@ -981,21 +971,22 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
+#if CYTHON_COMPILING_IN_PYPY
+#define __Pyx_PyObject_AsDouble(obj) \
+(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
+ likely(PyInt_CheckExact(obj)) ? \
+ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
+#else
#define __Pyx_PyObject_AsDouble(obj) \
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
+#endif
static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
- if (unlikely(d == Py_None)) {
- __Pyx_RaiseNoneIndexingError();
- return NULL;
- }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -1009,28 +1000,48 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
- return unlikely(b < 0) ? b : !b;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
- return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+ int result = PySequence_Contains(seq, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
+static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
+ int result = PyDict_Contains(dict, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+}
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len)) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
+ }
+ return PyList_Append(list, x);
+}
+#else
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#endif
+
static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (PyList_Append(L, x) < 0) return NULL;
+ if (unlikely(PyList_Append(L, x) < 0)) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- }
- else {
+ } else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -1040,6 +1051,18 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
}
}
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
+
+static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
+
+static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2,
+ int is_tuple, int has_known_size, int decref_tuple);
+
+static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
+ Py_ssize_t* p_orig_length, int* p_is_dict);
+static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
+ PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
+
#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_SetItemInt_Fast(o, i, v) : \
__Pyx_SetItemInt_Generic(o, to_py_func(i), v))
@@ -1051,6 +1074,7 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb
return r;
}
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -1060,13 +1084,26 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje
Py_DECREF(old);
return 1;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_SetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_ass_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return -1;
+ i += l;
+ }
return m->sq_ass_item(o, i, v);
}
}
+#else
+#if CYTHON_COMPILING_IN_PYPY
+ if (PySequence_Check(o) && !PyDict_Check(o)) {
+#else
+ if (PySequence_Check(o)) {
+#endif
+ return PySequence_SetItem(o, i, v);
+ }
+#endif
return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
}
@@ -1105,17 +1142,23 @@ static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
#endif /* PyAnySet_CheckExact (<= Py2.4) */
#endif /* < Py2.5 */
+static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
+
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
+
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level); /*proto*/
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name);
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases); /*proto*/
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
- PyObject *modname); /*proto*/
+ PyObject *qualname, PyObject *modname); /*proto*/
#define __Pyx_CyFunction_USED 1
#include <structmember.h>
@@ -1136,6 +1179,7 @@ typedef struct {
PyObject *func_dict;
PyObject *func_weakreflist;
PyObject *func_name;
+ PyObject *func_qualname;
PyObject *func_doc;
PyObject *func_code;
PyObject *func_closure;
@@ -1146,10 +1190,10 @@ typedef struct {
PyObject *(*defaults_getter)(PyObject *);
} __pyx_CyFunctionObject;
static PyTypeObject *__pyx_CyFunctionType = 0;
-#define __Pyx_CyFunction_NewEx(ml, flags, self, module, code) \
- __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, self, module, code)
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *,
- PyMethodDef *ml, int flags,
+#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, code) \
+ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, code)
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
+ int flags, PyObject* qualname,
PyObject *self, PyObject *module,
PyObject* code);
static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
@@ -1161,18 +1205,6 @@ static int __Pyx_CyFunction_init(void);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
-#include <string.h>
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
-
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
@@ -1209,22 +1241,30 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
#define __Pyx_Generator_USED
#include <structmember.h>
+#include <frameobject.h>
typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
typedef struct {
PyObject_HEAD
__pyx_generator_body_t body;
PyObject *closure;
- int is_running;
- int resume_label;
PyObject *exc_type;
PyObject *exc_value;
PyObject *exc_traceback;
PyObject *gi_weakreflist;
PyObject *classobj;
+ PyObject *yieldfrom;
+ int resume_label;
+ char is_running; // using T_BOOL for property below requires char value
} __pyx_GeneratorObject;
static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject *closure);
static int __pyx_Generator_init(void);
+static int __Pyx_Generator_clear(PyObject* self);
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
+#else
+#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
+#endif
static int __Pyx_check_binary_version(void);
@@ -1236,10 +1276,10 @@ static int __Pyx_check_binary_version(void);
#endif
#endif
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
@@ -1264,8 +1304,6 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from 'pysam' */
-
/* Module declarations from 'pysam.ctabix' */
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0;
@@ -1507,6 +1545,48 @@ static char __pyx_k_170[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must be
static char __pyx_k_171[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'";
static char __pyx_k_172[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s";
static char __pyx_k_173[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value";
+static char __pyx_k_176[] = "VCF.__init__";
+static char __pyx_k_180[] = "VCF.error";
+static char __pyx_k_183[] = "VCF.parse_format";
+static char __pyx_k_186[] = "VCF.format_format";
+static char __pyx_k_189[] = "VCF.get_expected";
+static char __pyx_k_192[] = "VCF._add_definition";
+static char __pyx_k_195[] = "VCF.format_formatdata";
+static char __pyx_k_198[] = "VCF.enter_default_format";
+static char __pyx_k_201[] = "VCF.parse_header";
+static char __pyx_k_204[] = "VCF.write_header";
+static char __pyx_k_207[] = "VCF.parse_heading";
+static char __pyx_k_210[] = "VCF.write_heading";
+static char __pyx_k_213[] = "VCF.convertGT";
+static char __pyx_k_216[] = "VCF.convertGTback";
+static char __pyx_k_219[] = "VCF.parse_formatdata";
+static char __pyx_k_222[] = "VCF.inregion";
+static char __pyx_k_225[] = "VCF.parse_data";
+static char __pyx_k_228[] = "VCF.write_data";
+static char __pyx_k_231[] = "VCF._parse_header";
+static char __pyx_k_234[] = "VCF._parse";
+static char __pyx_k_237[] = "VCF.getsamples";
+static char __pyx_k_240[] = "VCF.setsamples";
+static char __pyx_k_243[] = "VCF.getheader";
+static char __pyx_k_246[] = "VCF.setheader";
+static char __pyx_k_249[] = "VCF.getinfo";
+static char __pyx_k_252[] = "VCF.setinfo";
+static char __pyx_k_255[] = "VCF.getformat";
+static char __pyx_k_258[] = "VCF.setformat";
+static char __pyx_k_261[] = "VCF.getfilter";
+static char __pyx_k_264[] = "VCF.setfilter";
+static char __pyx_k_267[] = "VCF.setversion";
+static char __pyx_k_270[] = "VCF.setregions";
+static char __pyx_k_273[] = "VCF.setreference";
+static char __pyx_k_276[] = "VCF.ignoreerror";
+static char __pyx_k_279[] = "VCF.warnerror";
+static char __pyx_k_282[] = "VCF.parse";
+static char __pyx_k_285[] = "VCF.write";
+static char __pyx_k_288[] = "VCF.writeheader";
+static char __pyx_k_291[] = "VCF.compare_calls";
+static char __pyx_k_294[] = "VCF.connect";
+static char __pyx_k_298[] = "VCF.fetch";
+static char __pyx_k_301[] = "VCF.validate";
static char __pyx_k__DP[] = "DP";
static char __pyx_k__EC[] = "EC";
static char __pyx_k__FT[] = "FT";
@@ -1822,15 +1902,57 @@ static PyObject *__pyx_kp_s_170;
static PyObject *__pyx_kp_s_171;
static PyObject *__pyx_kp_s_172;
static PyObject *__pyx_kp_s_173;
+static PyObject *__pyx_n_s_176;
static PyObject *__pyx_n_s_18;
+static PyObject *__pyx_n_s_180;
+static PyObject *__pyx_n_s_183;
+static PyObject *__pyx_n_s_186;
+static PyObject *__pyx_n_s_189;
static PyObject *__pyx_kp_s_19;
+static PyObject *__pyx_n_s_192;
+static PyObject *__pyx_n_s_195;
+static PyObject *__pyx_n_s_198;
static PyObject *__pyx_kp_s_2;
static PyObject *__pyx_n_s_20;
+static PyObject *__pyx_n_s_201;
+static PyObject *__pyx_n_s_204;
+static PyObject *__pyx_n_s_207;
static PyObject *__pyx_kp_s_21;
+static PyObject *__pyx_n_s_210;
+static PyObject *__pyx_n_s_213;
+static PyObject *__pyx_n_s_216;
+static PyObject *__pyx_n_s_219;
+static PyObject *__pyx_n_s_222;
+static PyObject *__pyx_n_s_225;
+static PyObject *__pyx_n_s_228;
+static PyObject *__pyx_n_s_231;
+static PyObject *__pyx_n_s_234;
+static PyObject *__pyx_n_s_237;
static PyObject *__pyx_kp_s_24;
+static PyObject *__pyx_n_s_240;
+static PyObject *__pyx_n_s_243;
+static PyObject *__pyx_n_s_246;
+static PyObject *__pyx_n_s_249;
static PyObject *__pyx_kp_s_25;
+static PyObject *__pyx_n_s_252;
+static PyObject *__pyx_n_s_255;
+static PyObject *__pyx_n_s_258;
+static PyObject *__pyx_n_s_261;
+static PyObject *__pyx_n_s_264;
+static PyObject *__pyx_n_s_267;
static PyObject *__pyx_n_s_27;
+static PyObject *__pyx_n_s_270;
+static PyObject *__pyx_n_s_273;
+static PyObject *__pyx_n_s_276;
+static PyObject *__pyx_n_s_279;
static PyObject *__pyx_kp_s_28;
+static PyObject *__pyx_n_s_282;
+static PyObject *__pyx_n_s_285;
+static PyObject *__pyx_n_s_288;
+static PyObject *__pyx_n_s_291;
+static PyObject *__pyx_n_s_294;
+static PyObject *__pyx_n_s_298;
+static PyObject *__pyx_n_s_301;
static PyObject *__pyx_kp_s_32;
static PyObject *__pyx_n_s_36;
static PyObject *__pyx_n_s_37;
@@ -2258,93 +2380,93 @@ static PyObject *__pyx_k_tuple_132;
static PyObject *__pyx_k_tuple_136;
static PyObject *__pyx_k_tuple_139;
static PyObject *__pyx_k_tuple_174;
-static PyObject *__pyx_k_tuple_176;
-static PyObject *__pyx_k_tuple_178;
+static PyObject *__pyx_k_tuple_177;
static PyObject *__pyx_k_tuple_179;
static PyObject *__pyx_k_tuple_181;
-static PyObject *__pyx_k_tuple_183;
-static PyObject *__pyx_k_tuple_185;
+static PyObject *__pyx_k_tuple_184;
static PyObject *__pyx_k_tuple_187;
-static PyObject *__pyx_k_tuple_189;
-static PyObject *__pyx_k_tuple_191;
+static PyObject *__pyx_k_tuple_190;
static PyObject *__pyx_k_tuple_193;
-static PyObject *__pyx_k_tuple_195;
-static PyObject *__pyx_k_tuple_197;
+static PyObject *__pyx_k_tuple_196;
static PyObject *__pyx_k_tuple_199;
-static PyObject *__pyx_k_tuple_201;
-static PyObject *__pyx_k_tuple_203;
+static PyObject *__pyx_k_tuple_202;
static PyObject *__pyx_k_tuple_205;
-static PyObject *__pyx_k_tuple_207;
-static PyObject *__pyx_k_tuple_209;
+static PyObject *__pyx_k_tuple_208;
static PyObject *__pyx_k_tuple_211;
-static PyObject *__pyx_k_tuple_213;
-static PyObject *__pyx_k_tuple_215;
+static PyObject *__pyx_k_tuple_214;
static PyObject *__pyx_k_tuple_217;
-static PyObject *__pyx_k_tuple_219;
-static PyObject *__pyx_k_tuple_221;
+static PyObject *__pyx_k_tuple_220;
static PyObject *__pyx_k_tuple_223;
-static PyObject *__pyx_k_tuple_225;
-static PyObject *__pyx_k_tuple_227;
+static PyObject *__pyx_k_tuple_226;
static PyObject *__pyx_k_tuple_229;
-static PyObject *__pyx_k_tuple_231;
-static PyObject *__pyx_k_tuple_233;
+static PyObject *__pyx_k_tuple_232;
static PyObject *__pyx_k_tuple_235;
-static PyObject *__pyx_k_tuple_237;
-static PyObject *__pyx_k_tuple_239;
+static PyObject *__pyx_k_tuple_238;
static PyObject *__pyx_k_tuple_241;
-static PyObject *__pyx_k_tuple_243;
-static PyObject *__pyx_k_tuple_245;
+static PyObject *__pyx_k_tuple_244;
static PyObject *__pyx_k_tuple_247;
-static PyObject *__pyx_k_tuple_249;
-static PyObject *__pyx_k_tuple_251;
+static PyObject *__pyx_k_tuple_250;
static PyObject *__pyx_k_tuple_253;
-static PyObject *__pyx_k_tuple_255;
-static PyObject *__pyx_k_tuple_257;
-static PyObject *__pyx_k_tuple_258;
+static PyObject *__pyx_k_tuple_256;
+static PyObject *__pyx_k_tuple_259;
+static PyObject *__pyx_k_tuple_262;
+static PyObject *__pyx_k_tuple_265;
+static PyObject *__pyx_k_tuple_268;
+static PyObject *__pyx_k_tuple_271;
+static PyObject *__pyx_k_tuple_274;
+static PyObject *__pyx_k_tuple_277;
+static PyObject *__pyx_k_tuple_280;
+static PyObject *__pyx_k_tuple_283;
+static PyObject *__pyx_k_tuple_286;
+static PyObject *__pyx_k_tuple_289;
+static PyObject *__pyx_k_tuple_292;
+static PyObject *__pyx_k_tuple_295;
+static PyObject *__pyx_k_tuple_297;
+static PyObject *__pyx_k_tuple_299;
static PyObject *__pyx_k_codeobj_133;
static PyObject *__pyx_k_codeobj_137;
static PyObject *__pyx_k_codeobj_175;
-static PyObject *__pyx_k_codeobj_177;
-static PyObject *__pyx_k_codeobj_180;
+static PyObject *__pyx_k_codeobj_178;
static PyObject *__pyx_k_codeobj_182;
-static PyObject *__pyx_k_codeobj_184;
-static PyObject *__pyx_k_codeobj_186;
+static PyObject *__pyx_k_codeobj_185;
static PyObject *__pyx_k_codeobj_188;
-static PyObject *__pyx_k_codeobj_190;
-static PyObject *__pyx_k_codeobj_192;
+static PyObject *__pyx_k_codeobj_191;
static PyObject *__pyx_k_codeobj_194;
-static PyObject *__pyx_k_codeobj_196;
-static PyObject *__pyx_k_codeobj_198;
+static PyObject *__pyx_k_codeobj_197;
static PyObject *__pyx_k_codeobj_200;
-static PyObject *__pyx_k_codeobj_202;
-static PyObject *__pyx_k_codeobj_204;
+static PyObject *__pyx_k_codeobj_203;
static PyObject *__pyx_k_codeobj_206;
-static PyObject *__pyx_k_codeobj_208;
-static PyObject *__pyx_k_codeobj_210;
+static PyObject *__pyx_k_codeobj_209;
static PyObject *__pyx_k_codeobj_212;
-static PyObject *__pyx_k_codeobj_214;
-static PyObject *__pyx_k_codeobj_216;
+static PyObject *__pyx_k_codeobj_215;
static PyObject *__pyx_k_codeobj_218;
-static PyObject *__pyx_k_codeobj_220;
-static PyObject *__pyx_k_codeobj_222;
+static PyObject *__pyx_k_codeobj_221;
static PyObject *__pyx_k_codeobj_224;
-static PyObject *__pyx_k_codeobj_226;
-static PyObject *__pyx_k_codeobj_228;
+static PyObject *__pyx_k_codeobj_227;
static PyObject *__pyx_k_codeobj_230;
-static PyObject *__pyx_k_codeobj_232;
-static PyObject *__pyx_k_codeobj_234;
+static PyObject *__pyx_k_codeobj_233;
static PyObject *__pyx_k_codeobj_236;
-static PyObject *__pyx_k_codeobj_238;
-static PyObject *__pyx_k_codeobj_240;
+static PyObject *__pyx_k_codeobj_239;
static PyObject *__pyx_k_codeobj_242;
-static PyObject *__pyx_k_codeobj_244;
-static PyObject *__pyx_k_codeobj_246;
+static PyObject *__pyx_k_codeobj_245;
static PyObject *__pyx_k_codeobj_248;
-static PyObject *__pyx_k_codeobj_250;
-static PyObject *__pyx_k_codeobj_252;
+static PyObject *__pyx_k_codeobj_251;
static PyObject *__pyx_k_codeobj_254;
-static PyObject *__pyx_k_codeobj_256;
-static PyObject *__pyx_k_codeobj_259;
+static PyObject *__pyx_k_codeobj_257;
+static PyObject *__pyx_k_codeobj_260;
+static PyObject *__pyx_k_codeobj_263;
+static PyObject *__pyx_k_codeobj_266;
+static PyObject *__pyx_k_codeobj_269;
+static PyObject *__pyx_k_codeobj_272;
+static PyObject *__pyx_k_codeobj_275;
+static PyObject *__pyx_k_codeobj_278;
+static PyObject *__pyx_k_codeobj_281;
+static PyObject *__pyx_k_codeobj_284;
+static PyObject *__pyx_k_codeobj_287;
+static PyObject *__pyx_k_codeobj_290;
+static PyObject *__pyx_k_codeobj_293;
+static PyObject *__pyx_k_codeobj_296;
+static PyObject *__pyx_k_codeobj_300;
/* Python wrapper */
static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
@@ -2354,12 +2476,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObj
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_fa = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("get_sequence (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__chrom,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__fa,0};
PyObject* values[4] = {0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -2375,30 +2496,26 @@ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObj
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__end)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fa)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_sequence") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_sequence") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 4) {
goto __pyx_L5_argtuple_error;
@@ -2415,7 +2532,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObj
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.get_sequence", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -2426,7 +2543,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_1get_sequence(PyObject *__pyx_self, PyObj
return __pyx_r;
}
-/* "pysam/cvcf.pyx":58
+/* "pysam/cvcf.pyx":59
*
* # Utility function. Uses 0-based coordinates
* def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
@@ -2450,16 +2567,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("get_sequence", 0);
- /* "pysam/cvcf.pyx":60
+ /* "pysam/cvcf.pyx":61
* def get_sequence(chrom, start, end, fa):
* # obtain sequence from .fa file, without truncation
* if end<=start: return "" # <<<<<<<<<<<<<<
* if not fa: return "N"*(end-start)
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_end, __pyx_v_start, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
@@ -2470,20 +2586,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":61
+ /* "pysam/cvcf.pyx":62
* # obtain sequence from .fa file, without truncation
* if end<=start: return ""
* if not fa: return "N"*(end-start) # <<<<<<<<<<<<<<
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
* sequence = fa.fetch(chrom, start, end).upper()
*/
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_fa); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_fa); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (!__pyx_t_2);
if (__pyx_t_3) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = ((PyObject *)__pyx_t_4);
@@ -2493,27 +2609,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":62
+ /* "pysam/cvcf.pyx":63
* if end<=start: return ""
* if not fa: return "N"*(end-start)
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper() # <<<<<<<<<<<<<<
* sequence = fa.fetch(chrom, start, end).upper()
* if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
*/
- __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_start, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_3) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = PyNumber_Negative(__pyx_v_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Negative(__pyx_v_start); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_1 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_chrom);
@@ -2527,17 +2642,17 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
__Pyx_INCREF(__pyx_v_fa);
PyTuple_SET_ITEM(__pyx_t_5, 3, __pyx_v_fa);
__Pyx_GIVEREF(__pyx_v_fa);
- __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__upper); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__upper); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Add(((PyObject *)__pyx_t_1), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 62; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Add(((PyObject *)__pyx_t_1), __pyx_t_6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
@@ -2548,16 +2663,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":63
+ /* "pysam/cvcf.pyx":64
* if not fa: return "N"*(end-start)
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
* sequence = fa.fetch(chrom, start, end).upper() # <<<<<<<<<<<<<<
* if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
* return sequence
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_fa, __pyx_n_s__fetch); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_fa, __pyx_n_s__fetch); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_chrom);
@@ -2568,51 +2683,50 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
__Pyx_INCREF(__pyx_v_end);
PyTuple_SET_ITEM(__pyx_t_6, 2, __pyx_v_end);
__Pyx_GIVEREF(__pyx_v_end);
- __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__upper); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__upper); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_v_sequence = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":64
+ /* "pysam/cvcf.pyx":65
* if start<0: return "N"*(-start) + get_sequence(chrom, 0, end, fa).upper()
* sequence = fa.fetch(chrom, start, end).upper()
* if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence)) # <<<<<<<<<<<<<<
* return sequence
*
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_sequence); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_sequence); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_1, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_3) {
- __pyx_t_5 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Subtract(__pyx_v_end, __pyx_v_start); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Length(__pyx_v_sequence); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_sequence); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyNumber_Subtract(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Subtract(__pyx_t_5, __pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_sequence, ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_v_sequence, ((PyObject *)__pyx_t_6)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 65; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_v_sequence);
@@ -2622,7 +2736,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__py
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":65
+ /* "pysam/cvcf.pyx":66
* sequence = fa.fetch(chrom, start, end).upper()
* if len(sequence) < end-start: sequence += "N"*(end-start-len(sequence))
* return sequence # <<<<<<<<<<<<<<
@@ -2657,13 +2771,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3parse_regions(PyObject *__pyx_self, PyOb
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_regions (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_2parse_regions(__pyx_self, ((PyObject *)__pyx_v_string));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":68
+/* "pysam/cvcf.pyx":69
*
* # Utility function. Parses a region string
* def parse_regions( string ): # <<<<<<<<<<<<<<
@@ -2700,35 +2813,35 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("parse_regions", 0);
- /* "pysam/cvcf.pyx":69
+ /* "pysam/cvcf.pyx":70
* # Utility function. Parses a region string
* def parse_regions( string ):
* result = [] # <<<<<<<<<<<<<<
* for r in string.split(','):
* elts = r.split(':')
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_v_result = __pyx_t_1;
+ __pyx_v_result = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":70
+ /* "pysam/cvcf.pyx":71
* def parse_regions( string ):
* result = []
* for r in string.split(','): # <<<<<<<<<<<<<<
* elts = r.split(':')
* chrom, start, end = elts[0], 0, 3000000000
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_string, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_string, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
__pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_4 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
@@ -2736,16 +2849,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
for (;;) {
if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_3); __Pyx_INCREF(__pyx_t_2); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_4(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -2755,30 +2876,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
__pyx_v_r = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":71
+ /* "pysam/cvcf.pyx":72
* result = []
* for r in string.split(','):
* elts = r.split(':') # <<<<<<<<<<<<<<
* chrom, start, end = elts[0], 0, 3000000000
* if len(elts)==1: pass
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_r, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_5), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_5), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_elts);
__pyx_v_elts = __pyx_t_5;
__pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":72
+ /* "pysam/cvcf.pyx":73
* for r in string.split(','):
* elts = r.split(':')
* chrom, start, end = elts[0], 0, 3000000000 # <<<<<<<<<<<<<<
* if len(elts)==1: pass
* elif len(elts)==2:
*/
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_2 = __pyx_int_0;
__Pyx_INCREF(__pyx_t_2);
@@ -2794,81 +2915,81 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
__pyx_v_end = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":73
+ /* "pysam/cvcf.pyx":74
* elts = r.split(':')
* chrom, start, end = elts[0], 0, 3000000000
* if len(elts)==1: pass # <<<<<<<<<<<<<<
* elif len(elts)==2:
* if len(elts[1])>0:
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_8 = (__pyx_t_7 == 1);
if (__pyx_t_8) {
goto __pyx_L5;
}
- /* "pysam/cvcf.pyx":74
+ /* "pysam/cvcf.pyx":75
* chrom, start, end = elts[0], 0, 3000000000
* if len(elts)==1: pass
* elif len(elts)==2: # <<<<<<<<<<<<<<
* if len(elts[1])>0:
* ielts = elts[1].split('-')
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_8 = (__pyx_t_7 == 2);
if (__pyx_t_8) {
- /* "pysam/cvcf.pyx":75
+ /* "pysam/cvcf.pyx":76
* if len(elts)==1: pass
* elif len(elts)==2:
* if len(elts[1])>0: # <<<<<<<<<<<<<<
* ielts = elts[1].split('-')
* if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
*/
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_8 = (__pyx_t_7 > 0);
if (__pyx_t_8) {
- /* "pysam/cvcf.pyx":76
+ /* "pysam/cvcf.pyx":77
* elif len(elts)==2:
* if len(elts[1])>0:
* ielts = elts[1].split('-') # <<<<<<<<<<<<<<
* if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
* try: start, end = int(ielts[0])-1, int(ielts[1])
*/
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_ielts);
__pyx_v_ielts = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":77
+ /* "pysam/cvcf.pyx":78
* if len(elts[1])>0:
* ielts = elts[1].split('-')
* if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<<
* try: start, end = int(ielts[0])-1, int(ielts[1])
* except: raise ValueError("Don't understand region string '%s'" % r)
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_ielts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_ielts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_8 = (__pyx_t_7 != 2);
if (__pyx_t_8) {
- __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_8), __pyx_v_r); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_8), __pyx_v_r); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
@@ -2876,7 +2997,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":78
+ /* "pysam/cvcf.pyx":79
* ielts = elts[1].split('-')
* if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
* try: start, end = int(ielts[0])-1, int(ielts[1]) # <<<<<<<<<<<<<<
@@ -2889,27 +3010,27 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
__Pyx_XGOTREF(__pyx_t_10);
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ielts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ielts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Subtract(__pyx_t_6, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_2 = PyNumber_Subtract(__pyx_t_6, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ielts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ielts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
+ __pyx_t_6 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L8_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_v_start);
@@ -2928,7 +3049,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":79
+ /* "pysam/cvcf.pyx":80
* if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
* try: start, end = int(ielts[0])-1, int(ielts[1])
* except: raise ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<<
@@ -2937,23 +3058,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.parse_regions", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_2, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_8), __pyx_v_r); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_8), __pyx_v_r); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_12));
- __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
__Pyx_GOTREF(__pyx_t_13);
PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_12));
__Pyx_GIVEREF(((PyObject *)__pyx_t_12));
__pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ __pyx_t_12 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
__Pyx_Raise(__pyx_t_12, 0, 0, 0);
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 79; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L10_except_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -2979,37 +3100,37 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
}
/*else*/ {
- /* "pysam/cvcf.pyx":81
+ /* "pysam/cvcf.pyx":82
* except: raise ValueError("Don't understand region string '%s'" % r)
* else:
* raise ValueError("Don't understand region string '%s'" % r) # <<<<<<<<<<<<<<
* result.append( (chrom,start,end) )
* return result
*/
- __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_8), __pyx_v_r); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_8), __pyx_v_r); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_5, 0, 0, 0);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":82
+ /* "pysam/cvcf.pyx":83
* else:
* raise ValueError("Don't understand region string '%s'" % r)
* result.append( (chrom,start,end) ) # <<<<<<<<<<<<<<
* return result
*
*/
- __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_chrom);
@@ -3020,12 +3141,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
__Pyx_INCREF(__pyx_v_end);
PyTuple_SET_ITEM(__pyx_t_5, 2, __pyx_v_end);
__Pyx_GIVEREF(__pyx_v_end);
- __pyx_t_14 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_5)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyList_Append(__pyx_v_result, ((PyObject *)__pyx_t_5)); if (unlikely(__pyx_t_14 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":83
+ /* "pysam/cvcf.pyx":84
* raise ValueError("Don't understand region string '%s'" % r)
* result.append( (chrom,start,end) )
* return result # <<<<<<<<<<<<<<
@@ -3065,11 +3186,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_vcf = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -3082,12 +3203,11 @@ static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, Py
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -3098,7 +3218,7 @@ static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 104; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 105; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -3109,7 +3229,7 @@ static int __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__(PyObject *__pyx_v_self, Py
return __pyx_r;
}
-/* "pysam/cvcf.pyx":104
+/* "pysam/cvcf.pyx":105
* cdef uint32_t pos
*
* def __init__(self, vcf): # <<<<<<<<<<<<<<
@@ -3122,12 +3242,12 @@ static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cv
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__", 0);
- /* "pysam/cvcf.pyx":105
+ /* "pysam/cvcf.pyx":106
*
* def __init__(self, vcf):
* self.vcf = vcf # <<<<<<<<<<<<<<
* # if len(data) != len(self.vcf._samples):
- * # self.error(str(data),
+ * # self.vcf.error(str(data),
*/
__Pyx_INCREF(__pyx_v_vcf);
__Pyx_GIVEREF(__pyx_v_vcf);
@@ -3144,11 +3264,11 @@ static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cv
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_vcf = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcf,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -3161,12 +3281,11 @@ static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcf)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -3177,7 +3296,7 @@ static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 115; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCFRecord.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -3188,7 +3307,7 @@ static int __pyx_pw_5pysam_4cvcf_9VCFRecord_3__cinit__(PyObject *__pyx_v_self, P
return __pyx_r;
}
-/* "pysam/cvcf.pyx":115
+/* "pysam/cvcf.pyx":116
* # len(data)))
*
* def __cinit__(self, vcf ): # <<<<<<<<<<<<<<
@@ -3201,7 +3320,7 @@ static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
- /* "pysam/cvcf.pyx":117
+ /* "pysam/cvcf.pyx":118
* def __cinit__(self, vcf ):
* # start indexed access at genotypes
* self.offset = 9 # <<<<<<<<<<<<<<
@@ -3210,7 +3329,7 @@ static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4
*/
__pyx_v_self->__pyx_base.offset = 9;
- /* "pysam/cvcf.pyx":119
+ /* "pysam/cvcf.pyx":120
* self.offset = 9
*
* self.vcf = vcf # <<<<<<<<<<<<<<
@@ -3235,14 +3354,14 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self,
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_error = 0;
PyObject *__pyx_v_opt = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("error (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject* values[3] = {0,0,0};
- /* "pysam/cvcf.pyx":121
+ /* "pysam/cvcf.pyx":122
* self.vcf = vcf
*
* def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
@@ -3263,14 +3382,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (kw_args > 0) {
@@ -3279,7 +3396,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self,
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "error") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "error") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -3296,7 +3413,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_5error(PyObject *__pyx_v_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 121; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("error", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 122; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCFRecord.error", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -3318,7 +3435,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("error", 0);
- /* "pysam/cvcf.pyx":124
+ /* "pysam/cvcf.pyx":125
* '''raise error.'''
* # pass to vcf file for error handling
* return self.vcf.error( line, error, opt ) # <<<<<<<<<<<<<<
@@ -3326,9 +3443,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam
* cdef update( self, char * buffer, size_t nbytes ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
@@ -3339,7 +3456,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam
__Pyx_INCREF(__pyx_v_opt);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_opt);
__Pyx_GIVEREF(__pyx_v_opt);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 124; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 125; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -3361,7 +3478,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam
return __pyx_r;
}
-/* "pysam/cvcf.pyx":126
+/* "pysam/cvcf.pyx":127
* return self.vcf.error( line, error, opt )
*
* cdef update( self, char * buffer, size_t nbytes ): # <<<<<<<<<<<<<<
@@ -3378,18 +3495,18 @@ static PyObject *__pyx_f_5pysam_4cvcf_9VCFRecord_update(struct __pyx_obj_5pysam_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("update", 0);
- /* "pysam/cvcf.pyx":131
+ /* "pysam/cvcf.pyx":132
* nbytes does not include the terminal '\0'.
* '''
* TabProxies.TupleProxy.update( self, buffer, nbytes ) # <<<<<<<<<<<<<<
*
* self.contig = self.fields[0]
*/
- __pyx_t_1 = __pyx_vtabptr_5pysam_10TabProxies_TupleProxy->update(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 131; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __pyx_vtabptr_5pysam_10TabProxies_TupleProxy->update(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_self), __pyx_v_buffer, __pyx_v_nbytes); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":133
+ /* "pysam/cvcf.pyx":134
* TabProxies.TupleProxy.update( self, buffer, nbytes )
*
* self.contig = self.fields[0] # <<<<<<<<<<<<<<
@@ -3398,7 +3515,7 @@ static PyObject *__pyx_f_5pysam_4cvcf_9VCFRecord_update(struct __pyx_obj_5pysam_
*/
__pyx_v_self->contig = (__pyx_v_self->__pyx_base.fields[0]);
- /* "pysam/cvcf.pyx":135
+ /* "pysam/cvcf.pyx":136
* self.contig = self.fields[0]
* # vcf counts from 1 - correct here
* self.pos = atoi( self.fields[1] ) - 1 # <<<<<<<<<<<<<<
@@ -3430,7 +3547,7 @@ static Py_ssize_t __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__(PyObject *__pyx_v_se
return __pyx_r;
}
-/* "pysam/cvcf.pyx":137
+/* "pysam/cvcf.pyx":138
* self.pos = atoi( self.fields[1] ) - 1
*
* def __len__(self): # <<<<<<<<<<<<<<
@@ -3446,7 +3563,7 @@ static Py_ssize_t __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_5py
long __pyx_t_3;
__Pyx_RefNannySetupContext("__len__", 0);
- /* "pysam/cvcf.pyx":138
+ /* "pysam/cvcf.pyx":139
*
* def __len__(self):
* return max(0, self.nfields - 9) # <<<<<<<<<<<<<<
@@ -3480,7 +3597,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(PyObject *__p
return __pyx_r;
}
-/* "pysam/cvcf.pyx":141
+/* "pysam/cvcf.pyx":142
*
* property contig:
* def __get__(self): return self.contig # <<<<<<<<<<<<<<
@@ -3497,7 +3614,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(struct __pyx_o
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyBytes_FromString(__pyx_v_self->contig); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString(__pyx_v_self->contig); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
@@ -3526,7 +3643,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(PyObject *__pyx_
return __pyx_r;
}
-/* "pysam/cvcf.pyx":144
+/* "pysam/cvcf.pyx":145
*
* property pos:
* def __get__(self): return self.pos # <<<<<<<<<<<<<<
@@ -3543,7 +3660,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyInt_to_py_uint32_t(__pyx_v_self->pos); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -3572,7 +3689,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(PyObject *__pyx_v
return __pyx_r;
}
-/* "pysam/cvcf.pyx":147
+/* "pysam/cvcf.pyx":148
*
* property id:
* def __get__(self): return self.fields[2] # <<<<<<<<<<<<<<
@@ -3589,7 +3706,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_5
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[2])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[2])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 148; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
@@ -3618,12 +3735,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(PyObject *__pyx_
return __pyx_r;
}
-/* "pysam/cvcf.pyx":150
+/* "pysam/cvcf.pyx":151
*
* property ref:
- * def __get__(self): return self.fields[3] # <<<<<<<<<<<<<<
+ * def __get__(self): # <<<<<<<<<<<<<<
+ * return self.fields[3]
*
- * property alt:
*/
static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self) {
@@ -3634,8 +3751,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
+
+ /* "pysam/cvcf.pyx":152
+ * property ref:
+ * def __get__(self):
+ * return self.fields[3] # <<<<<<<<<<<<<<
+ *
+ * property alt:
+ */
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[3])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 150; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[3])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_r = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
@@ -3664,7 +3789,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(PyObject *__pyx_
return __pyx_r;
}
-/* "pysam/cvcf.pyx":153
+/* "pysam/cvcf.pyx":155
*
* property alt:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -3684,28 +3809,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "pysam/cvcf.pyx":155
+ /* "pysam/cvcf.pyx":157
* def __get__(self):
* # convert v3.3 to v4.0 alleles below
* alt = self.fields[4] # <<<<<<<<<<<<<<
* if alt == ".": alt = []
* else: alt = alt.upper().split(',')
*/
- __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[4])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[4])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_alt = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":156
+ /* "pysam/cvcf.pyx":158
* # convert v3.3 to v4.0 alleles below
* alt = self.fields[4]
* if alt == ".": alt = [] # <<<<<<<<<<<<<<
* else: alt = alt.upper().split(',')
* return alt
*/
- __pyx_t_2 = __Pyx_PyString_Equals(__pyx_v_alt, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_alt);
__pyx_v_alt = ((PyObject *)__pyx_t_1);
@@ -3714,22 +3841,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_
}
/*else*/ {
- /* "pysam/cvcf.pyx":157
+ /* "pysam/cvcf.pyx":159
* alt = self.fields[4]
* if alt == ".": alt = []
* else: alt = alt.upper().split(',') # <<<<<<<<<<<<<<
* return alt
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_alt, __pyx_n_s__upper); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_alt, __pyx_n_s__upper); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_10), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_v_alt);
@@ -3738,7 +3865,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":158
+ /* "pysam/cvcf.pyx":160
* if alt == ".": alt = []
* else: alt = alt.upper().split(',')
* return alt # <<<<<<<<<<<<<<
@@ -3775,7 +3902,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(PyObject *__pyx
return __pyx_r;
}
-/* "pysam/cvcf.pyx":161
+/* "pysam/cvcf.pyx":163
*
* property qual:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -3804,26 +3931,28 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "pysam/cvcf.pyx":162
+ /* "pysam/cvcf.pyx":164
* property qual:
* def __get__(self):
* qual = self.fields[5] # <<<<<<<<<<<<<<
* if qual == b".": qual = -1
* else:
*/
- __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[5])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 162; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[5])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__pyx_v_qual = ((PyObject *)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":163
+ /* "pysam/cvcf.pyx":165
* def __get__(self):
* qual = self.fields[5]
* if qual == b".": qual = -1 # <<<<<<<<<<<<<<
* else:
* try: qual = float(qual)
*/
- __pyx_t_2 = __Pyx_PyBytes_Equals(__pyx_v_qual, ((PyObject *)__pyx_kp_b_9), Py_EQ); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 163; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_qual, ((PyObject *)__pyx_kp_b_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_INCREF(__pyx_int_neg_1);
__Pyx_DECREF(__pyx_v_qual);
@@ -3832,12 +3961,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj
}
/*else*/ {
- /* "pysam/cvcf.pyx":165
+ /* "pysam/cvcf.pyx":167
* if qual == b".": qual = -1
* else:
* try: qual = float(qual) # <<<<<<<<<<<<<<
* except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
- *
+ * return qual
*/
{
__Pyx_ExceptionSave(&__pyx_t_3, &__pyx_t_4, &__pyx_t_5);
@@ -3845,8 +3974,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj
__Pyx_XGOTREF(__pyx_t_4);
__Pyx_XGOTREF(__pyx_t_5);
/*try:*/ {
- __pyx_t_6 = __Pyx_PyObject_AsDouble(__pyx_v_qual); if (unlikely(__pyx_t_6 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_1 = PyFloat_FromDouble(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_PyObject_AsDouble(__pyx_v_qual); if (unlikely(__pyx_t_6 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 167; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_1 = PyFloat_FromDouble(__pyx_t_6); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 167; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_qual);
__pyx_v_qual = __pyx_t_1;
@@ -3859,32 +3988,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj
__pyx_L4_error:;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":166
+ /* "pysam/cvcf.pyx":168
* else:
* try: qual = float(qual)
* except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL) # <<<<<<<<<<<<<<
+ * return qual
*
- * property filter:
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCFRecord.qual.__get__", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_7, &__pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_7, &__pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(((PyObject *)__pyx_v_self));
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_v_self));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_11 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_12);
PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_11);
__Pyx_GIVEREF(__pyx_t_11);
@@ -3892,7 +4021,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_11 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 166; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
@@ -3918,6 +4047,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj
}
__pyx_L3:;
+ /* "pysam/cvcf.pyx":169
+ * try: qual = float(qual)
+ * except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
+ * return qual # <<<<<<<<<<<<<<
+ *
+ * property filter:
+ */
+ __Pyx_XDECREF(__pyx_r);
+ __Pyx_INCREF(__pyx_v_qual);
+ __pyx_r = __pyx_v_qual;
+ goto __pyx_L0;
+
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
@@ -3948,7 +4089,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(PyObject *__p
return __pyx_r;
}
-/* "pysam/cvcf.pyx":169
+/* "pysam/cvcf.pyx":172
*
* property filter:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -3971,7 +4112,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_o
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "pysam/cvcf.pyx":170
+ /* "pysam/cvcf.pyx":173
* property filter:
* def __get__(self):
* f = self.fields[6] # <<<<<<<<<<<<<<
@@ -3980,35 +4121,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_o
*/
__pyx_v_f = (__pyx_v_self->__pyx_base.fields[6]);
- /* "pysam/cvcf.pyx":172
+ /* "pysam/cvcf.pyx":175
* f = self.fields[6]
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if f == b"." or f == b"PASS" or f == b"0": return [] # <<<<<<<<<<<<<<
* else: return f.split(';')
*
*/
- __pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!__pyx_t_3) {
- __pyx_t_2 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_n_b__PASS), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_n_b__PASS), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!__pyx_t_4) {
- __pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b__0), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b__0), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_6 = __pyx_t_5;
} else {
@@ -4020,7 +4158,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_o
}
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 175; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -4029,7 +4167,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_o
}
/*else*/ {
- /* "pysam/cvcf.pyx":173
+ /* "pysam/cvcf.pyx":176
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if f == b"." or f == b"PASS" or f == b"0": return []
* else: return f.split(';') # <<<<<<<<<<<<<<
@@ -4037,12 +4175,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_o
* property info:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_f); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_t_2), __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_t_2), __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_12), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_12), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_r = __pyx_t_2;
@@ -4075,7 +4213,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(PyObject *__pyx
return __pyx_r;
}
-/* "pysam/cvcf.pyx":176
+/* "pysam/cvcf.pyx":179
*
* property info:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -4106,7 +4244,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "pysam/cvcf.pyx":177
+ /* "pysam/cvcf.pyx":180
* property info:
* def __get__(self):
* col = self.fields[7] # <<<<<<<<<<<<<<
@@ -4115,54 +4253,53 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
*/
__pyx_v_col = (__pyx_v_self->__pyx_base.fields[7]);
- /* "pysam/cvcf.pyx":179
+ /* "pysam/cvcf.pyx":182
* col = self.fields[7]
* # dictionary of keys, and list of values
* info = {} # <<<<<<<<<<<<<<
* if col != b".":
* for blurp in col.split(';'):
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 179; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_info = __pyx_t_1;
+ __pyx_v_info = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":180
+ /* "pysam/cvcf.pyx":183
* # dictionary of keys, and list of values
* info = {}
* if col != b".": # <<<<<<<<<<<<<<
* for blurp in col.split(';'):
* elts = blurp.split('=')
*/
- __pyx_t_1 = PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_kp_b_9), Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 180; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":181
+ /* "pysam/cvcf.pyx":184
* info = {}
* if col != b".":
* for blurp in col.split(';'): # <<<<<<<<<<<<<<
* elts = blurp.split('=')
* if len(elts) == 1: v = None
*/
- __pyx_t_2 = PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_col); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_t_2), __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_t_2), __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_13), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_13), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
__pyx_t_1 = __pyx_t_2; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
@@ -4170,16 +4307,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -4189,30 +4334,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
__pyx_v_blurp = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":182
+ /* "pysam/cvcf.pyx":185
* if col != b".":
* for blurp in col.split(';'):
* elts = blurp.split('=') # <<<<<<<<<<<<<<
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_15), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_15), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_elts);
__pyx_v_elts = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":183
+ /* "pysam/cvcf.pyx":186
* for blurp in col.split(';'):
* elts = blurp.split('=')
* if len(elts) == 1: v = None # <<<<<<<<<<<<<<
* elif len(elts) == 2: v = elts[1]
* else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 183; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (__pyx_t_7 == 1);
if (__pyx_t_3) {
__Pyx_INCREF(Py_None);
@@ -4221,17 +4366,17 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
goto __pyx_L6;
}
- /* "pysam/cvcf.pyx":184
+ /* "pysam/cvcf.pyx":187
* elts = blurp.split('=')
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1] # <<<<<<<<<<<<<<
* else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
* info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self))
*/
- __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (__pyx_t_7 == 2);
if (__pyx_t_3) {
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 187; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_v);
__pyx_v_v = __pyx_t_6;
@@ -4240,26 +4385,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
}
/*else*/ {
- /* "pysam/cvcf.pyx":185
+ /* "pysam/cvcf.pyx":188
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
* else: self.vcf.error(str(self),self.ERROR_INFO_STRING) # <<<<<<<<<<<<<<
* info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self))
* return info
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_v_self));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_v_self));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_8 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
@@ -4267,7 +4412,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_8 = 0;
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
@@ -4275,29 +4420,29 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":186
+ /* "pysam/cvcf.pyx":189
* elif len(elts) == 2: v = elts[1]
* else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
* info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self)) # <<<<<<<<<<<<<<
* return info
*
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___info); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___info); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(((PyObject *)__pyx_v_self));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_v_self));
__Pyx_GIVEREF(((PyObject *)__pyx_v_self));
- __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
@@ -4311,13 +4456,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
__pyx_t_9 = 0;
__pyx_t_6 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- if (PyDict_SetItem(((PyObject *)__pyx_v_info), __pyx_t_8, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_info), __pyx_t_8, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 189; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
@@ -4326,7 +4471,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":187
+ /* "pysam/cvcf.pyx":190
* else: self.vcf.error(str(self),self.ERROR_INFO_STRING)
* info[elts[0]] = self.vcf.parse_formatdata(elts[0], v, self.vcf._info, str(self))
* return info # <<<<<<<<<<<<<<
@@ -4370,7 +4515,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(PyObject *__p
return __pyx_r;
}
-/* "pysam/cvcf.pyx":190
+/* "pysam/cvcf.pyx":193
*
* property format:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -4388,7 +4533,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_o
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "pysam/cvcf.pyx":191
+ /* "pysam/cvcf.pyx":194
* property format:
* def __get__(self):
* return self.fields[8].split(':') # <<<<<<<<<<<<<<
@@ -4396,12 +4541,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_o
* property samples:
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[8])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[8])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_t_1), __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_t_1), __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_16), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_16), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = __pyx_t_1;
@@ -4432,7 +4577,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(PyObject *__
return __pyx_r;
}
-/* "pysam/cvcf.pyx":194
+/* "pysam/cvcf.pyx":197
*
* property samples:
* def __get__(self): # <<<<<<<<<<<<<<
@@ -4449,7 +4594,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__get__", 0);
- /* "pysam/cvcf.pyx":195
+ /* "pysam/cvcf.pyx":198
* property samples:
* def __get__(self):
* return self.vcf._samples # <<<<<<<<<<<<<<
@@ -4457,7 +4602,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_
* def __getitem__(self, key):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___samples); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 195; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___samples); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 198; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -4486,7 +4631,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__(PyObject *__pyx_v
return __pyx_r;
}
-/* "pysam/cvcf.pyx":197
+/* "pysam/cvcf.pyx":200
* return self.vcf._samples
*
* def __getitem__(self, key): # <<<<<<<<<<<<<<
@@ -4522,103 +4667,103 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__getitem__", 0);
- /* "pysam/cvcf.pyx":200
+ /* "pysam/cvcf.pyx":203
*
* # parse sample columns
* values = self.fields[self.vcf._sample2column[key]].split(':') # <<<<<<<<<<<<<<
* alt = self.alt
* format = self.format
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___sample2column); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___sample2column); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_t_1, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyIndex_AsSsize_t(__pyx_t_2); if (unlikely((__pyx_t_3 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyIndex_AsSsize_t(__pyx_t_2); if (unlikely((__pyx_t_3 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[__pyx_t_3])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString((__pyx_v_self->__pyx_base.fields[__pyx_t_3])); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_t_2), __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_t_2), __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_17), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_17), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_values = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":201
+ /* "pysam/cvcf.pyx":204
* # parse sample columns
* values = self.fields[self.vcf._sample2column[key]].split(':')
* alt = self.alt # <<<<<<<<<<<<<<
* format = self.format
*
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 201; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_alt = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":202
+ /* "pysam/cvcf.pyx":205
* values = self.fields[self.vcf._sample2column[key]].split(':')
* alt = self.alt
* format = self.format # <<<<<<<<<<<<<<
*
* if len(values) > len(format):
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_format = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":204
+ /* "pysam/cvcf.pyx":207
* format = self.format
*
* if len(values) > len(format): # <<<<<<<<<<<<<<
- * self.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
+ * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
* (len(values),key,len(format)))
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 204; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_3 > __pyx_t_4);
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":205
+ /* "pysam/cvcf.pyx":208
*
* if len(values) > len(format):
- * self.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ # <<<<<<<<<<<<<<
+ * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\ # <<<<<<<<<<<<<<
* (len(values),key,len(format)))
*
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__line); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_18); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_18); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "pysam/cvcf.pyx":206
+ /* "pysam/cvcf.pyx":209
* if len(values) > len(format):
- * self.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
+ * self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
* (len(values),key,len(format))) # <<<<<<<<<<<<<<
*
* result = {}
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 206; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
@@ -4629,10 +4774,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_7 = 0;
__pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
@@ -4643,7 +4788,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__pyx_t_1 = 0;
__pyx_t_6 = 0;
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
@@ -4652,41 +4797,41 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":208
+ /* "pysam/cvcf.pyx":211
* (len(values),key,len(format)))
*
* result = {} # <<<<<<<<<<<<<<
* for idx in range(len(format)):
* expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
*/
- __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 208; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_v_result = __pyx_t_8;
+ __pyx_v_result = ((PyObject*)__pyx_t_8);
__pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":209
+ /* "pysam/cvcf.pyx":212
*
* result = {}
* for idx in range(len(format)): # <<<<<<<<<<<<<<
* expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
* if idx < len(values): value = values[idx]
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
__pyx_t_9 = __pyx_t_8; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
@@ -4694,16 +4839,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
for (;;) {
if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_8 = __pyx_t_10(__pyx_t_9);
if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -4713,20 +4866,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__pyx_v_idx = __pyx_t_8;
__pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":210
+ /* "pysam/cvcf.pyx":213
* result = {}
* for idx in range(len(format)):
* expected = self.vcf.get_expected(format[idx], self.vcf._format, alt) # <<<<<<<<<<<<<<
* if idx < len(values): value = values[idx]
* else:
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__get_expected); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__get_expected); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___format); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
@@ -4737,7 +4890,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__Pyx_GIVEREF(__pyx_v_alt);
__pyx_t_2 = 0;
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -4745,23 +4898,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__pyx_v_expected = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":211
+ /* "pysam/cvcf.pyx":214
* for idx in range(len(format)):
* expected = self.vcf.get_expected(format[idx], self.vcf._format, alt)
* if idx < len(values): value = values[idx] # <<<<<<<<<<<<<<
* else:
* if expected == -1: value = "."
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_6, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_6, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
- __pyx_t_1 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_1;
@@ -4770,16 +4922,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
}
/*else*/ {
- /* "pysam/cvcf.pyx":213
+ /* "pysam/cvcf.pyx":216
* if idx < len(values): value = values[idx]
* else:
* if expected == -1: value = "." # <<<<<<<<<<<<<<
* else: value = ",".join(["."]*expected)
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 213; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
@@ -4789,31 +4940,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
}
/*else*/ {
- /* "pysam/cvcf.pyx":214
+ /* "pysam/cvcf.pyx":217
* else:
* if expected == -1: value = "."
* else: value = ",".join(["."]*expected) # <<<<<<<<<<<<<<
*
* result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyList_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyList_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
PyList_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
- { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_6, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_6, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_temp);
__Pyx_DECREF(__pyx_t_6);
__pyx_t_6 = __pyx_temp;
}
- __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
@@ -4825,30 +4976,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":216
+ /* "pysam/cvcf.pyx":219
* else: value = ",".join(["."]*expected)
*
* result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data)) # <<<<<<<<<<<<<<
* if expected != -1 and len(result[format[idx]]) != expected:
- * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+ * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyBytes_FromString(__pyx_v_self->__pyx_base.data); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromString(__pyx_v_self->__pyx_base.data); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
@@ -4862,41 +5013,39 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__pyx_t_8 = 0;
__pyx_t_1 = 0;
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_t_7, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_t_7, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":217
+ /* "pysam/cvcf.pyx":220
*
* result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
* if expected != -1 and len(result[format[idx]]) != expected: # <<<<<<<<<<<<<<
- * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
- * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+ * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+ * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_5) {
- __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_2); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_2); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_12 = __pyx_t_11;
} else {
@@ -4904,43 +5053,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
}
if (__pyx_t_12) {
- /* "pysam/cvcf.pyx":218
+ /* "pysam/cvcf.pyx":221
* result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
* if expected != -1 and len(result[format[idx]]) != expected:
- * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<<
- * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+ * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<<
+ * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
* if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self->vcf, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyBytes_FromString(__pyx_v_self->__pyx_base.data); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyBytes_FromString(__pyx_v_self->__pyx_base.data); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_20); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(((PyObject *)__pyx_v_self), __pyx_n_s_20); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- /* "pysam/cvcf.pyx":219
+ /* "pysam/cvcf.pyx":222
* if expected != -1 and len(result[format[idx]]) != expected:
- * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
- * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) # <<<<<<<<<<<<<<
+ * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+ * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]])) # <<<<<<<<<<<<<<
* if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
* result[format[idx]] = result[format[idx]][:expected]
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_13 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_8); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_8); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
@@ -4951,10 +5100,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__Pyx_GIVEREF(__pyx_t_13);
__pyx_t_1 = 0;
__pyx_t_13 = 0;
- __pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_13));
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
@@ -4965,99 +5114,98 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
__pyx_t_7 = 0;
__pyx_t_6 = 0;
__pyx_t_13 = 0;
- __pyx_t_13 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- /* "pysam/cvcf.pyx":220
- * self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
- * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+ /* "pysam/cvcf.pyx":223
+ * self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+ * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
* if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]])) # <<<<<<<<<<<<<<
* result[format[idx]] = result[format[idx]][:expected]
*
*/
- __pyx_t_13 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_13); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_13); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_3 = PyObject_Length(__pyx_t_8); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_t_8); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_13 = PyObject_RichCompare(__pyx_t_8, __pyx_v_expected, Py_LT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_13);
+ __pyx_t_13 = PyObject_RichCompare(__pyx_t_8, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_13); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_PyObject_IsTrue(__pyx_t_13); if (unlikely(__pyx_t_12 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
if (__pyx_t_12) {
- __pyx_t_13 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_13); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_13); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_2); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_2); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_6, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_6, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_6); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_6); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_3 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_6 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_7); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyList_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyList_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_7, __pyx_t_6); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_temp);
__Pyx_DECREF(__pyx_t_7);
__pyx_t_7 = __pyx_temp;
}
__pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_InPlaceAdd(__pyx_t_8, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_InPlaceAdd(__pyx_t_8, ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_t_13, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_t_13, __pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 223; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
goto __pyx_L9;
}
__pyx_L9:;
- /* "pysam/cvcf.pyx":221
- * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+ /* "pysam/cvcf.pyx":224
+ * "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
* if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
* result[format[idx]] = result[format[idx]][:expected] # <<<<<<<<<<<<<<
*
* return result
*/
- __pyx_t_13 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_13) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_6 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_13); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_result), __pyx_t_13); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
- __pyx_t_3 = __Pyx_PyIndex_AsSsize_t(__pyx_v_expected); if (unlikely((__pyx_t_3 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_13 = __Pyx_PySequence_GetSlice(__pyx_t_6, 0, __pyx_t_3); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyIndex_AsSsize_t(__pyx_v_expected); if (unlikely((__pyx_t_3 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PySequence_GetSlice(__pyx_t_6, 0, __pyx_t_3); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_t_6, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 221; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_result), __pyx_t_6, __pyx_t_13) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 224; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
goto __pyx_L8;
@@ -5066,7 +5214,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":223
+ /* "pysam/cvcf.pyx":226
* result[format[idx]] = result[format[idx]][:expected]
*
* return result # <<<<<<<<<<<<<<
@@ -5107,11 +5255,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_
static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_vcffile = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcffile,0};
int __pyx_r;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__vcffile,0};
PyObject* values[1] = {0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5124,12 +5272,11 @@ static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcffile);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__vcffile)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -5140,7 +5287,7 @@ static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 232; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.asVCFRecord.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -5151,7 +5298,7 @@ static int __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__(PyObject *__pyx_v_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":229
+/* "pysam/cvcf.pyx":232
* '''converts a :term:`tabix row` into a VCF record.'''
* cdef vcffile
* def __init__(self, vcffile ): # <<<<<<<<<<<<<<
@@ -5164,7 +5311,7 @@ static int __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__", 0);
- /* "pysam/cvcf.pyx":230
+ /* "pysam/cvcf.pyx":233
* cdef vcffile
* def __init__(self, vcffile ):
* self.vcffile = vcffile # <<<<<<<<<<<<<<
@@ -5187,11 +5334,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v
static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
char *__pyx_v_buffer;
int __pyx_v_len;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__call__ (wrapper)", 0);
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__buffer,&__pyx_n_s__len,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -5205,18 +5352,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__buffer)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__len)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__call__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__call__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -5224,12 +5369,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
values[1] = PyTuple_GET_ITEM(__pyx_args, 1);
}
- __pyx_v_buffer = PyBytes_AsString(values[0]); if (unlikely((!__pyx_v_buffer) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
- __pyx_v_len = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_len == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_buffer = PyBytes_AsString(values[0]); if (unlikely((!__pyx_v_buffer) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_v_len = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_len == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 231; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__call__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.asVCFRecord.__call__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -5240,7 +5385,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__(PyObject *__pyx_v
return __pyx_r;
}
-/* "pysam/cvcf.pyx":231
+/* "pysam/cvcf.pyx":234
* def __init__(self, vcffile ):
* self.vcffile = vcffile
* def __call__(self, char * buffer, int len ): # <<<<<<<<<<<<<<
@@ -5259,36 +5404,36 @@ static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__call__", 0);
- /* "pysam/cvcf.pyx":233
+ /* "pysam/cvcf.pyx":236
* def __call__(self, char * buffer, int len ):
* cdef VCFRecord r
* r = VCFRecord( self.vcffile ) # <<<<<<<<<<<<<<
* r.copy( buffer, len )
* return r
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_self->vcffile);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_self->vcffile);
__Pyx_GIVEREF(__pyx_v_self->vcffile);
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_4cvcf_VCFRecord)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_4cvcf_VCFRecord)), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 236; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_r = ((struct __pyx_obj_5pysam_4cvcf_VCFRecord *)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":234
+ /* "pysam/cvcf.pyx":237
* cdef VCFRecord r
* r = VCFRecord( self.vcffile )
* r.copy( buffer, len ) # <<<<<<<<<<<<<<
* return r
*
*/
- __pyx_t_2 = ((struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 234; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *)__pyx_v_r->__pyx_base.__pyx_vtab)->__pyx_base.copy(((struct __pyx_obj_5pysam_10TabProxies_TupleProxy *)__pyx_v_r), __pyx_v_buffer, __pyx_v_len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":235
+ /* "pysam/cvcf.pyx":238
* r = VCFRecord( self.vcffile )
* r.copy( buffer, len )
* return r # <<<<<<<<<<<<<<
@@ -5314,7 +5459,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_
return __pyx_r;
}
-/* "pysam/cvcf.pyx":314
+/* "pysam/cvcf.pyx":317
* _lines = None
*
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # <<<<<<<<<<<<<<
@@ -5331,7 +5476,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__defaults__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)Py_None));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)Py_None));
@@ -5374,12 +5519,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyOb
PyObject *__pyx_v_regions = 0;
PyObject *__pyx_v_lines = 0;
PyObject *__pyx_v_leftalign = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s___copy,&__pyx_n_s__reference,&__pyx_n_s__regions,&__pyx_n_s__lines,&__pyx_n_s__leftalign,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__init__ (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s___copy,&__pyx_n_s__reference,&__pyx_n_s__regions,&__pyx_n_s__lines,&__pyx_n_s__leftalign,0};
PyObject* values[6] = {0,0,0,0,0,0};
__pyx_defaults *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults, __pyx_self);
values[1] = ((PyObject *)((PyObject *)Py_None));
@@ -5403,8 +5547,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyOb
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -5433,7 +5576,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyOb
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -5456,7 +5599,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_1__init__(PyObject *__pyx_self, PyOb
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("__init__", 0, 1, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -5483,26 +5626,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__p
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__init__", 0);
- /* "pysam/cvcf.pyx":316
+ /* "pysam/cvcf.pyx":319
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
* # make error identifiers accessible by name
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id # <<<<<<<<<<<<<<
* if _copy != None:
* self._leftalign = _copy._leftalign
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__keys); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__keys); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
__pyx_t_4 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_4 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
@@ -5510,16 +5653,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__p
for (;;) {
if (!__pyx_t_4 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_4 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_1); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_1 = __pyx_t_4(__pyx_t_2);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -5528,328 +5679,327 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__p
__Pyx_XDECREF(__pyx_v_id);
__pyx_v_id = __pyx_t_1;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___errors); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___errors); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_GetItem(__pyx_t_5, __pyx_v_id); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_5, __pyx_v_id); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__split); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__split); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_22), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_22), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_6, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_t_6, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- if (PyObject_SetItem(__pyx_t_1, __pyx_t_5, __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_t_5, __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":317
+ /* "pysam/cvcf.pyx":320
* # make error identifiers accessible by name
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
* if _copy != None: # <<<<<<<<<<<<<<
* self._leftalign = _copy._leftalign
* self._header = _copy._header[:]
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v__copy, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_7) {
- /* "pysam/cvcf.pyx":318
+ /* "pysam/cvcf.pyx":321
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
* if _copy != None:
* self._leftalign = _copy._leftalign # <<<<<<<<<<<<<<
* self._header = _copy._header[:]
* self._version = _copy._version
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___leftalign, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 318; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___leftalign, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":319
+ /* "pysam/cvcf.pyx":322
* if _copy != None:
* self._leftalign = _copy._leftalign
* self._header = _copy._header[:] # <<<<<<<<<<<<<<
* self._version = _copy._version
* self._info = copy.deepcopy(_copy._info)
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___header); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___header); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PySequence_GetSlice(__pyx_t_2, 0, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PySequence_GetSlice(__pyx_t_2, 0, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___header, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___header, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":320
+ /* "pysam/cvcf.pyx":323
* self._leftalign = _copy._leftalign
* self._header = _copy._header[:]
* self._version = _copy._version # <<<<<<<<<<<<<<
* self._info = copy.deepcopy(_copy._info)
* self._filter = copy.deepcopy(_copy._filter)
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___version); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___version); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 320; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":321
+ /* "pysam/cvcf.pyx":324
* self._header = _copy._header[:]
* self._version = _copy._version
* self._info = copy.deepcopy(_copy._info) # <<<<<<<<<<<<<<
* self._filter = copy.deepcopy(_copy._filter)
* self._format = copy.deepcopy(_copy._format)
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___info); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___info, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___info, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":322
+ /* "pysam/cvcf.pyx":325
* self._version = _copy._version
* self._info = copy.deepcopy(_copy._info)
* self._filter = copy.deepcopy(_copy._filter) # <<<<<<<<<<<<<<
* self._format = copy.deepcopy(_copy._format)
* self._samples = _copy._samples[:]
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___filter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___filter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___filter, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 322; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___filter, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":323
+ /* "pysam/cvcf.pyx":326
* self._info = copy.deepcopy(_copy._info)
* self._filter = copy.deepcopy(_copy._filter)
* self._format = copy.deepcopy(_copy._format) # <<<<<<<<<<<<<<
* self._samples = _copy._samples[:]
* self._sample2column = copy.deepcopy(_copy._sample2column)
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_5, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___format); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___format, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 323; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___format, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":324
+ /* "pysam/cvcf.pyx":327
* self._filter = copy.deepcopy(_copy._filter)
* self._format = copy.deepcopy(_copy._format)
* self._samples = _copy._samples[:] # <<<<<<<<<<<<<<
* self._sample2column = copy.deepcopy(_copy._sample2column)
* self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___samples); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___samples); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_t_5, 0, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_t_5, 0, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 324; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":325
+ /* "pysam/cvcf.pyx":328
* self._format = copy.deepcopy(_copy._format)
* self._samples = _copy._samples[:]
* self._sample2column = copy.deepcopy(_copy._sample2column) # <<<<<<<<<<<<<<
* self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
* self._warn_errors = copy.deepcopy(_copy._warn_errors)
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___sample2column); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___sample2column); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 325; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":326
+ /* "pysam/cvcf.pyx":329
* self._samples = _copy._samples[:]
* self._sample2column = copy.deepcopy(_copy._sample2column)
* self._ignored_errors = copy.deepcopy(_copy._ignored_errors) # <<<<<<<<<<<<<<
* self._warn_errors = copy.deepcopy(_copy._warn_errors)
* self._reference = _copy._reference
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___ignored_errors, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___ignored_errors, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":327
+ /* "pysam/cvcf.pyx":330
* self._sample2column = copy.deepcopy(_copy._sample2column)
* self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
* self._warn_errors = copy.deepcopy(_copy._warn_errors) # <<<<<<<<<<<<<<
* self._reference = _copy._reference
* self._regions = _copy._regions
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__copy); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__deepcopy); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___warn_errors, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 327; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___warn_errors, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":328
+ /* "pysam/cvcf.pyx":331
* self._ignored_errors = copy.deepcopy(_copy._ignored_errors)
* self._warn_errors = copy.deepcopy(_copy._warn_errors)
* self._reference = _copy._reference # <<<<<<<<<<<<<<
* self._regions = _copy._regions
* if reference: self._reference = reference
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___reference); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___reference); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 328; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":329
+ /* "pysam/cvcf.pyx":332
* self._warn_errors = copy.deepcopy(_copy._warn_errors)
* self._reference = _copy._reference
* self._regions = _copy._regions # <<<<<<<<<<<<<<
* if reference: self._reference = reference
* if regions: self._regions = regions
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___regions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v__copy, __pyx_n_s___regions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___regions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 329; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___regions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L5;
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":330
+ /* "pysam/cvcf.pyx":333
* self._reference = _copy._reference
* self._regions = _copy._regions
* if reference: self._reference = reference # <<<<<<<<<<<<<<
* if regions: self._regions = regions
* if leftalign: self._leftalign = leftalign
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_reference); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_7) {
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_v_reference) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 330; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_v_reference) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L6;
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":331
+ /* "pysam/cvcf.pyx":334
* self._regions = _copy._regions
* if reference: self._reference = reference
* if regions: self._regions = regions # <<<<<<<<<<<<<<
* if leftalign: self._leftalign = leftalign
* self._lines = lines
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_regions); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_regions); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_7) {
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___regions, __pyx_v_regions) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 331; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___regions, __pyx_v_regions) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L7;
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":332
+ /* "pysam/cvcf.pyx":335
* if reference: self._reference = reference
* if regions: self._regions = regions
* if leftalign: self._leftalign = leftalign # <<<<<<<<<<<<<<
* self._lines = lines
*
*/
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_leftalign); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_v_leftalign); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_7) {
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___leftalign, __pyx_v_leftalign) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 332; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___leftalign, __pyx_v_leftalign) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L8;
}
__pyx_L8:;
- /* "pysam/cvcf.pyx":333
+ /* "pysam/cvcf.pyx":336
* if regions: self._regions = regions
* if leftalign: self._leftalign = leftalign
* self._lines = lines # <<<<<<<<<<<<<<
*
* def error(self,line,error,opt=None):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lines, __pyx_v_lines) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 333; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lines, __pyx_v_lines) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -5875,15 +6025,14 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObjec
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_error = 0;
PyObject *__pyx_v_opt = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("error (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__error,&__pyx_n_s__opt,0};
PyObject* values[4] = {0,0,0,0};
- /* "pysam/cvcf.pyx":335
+ /* "pysam/cvcf.pyx":338
* self._lines = lines
*
* def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
@@ -5905,20 +6054,17 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObjec
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__error)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (kw_args > 0) {
@@ -5927,7 +6073,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObjec
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "error") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "error") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -5946,7 +6092,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_3error(PyObject *__pyx_self, PyObjec
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("error", 0, 3, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.error", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -5974,16 +6120,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("error", 0);
- /* "pysam/cvcf.pyx":336
+ /* "pysam/cvcf.pyx":339
*
* def error(self,line,error,opt=None):
* if error in self._ignored_errors: return # <<<<<<<<<<<<<<
* errorlabel, errorstring = self._errors[error].split(':')
* if opt: errorstring = errorstring % opt
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = ((PySequence_Contains(__pyx_t_1, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 336; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_1, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
@@ -5993,49 +6139,57 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":337
+ /* "pysam/cvcf.pyx":340
* def error(self,line,error,opt=None):
* if error in self._ignored_errors: return
* errorlabel, errorstring = self._errors[error].split(':') # <<<<<<<<<<<<<<
* if opt: errorstring = errorstring % opt
* errwarn = ["Error","Warning"][error in self._warn_errors]
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___errors); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetItem(__pyx_t_1, __pyx_v_error); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_t_1, __pyx_v_error); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_23), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_23), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if ((likely(PyTuple_CheckExact(__pyx_t_3))) || (PyList_CheckExact(__pyx_t_3))) {
PyObject* sequence = __pyx_t_3;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_4 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_4 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_4);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_4);
+ #endif
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_5 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetIter(__pyx_t_3); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_6 = Py_TYPE(__pyx_t_5)->tp_iternext;
@@ -6043,14 +6197,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
__Pyx_GOTREF(__pyx_t_1);
index = 1; __pyx_t_4 = __pyx_t_6(__pyx_t_5); if (unlikely(!__pyx_t_4)) goto __pyx_L4_unpacking_failed;
__Pyx_GOTREF(__pyx_t_4);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_5), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = NULL;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
goto __pyx_L5_unpacking_done;
__pyx_L4_unpacking_failed:;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L5_unpacking_done:;
}
__pyx_v_errorlabel = __pyx_t_1;
@@ -6058,16 +6213,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
__pyx_v_errorstring = __pyx_t_4;
__pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":338
+ /* "pysam/cvcf.pyx":341
* if error in self._ignored_errors: return
* errorlabel, errorstring = self._errors[error].split(':')
* if opt: errorstring = errorstring % opt # <<<<<<<<<<<<<<
* errwarn = ["Error","Warning"][error in self._warn_errors]
* errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
*/
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_opt); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_v_opt); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_2) {
- __pyx_t_3 = PyNumber_Remainder(__pyx_v_errorstring, __pyx_v_opt); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Remainder(__pyx_v_errorstring, __pyx_v_opt); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_v_errorstring);
__pyx_v_errorstring = __pyx_t_3;
@@ -6076,14 +6231,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":339
+ /* "pysam/cvcf.pyx":342
* errorlabel, errorstring = self._errors[error].split(':')
* if opt: errorstring = errorstring % opt
* errwarn = ["Error","Warning"][error in self._warn_errors] # <<<<<<<<<<<<<<
* errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
* if error in self._warn_errors: return
*/
- __pyx_t_3 = PyList_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyList_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Error));
PyList_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_n_s__Error));
@@ -6091,26 +6246,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
__Pyx_INCREF(((PyObject *)__pyx_n_s__Warning));
PyList_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__Warning));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__Warning));
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = ((PySequence_Contains(__pyx_t_4, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_4, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetItemInt_List(((PyObject *)__pyx_t_3), __pyx_t_2, sizeof(int), __Pyx_PyBool_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 339; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetItemInt_List(((PyObject *)__pyx_t_3), __pyx_t_2, sizeof(int), __Pyx_PyBool_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__pyx_v_errwarn = __pyx_t_4;
__pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":340
+ /* "pysam/cvcf.pyx":343
* if opt: errorstring = errorstring % opt
* errwarn = ["Error","Warning"][error in self._warn_errors]
* errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring) # <<<<<<<<<<<<<<
* if error in self._warn_errors: return
* raise ValueError(errorstring)
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(5); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
@@ -6127,26 +6282,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
PyTuple_SET_ITEM(__pyx_t_3, 4, __pyx_v_errorstring);
__Pyx_GIVEREF(__pyx_v_errorstring);
__pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_24), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_24), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_errorstring, ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_InPlaceAdd(__pyx_v_errorstring, ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 343; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_v_errorstring);
__pyx_v_errorstring = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":341
+ /* "pysam/cvcf.pyx":344
* errwarn = ["Error","Warning"][error in self._warn_errors]
* errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
* if error in self._warn_errors: return # <<<<<<<<<<<<<<
* raise ValueError(errorstring)
*
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = ((PySequence_Contains(__pyx_t_3, __pyx_v_error))); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 341; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = (__Pyx_PySequence_Contains(__pyx_v_error, __pyx_t_3, Py_EQ)); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
@@ -6156,24 +6311,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":342
+ /* "pysam/cvcf.pyx":345
* errorstring += " in line %s: '%s'\n%s %s: %s\n" % (self._lineno,line,errwarn,errorlabel,errorstring)
* if error in self._warn_errors: return
* raise ValueError(errorstring) # <<<<<<<<<<<<<<
*
* def parse_format(self,line,format,filter=False):
*/
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_errorstring);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_errorstring);
__Pyx_GIVEREF(__pyx_v_errorstring);
- __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
__Pyx_Raise(__pyx_t_4, 0, 0, 0);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 342; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -6193,7 +6348,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx
return __pyx_r;
}
-/* "pysam/cvcf.pyx":344
+/* "pysam/cvcf.pyx":347
* raise ValueError(errorstring)
*
* def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
@@ -6210,7 +6365,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__defaults__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_self)->__pyx_arg_filter);
PyTuple_SET_ITEM(__pyx_t_1, 0, __Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_self)->__pyx_arg_filter);
@@ -6239,12 +6394,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_5parse_format(PyObject *__pyx_self,
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_format = 0;
PyObject *__pyx_v_filter = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__format,&__pyx_n_s__filter,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_format (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__format,&__pyx_n_s__filter,0};
PyObject* values[4] = {0,0,0,0};
__pyx_defaults1 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_self);
values[3] = __pyx_dynamic_args->__pyx_arg_filter;
@@ -6262,20 +6416,17 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_5parse_format(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (kw_args > 0) {
@@ -6284,7 +6435,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_5parse_format(PyObject *__pyx_self,
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_format") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_format") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -6303,7 +6454,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_5parse_format(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_format", 0, 3, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -6345,51 +6496,50 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_RefNannySetupContext("parse_format", 0);
__Pyx_INCREF(__pyx_v_format);
- /* "pysam/cvcf.pyx":345
+ /* "pysam/cvcf.pyx":348
*
* def parse_format(self,line,format,filter=False):
* if self._version == 40: # <<<<<<<<<<<<<<
* if not format.startswith('<'):
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 345; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":346
+ /* "pysam/cvcf.pyx":349
* def parse_format(self,line,format,filter=False):
* if self._version == 40:
* if not format.startswith('<'): # <<<<<<<<<<<<<<
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format = "<"+format
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_26), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_26), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":347
+ /* "pysam/cvcf.pyx":350
* if self._version == 40:
* if not format.startswith('<'):
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS) # <<<<<<<<<<<<<<
* format = "<"+format
* if not format.endswith('>'):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_27); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_27); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
@@ -6397,20 +6547,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":348
+ /* "pysam/cvcf.pyx":351
* if not format.startswith('<'):
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format = "<"+format # <<<<<<<<<<<<<<
* if not format.endswith('>'):
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
*/
- __pyx_t_2 = PyNumber_Add(((PyObject *)__pyx_kp_s_25), __pyx_v_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 348; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(((PyObject *)__pyx_kp_s_25), __pyx_v_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_format);
__pyx_v_format = __pyx_t_2;
@@ -6419,35 +6569,35 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":349
+ /* "pysam/cvcf.pyx":352
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format = "<"+format
* if not format.endswith('>'): # <<<<<<<<<<<<<<
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format += ">"
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__endswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__endswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_29), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_29), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_3 = (!__pyx_t_4);
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":350
+ /* "pysam/cvcf.pyx":353
* format = "<"+format
* if not format.endswith('>'):
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS) # <<<<<<<<<<<<<<
* format += ">"
* format = format[1:-1]
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_27); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_27); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
@@ -6455,20 +6605,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":351
+ /* "pysam/cvcf.pyx":354
* if not format.endswith('>'):
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format += ">" # <<<<<<<<<<<<<<
* format = format[1:-1]
* data = {'id':None,'number':None,'type':None,'descr':None}
*/
- __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_format, ((PyObject *)__pyx_kp_s_28)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_format, ((PyObject *)__pyx_kp_s_28)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 354; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_format);
__pyx_v_format = __pyx_t_2;
@@ -6477,14 +6627,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":352
+ /* "pysam/cvcf.pyx":355
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format += ">"
* format = format[1:-1] # <<<<<<<<<<<<<<
* data = {'id':None,'number':None,'type':None,'descr':None}
* idx = 0
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_format, 1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_format, 1, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_format);
__pyx_v_format = __pyx_t_2;
@@ -6493,23 +6643,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":353
+ /* "pysam/cvcf.pyx":356
* format += ">"
* format = format[1:-1]
* data = {'id':None,'number':None,'type':None,'descr':None} # <<<<<<<<<<<<<<
* idx = 0
* while len(format.strip())>0:
*/
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__id), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__number), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__type), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__descr), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_data = __pyx_t_2;
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__id), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__number), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__type), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_2, ((PyObject *)__pyx_n_s__descr), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_data = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":354
+ /* "pysam/cvcf.pyx":357
* format = format[1:-1]
* data = {'id':None,'number':None,'type':None,'descr':None}
* idx = 0 # <<<<<<<<<<<<<<
@@ -6519,7 +6669,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_INCREF(__pyx_int_0);
__pyx_v_idx = __pyx_int_0;
- /* "pysam/cvcf.pyx":355
+ /* "pysam/cvcf.pyx":358
* data = {'id':None,'number':None,'type':None,'descr':None}
* idx = 0
* while len(format.strip())>0: # <<<<<<<<<<<<<<
@@ -6527,57 +6677,57 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
* first, rest = elts[0], ','.join(elts[1:])
*/
while (1) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_6 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 355; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (__pyx_t_6 > 0);
if (!__pyx_t_3) break;
- /* "pysam/cvcf.pyx":356
+ /* "pysam/cvcf.pyx":359
* idx = 0
* while len(format.strip())>0:
* elts = format.strip().split(',') # <<<<<<<<<<<<<<
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_30), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_30), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_v_elts);
__pyx_v_elts = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":357
+ /* "pysam/cvcf.pyx":360
* while len(format.strip())>0:
* elts = format.strip().split(',')
* first, rest = elts[0], ','.join(elts[1:]) # <<<<<<<<<<<<<<
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PySequence_GetSlice(__pyx_v_elts, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PySequence_GetSlice(__pyx_v_elts, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -6588,50 +6738,47 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_v_rest = __pyx_t_5;
__pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":358
+ /* "pysam/cvcf.pyx":361
* elts = format.strip().split(',')
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<<
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_31), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_31), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (!__pyx_t_3) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_33), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_33), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_4) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_34), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_34), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__find); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_35), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_35), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = __pyx_t_8;
} else {
@@ -6643,26 +6790,25 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":359
+ /* "pysam/cvcf.pyx":362
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS) # <<<<<<<<<<<<<<
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_4) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_36); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_36); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
@@ -6670,7 +6816,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -6679,23 +6825,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L9:;
- /* "pysam/cvcf.pyx":360
+ /* "pysam/cvcf.pyx":363
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
*/
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_4) {
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
@@ -6703,7 +6848,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -6712,14 +6857,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L10:;
- /* "pysam/cvcf.pyx":361
+ /* "pysam/cvcf.pyx":364
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first # <<<<<<<<<<<<<<
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
*/
- __pyx_t_2 = PyList_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_38));
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_38));
@@ -6733,10 +6878,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_INCREF(((PyObject *)__pyx_kp_s_41));
PyList_SET_ITEM(__pyx_t_2, 3, ((PyObject *)__pyx_kp_s_41));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_41));
- __pyx_t_7 = PyObject_GetItem(((PyObject *)__pyx_t_2), __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(((PyObject *)__pyx_t_2), __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Add(__pyx_t_7, __pyx_v_first); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_7, __pyx_v_first); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_v_first);
@@ -6746,145 +6891,145 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L8:;
- /* "pysam/cvcf.pyx":362
+ /* "pysam/cvcf.pyx":365
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<<
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_42), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_42), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_4) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_43), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_43), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_2, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_2, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L11;
}
- /* "pysam/cvcf.pyx":363
+ /* "pysam/cvcf.pyx":366
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<<
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='):
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_44), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_44), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_45), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_45), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_7, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_7, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number), __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L11;
}
- /* "pysam/cvcf.pyx":364
+ /* "pysam/cvcf.pyx":367
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<<
* elif first.startswith('Description='):
* elts = format.split('"')
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_46), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_46), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_4) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_47), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_2, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_t_2, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L11;
}
- /* "pysam/cvcf.pyx":365
+ /* "pysam/cvcf.pyx":368
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='): # <<<<<<<<<<<<<<
* elts = format.split('"')
* if len(elts)<3:
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_48), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_48), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":366
+ /* "pysam/cvcf.pyx":369
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='):
* elts = format.split('"') # <<<<<<<<<<<<<<
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES)
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_format, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_49), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_49), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_elts);
__pyx_v_elts = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":367
+ /* "pysam/cvcf.pyx":370
* elif first.startswith('Description='):
* elts = format.split('"')
* if len(elts)<3: # <<<<<<<<<<<<<<
* self.error(line,self.FORMAT_MISSING_QUOTES)
* elts = first.split('=') + [rest]
*/
- __pyx_t_6 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_6 < 3);
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":368
+ /* "pysam/cvcf.pyx":371
* elts = format.split('"')
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES) # <<<<<<<<<<<<<<
* elts = first.split('=') + [rest]
* data['descr'] = elts[1]
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_50); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_50); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
@@ -6892,30 +7037,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":369
+ /* "pysam/cvcf.pyx":372
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES)
* elts = first.split('=') + [rest] # <<<<<<<<<<<<<<
* data['descr'] = elts[1]
* rest = '"'.join(elts[2:])
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_first, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_51), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_51), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_rest);
PyList_SET_ITEM(__pyx_t_2, 0, __pyx_v_rest);
__Pyx_GIVEREF(__pyx_v_rest);
- __pyx_t_7 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_5, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -6926,35 +7071,35 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L12:;
- /* "pysam/cvcf.pyx":370
+ /* "pysam/cvcf.pyx":373
* self.error(line,self.FORMAT_MISSING_QUOTES)
* elts = first.split('=') + [rest]
* data['descr'] = elts[1] # <<<<<<<<<<<<<<
* rest = '"'.join(elts[2:])
* if rest.startswith(','): rest = rest[1:]
*/
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 370; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr), __pyx_t_7) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 373; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":371
+ /* "pysam/cvcf.pyx":374
* elts = first.split('=') + [rest]
* data['descr'] = elts[1]
* rest = '"'.join(elts[2:]) # <<<<<<<<<<<<<<
* if rest.startswith(','): rest = rest[1:]
* else:
*/
- __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_32), __pyx_n_s__join); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_32), __pyx_n_s__join); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_elts, 2, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_elts, 2, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 371; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
@@ -6962,22 +7107,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_v_rest = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":372
+ /* "pysam/cvcf.pyx":375
* data['descr'] = elts[1]
* rest = '"'.join(elts[2:])
* if rest.startswith(','): rest = rest[1:] # <<<<<<<<<<<<<<
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_rest, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_rest, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_52), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_52), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_4) {
- __pyx_t_5 = __Pyx_PySequence_GetSlice(__pyx_v_rest, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PySequence_GetSlice(__pyx_v_rest, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_v_rest);
__pyx_v_rest = __pyx_t_5;
@@ -6989,18 +7134,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":374
+ /* "pysam/cvcf.pyx":377
* if rest.startswith(','): rest = rest[1:]
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* format = rest
* idx += 1
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
@@ -7008,7 +7153,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 374; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -7016,7 +7161,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L11:;
- /* "pysam/cvcf.pyx":375
+ /* "pysam/cvcf.pyx":378
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* format = rest # <<<<<<<<<<<<<<
@@ -7027,31 +7172,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_DECREF(__pyx_v_format);
__pyx_v_format = __pyx_v_rest;
- /* "pysam/cvcf.pyx":376
+ /* "pysam/cvcf.pyx":379
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* format = rest
* idx += 1 # <<<<<<<<<<<<<<
* if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
* if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_idx, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 376; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_InPlaceAdd(__pyx_v_idx, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_idx);
__pyx_v_idx = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":377
+ /* "pysam/cvcf.pyx":380
* format = rest
* idx += 1
* if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings # <<<<<<<<<<<<<<
* if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* if 'descr' not in data:
*/
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 377; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 380; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_9 = __pyx_t_3;
} else {
@@ -7066,24 +7210,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_L14:;
}
- /* "pysam/cvcf.pyx":378
+ /* "pysam/cvcf.pyx":381
* idx += 1
* if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
* if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* if 'descr' not in data:
* # missing description
*/
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = (!__pyx_t_9);
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
@@ -7091,7 +7235,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 378; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
@@ -7100,28 +7244,28 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L15:;
- /* "pysam/cvcf.pyx":379
+ /* "pysam/cvcf.pyx":382
* if filter and idx==1: idx=3 # skip number and type fields for FILTER format strings
* if not data['id']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* if 'descr' not in data: # <<<<<<<<<<<<<<
* # missing description
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_4 = (__Pyx_NegateNonNeg(PyDict_Contains(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)))); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 379; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = (__Pyx_PyDict_Contains(((PyObject *)__pyx_n_s__descr), ((PyObject *)__pyx_v_data), Py_NE)); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":381
+ /* "pysam/cvcf.pyx":384
* if 'descr' not in data:
* # missing description
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* data['descr'] = ""
* if not data['type'] and not data['number']:
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
@@ -7129,40 +7273,40 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 381; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":382
+ /* "pysam/cvcf.pyx":385
* # missing description
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* data['descr'] = "" # <<<<<<<<<<<<<<
* if not data['type'] and not data['number']:
* # fine, ##filter format
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr), ((PyObject *)__pyx_kp_s_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr), ((PyObject *)__pyx_kp_s_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L16;
}
__pyx_L16:;
- /* "pysam/cvcf.pyx":383
+ /* "pysam/cvcf.pyx":386
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* data['descr'] = ""
* if not data['type'] and not data['number']: # <<<<<<<<<<<<<<
* # fine, ##filter format
* return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
*/
- __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = (!__pyx_t_4);
if (__pyx_t_9) {
- __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 383; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_3 = (!__pyx_t_4);
__pyx_t_4 = __pyx_t_3;
@@ -7171,7 +7315,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":385
+ /* "pysam/cvcf.pyx":388
* if not data['type'] and not data['number']:
* # fine, ##filter format
* return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.') # <<<<<<<<<<<<<<
@@ -7179,15 +7323,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = PyTuple_New(6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
@@ -7207,7 +7351,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_t_2 = 0;
__pyx_t_7 = 0;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
@@ -7218,36 +7362,46 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L17:;
- /* "pysam/cvcf.pyx":386
+ /* "pysam/cvcf.pyx":389
* # fine, ##filter format
* return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
* if not data['type'] in ["Integer","Float","Character","String","Flag"]: # <<<<<<<<<<<<<<
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* # I would like a missing-value field, but it isn't there
*/
- __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (!((int)__pyx_t_4)) {
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_3 = ((int)__pyx_t_9);
} else {
__pyx_t_3 = ((int)__pyx_t_4);
}
if (!__pyx_t_3) {
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Character), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Character), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_9 = ((int)__pyx_t_4);
} else {
__pyx_t_9 = __pyx_t_3;
}
if (!__pyx_t_9) {
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__String), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__String), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_4 = ((int)__pyx_t_3);
} else {
__pyx_t_4 = __pyx_t_9;
}
if (!__pyx_t_4) {
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely((__pyx_t_9 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_3 = ((int)__pyx_t_9);
} else {
__pyx_t_3 = __pyx_t_4;
@@ -7256,18 +7410,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":387
+ /* "pysam/cvcf.pyx":390
* return FORMAT(data['id'],self.NT_NUMBER,0,"Flag",data['descr'],'.')
* if not data['type'] in ["Integer","Float","Character","String","Flag"]:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* # I would like a missing-value field, but it isn't there
* if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
@@ -7275,7 +7429,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
@@ -7284,18 +7438,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L18:;
- /* "pysam/cvcf.pyx":389
+ /* "pysam/cvcf.pyx":392
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* # I would like a missing-value field, but it isn't there
* if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value # <<<<<<<<<<<<<<
* else: data['missing'] = '.'
* if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (!((int)__pyx_t_4)) {
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = ((int)__pyx_t_3);
} else {
__pyx_t_9 = ((int)__pyx_t_4);
@@ -7303,40 +7461,40 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_4 = __pyx_t_9;
if (__pyx_t_4) {
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 389; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing), Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L19;
}
/*else*/ {
- /* "pysam/cvcf.pyx":390
+ /* "pysam/cvcf.pyx":393
* # I would like a missing-value field, but it isn't there
* if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
* else: data['missing'] = '.' # <<<<<<<<<<<<<<
* if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* try:
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing), ((PyObject *)__pyx_kp_s_9)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 390; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing), ((PyObject *)__pyx_kp_s_9)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L19:;
- /* "pysam/cvcf.pyx":391
+ /* "pysam/cvcf.pyx":394
* if data['type'] in ['Integer','Float']: data['missing'] = None # Do NOT use arbitrary int/float as missing value
* else: data['missing'] = '.'
* if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* try:
* n = int(data['number'])
*/
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_9 = (!__pyx_t_4);
if (__pyx_t_9) {
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
@@ -7344,7 +7502,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 391; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -7353,7 +7511,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
__pyx_L20:;
- /* "pysam/cvcf.pyx":392
+ /* "pysam/cvcf.pyx":395
* else: data['missing'] = '.'
* if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* try: # <<<<<<<<<<<<<<
@@ -7367,34 +7525,34 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_XGOTREF(__pyx_t_13);
/*try:*/ {
- /* "pysam/cvcf.pyx":393
+ /* "pysam/cvcf.pyx":396
* if not data['number']: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* try:
* n = int(data['number']) # <<<<<<<<<<<<<<
* t = self.NT_NUMBER
* except ValueError:
*/
- __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
+ __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 393; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
+ __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_n = __pyx_t_5;
__pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":394
+ /* "pysam/cvcf.pyx":397
* try:
* n = int(data['number'])
* t = self.NT_NUMBER # <<<<<<<<<<<<<<
* except ValueError:
* n = -1
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L21_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_v_t = __pyx_t_5;
__pyx_t_5 = 0;
@@ -7410,7 +7568,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":395
+ /* "pysam/cvcf.pyx":398
* n = int(data['number'])
* t = self.NT_NUMBER
* except ValueError: # <<<<<<<<<<<<<<
@@ -7420,12 +7578,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_t_14 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_14) {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_1, &__pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ if (__Pyx_GetException(&__pyx_t_5, &__pyx_t_1, &__pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_10);
- /* "pysam/cvcf.pyx":396
+ /* "pysam/cvcf.pyx":399
* t = self.NT_NUMBER
* except ValueError:
* n = -1 # <<<<<<<<<<<<<<
@@ -7436,39 +7594,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_XDECREF(__pyx_v_n);
__pyx_v_n = __pyx_int_neg_1;
- /* "pysam/cvcf.pyx":397
+ /* "pysam/cvcf.pyx":400
* except ValueError:
* n = -1
* if data['number'] == '.': t = self.NT_UNKNOWN # <<<<<<<<<<<<<<
* elif data['number'] == '#alleles': t = self.NT_ALLELES
* elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":398
+ /* "pysam/cvcf.pyx":401
* n = -1
* if data['number'] == '.': t = self.NT_UNKNOWN
* elif data['number'] == '#alleles': t = self.NT_ALLELES # <<<<<<<<<<<<<<
* elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
* elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_53), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_53), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
__pyx_v_t = __pyx_t_7;
@@ -7476,39 +7638,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":399
+ /* "pysam/cvcf.pyx":402
* if data['number'] == '.': t = self.NT_UNKNOWN
* elif data['number'] == '#alleles': t = self.NT_ALLELES
* elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES # <<<<<<<<<<<<<<
* elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_54), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_54), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":400
+ /* "pysam/cvcf.pyx":403
* elif data['number'] == '#alleles': t = self.NT_ALLELES
* elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
* elif data['number'] == '#genotypes': t = self.NT_GENOTYPES # <<<<<<<<<<<<<<
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_55), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_55), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 400; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 403; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
__pyx_v_t = __pyx_t_7;
@@ -7516,39 +7682,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":401
+ /* "pysam/cvcf.pyx":404
* elif data['number'] == '#nonref_alleles': t = self.NT_NR_ALLELES
* elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # <<<<<<<<<<<<<<
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
* # abbreviations added in VCF version v4.1
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 401; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":402
+ /* "pysam/cvcf.pyx":405
* elif data['number'] == '#genotypes': t = self.NT_GENOTYPES
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES # <<<<<<<<<<<<<<
* # abbreviations added in VCF version v4.1
* elif data['number'] == 'A': t = self.NT_ALLELES
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_kp_s_56), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_kp_s_56), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 402; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
__pyx_v_t = __pyx_t_7;
@@ -7556,39 +7726,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":404
+ /* "pysam/cvcf.pyx":407
* elif data['number'] == '#phased_genotypes': t = self.NT_PHASED_GENOTYPES
* # abbreviations added in VCF version v4.1
* elif data['number'] == 'A': t = self.NT_ALLELES # <<<<<<<<<<<<<<
* elif data['number'] == 'G': t = self.NT_GENOTYPES
* else:
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_n_s__A), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_n_s__A), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 404; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_t);
- __pyx_v_t = __pyx_t_7;
- __pyx_t_7 = 0;
+ __pyx_v_t = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L31;
}
- /* "pysam/cvcf.pyx":405
+ /* "pysam/cvcf.pyx":408
* # abbreviations added in VCF version v4.1
* elif data['number'] == 'A': t = self.NT_ALLELES
* elif data['number'] == 'G': t = self.NT_GENOTYPES # <<<<<<<<<<<<<<
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_7, ((PyObject *)__pyx_n_s__G), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__number)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__G), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_9) {
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 405; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 408; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_t);
__pyx_v_t = __pyx_t_7;
@@ -7597,18 +7771,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":407
+ /* "pysam/cvcf.pyx":410
* elif data['number'] == 'G': t = self.NT_GENOTYPES
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* # if number is 0 - type must be Flag
* if n == 0 and data['type'] != 'Flag':
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_37); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = PyTuple_New(2); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_15 = PyTuple_New(2); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_15, 0, __pyx_v_line);
@@ -7616,7 +7790,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_15, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 407; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L23_except_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
@@ -7642,66 +7816,67 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__pyx_L28_try_end:;
}
- /* "pysam/cvcf.pyx":409
+ /* "pysam/cvcf.pyx":412
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* # if number is 0 - type must be Flag
* if n == 0 and data['type'] != 'Flag': # <<<<<<<<<<<<<<
* self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
* # force type 'Flag' if no number
*/
- __pyx_t_10 = PyObject_RichCompare(__pyx_v_n, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_v_n, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_9) {
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_n_s__Flag), Py_NE); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 409; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_n_s__Flag), Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = __pyx_t_4;
} else {
__pyx_t_3 = __pyx_t_9;
}
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":410
+ /* "pysam/cvcf.pyx":413
* # if number is 0 - type must be Flag
* if n == 0 and data['type'] != 'Flag':
* self.error( line, self.ZERO_FOR_NON_FLAG_FIELD) # <<<<<<<<<<<<<<
* # force type 'Flag' if no number
* data['type'] = 'Flag'
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_57); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_57); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 410; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":412
+ /* "pysam/cvcf.pyx":415
* self.error( line, self.ZERO_FOR_NON_FLAG_FIELD)
* # force type 'Flag' if no number
* data['type'] = 'Flag' # <<<<<<<<<<<<<<
*
* return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type), ((PyObject *)__pyx_n_s__Flag)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 412; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type), ((PyObject *)__pyx_n_s__Flag)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 415; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L32;
}
__pyx_L32:;
- /* "pysam/cvcf.pyx":414
+ /* "pysam/cvcf.pyx":417
* data['type'] = 'Flag'
*
* return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing']) # <<<<<<<<<<<<<<
@@ -7709,18 +7884,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
* def format_format( self, fmt, filter=False ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
- if (unlikely(!__pyx_v_t)) { __Pyx_RaiseUnboundLocalError("t"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_5);
+ if (unlikely(!__pyx_v_t)) { __Pyx_RaiseUnboundLocalError("t"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_1 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__type)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__descr)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_15 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing)); if (!__pyx_t_15) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_data), ((PyObject *)__pyx_n_s__missing)); if (!__pyx_t_15) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
@@ -7730,19 +7905,19 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
__Pyx_INCREF(__pyx_v_n);
PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_v_n);
__Pyx_GIVEREF(__pyx_v_n);
- PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_7, 3, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_7, 4, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_7, 5, __pyx_t_15);
__Pyx_GIVEREF(__pyx_t_15);
__pyx_t_5 = 0;
- __pyx_t_10 = 0;
+ __pyx_t_1 = 0;
__pyx_t_2 = 0;
__pyx_t_15 = 0;
- __pyx_t_15 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 414; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__pyx_r = __pyx_t_15;
__pyx_t_15 = 0;
@@ -7773,7 +7948,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject
return __pyx_r;
}
-/* "pysam/cvcf.pyx":416
+/* "pysam/cvcf.pyx":419
* return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
*
* def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
@@ -7790,7 +7965,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__defaults__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_self)->__pyx_arg_filter);
PyTuple_SET_ITEM(__pyx_t_1, 0, __Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_self)->__pyx_arg_filter);
@@ -7818,12 +7993,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_7format_format(PyObject *__pyx_self,
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_fmt = 0;
PyObject *__pyx_v_filter = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fmt,&__pyx_n_s__filter,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("format_format (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__fmt,&__pyx_n_s__filter,0};
PyObject* values[3] = {0,0,0};
__pyx_defaults2 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_self);
values[2] = __pyx_dynamic_args->__pyx_arg_filter;
@@ -7840,14 +8014,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_7format_format(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fmt);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fmt)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (kw_args > 0) {
@@ -7856,7 +8028,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_7format_format(PyObject *__pyx_self,
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "format_format") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "format_format") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -7873,7 +8045,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_7format_format(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("format_format", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.format_format", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -7910,16 +8082,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("format_format", 0);
- /* "pysam/cvcf.pyx":417
+ /* "pysam/cvcf.pyx":420
*
* def format_format( self, fmt, filter=False ):
* values = [('ID',fmt.id)] # <<<<<<<<<<<<<<
* if fmt.number != None and not filter:
* if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__id); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_n_s__ID));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__ID));
@@ -7927,30 +8099,29 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 417; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
- __pyx_v_values = __pyx_t_1;
+ __pyx_v_values = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":418
+ /* "pysam/cvcf.pyx":421
* def format_format( self, fmt, filter=False ):
* values = [('ID',fmt.id)]
* if fmt.number != None and not filter: # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
* elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 418; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_v_filter); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (!__pyx_t_4);
__pyx_t_4 = __pyx_t_5;
} else {
@@ -7958,22 +8129,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
}
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":419
+ /* "pysam/cvcf.pyx":422
* values = [('ID',fmt.id)]
* if fmt.number != None and not filter:
* if fmt.numbertype == self.NT_UNKNOWN: nmb = "." # <<<<<<<<<<<<<<
* elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
* elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_4) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
@@ -7981,32 +8151,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":420
+ /* "pysam/cvcf.pyx":423
* if fmt.number != None and not filter:
* if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
* elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number) # <<<<<<<<<<<<<<
* elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
* elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_nmb = __pyx_t_2;
@@ -8014,22 +8183,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":421
+ /* "pysam/cvcf.pyx":424
* if fmt.numbertype == self.NT_UNKNOWN: nmb = "."
* elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
* elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles" # <<<<<<<<<<<<<<
* elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
* elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 421; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_4) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_53));
@@ -8037,22 +8205,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":422
+ /* "pysam/cvcf.pyx":425
* elif fmt.numbertype == self.NT_NUMBER: nmb = str(fmt.number)
* elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
* elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles" # <<<<<<<<<<<<<<
* elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
* elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_54));
@@ -8060,22 +8227,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":423
+ /* "pysam/cvcf.pyx":426
* elif fmt.numbertype == self.NT_ALLELES: nmb = "#alleles"
* elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
* elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes" # <<<<<<<<<<<<<<
* elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
* else:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_2, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 423; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_4) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_55));
@@ -8083,22 +8249,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":424
+ /* "pysam/cvcf.pyx":427
* elif fmt.numbertype == self.NT_NR_ALLELES: nmb = "#nonref_alleles"
* elif fmt.numbertype == self.NT_GENOTYPES: nmb = "#genotypes"
* elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes" # <<<<<<<<<<<<<<
* else:
* raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_6, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 424; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_56));
@@ -8107,40 +8272,40 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
}
/*else*/ {
- /* "pysam/cvcf.pyx":426
+ /* "pysam/cvcf.pyx":429
* elif fmt.numbertype == self.NT_PHASED_GENOTYPES: nmb = "#phased_genotypes"
* else:
* raise ValueError("Unknown number type encountered: %s" % fmt.numbertype) # <<<<<<<<<<<<<<
* values.append( ('Number',nmb) )
* values.append( ('Type', fmt.type) )
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_58), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_58), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 426; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":427
+ /* "pysam/cvcf.pyx":430
* else:
* raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
* values.append( ('Number',nmb) ) # <<<<<<<<<<<<<<
* values.append( ('Type', fmt.type) )
* values.append( ('Description', '"' + fmt.description + '"') )
*/
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Number));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Number));
@@ -8148,19 +8313,19 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_nmb);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_nmb);
__Pyx_GIVEREF(__pyx_v_nmb);
- __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":428
+ /* "pysam/cvcf.pyx":431
* raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
* values.append( ('Number',nmb) )
* values.append( ('Type', fmt.type) ) # <<<<<<<<<<<<<<
* values.append( ('Description', '"' + fmt.description + '"') )
* if self._version == 33:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__type); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__type); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Type));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__Type));
@@ -8168,28 +8333,28 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 428; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":429
+ /* "pysam/cvcf.pyx":432
* values.append( ('Number',nmb) )
* values.append( ('Type', fmt.type) )
* values.append( ('Description', '"' + fmt.description + '"') ) # <<<<<<<<<<<<<<
* if self._version == 33:
* format = ",".join([v for k,v in values])
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__description); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__description); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyNumber_Add(((PyObject *)__pyx_kp_s_32), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(((PyObject *)__pyx_kp_s_32), __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Add(__pyx_t_1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__Description));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__Description));
@@ -8197,65 +8362,76 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 429; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyList_Append(__pyx_v_values, ((PyObject *)__pyx_t_1)); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 432; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":430
+ /* "pysam/cvcf.pyx":433
* values.append( ('Type', fmt.type) )
* values.append( ('Description', '"' + fmt.description + '"') )
* if self._version == 33: # <<<<<<<<<<<<<<
* format = ",".join([v for k,v in values])
* else:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 430; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":431
+ /* "pysam/cvcf.pyx":434
* values.append( ('Description', '"' + fmt.description + '"') )
* if self._version == 33:
* format = ",".join([v for k,v in values]) # <<<<<<<<<<<<<<
* else:
* format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_6 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_6); __pyx_t_8 = 0;
for (;;) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_6, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_11 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_10 = PyList_GET_ITEM(sequence, 0);
__pyx_t_11 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_10);
__Pyx_INCREF(__pyx_t_11);
+ #else
+ __pyx_t_10 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_11 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ #endif
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
@@ -8263,14 +8439,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
__Pyx_GOTREF(__pyx_t_10);
index = 1; __pyx_t_11 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_11)) goto __pyx_L8_unpacking_failed;
__Pyx_GOTREF(__pyx_t_11);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
goto __pyx_L9_unpacking_done;
__pyx_L8_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L9_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_k);
@@ -8279,16 +8456,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
__Pyx_XDECREF(__pyx_v_v);
__pyx_v_v = __pyx_t_11;
__pyx_t_11 = 0;
- if (unlikely(PyList_Append(__pyx_t_1, (PyObject*)__pyx_v_v))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_1, (PyObject*)__pyx_v_v))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(((PyObject *)__pyx_t_1));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 434; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
@@ -8298,46 +8475,58 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
}
/*else*/ {
- /* "pysam/cvcf.pyx":433
+ /* "pysam/cvcf.pyx":436
* format = ",".join([v for k,v in values])
* else:
* format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">" # <<<<<<<<<<<<<<
* return format
*
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyList_New(0); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__pyx_t_2 = ((PyObject *)__pyx_v_values); __Pyx_INCREF(__pyx_t_2); __pyx_t_8 = 0;
for (;;) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_11 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_11 = PyList_GET_ITEM(sequence, 0);
__pyx_t_10 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_11);
__Pyx_INCREF(__pyx_t_10);
+ #else
+ __pyx_t_11 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_11);
+ __pyx_t_10 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ #endif
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_13 = Py_TYPE(__pyx_t_12)->tp_iternext;
@@ -8345,14 +8534,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
__Pyx_GOTREF(__pyx_t_11);
index = 1; __pyx_t_10 = __pyx_t_13(__pyx_t_12); if (unlikely(!__pyx_t_10)) goto __pyx_L12_unpacking_failed;
__Pyx_GOTREF(__pyx_t_10);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_13(__pyx_t_12), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
goto __pyx_L13_unpacking_done;
__pyx_L12_unpacking_failed:;
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L13_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_k);
@@ -8361,7 +8551,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
__Pyx_XDECREF(__pyx_v_v);
__pyx_v_v = __pyx_t_10;
__pyx_t_10 = 0;
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_k);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_k);
@@ -8369,27 +8559,27 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_v);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_v);
__Pyx_GIVEREF(__pyx_v_v);
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- if (unlikely(PyList_Append(__pyx_t_6, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_6, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_t_6));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Add(((PyObject *)__pyx_kp_s_25), __pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(((PyObject *)__pyx_kp_s_25), __pyx_t_6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Add(__pyx_t_2, ((PyObject *)__pyx_kp_s_28)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Add(__pyx_t_2, ((PyObject *)__pyx_kp_s_28)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_format = __pyx_t_6;
@@ -8397,7 +8587,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObjec
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":434
+ /* "pysam/cvcf.pyx":437
* else:
* format = "<" + (",".join( ["%s=%s" % (k,v) for (k,v) in values] )) + ">"
* return format # <<<<<<<<<<<<<<
@@ -8440,12 +8630,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_9get_expected(PyObject *__pyx_self,
PyObject *__pyx_v_format = 0;
PyObject *__pyx_v_formatdict = 0;
PyObject *__pyx_v_alt = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("get_expected (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,&__pyx_n_s__formatdict,&__pyx_n_s__alt,0};
PyObject* values[4] = {0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -8461,30 +8650,26 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_9get_expected(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_expected") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "get_expected") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 4) {
goto __pyx_L5_argtuple_error;
@@ -8501,7 +8686,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_9get_expected(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("get_expected", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.get_expected", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -8512,7 +8697,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_9get_expected(PyObject *__pyx_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":436
+/* "pysam/cvcf.pyx":439
* return format
*
* def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
@@ -8535,34 +8720,33 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("get_expected", 0);
- /* "pysam/cvcf.pyx":437
+ /* "pysam/cvcf.pyx":440
*
* def get_expected(self, format, formatdict, alt):
* fmt = formatdict[format] # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_UNKNOWN: return -1
* if fmt.numbertype == self.NT_NUMBER: return fmt.number
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_formatdict, __pyx_v_format); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_formatdict, __pyx_v_format); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_v_fmt = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":438
+ /* "pysam/cvcf.pyx":441
* def get_expected(self, format, formatdict, alt):
* fmt = formatdict[format]
* if fmt.numbertype == self.NT_UNKNOWN: return -1 # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_NUMBER: return fmt.number
* if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
@@ -8573,26 +8757,25 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":439
+ /* "pysam/cvcf.pyx":442
* fmt = formatdict[format]
* if fmt.numbertype == self.NT_UNKNOWN: return -1
* if fmt.numbertype == self.NT_NUMBER: return fmt.number # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
* if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__number); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -8601,27 +8784,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":440
+ /* "pysam/cvcf.pyx":443
* if fmt.numbertype == self.NT_UNKNOWN: return -1
* if fmt.numbertype == self.NT_NUMBER: return fmt.number
* if fmt.numbertype == self.NT_ALLELES: return len(alt)+1 # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
* if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyInt_FromSsize_t((__pyx_t_5 + 1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 440; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromSsize_t((__pyx_t_5 + 1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_r = __pyx_t_3;
__pyx_t_3 = 0;
@@ -8630,27 +8812,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":441
+ /* "pysam/cvcf.pyx":444
* if fmt.numbertype == self.NT_NUMBER: return fmt.number
* if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
* if fmt.numbertype == self.NT_NR_ALLELES: return len(alt) # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
* if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NR_ALLELES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 444; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -8659,28 +8840,27 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":442
+ /* "pysam/cvcf.pyx":445
* if fmt.numbertype == self.NT_ALLELES: return len(alt)+1
* if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
* if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2 # <<<<<<<<<<<<<<
* if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
* return 0
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_6 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyInt_FromSsize_t(__Pyx_div_Py_ssize_t(((__pyx_t_5 + 1) * (__pyx_t_6 + 2)), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 442; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyInt_FromSsize_t(__Pyx_div_Py_ssize_t(((__pyx_t_5 + 1) * (__pyx_t_6 + 2)), 2)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 445; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_r = __pyx_t_3;
__pyx_t_3 = 0;
@@ -8689,28 +8869,27 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":443
+ /* "pysam/cvcf.pyx":446
* if fmt.numbertype == self.NT_NR_ALLELES: return len(alt)
* if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
* if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1) # <<<<<<<<<<<<<<
* return 0
*
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_fmt, __pyx_n_s__numbertype); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_PHASED_GENOTYPES); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_t_2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_4) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_1 = PyInt_FromSsize_t(((__pyx_t_6 + 1) * (__pyx_t_5 + 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_6 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Length(__pyx_v_alt); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(((__pyx_t_6 + 1) * (__pyx_t_5 + 1))); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 446; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -8719,7 +8898,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject
}
__pyx_L8:;
- /* "pysam/cvcf.pyx":444
+ /* "pysam/cvcf.pyx":447
* if fmt.numbertype == self.NT_GENOTYPES: return ((len(alt)+1)*(len(alt)+2)) // 2
* if fmt.numbertype == self.NT_PHASED_GENOTYPES: return (len(alt)+1)*(len(alt)+1)
* return 0 # <<<<<<<<<<<<<<
@@ -8755,12 +8934,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition(PyObject *__pyx_se
PyObject *__pyx_v_key = 0;
PyObject *__pyx_v_data = 0;
PyObject *__pyx_v_line = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__formatdict,&__pyx_n_s__key,&__pyx_n_s__data,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_add_definition (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__formatdict,&__pyx_n_s__key,&__pyx_n_s__data,&__pyx_n_s__line,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -8777,36 +8955,31 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition(PyObject *__pyx_se
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[4])) kw_args--;
+ if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_add_definition") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_add_definition") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 5) {
goto __pyx_L5_argtuple_error;
@@ -8825,7 +8998,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition(PyObject *__pyx_se
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_add_definition", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF._add_definition", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -8836,7 +9009,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_11_add_definition(PyObject *__pyx_se
return __pyx_r;
}
-/* "pysam/cvcf.pyx":447
+/* "pysam/cvcf.pyx":450
*
*
* def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
@@ -8857,14 +9030,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
__Pyx_RefNannySetupContext("_add_definition", 0);
__Pyx_INCREF(__pyx_v_data);
- /* "pysam/cvcf.pyx":448
+ /* "pysam/cvcf.pyx":451
*
* def _add_definition(self, formatdict, key, data, line ):
* if key in formatdict: return # <<<<<<<<<<<<<<
* self.error(line,self.ERROR_UNKNOWN_KEY,key)
* if data == None:
*/
- __pyx_t_1 = ((PySequence_Contains(__pyx_v_formatdict, __pyx_v_key))); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 448; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = (__Pyx_PySequence_Contains(__pyx_v_key, __pyx_v_formatdict, Py_EQ)); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
__Pyx_XDECREF(__pyx_r);
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -8873,18 +9046,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":449
+ /* "pysam/cvcf.pyx":452
* def _add_definition(self, formatdict, key, data, line ):
* if key in formatdict: return
* self.error(line,self.ERROR_UNKNOWN_KEY,key) # <<<<<<<<<<<<<<
* if data == None:
* formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 449; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_UNKNOWN_KEY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 449; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_UNKNOWN_KEY); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 449; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_line);
@@ -8895,37 +9068,36 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
PyTuple_SET_ITEM(__pyx_t_4, 2, __pyx_v_key);
__Pyx_GIVEREF(__pyx_v_key);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 449; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":450
+ /* "pysam/cvcf.pyx":453
* if key in formatdict: return
* self.error(line,self.ERROR_UNKNOWN_KEY,key)
* if data == None: # <<<<<<<<<<<<<<
* formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
* return
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_data, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_1) {
- /* "pysam/cvcf.pyx":451
+ /* "pysam/cvcf.pyx":454
* self.error(line,self.ERROR_UNKNOWN_KEY,key)
* if data == None:
* formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".") # <<<<<<<<<<<<<<
* return
* if data == []: data = [""] # unsure what type -- say string
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
@@ -8945,14 +9117,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 451; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":452
+ /* "pysam/cvcf.pyx":455
* if data == None:
* formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
* return # <<<<<<<<<<<<<<
@@ -8966,22 +9138,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":453
+ /* "pysam/cvcf.pyx":456
* formatdict[key] = FORMAT(key,self.NT_NUMBER,0,"Flag","(Undefined tag)",".")
* return
* if data == []: data = [""] # unsure what type -- say string # <<<<<<<<<<<<<<
* if type(data[0]) == type(0.0):
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
*/
- __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyList_New(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, ((PyObject *)__pyx_t_4), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_data, ((PyObject *)__pyx_t_4), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_1) {
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 456; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_1));
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_1));
@@ -8993,37 +9164,36 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":454
+ /* "pysam/cvcf.pyx":457
* return
* if data == []: data = [""] # unsure what type -- say string
* if type(data[0]) == type(0.0): # <<<<<<<<<<<<<<
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
* return
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_data, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_data, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_t_4)), Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_2)), ((PyObject *)Py_TYPE(__pyx_t_4)), Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 454; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_1) {
- /* "pysam/cvcf.pyx":455
+ /* "pysam/cvcf.pyx":458
* if data == []: data = [""] # unsure what type -- say string
* if type(data[0]) == type(0.0):
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None) # <<<<<<<<<<<<<<
* return
* if type(data[0]) == type(0):
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
@@ -9043,14 +9213,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
PyTuple_SET_ITEM(__pyx_t_2, 5, Py_None);
__Pyx_GIVEREF(Py_None);
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 455; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":456
+ /* "pysam/cvcf.pyx":459
* if type(data[0]) == type(0.0):
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
* return # <<<<<<<<<<<<<<
@@ -9064,34 +9234,33 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":457
+ /* "pysam/cvcf.pyx":460
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Float","(Undefined tag)",None)
* return
* if type(data[0]) == type(0): # <<<<<<<<<<<<<<
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
* return
*/
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_data, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_v_data, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_4)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_t_4)), ((PyObject *)Py_TYPE(__pyx_int_0)), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_1) {
- /* "pysam/cvcf.pyx":458
+ /* "pysam/cvcf.pyx":461
* return
* if type(data[0]) == type(0):
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None) # <<<<<<<<<<<<<<
* return
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".")
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_key);
@@ -9111,14 +9280,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
PyTuple_SET_ITEM(__pyx_t_3, 5, Py_None);
__Pyx_GIVEREF(Py_None);
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":459
+ /* "pysam/cvcf.pyx":462
* if type(data[0]) == type(0):
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
* return # <<<<<<<<<<<<<<
@@ -9132,18 +9301,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":460
+ /* "pysam/cvcf.pyx":463
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"Integer","(Undefined tag)",None)
* return
* formatdict[key] = FORMAT(key,self.NT_UNKNOWN,-1,"String","(Undefined tag)",".") # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(6); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
@@ -9163,11 +9332,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
PyTuple_SET_ITEM(__pyx_t_2, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 460; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_v_formatdict, __pyx_v_key, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -9185,7 +9354,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyOb
return __pyx_r;
}
-/* "pysam/cvcf.pyx":464
+/* "pysam/cvcf.pyx":467
*
* # todo: trim trailing missing values
* def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
@@ -9202,7 +9371,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__defaults__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_self)->__pyx_arg_key);
PyTuple_SET_ITEM(__pyx_t_1, 0, __Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_self)->__pyx_arg_key);
@@ -9239,12 +9408,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_
PyObject *__pyx_v_key = 0;
PyObject *__pyx_v_value = 0;
PyObject *__pyx_v_separator = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__data,&__pyx_n_s__format,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__separator,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("format_formatdata (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__data,&__pyx_n_s__format,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__separator,0};
PyObject* values[6] = {0,0,0,0,0,0};
__pyx_defaults3 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_self);
values[3] = __pyx_dynamic_args->__pyx_arg_key;
@@ -9266,20 +9434,17 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
if (kw_args > 0) {
@@ -9298,7 +9463,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "format_formatdata") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "format_formatdata") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -9321,7 +9486,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_13format_formatdata(PyObject *__pyx_
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("format_formatdata", 0, 3, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.format_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -9362,51 +9527,50 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_RefNannySetupContext("format_formatdata", 0);
__Pyx_INCREF(__pyx_v_data);
- /* "pysam/cvcf.pyx":465
+ /* "pysam/cvcf.pyx":468
* # todo: trim trailing missing values
* def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
* output, sdata = [], [] # <<<<<<<<<<<<<<
* if type(data) == type([]): # for FORMAT field, make data with dummy values
* d = {}
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 465; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_v_output = __pyx_t_1;
+ __pyx_v_output = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_v_sdata = __pyx_t_2;
+ __pyx_v_sdata = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":466
+ /* "pysam/cvcf.pyx":469
* def format_formatdata( self, data, format, key=True, value=True, separator=":" ):
* output, sdata = [], []
* if type(data) == type([]): # for FORMAT field, make data with dummy values # <<<<<<<<<<<<<<
* d = {}
* for k in data: d[k] = []
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(((PyObject *)__pyx_t_2))), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(((PyObject *)Py_TYPE(__pyx_v_data)), ((PyObject *)Py_TYPE(((PyObject *)__pyx_t_2))), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 466; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":467
+ /* "pysam/cvcf.pyx":470
* output, sdata = [], []
* if type(data) == type([]): # for FORMAT field, make data with dummy values
* d = {} # <<<<<<<<<<<<<<
* for k in data: d[k] = []
* data = d
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 470; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- __pyx_v_d = __pyx_t_1;
+ __pyx_v_d = ((PyObject*)__pyx_t_1);
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":468
+ /* "pysam/cvcf.pyx":471
* if type(data) == type([]): # for FORMAT field, make data with dummy values
* d = {}
* for k in data: d[k] = [] # <<<<<<<<<<<<<<
@@ -9417,23 +9581,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_t_1 = __pyx_v_data; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -9442,14 +9614,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_XDECREF(__pyx_v_k);
__pyx_v_k = __pyx_t_2;
__pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyDict_SetItem(((PyObject *)__pyx_v_d), __pyx_v_k, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_d), __pyx_v_k, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":469
+ /* "pysam/cvcf.pyx":472
* d = {}
* for k in data: d[k] = []
* data = d # <<<<<<<<<<<<<<
@@ -9463,7 +9635,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":471
+ /* "pysam/cvcf.pyx":474
* data = d
* # convert missing values; and silently add definitions if required
* for k in data: # <<<<<<<<<<<<<<
@@ -9474,23 +9646,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_t_1 = __pyx_v_data; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -9500,18 +9680,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_v_k = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":472
+ /* "pysam/cvcf.pyx":475
* # convert missing values; and silently add definitions if required
* for k in data:
* self._add_definition( format, k, data[k], "(output)" ) # <<<<<<<<<<<<<<
* for idx,v in enumerate(data[k]):
* if v == format[k].missingvalue: data[k][idx] = "."
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___add_definition); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___add_definition); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_format);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_format);
@@ -9525,13 +9705,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
PyTuple_SET_ITEM(__pyx_t_7, 3, ((PyObject *)__pyx_kp_s_61));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_61));
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 472; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 475; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":473
+ /* "pysam/cvcf.pyx":476
* for k in data:
* self._add_definition( format, k, data[k], "(output)" )
* for idx,v in enumerate(data[k]): # <<<<<<<<<<<<<<
@@ -9540,13 +9720,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
*/
__Pyx_INCREF(__pyx_int_0);
__pyx_t_6 = __pyx_int_0;
- __pyx_t_7 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
__pyx_t_2 = __pyx_t_7; __Pyx_INCREF(__pyx_t_2); __pyx_t_8 = 0;
__pyx_t_9 = NULL;
} else {
- __pyx_t_8 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_9 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
@@ -9554,16 +9734,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
for (;;) {
if (!__pyx_t_9 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_8 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_9 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_8 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_7 = __pyx_t_9(__pyx_t_2);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -9575,33 +9763,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_INCREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_v_idx);
__pyx_v_idx = __pyx_t_6;
- __pyx_t_7 = PyNumber_Add(__pyx_t_6, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_6, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6);
__pyx_t_6 = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":474
+ /* "pysam/cvcf.pyx":477
* self._add_definition( format, k, data[k], "(output)" )
* for idx,v in enumerate(data[k]):
* if v == format[k].missingvalue: data[k][idx] = "." # <<<<<<<<<<<<<<
* # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
* for k in data:
*/
- __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_k); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_k); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_7, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, __pyx_t_10, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, __pyx_t_10, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_3) {
- __pyx_t_7 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (PyObject_SetItem(__pyx_t_7, __pyx_v_idx, ((PyObject *)__pyx_kp_s_9)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 474; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_7, __pyx_v_idx, ((PyObject *)__pyx_kp_s_9)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L10;
}
@@ -9612,7 +9799,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":476
+ /* "pysam/cvcf.pyx":479
* if v == format[k].missingvalue: data[k][idx] = "."
* # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
* for k in data: # <<<<<<<<<<<<<<
@@ -9623,23 +9810,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_t_1 = __pyx_v_data; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_6 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_6 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_6 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_6)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -9649,18 +9844,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_v_k = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":477
+ /* "pysam/cvcf.pyx":480
* # make sure GT comes first; and ensure fixed ordering; also convert GT data back to string
* for k in data:
* if k != 'GT': sdata.append( (k,data[k]) ) # <<<<<<<<<<<<<<
* sdata.sort()
* if 'GT' in data:
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_k, ((PyObject *)__pyx_n_s__GT), Py_NE); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_RichCompare(__pyx_v_k, ((PyObject *)__pyx_n_s__GT), Py_NE); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
if (__pyx_t_3) {
- __pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_v_data, __pyx_v_k); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_k);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_k);
@@ -9668,7 +9865,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_11 = PyList_Append(__pyx_v_sdata, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 477; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_Append(__pyx_v_sdata, ((PyObject *)__pyx_t_2)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
goto __pyx_L13;
}
@@ -9676,37 +9873,37 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":478
+ /* "pysam/cvcf.pyx":481
* for k in data:
* if k != 'GT': sdata.append( (k,data[k]) )
* sdata.sort() # <<<<<<<<<<<<<<
* if 'GT' in data:
* sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
*/
- __pyx_t_11 = PyList_Sort(((PyObject *)__pyx_v_sdata)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 478; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_Sort(((PyObject *)__pyx_v_sdata)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":479
+ /* "pysam/cvcf.pyx":482
* if k != 'GT': sdata.append( (k,data[k]) )
* sdata.sort()
* if 'GT' in data: # <<<<<<<<<<<<<<
* sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
* for k,v in sdata:
*/
- __pyx_t_3 = ((PySequence_Contains(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)))); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 479; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__GT), __pyx_v_data, Py_EQ)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":480
+ /* "pysam/cvcf.pyx":483
* sdata.sort()
* if 'GT' in data:
* sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata # <<<<<<<<<<<<<<
* for k,v in sdata:
* if v == []: v = None
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGTback); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGTback); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__GT)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
@@ -9714,10 +9911,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_1 = 0;
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GT));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_n_s__GT));
@@ -9725,22 +9922,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
PyTuple_SET_ITEM(__pyx_t_6, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
__pyx_t_6 = 0;
- __pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_sdata)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyNumber_Add(((PyObject *)__pyx_t_2), ((PyObject *)__pyx_v_sdata)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_v_sdata));
- __pyx_v_sdata = __pyx_t_6;
+ __pyx_v_sdata = ((PyObject*)__pyx_t_6);
__pyx_t_6 = 0;
goto __pyx_L14;
}
__pyx_L14:;
- /* "pysam/cvcf.pyx":481
+ /* "pysam/cvcf.pyx":484
* if 'GT' in data:
* sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
* for k,v in sdata: # <<<<<<<<<<<<<<
@@ -9750,32 +9947,44 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_t_6 = ((PyObject *)__pyx_v_sdata); __Pyx_INCREF(__pyx_t_6); __pyx_t_4 = 0;
for (;;) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_6)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_6, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_7 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_10 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_12 = Py_TYPE(__pyx_t_10)->tp_iternext;
@@ -9783,14 +9992,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_GOTREF(__pyx_t_1);
index = 1; __pyx_t_7 = __pyx_t_12(__pyx_t_10); if (unlikely(!__pyx_t_7)) goto __pyx_L17_unpacking_failed;
__Pyx_GOTREF(__pyx_t_7);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_12(__pyx_t_10), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L18_unpacking_done;
__pyx_L17_unpacking_failed:;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 481; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L18_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_k);
@@ -9800,19 +10010,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__pyx_v_v = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":482
+ /* "pysam/cvcf.pyx":485
* sdata = [('GT',map(self.convertGTback,data['GT']))] + sdata
* for k,v in sdata:
* if v == []: v = None # <<<<<<<<<<<<<<
* if key and value:
* if v != None: output.append( k+"="+','.join(map(str,v)) )
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 482; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_3) {
__Pyx_INCREF(Py_None);
@@ -9822,39 +10031,38 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
}
__pyx_L19:;
- /* "pysam/cvcf.pyx":483
+ /* "pysam/cvcf.pyx":486
* for k,v in sdata:
* if v == []: v = None
* if key and value: # <<<<<<<<<<<<<<
* if v != None: output.append( k+"="+','.join(map(str,v)) )
* else: output.append( k )
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_key); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_key); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
- __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely(__pyx_t_13 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = __pyx_t_13;
} else {
__pyx_t_14 = __pyx_t_3;
}
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":484
+ /* "pysam/cvcf.pyx":487
* if v == []: v = None
* if key and value:
* if v != None: output.append( k+"="+','.join(map(str,v)) ) # <<<<<<<<<<<<<<
* else: output.append( k )
* elif key: output.append(k)
*/
- __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_14) {
- __pyx_t_7 = PyNumber_Add(__pyx_v_k, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_v_k, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
@@ -9862,79 +10070,78 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_INCREF(__pyx_v_v);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_v);
__Pyx_GIVEREF(__pyx_v_v);
- __pyx_t_10 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyNumber_Add(__pyx_t_7, __pyx_t_10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Add(__pyx_t_7, __pyx_t_10); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_t_1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 484; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_t_1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L21;
}
/*else*/ {
- /* "pysam/cvcf.pyx":485
+ /* "pysam/cvcf.pyx":488
* if key and value:
* if v != None: output.append( k+"="+','.join(map(str,v)) )
* else: output.append( k ) # <<<<<<<<<<<<<<
* elif key: output.append(k)
* elif value:
*/
- __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_v_k); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 485; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_v_k); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L21:;
goto __pyx_L20;
}
- /* "pysam/cvcf.pyx":486
+ /* "pysam/cvcf.pyx":489
* if v != None: output.append( k+"="+','.join(map(str,v)) )
* else: output.append( k )
* elif key: output.append(k) # <<<<<<<<<<<<<<
* elif value:
* if v != None: output.append( ','.join(map(str,v)) )
*/
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_key); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_key); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_v_k); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 486; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_v_k); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L20;
}
- /* "pysam/cvcf.pyx":487
+ /* "pysam/cvcf.pyx":490
* else: output.append( k )
* elif key: output.append(k)
* elif value: # <<<<<<<<<<<<<<
* if v != None: output.append( ','.join(map(str,v)) )
* else: output.append( "." ) # should not happen
*/
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 487; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_value); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":488
+ /* "pysam/cvcf.pyx":491
* elif key: output.append(k)
* elif value:
* if v != None: output.append( ','.join(map(str,v)) ) # <<<<<<<<<<<<<<
* else: output.append( "." ) # should not happen
* # snip off trailing missing data
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, Py_None, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_14) {
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
@@ -9942,35 +10149,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
__Pyx_INCREF(__pyx_v_v);
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_v);
__Pyx_GIVEREF(__pyx_v_v);
- __pyx_t_7 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_t_7); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_t_7); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L22;
}
/*else*/ {
- /* "pysam/cvcf.pyx":489
+ /* "pysam/cvcf.pyx":492
* elif value:
* if v != None: output.append( ','.join(map(str,v)) )
* else: output.append( "." ) # should not happen # <<<<<<<<<<<<<<
* # snip off trailing missing data
* while len(output) > 1:
*/
- __pyx_t_7 = ((PyObject *)__pyx_kp_s_9);
- __Pyx_INCREF(__pyx_t_7);
- __pyx_t_11 = PyList_Append(__pyx_v_output, __pyx_t_7); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 489; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_11 = PyList_Append(__pyx_v_output, ((PyObject *)__pyx_kp_s_9)); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__pyx_L22:;
goto __pyx_L20;
@@ -9979,7 +10183,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":491
+ /* "pysam/cvcf.pyx":494
* else: output.append( "." ) # should not happen
* # snip off trailing missing data
* while len(output) > 1: # <<<<<<<<<<<<<<
@@ -9988,45 +10192,50 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
*/
while (1) {
if (unlikely(((PyObject *)__pyx_v_output) == Py_None)) {
- PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 491; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetString(PyExc_TypeError, "object of type 'NoneType' has no len()");
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __pyx_t_4 = PyList_GET_SIZE(((PyObject *)__pyx_v_output));
+ __pyx_t_4 = PyList_GET_SIZE(((PyObject *)__pyx_v_output)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_4 > 1);
if (!__pyx_t_14) break;
- /* "pysam/cvcf.pyx":492
+ /* "pysam/cvcf.pyx":495
* # snip off trailing missing data
* while len(output) > 1:
* last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<<
* if len(last)>0: break
* output = output[:-1]
*/
- __pyx_t_6 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_output), -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(((PyObject *)__pyx_v_output) == Py_None)) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not subscriptable");
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_t_6 = __Pyx_GetItemInt_List(((PyObject *)__pyx_v_output), -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__replace); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__replace); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_62), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_62), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__replace); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_6, __pyx_n_s__replace); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_63), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_63), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_last);
__pyx_v_last = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":493
+ /* "pysam/cvcf.pyx":496
* while len(output) > 1:
* last = output[-1].replace(',','').replace('.','')
* if len(last)>0: break # <<<<<<<<<<<<<<
* output = output[:-1]
* return separator.join(output)
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_last); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 493; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_last); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 496; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_4 > 0);
if (__pyx_t_14) {
goto __pyx_L24_break;
@@ -10034,22 +10243,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
}
__pyx_L25:;
- /* "pysam/cvcf.pyx":494
+ /* "pysam/cvcf.pyx":497
* last = output[-1].replace(',','').replace('.','')
* if len(last)>0: break
* output = output[:-1] # <<<<<<<<<<<<<<
* return separator.join(output)
*
*/
- __pyx_t_6 = __Pyx_PySequence_GetSlice(((PyObject *)__pyx_v_output), 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 494; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PySequence_GetSlice(((PyObject *)__pyx_v_output), 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 497; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_6));
__Pyx_DECREF(((PyObject *)__pyx_v_output));
- __pyx_v_output = __pyx_t_6;
+ __pyx_v_output = ((PyObject*)__pyx_t_6);
__pyx_t_6 = 0;
}
__pyx_L24_break:;
- /* "pysam/cvcf.pyx":495
+ /* "pysam/cvcf.pyx":498
* if len(last)>0: break
* output = output[:-1]
* return separator.join(output) # <<<<<<<<<<<<<<
@@ -10057,14 +10266,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED Py
*
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_separator, __pyx_n_s__join); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_separator, __pyx_n_s__join); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(((PyObject *)__pyx_v_output));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_output));
__Pyx_GIVEREF(((PyObject *)__pyx_v_output));
- __pyx_t_10 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -10103,13 +10312,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_15enter_default_format(PyObject *__p
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("enter_default_format (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":498
+/* "pysam/cvcf.pyx":501
*
*
* def enter_default_format(self): # <<<<<<<<<<<<<<
@@ -10144,18 +10352,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("enter_default_format", 0);
- /* "pysam/cvcf.pyx":499
+ /* "pysam/cvcf.pyx":502
*
* def enter_default_format(self):
* for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<<
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(6); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GT));
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_n_s__GT));
@@ -10175,23 +10383,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_3, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":500
+ /* "pysam/cvcf.pyx":503
* def enter_default_format(self):
* for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1), # <<<<<<<<<<<<<<
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
* FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
*/
- __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyTuple_New(6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(6); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(((PyObject *)__pyx_n_s__DP));
PyTuple_SET_ITEM(__pyx_t_4, 0, ((PyObject *)__pyx_n_s__DP));
@@ -10211,23 +10419,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_4, 5, __pyx_int_neg_1);
__Pyx_GIVEREF(__pyx_int_neg_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 500; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":501
+ /* "pysam/cvcf.pyx":504
* for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'), # <<<<<<<<<<<<<<
* FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
* FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
*/
- __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_5 = PyTuple_New(6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(6); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(((PyObject *)__pyx_n_s__FT));
PyTuple_SET_ITEM(__pyx_t_5, 0, ((PyObject *)__pyx_n_s__FT));
@@ -10247,23 +10455,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_5, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":502
+ /* "pysam/cvcf.pyx":505
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
* FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), # <<<<<<<<<<<<<<
* FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
* FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
*/
- __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyTuple_New(6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyTuple_New(6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GL));
PyTuple_SET_ITEM(__pyx_t_6, 0, ((PyObject *)__pyx_n_s__GL));
@@ -10283,23 +10491,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_6, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":503
+ /* "pysam/cvcf.pyx":506
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
* FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
* FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'), # <<<<<<<<<<<<<<
* FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
* FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
*/
- __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(6); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GLE));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_n_s__GLE));
@@ -10319,23 +10527,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_7, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":504
+ /* "pysam/cvcf.pyx":507
* FORMAT('GL',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
* FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
* FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1), # <<<<<<<<<<<<<<
* FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
* FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
*/
- __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyTuple_New(6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(6); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GQ));
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_n_s__GQ));
@@ -10355,23 +10563,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_8, 5, __pyx_int_neg_1);
__Pyx_GIVEREF(__pyx_int_neg_1);
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 504; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":505
+ /* "pysam/cvcf.pyx":508
* FORMAT('GLE',self.NT_UNKNOWN,-1,'Float','Genotype likelihoods','.'),
* FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
* FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'), # <<<<<<<<<<<<<<
* FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
* FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_9 = PyTuple_New(6); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(6); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(((PyObject *)__pyx_n_s__PL));
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_n_s__PL));
@@ -10391,23 +10599,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_9, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 505; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":506
+ /* "pysam/cvcf.pyx":509
* FORMAT('GQ',self.NT_NUMBER,1,'Integer','Genotype Quality',-1),
* FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
* FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'), # <<<<<<<<<<<<<<
* FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
* FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
*/
- __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyTuple_New(6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(6); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GP));
PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_n_s__GP));
@@ -10427,23 +10635,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_10, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 506; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":507
+ /* "pysam/cvcf.pyx":510
* FORMAT('PL',self.NT_GENOTYPES,-1,'Integer','Phred-scaled genotype likelihoods', '.'),
* FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
* FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'), # <<<<<<<<<<<<<<
* FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
* FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
*/
- __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_GENOTYPES); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_11 = PyTuple_New(6); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyTuple_New(6); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_INCREF(((PyObject *)__pyx_n_s__GQ));
PyTuple_SET_ITEM(__pyx_t_11, 0, ((PyObject *)__pyx_n_s__GQ));
@@ -10463,23 +10671,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_11, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 507; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
- /* "pysam/cvcf.pyx":508
+ /* "pysam/cvcf.pyx":511
* FORMAT('GP',self.NT_GENOTYPES,-1,'Float','Genotype posterior probabilities','.'),
* FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
* FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid # <<<<<<<<<<<<<<
* FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
* FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
*/
- __pyx_t_11 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_12 = PyTuple_New(6); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyTuple_New(6); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_INCREF(((PyObject *)__pyx_n_s__HQ));
PyTuple_SET_ITEM(__pyx_t_12, 0, ((PyObject *)__pyx_n_s__HQ));
@@ -10499,23 +10707,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_12, 5, __pyx_int_neg_1);
__Pyx_GIVEREF(__pyx_int_neg_1);
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_12), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
- /* "pysam/cvcf.pyx":509
+ /* "pysam/cvcf.pyx":512
* FORMAT('GQ',self.NT_GENOTYPES,-1,'Integer','Conditional genotype quality','.'),
* FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
* FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'), # <<<<<<<<<<<<<<
* FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
* FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
*/
- __pyx_t_12 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
- __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_UNKNOWN); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_13 = PyTuple_New(6); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyTuple_New(6); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_INCREF(((PyObject *)__pyx_n_s__PS));
PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_n_s__PS));
@@ -10535,23 +10743,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_13, 5, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_t_11 = 0;
- __pyx_t_11 = PyObject_Call(__pyx_t_12, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_Call(__pyx_t_12, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
- /* "pysam/cvcf.pyx":510
+ /* "pysam/cvcf.pyx":513
* FORMAT('HQ',self.NT_UNKNOWN,-1,'Integer','Haplotype Quality',-1), # unknown number, since may be haploid
* FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
* FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1), # <<<<<<<<<<<<<<
* FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
* FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
*/
- __pyx_t_13 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
- __pyx_t_14 = PyTuple_New(6); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyTuple_New(6); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
__Pyx_INCREF(((PyObject *)__pyx_n_s__PQ));
PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)__pyx_n_s__PQ));
@@ -10571,23 +10779,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_14, 5, __pyx_int_neg_1);
__Pyx_GIVEREF(__pyx_int_neg_1);
__pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyObject_Call(__pyx_t_13, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 513; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- /* "pysam/cvcf.pyx":511
+ /* "pysam/cvcf.pyx":514
* FORMAT('PS',self.NT_UNKNOWN,-1,'Integer','Phase set','.'),
* FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
* FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1), # <<<<<<<<<<<<<<
* FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
* ]:
*/
- __pyx_t_14 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_ALLELES); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_15 = PyTuple_New(6); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyTuple_New(6); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(((PyObject *)__pyx_n_s__EC));
PyTuple_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_n_s__EC));
@@ -10607,23 +10815,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_15, 5, __pyx_int_neg_1);
__Pyx_GIVEREF(__pyx_int_neg_1);
__pyx_t_13 = 0;
- __pyx_t_13 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 511; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_Call(__pyx_t_14, ((PyObject *)__pyx_t_15), NULL); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_15)); __pyx_t_15 = 0;
- /* "pysam/cvcf.pyx":512
+ /* "pysam/cvcf.pyx":515
* FORMAT('PQ',self.NT_NUMBER,1,'Integer','Phasing quality',-1),
* FORMAT('EC',self.NT_ALLELES,1,'Integer','Expected alternate allel counts',-1),
* FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1), # <<<<<<<<<<<<<<
* ]:
* if f.id not in self._format:
*/
- __pyx_t_15 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = __Pyx_GetName(__pyx_m, __pyx_n_s__FORMAT); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__NT_NUMBER); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_16 = PyTuple_New(6); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyTuple_New(6); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
__Pyx_INCREF(((PyObject *)__pyx_n_s__MQ));
PyTuple_SET_ITEM(__pyx_t_16, 0, ((PyObject *)__pyx_n_s__MQ));
@@ -10643,39 +10851,39 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
PyTuple_SET_ITEM(__pyx_t_16, 5, __pyx_int_neg_1);
__Pyx_GIVEREF(__pyx_int_neg_1);
__pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_16), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 512; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_16), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_16)); __pyx_t_16 = 0;
- __pyx_t_16 = PyList_New(14); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 499; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyTuple_New(14); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
- PyList_SET_ITEM(__pyx_t_16, 0, __pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyList_SET_ITEM(__pyx_t_16, 1, __pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_16, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
- PyList_SET_ITEM(__pyx_t_16, 2, __pyx_t_3);
+ PyTuple_SET_ITEM(__pyx_t_16, 2, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- PyList_SET_ITEM(__pyx_t_16, 3, __pyx_t_4);
+ PyTuple_SET_ITEM(__pyx_t_16, 3, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
- PyList_SET_ITEM(__pyx_t_16, 4, __pyx_t_5);
+ PyTuple_SET_ITEM(__pyx_t_16, 4, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
- PyList_SET_ITEM(__pyx_t_16, 5, __pyx_t_6);
+ PyTuple_SET_ITEM(__pyx_t_16, 5, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- PyList_SET_ITEM(__pyx_t_16, 6, __pyx_t_7);
+ PyTuple_SET_ITEM(__pyx_t_16, 6, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
- PyList_SET_ITEM(__pyx_t_16, 7, __pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_16, 7, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
- PyList_SET_ITEM(__pyx_t_16, 8, __pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_16, 8, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
- PyList_SET_ITEM(__pyx_t_16, 9, __pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_16, 9, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
- PyList_SET_ITEM(__pyx_t_16, 10, __pyx_t_11);
+ PyTuple_SET_ITEM(__pyx_t_16, 10, __pyx_t_11);
__Pyx_GIVEREF(__pyx_t_11);
- PyList_SET_ITEM(__pyx_t_16, 11, __pyx_t_12);
+ PyTuple_SET_ITEM(__pyx_t_16, 11, __pyx_t_12);
__Pyx_GIVEREF(__pyx_t_12);
- PyList_SET_ITEM(__pyx_t_16, 12, __pyx_t_13);
+ PyTuple_SET_ITEM(__pyx_t_16, 12, __pyx_t_13);
__Pyx_GIVEREF(__pyx_t_13);
- PyList_SET_ITEM(__pyx_t_16, 13, __pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_16, 13, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
__pyx_t_2 = 0;
__pyx_t_1 = 0;
@@ -10695,47 +10903,51 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED
__Pyx_DECREF(((PyObject *)__pyx_t_16)); __pyx_t_16 = 0;
for (;;) {
- /* "pysam/cvcf.pyx":499
+ /* "pysam/cvcf.pyx":502
*
* def enter_default_format(self):
* for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'), # <<<<<<<<<<<<<<
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
* FORMAT('FT',self.NT_NUMBER,1,'String','Sample Genotype Filter','.'),
*/
- if (__pyx_t_17 >= PyList_GET_SIZE(__pyx_t_14)) break;
- __pyx_t_16 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_17); __Pyx_INCREF(__pyx_t_16); __pyx_t_17++;
+ if (__pyx_t_17 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_16 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_17); __Pyx_INCREF(__pyx_t_16); __pyx_t_17++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_16 = PySequence_ITEM(__pyx_t_14, __pyx_t_17); __pyx_t_17++; if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 502; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
__Pyx_XDECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_16;
__pyx_t_16 = 0;
- /* "pysam/cvcf.pyx":514
+ /* "pysam/cvcf.pyx":517
* FORMAT('MQ',self.NT_NUMBER,1,'Integer','RMS mapping quality',-1),
* ]:
* if f.id not in self._format: # <<<<<<<<<<<<<<
* self._format[f.id] = f
*
*/
- __pyx_t_16 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
- __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_18 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_13, __pyx_t_16))); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_18 = (__Pyx_PySequence_Contains(__pyx_t_16, __pyx_t_13, Py_NE)); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
if (__pyx_t_18) {
- /* "pysam/cvcf.pyx":515
+ /* "pysam/cvcf.pyx":518
* ]:
* if f.id not in self._format:
* self._format[f.id] = f # <<<<<<<<<<<<<<
*
* def parse_header( self, line ):
*/
- __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_13);
- __pyx_t_16 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_16 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_16);
- if (PyObject_SetItem(__pyx_t_13, __pyx_t_16, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_13, __pyx_t_16, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_13); __pyx_t_13 = 0;
__Pyx_DECREF(__pyx_t_16); __pyx_t_16 = 0;
goto __pyx_L5;
@@ -10778,12 +10990,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_17parse_header = {__Pyx_NAMESTR(
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_header (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -10797,18 +11008,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_header") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_header") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -10821,7 +11030,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -10832,7 +11041,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_17parse_header(PyObject *__pyx_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":517
+/* "pysam/cvcf.pyx":520
* self._format[f.id] = f
*
* def parse_header( self, line ): # <<<<<<<<<<<<<<
@@ -10857,7 +11066,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("parse_header", 0);
- /* "pysam/cvcf.pyx":518
+ /* "pysam/cvcf.pyx":521
*
* def parse_header( self, line ):
* assert line.startswith('##') # <<<<<<<<<<<<<<
@@ -10865,170 +11074,178 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
* key = elts[0].strip()
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_77), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (unlikely(!__pyx_t_3)) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/cvcf.pyx":519
+ /* "pysam/cvcf.pyx":522
* def parse_header( self, line ):
* assert line.startswith('##')
* elts = line[2:].split('=') # <<<<<<<<<<<<<<
* key = elts[0].strip()
* value = '='.join(elts[1:]).strip()
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_line, 2, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_line, 2, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_78), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_78), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_elts = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":520
+ /* "pysam/cvcf.pyx":523
* assert line.startswith('##')
* elts = line[2:].split('=')
* key = elts[0].strip() # <<<<<<<<<<<<<<
* value = '='.join(elts[1:]).strip()
* if key == "fileformat":
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__strip); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_key = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":521
+ /* "pysam/cvcf.pyx":524
* elts = line[2:].split('=')
* key = elts[0].strip()
* value = '='.join(elts[1:]).strip() # <<<<<<<<<<<<<<
* if key == "fileformat":
* if value == "VCFv3.3":
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_14), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_14), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_elts, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_elts, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__strip); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__strip); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_v_value = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":522
+ /* "pysam/cvcf.pyx":525
* key = elts[0].strip()
* value = '='.join(elts[1:]).strip()
* if key == "fileformat": # <<<<<<<<<<<<<<
* if value == "VCFv3.3":
* self._version = 33
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__fileformat), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__fileformat), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":523
+ /* "pysam/cvcf.pyx":526
* value = '='.join(elts[1:]).strip()
* if key == "fileformat":
* if value == "VCFv3.3": # <<<<<<<<<<<<<<
* self._version = 33
* elif value == "VCFv4.0":
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_79), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_79), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":524
+ /* "pysam/cvcf.pyx":527
* if key == "fileformat":
* if value == "VCFv3.3":
* self._version = 33 # <<<<<<<<<<<<<<
* elif value == "VCFv4.0":
* self._version = 40
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_int_33) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 524; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_int_33) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":525
+ /* "pysam/cvcf.pyx":528
* if value == "VCFv3.3":
* self._version = 33
* elif value == "VCFv4.0": # <<<<<<<<<<<<<<
* self._version = 40
* elif value == "VCFv4.1":
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_80), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 525; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_80), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 528; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 528; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":526
+ /* "pysam/cvcf.pyx":529
* self._version = 33
* elif value == "VCFv4.0":
* self._version = 40 # <<<<<<<<<<<<<<
* elif value == "VCFv4.1":
* # AH - for testing
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 526; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L4;
}
- /* "pysam/cvcf.pyx":527
+ /* "pysam/cvcf.pyx":530
* elif value == "VCFv4.0":
* self._version = 40
* elif value == "VCFv4.1": # <<<<<<<<<<<<<<
* # AH - for testing
* self._version = 40
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_value, ((PyObject *)__pyx_kp_s_81), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 527; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_value, ((PyObject *)__pyx_kp_s_81), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 530; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":529
+ /* "pysam/cvcf.pyx":532
* elif value == "VCFv4.1":
* # AH - for testing
* self._version = 40 # <<<<<<<<<<<<<<
* else:
* self.error(line,self.UNKNOWN_FORMAT_STRING)
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 529; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L4;
}
/*else*/ {
- /* "pysam/cvcf.pyx":531
+ /* "pysam/cvcf.pyx":534
* self._version = 40
* else:
* self.error(line,self.UNKNOWN_FORMAT_STRING) # <<<<<<<<<<<<<<
* elif key == "INFO":
* f = self.parse_format(line, value)
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_82); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_82); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
@@ -11036,7 +11253,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 531; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -11046,26 +11263,28 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
goto __pyx_L3;
}
- /* "pysam/cvcf.pyx":532
+ /* "pysam/cvcf.pyx":535
* else:
* self.error(line,self.UNKNOWN_FORMAT_STRING)
* elif key == "INFO": # <<<<<<<<<<<<<<
* f = self.parse_format(line, value)
* self._info[ f.id ] = f
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__INFO), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 532; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__INFO), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":533
+ /* "pysam/cvcf.pyx":536
* self.error(line,self.UNKNOWN_FORMAT_STRING)
* elif key == "INFO":
* f = self.parse_format(line, value) # <<<<<<<<<<<<<<
* self._info[ f.id ] = f
* elif key == "FILTER":
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
@@ -11073,50 +11292,52 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 533; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":534
+ /* "pysam/cvcf.pyx":537
* elif key == "INFO":
* f = self.parse_format(line, value)
* self._info[ f.id ] = f # <<<<<<<<<<<<<<
* elif key == "FILTER":
* f = self.parse_format(line, value, filter=True)
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_t_1, __pyx_t_2, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 534; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_t_2, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L3;
}
- /* "pysam/cvcf.pyx":535
+ /* "pysam/cvcf.pyx":538
* f = self.parse_format(line, value)
* self._info[ f.id ] = f
* elif key == "FILTER": # <<<<<<<<<<<<<<
* f = self.parse_format(line, value, filter=True)
* self._filter[ f.id ] = f
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 535; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":536
+ /* "pysam/cvcf.pyx":539
* self._info[ f.id ] = f
* elif key == "FILTER":
* f = self.parse_format(line, value, filter=True) # <<<<<<<<<<<<<<
* self._filter[ f.id ] = f
* elif key == "FORMAT":
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
@@ -11124,13 +11345,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
- __pyx_t_5 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__filter), __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_4, ((PyObject *)__pyx_n_s__filter), __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 536; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_4)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -11138,43 +11359,45 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
__pyx_v_f = __pyx_t_5;
__pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":537
+ /* "pysam/cvcf.pyx":540
* elif key == "FILTER":
* f = self.parse_format(line, value, filter=True)
* self._filter[ f.id ] = f # <<<<<<<<<<<<<<
* elif key == "FORMAT":
* f = self.parse_format(line, value)
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- if (PyObject_SetItem(__pyx_t_5, __pyx_t_4, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 537; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_5, __pyx_t_4, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L3;
}
- /* "pysam/cvcf.pyx":538
+ /* "pysam/cvcf.pyx":541
* f = self.parse_format(line, value, filter=True)
* self._filter[ f.id ] = f
* elif key == "FORMAT": # <<<<<<<<<<<<<<
* f = self.parse_format(line, value)
* self._format[ f.id ] = f
*/
- __pyx_t_3 = __Pyx_PyString_Equals(__pyx_v_key, ((PyObject *)__pyx_n_s__FORMAT), Py_EQ); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 538; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_RichCompare(__pyx_v_key, ((PyObject *)__pyx_n_s__FORMAT), Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 541; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":539
+ /* "pysam/cvcf.pyx":542
* self._filter[ f.id ] = f
* elif key == "FORMAT":
* f = self.parse_format(line, value) # <<<<<<<<<<<<<<
* self._format[ f.id ] = f
* else:
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_format); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_v_line);
@@ -11182,41 +11405,41 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_5, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 539; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 542; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":540
+ /* "pysam/cvcf.pyx":543
* elif key == "FORMAT":
* f = self.parse_format(line, value)
* self._format[ f.id ] = f # <<<<<<<<<<<<<<
* else:
* # keep other keys in the header field
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- if (PyObject_SetItem(__pyx_t_1, __pyx_t_5, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 540; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_1, __pyx_t_5, __pyx_v_f) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
goto __pyx_L3;
}
/*else*/ {
- /* "pysam/cvcf.pyx":543
+ /* "pysam/cvcf.pyx":546
* else:
* # keep other keys in the header field
* self._header.append( (key,value) ) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___header); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___header); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_key);
@@ -11224,7 +11447,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_4 = __Pyx_PyObject_Append(__pyx_t_5, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 543; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_Append(__pyx_t_5, ((PyObject *)__pyx_t_1)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -11257,12 +11480,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_19write_header = {__Pyx_NAMESTR(
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write_header (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -11276,18 +11498,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write_header") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write_header") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -11300,7 +11520,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -11311,7 +11531,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_19write_header(PyObject *__pyx_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":546
+/* "pysam/cvcf.pyx":549
*
*
* def write_header( self, stream ): # <<<<<<<<<<<<<<
@@ -11336,34 +11556,36 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
PyObject *__pyx_t_7 = NULL;
PyObject *(*__pyx_t_8)(PyObject *);
Py_ssize_t __pyx_t_9;
- PyObject *__pyx_t_10 = NULL;
+ Py_ssize_t __pyx_t_10;
int __pyx_t_11;
- PyObject *__pyx_t_12 = NULL;
+ int __pyx_t_12;
+ PyObject *__pyx_t_13 = NULL;
+ PyObject *__pyx_t_14 = NULL;
int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("write_header", 0);
- /* "pysam/cvcf.pyx":547
+ /* "pysam/cvcf.pyx":550
*
* def write_header( self, stream ):
* stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10)) # <<<<<<<<<<<<<<
* for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
* for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_FloorDivide(__pyx_t_2, __pyx_int_10); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_FloorDivide(__pyx_t_2, __pyx_int_10); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyNumber_Remainder(__pyx_t_2, __pyx_int_10); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(__pyx_t_2, __pyx_int_10); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
@@ -11371,34 +11593,34 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__Pyx_GIVEREF(__pyx_t_4);
__pyx_t_3 = 0;
__pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_83), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_83), ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_4));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 547; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":548
+ /* "pysam/cvcf.pyx":551
* def write_header( self, stream ):
* stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
* for key,value in self._header: stream.write("##%s=%s\n" % (key,value)) # <<<<<<<<<<<<<<
* for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
* for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___header); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___header); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
if (PyList_CheckExact(__pyx_t_4) || PyTuple_CheckExact(__pyx_t_4)) {
__pyx_t_2 = __pyx_t_4; __Pyx_INCREF(__pyx_t_2); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_6 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
@@ -11406,16 +11628,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
for (;;) {
if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_5); __Pyx_INCREF(__pyx_t_4); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_2, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_4 = __pyx_t_6(__pyx_t_2);
if (unlikely(!__pyx_t_4)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -11423,29 +11653,37 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
}
if ((likely(PyTuple_CheckExact(__pyx_t_4))) || (PyList_CheckExact(__pyx_t_4))) {
PyObject* sequence = __pyx_t_4;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_3 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_1);
__Pyx_INCREF(__pyx_t_3);
+ #else
+ __pyx_t_1 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ #endif
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_7 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetIter(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext;
@@ -11453,14 +11691,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__Pyx_GOTREF(__pyx_t_1);
index = 1; __pyx_t_3 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_3)) goto __pyx_L5_unpacking_failed;
__Pyx_GOTREF(__pyx_t_3);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L6_unpacking_done;
__pyx_L5_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L6_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_key);
@@ -11469,9 +11708,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_key);
@@ -11479,15 +11718,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__Pyx_INCREF(__pyx_v_value);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 548; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 551; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -11495,16 +11734,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":549
+ /* "pysam/cvcf.pyx":552
* stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
* for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
* for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]: # <<<<<<<<<<<<<<
* for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER"))))
*
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
@@ -11512,9 +11751,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_1, 1, ((PyObject *)__pyx_n_s__INFO));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__INFO));
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
@@ -11522,9 +11761,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__FILTER));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__FILTER));
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
@@ -11532,13 +11771,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
PyTuple_SET_ITEM(__pyx_t_4, 1, ((PyObject *)__pyx_n_s__FORMAT));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__FORMAT));
__pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_1));
__Pyx_GIVEREF(((PyObject *)__pyx_t_1));
- PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_t_3));
+ PyTuple_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_t_3));
__Pyx_GIVEREF(((PyObject *)__pyx_t_3));
- PyList_SET_ITEM(__pyx_t_2, 2, ((PyObject *)__pyx_t_4));
+ PyTuple_SET_ITEM(__pyx_t_2, 2, ((PyObject *)__pyx_t_4));
__Pyx_GIVEREF(((PyObject *)__pyx_t_4));
__pyx_t_1 = 0;
__pyx_t_3 = 0;
@@ -11546,33 +11785,45 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__pyx_t_4 = ((PyObject *)__pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
for (;;) {
- if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++;
+ if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_2); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
if ((likely(PyTuple_CheckExact(__pyx_t_2))) || (PyList_CheckExact(__pyx_t_2))) {
PyObject* sequence = __pyx_t_2;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_3 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_1 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_3 = PyList_GET_ITEM(sequence, 0);
__pyx_t_1 = PyList_GET_ITEM(sequence, 1);
}
__Pyx_INCREF(__pyx_t_3);
__Pyx_INCREF(__pyx_t_1);
+ #else
+ __pyx_t_3 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_1 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ #endif
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_8 = Py_TYPE(__pyx_t_7)->tp_iternext;
@@ -11580,14 +11831,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__Pyx_GOTREF(__pyx_t_3);
index = 1; __pyx_t_1 = __pyx_t_8(__pyx_t_7); if (unlikely(!__pyx_t_1)) goto __pyx_L9_unpacking_failed;
__Pyx_GOTREF(__pyx_t_1);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_8(__pyx_t_7), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = NULL;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L10_unpacking_done;
__pyx_L9_unpacking_failed:;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 552; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L10_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_var);
@@ -11597,90 +11849,71 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__pyx_v_label = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":550
+ /* "pysam/cvcf.pyx":553
* for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
* for var,label in [(self._info,"INFO"),(self._filter,"FILTER"),(self._format,"FORMAT")]:
* for f in var.itervalues(): stream.write("##%s=%s\n" % (label,self.format_format(f,filter=(label=="FILTER")))) # <<<<<<<<<<<<<<
*
*
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_var, __pyx_n_s__itervalues); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
- __pyx_t_2 = __pyx_t_1; __Pyx_INCREF(__pyx_t_2); __pyx_t_9 = 0;
- __pyx_t_6 = NULL;
- } else {
- __pyx_t_9 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ __pyx_t_9 = 0;
+ if (unlikely(__pyx_v_var == Py_None)) {
+ PyErr_Format(PyExc_AttributeError, "'NoneType' object has no attribute '%s'", "itervalues");
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- for (;;) {
- if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_2)) {
- if (__pyx_t_9 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++;
- } else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_2)) {
- if (__pyx_t_9 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_9); __Pyx_INCREF(__pyx_t_1); __pyx_t_9++;
- } else {
- __pyx_t_1 = __pyx_t_6(__pyx_t_2);
- if (unlikely(!__pyx_t_1)) {
- if (PyErr_Occurred()) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- break;
- }
- __Pyx_GOTREF(__pyx_t_1);
- }
+ __pyx_t_1 = __Pyx_dict_iterator(__pyx_v_var, 0, ((PyObject *)__pyx_n_s__itervalues), (&__pyx_t_10), (&__pyx_t_11)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_XDECREF(__pyx_t_2);
+ __pyx_t_2 = __pyx_t_1;
+ __pyx_t_1 = 0;
+ while (1) {
+ __pyx_t_12 = __Pyx_dict_iter_next(__pyx_t_2, __pyx_t_10, &__pyx_t_9, NULL, &__pyx_t_1, NULL, __pyx_t_11);
+ if (unlikely(__pyx_t_12 == 0)) break;
+ if (unlikely(__pyx_t_12 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_format); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_f);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_10 = PyDict_New(); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __pyx_t_11 = __Pyx_PyString_Equals(__pyx_v_label, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_12 = __Pyx_PyBool_FromLong(__pyx_t_11); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
- if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__filter), __pyx_t_12) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ __pyx_t_13 = PyDict_New(); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_13));
+ __pyx_t_14 = PyObject_RichCompare(__pyx_v_label, ((PyObject *)__pyx_n_s__FILTER), Py_EQ); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_13, ((PyObject *)__pyx_n_s__filter), __pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_7), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __pyx_t_13 = PyTuple_New(2); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
__Pyx_INCREF(__pyx_v_label);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_label);
+ PyTuple_SET_ITEM(__pyx_t_13, 0, __pyx_v_label);
__Pyx_GIVEREF(__pyx_v_label);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_12);
- __Pyx_GIVEREF(__pyx_t_12);
- __pyx_t_12 = 0;
- __pyx_t_12 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_12));
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, ((PyObject *)__pyx_t_12));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_12));
- __pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 550; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_12);
+ PyTuple_SET_ITEM(__pyx_t_13, 1, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_84), ((PyObject *)__pyx_t_13)); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_14));
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __pyx_t_13 = PyTuple_New(1); if (unlikely(!__pyx_t_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_13);
+ PyTuple_SET_ITEM(__pyx_t_13, 0, ((PyObject *)__pyx_t_14));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_14));
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_13), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_13)); __pyx_t_13 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
@@ -11694,8 +11927,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObjec
__Pyx_XDECREF(__pyx_t_3);
__Pyx_XDECREF(__pyx_t_4);
__Pyx_XDECREF(__pyx_t_7);
- __Pyx_XDECREF(__pyx_t_10);
- __Pyx_XDECREF(__pyx_t_12);
+ __Pyx_XDECREF(__pyx_t_13);
+ __Pyx_XDECREF(__pyx_t_14);
__Pyx_AddTraceback("pysam.cvcf.VCF.write_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = NULL;
__pyx_L0:;
@@ -11715,12 +11948,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_21parse_heading = {__Pyx_NAMESTR
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_heading (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -11734,18 +11966,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_heading") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_heading") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -11758,7 +11988,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_heading", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_heading", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -11769,7 +11999,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_21parse_heading(PyObject *__pyx_self
return __pyx_r;
}
-/* "pysam/cvcf.pyx":553
+/* "pysam/cvcf.pyx":556
*
*
* def parse_heading( self, line ): # <<<<<<<<<<<<<<
@@ -11802,7 +12032,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("parse_heading", 0);
- /* "pysam/cvcf.pyx":554
+ /* "pysam/cvcf.pyx":557
*
* def parse_heading( self, line ):
* assert line.startswith('#') # <<<<<<<<<<<<<<
@@ -11810,20 +12040,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
* headings = line[1:].split('\t')
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_86), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (unlikely(!__pyx_t_3)) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/cvcf.pyx":555
+ /* "pysam/cvcf.pyx":558
* def parse_heading( self, line ):
* assert line.startswith('#')
* assert not line.startswith('##') # <<<<<<<<<<<<<<
@@ -11831,56 +12061,56 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
* # test for 8, as FORMAT field might be missing
*/
#ifndef CYTHON_WITHOUT_ASSERTIONS
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_87), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_87), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (unlikely(!(!__pyx_t_3))) {
PyErr_SetNone(PyExc_AssertionError);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/cvcf.pyx":556
+ /* "pysam/cvcf.pyx":559
* assert line.startswith('#')
* assert not line.startswith('##')
* headings = line[1:].split('\t') # <<<<<<<<<<<<<<
* # test for 8, as FORMAT field might be missing
* if len(headings)==1 and len(line[1:].split()) >= 8:
*/
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_89), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_headings = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":558
+ /* "pysam/cvcf.pyx":561
* headings = line[1:].split('\t')
* # test for 8, as FORMAT field might be missing
* if len(headings)==1 and len(line[1:].split()) >= 8: # <<<<<<<<<<<<<<
* self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
* headings = line[1:].split()
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_3 = (__pyx_t_4 == 1);
if (__pyx_t_3) {
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 561; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_5 = (__pyx_t_4 >= 8);
__pyx_t_6 = __pyx_t_5;
@@ -11889,18 +12119,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
}
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":559
+ /* "pysam/cvcf.pyx":562
* # test for 8, as FORMAT field might be missing
* if len(headings)==1 and len(line[1:].split()) >= 8:
* self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS) # <<<<<<<<<<<<<<
* headings = line[1:].split()
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_90); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_90); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
@@ -11908,25 +12138,25 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":560
+ /* "pysam/cvcf.pyx":563
* if len(headings)==1 and len(line[1:].split()) >= 8:
* self.error(line,self.HEADING_NOT_SEPARATED_BY_TABS)
* headings = line[1:].split() # <<<<<<<<<<<<<<
*
* for i,s in enumerate(self._required):
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_line, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 560; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 563; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_v_headings);
@@ -11936,7 +12166,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":562
+ /* "pysam/cvcf.pyx":565
* headings = line[1:].split()
*
* for i,s in enumerate(self._required): # <<<<<<<<<<<<<<
@@ -11945,13 +12175,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
*/
__Pyx_INCREF(__pyx_int_0);
__pyx_t_2 = __pyx_int_0;
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___required); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___required); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
__pyx_t_1 = __pyx_t_7; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
__pyx_t_8 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_8 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
@@ -11959,16 +12189,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
for (;;) {
if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_7); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_7 = __pyx_t_8(__pyx_t_1);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -11980,34 +12218,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
__Pyx_INCREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_i);
__pyx_v_i = __pyx_t_2;
- __pyx_t_7 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 562; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 565; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2);
__pyx_t_2 = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":564
+ /* "pysam/cvcf.pyx":567
* for i,s in enumerate(self._required):
*
* if len(headings)<=i or headings[i] != s: # <<<<<<<<<<<<<<
*
* if len(headings) <= i:
*/
- __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (!__pyx_t_6) {
- __pyx_t_10 = PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_10, __pyx_v_s, Py_NE); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_10, __pyx_v_s, Py_NE); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_5 = __pyx_t_3;
} else {
@@ -12015,33 +12251,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
}
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":566
+ /* "pysam/cvcf.pyx":569
* if len(headings)<=i or headings[i] != s:
*
* if len(headings) <= i: # <<<<<<<<<<<<<<
* err = "(%sth entry not found)" % (i+1)
* else:
*/
- __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_9); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_7, __pyx_v_i, Py_LE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 566; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":567
+ /* "pysam/cvcf.pyx":570
*
* if len(headings) <= i:
* err = "(%sth entry not found)" % (i+1) # <<<<<<<<<<<<<<
* else:
* err = "(found %s, expected %s)" % (headings[i],s)
*/
- __pyx_t_10 = PyNumber_Add(__pyx_v_i, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_v_i, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_91), __pyx_t_10); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 567; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_91), __pyx_t_10); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 570; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_v_err);
@@ -12051,16 +12286,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
}
/*else*/ {
- /* "pysam/cvcf.pyx":569
+ /* "pysam/cvcf.pyx":572
* err = "(%sth entry not found)" % (i+1)
* else:
* err = "(found %s, expected %s)" % (headings[i],s) # <<<<<<<<<<<<<<
*
* #self.error(line,self.BADLY_FORMATTED_HEADING,err)
*/
- __pyx_t_7 = PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_headings, __pyx_v_i); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
@@ -12068,7 +12303,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_s);
__Pyx_GIVEREF(__pyx_v_s);
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_92), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_92), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 572; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_v_err);
@@ -12077,43 +12312,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":573
+ /* "pysam/cvcf.pyx":576
* #self.error(line,self.BADLY_FORMATTED_HEADING,err)
* # allow FORMAT column to be absent
* if len(headings) == 8: # <<<<<<<<<<<<<<
* headings.append("FORMAT")
* else:
*/
- __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Length(__pyx_v_headings); if (unlikely(__pyx_t_9 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_9 == 8);
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":574
+ /* "pysam/cvcf.pyx":577
* # allow FORMAT column to be absent
* if len(headings) == 8:
* headings.append("FORMAT") # <<<<<<<<<<<<<<
* else:
* self.error(line,self.BADLY_FORMATTED_HEADING,err)
*/
- __pyx_t_7 = __Pyx_PyObject_Append(__pyx_v_headings, ((PyObject *)__pyx_n_s__FORMAT)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 574; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_Append(__pyx_v_headings, ((PyObject *)__pyx_n_s__FORMAT)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 577; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L8;
}
/*else*/ {
- /* "pysam/cvcf.pyx":576
+ /* "pysam/cvcf.pyx":579
* headings.append("FORMAT")
* else:
* self.error(line,self.BADLY_FORMATTED_HEADING,err) # <<<<<<<<<<<<<<
*
* self._samples = headings[9:]
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_93); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_93); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_11 = PyTuple_New(3); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyTuple_New(3); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_v_line);
@@ -12124,7 +12359,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
PyTuple_SET_ITEM(__pyx_t_11, 2, __pyx_v_err);
__Pyx_GIVEREF(__pyx_v_err);
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 576; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_11), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
@@ -12138,36 +12373,36 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":578
+ /* "pysam/cvcf.pyx":581
* self.error(line,self.BADLY_FORMATTED_HEADING,err)
*
* self._samples = headings[9:] # <<<<<<<<<<<<<<
* self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
*
*/
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_headings, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_headings, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 578; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":579
+ /* "pysam/cvcf.pyx":582
*
* self._samples = headings[9:]
* self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] ) # <<<<<<<<<<<<<<
*
* def write_heading( self, stream ):
*/
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_int_0);
__pyx_t_1 = __pyx_int_0;
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
if (PyList_CheckExact(__pyx_t_10) || PyTuple_CheckExact(__pyx_t_10)) {
__pyx_t_11 = __pyx_t_10; __Pyx_INCREF(__pyx_t_11); __pyx_t_4 = 0;
__pyx_t_8 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_t_10); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_t_10); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__pyx_t_8 = Py_TYPE(__pyx_t_11)->tp_iternext;
}
@@ -12175,16 +12410,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
for (;;) {
if (!__pyx_t_8 && PyList_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_11)) break;
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_8 && PyTuple_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_11)) break;
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_10 = __pyx_t_8(__pyx_t_11);
if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -12196,14 +12439,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
__Pyx_INCREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_v_x);
__pyx_v_x = __pyx_t_1;
- __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1);
__pyx_t_1 = __pyx_t_10;
__pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Add(__pyx_v_x, __pyx_int_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_v_x, __pyx_int_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_y);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_y);
@@ -12211,21 +12454,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObje
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_t_2));
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyDict_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyDict_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___sample2column, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
@@ -12256,12 +12499,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_23write_heading = {__Pyx_NAMESTR
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write_heading (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -12275,18 +12517,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write_heading") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write_heading") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -12299,7 +12539,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_heading", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.write_heading", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -12310,7 +12550,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_23write_heading(PyObject *__pyx_self
return __pyx_r;
}
-/* "pysam/cvcf.pyx":581
+/* "pysam/cvcf.pyx":584
* self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
*
* def write_heading( self, stream ): # <<<<<<<<<<<<<<
@@ -12331,46 +12571,46 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObje
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("write_heading", 0);
- /* "pysam/cvcf.pyx":582
+ /* "pysam/cvcf.pyx":585
*
* def write_heading( self, stream ):
* stream.write("#" + "\t".join(self._required + self._samples) + "\n") # <<<<<<<<<<<<<<
*
* def convertGT(self, GTstring):
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_88), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_88), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___required); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___required); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Add(__pyx_t_3, __pyx_t_4); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- __pyx_t_4 = PyNumber_Add(((PyObject *)__pyx_kp_s_85), __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyNumber_Add(((PyObject *)__pyx_kp_s_85), __pyx_t_5); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyNumber_Add(__pyx_t_4, ((PyObject *)__pyx_kp_s_94)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_Add(__pyx_t_4, ((PyObject *)__pyx_kp_s_94)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 582; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
@@ -12398,12 +12638,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_25convertGT = {__Pyx_NAMESTR("co
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_GTstring = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTstring,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("convertGT (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTstring,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -12417,18 +12656,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, Py
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTstring);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTstring)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "convertGT") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "convertGT") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -12441,7 +12678,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("convertGT", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -12452,7 +12689,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_25convertGT(PyObject *__pyx_self, Py
return __pyx_r;
}
-/* "pysam/cvcf.pyx":584
+/* "pysam/cvcf.pyx":587
* stream.write("#" + "\t".join(self._required + self._samples) + "\n")
*
* def convertGT(self, GTstring): # <<<<<<<<<<<<<<
@@ -12464,8 +12701,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
PyObject *__pyx_v_gts = NULL;
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
- int __pyx_t_1;
- PyObject *__pyx_t_2 = NULL;
+ PyObject *__pyx_t_1 = NULL;
+ int __pyx_t_2;
PyObject *__pyx_t_3 = NULL;
PyObject *__pyx_t_4 = NULL;
PyObject *__pyx_t_5 = NULL;
@@ -12485,29 +12722,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("convertGT", 0);
- /* "pysam/cvcf.pyx":585
+ /* "pysam/cvcf.pyx":588
*
* def convertGT(self, GTstring):
* if GTstring == ".": return ["."] # <<<<<<<<<<<<<<
* try:
* gts = gtsRegEx.split(GTstring)
*/
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_t_1) {
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_GTstring, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
- PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_9));
+ PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L3;
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":586
+ /* "pysam/cvcf.pyx":589
* def convertGT(self, GTstring):
* if GTstring == ".": return ["."]
* try: # <<<<<<<<<<<<<<
@@ -12521,127 +12760,131 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
__Pyx_XGOTREF(__pyx_t_5);
/*try:*/ {
- /* "pysam/cvcf.pyx":587
+ /* "pysam/cvcf.pyx":590
* if GTstring == ".": return ["."]
* try:
* gts = gtsRegEx.split(GTstring) # <<<<<<<<<<<<<<
* if len(gts) == 1: return [int(gts[0])]
* if len(gts) != 2: raise ValueError()
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__gtsRegEx); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_6 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__gtsRegEx); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_6 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_GTstring);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_GTstring);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_GTstring);
__Pyx_GIVEREF(__pyx_v_GTstring);
- __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_6, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_gts = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":588
+ /* "pysam/cvcf.pyx":591
* try:
* gts = gtsRegEx.split(GTstring)
* if len(gts) == 1: return [int(gts[0])] # <<<<<<<<<<<<<<
* if len(gts) != 2: raise ValueError()
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
*/
- __pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_1 = (__pyx_t_8 == 1);
- if (__pyx_t_1) {
+ __pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_2 = (__pyx_t_8 == 1);
+ if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 588; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyList_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
goto __pyx_L8_try_return;
goto __pyx_L12;
}
__pyx_L12:;
- /* "pysam/cvcf.pyx":589
+ /* "pysam/cvcf.pyx":592
* gts = gtsRegEx.split(GTstring)
* if len(gts) == 1: return [int(gts[0])]
* if len(gts) != 2: raise ValueError() # <<<<<<<<<<<<<<
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
*/
- __pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __pyx_t_1 = (__pyx_t_8 != 2);
- if (__pyx_t_1) {
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_Raise(__pyx_t_2, 0, 0, 0);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_8 = PyObject_Length(__pyx_v_gts); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_2 = (__pyx_t_8 != 2);
+ if (__pyx_t_2) {
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_Raise(__pyx_t_1, 0, 0, 0);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
goto __pyx_L13;
}
__pyx_L13:;
- /* "pysam/cvcf.pyx":590
+ /* "pysam/cvcf.pyx":593
* if len(gts) == 1: return [int(gts[0])]
* if len(gts) != 2: raise ValueError()
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]] # <<<<<<<<<<<<<<
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
* except ValueError:
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (__pyx_t_1) {
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = __Pyx_PyString_Equals(__pyx_t_2, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ if (__pyx_t_2) {
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_10 = __pyx_t_9;
} else {
- __pyx_t_10 = __pyx_t_1;
+ __pyx_t_10 = __pyx_t_2;
}
if (__pyx_t_10) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_8 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_11 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_11 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_GTstring, __pyx_t_8, (-__pyx_t_11)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_GTstring, __pyx_t_8, (-__pyx_t_11)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_12 = PyList_New(3); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 590; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_12 = PyList_New(3); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_12);
- PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_12, 0, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
PyList_SET_ITEM(__pyx_t_12, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
PyList_SET_ITEM(__pyx_t_12, 2, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- __pyx_t_2 = 0;
+ __pyx_t_1 = 0;
__pyx_t_7 = 0;
__pyx_t_6 = 0;
__pyx_r = ((PyObject *)__pyx_t_12);
@@ -12651,7 +12894,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
}
__pyx_L14:;
- /* "pysam/cvcf.pyx":591
+ /* "pysam/cvcf.pyx":594
* if len(gts) != 2: raise ValueError()
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])] # <<<<<<<<<<<<<<
@@ -12659,49 +12902,49 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
* self.error(self._line,self.BAD_GENOTYPE,GTstring)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_12) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_12 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_12) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_12);
- __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = PyTuple_New(1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_12);
__Pyx_GIVEREF(__pyx_t_12);
__pyx_t_12 = 0;
- __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_12 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_6), NULL); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_12);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_11 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_11 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_8 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_8 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_8 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_GTstring, __pyx_t_11, (-__pyx_t_8)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_GTstring, __pyx_t_11, (-__pyx_t_8)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_gts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_7);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyList_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 591; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
- __Pyx_GOTREF(__pyx_t_2);
- PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_12);
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ __pyx_t_1 = PyList_New(3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ PyList_SET_ITEM(__pyx_t_1, 0, __pyx_t_12);
__Pyx_GIVEREF(__pyx_t_12);
- PyList_SET_ITEM(__pyx_t_2, 1, __pyx_t_6);
+ PyList_SET_ITEM(__pyx_t_1, 1, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
- PyList_SET_ITEM(__pyx_t_2, 2, __pyx_t_7);
+ PyList_SET_ITEM(__pyx_t_1, 2, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_12 = 0;
__pyx_t_6 = 0;
__pyx_t_7 = 0;
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
goto __pyx_L8_try_return;
}
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
@@ -12718,9 +12961,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
__Pyx_XDECREF(__pyx_t_12); __pyx_t_12 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":592
+ /* "pysam/cvcf.pyx":595
* if gts[0] == "." and gts[1] == ".": return [gts[0],GTstring[len(gts[0]):-len(gts[1])],gts[1]]
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
* except ValueError: # <<<<<<<<<<<<<<
@@ -12730,25 +12973,25 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
__pyx_t_13 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_13) {
__Pyx_AddTraceback("pysam.cvcf.VCF.convertGT", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_2, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 592; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ if (__Pyx_GetException(&__pyx_t_1, &__pyx_t_7, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 595; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_6);
- /* "pysam/cvcf.pyx":593
+ /* "pysam/cvcf.pyx":596
* return [int(gts[0]),GTstring[len(gts[0]):-len(gts[1])],int(gts[1])]
* except ValueError:
* self.error(self._line,self.BAD_GENOTYPE,GTstring) # <<<<<<<<<<<<<<
* return [".","|","."]
*
*/
- __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_12 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_12);
- __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___line); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___line); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_14);
- __pyx_t_15 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__BAD_GENOTYPE); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_15 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__BAD_GENOTYPE); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_16 = PyTuple_New(3); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_16 = PyTuple_New(3); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_16);
PyTuple_SET_ITEM(__pyx_t_16, 0, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
@@ -12759,13 +13002,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
__Pyx_GIVEREF(__pyx_v_GTstring);
__pyx_t_14 = 0;
__pyx_t_15 = 0;
- __pyx_t_15 = PyObject_Call(__pyx_t_12, ((PyObject *)__pyx_t_16), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_15 = PyObject_Call(__pyx_t_12, ((PyObject *)__pyx_t_16), NULL); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_16)); __pyx_t_16 = 0;
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
- /* "pysam/cvcf.pyx":594
+ /* "pysam/cvcf.pyx":597
* except ValueError:
* self.error(self._line,self.BAD_GENOTYPE,GTstring)
* return [".","|","."] # <<<<<<<<<<<<<<
@@ -12773,7 +13016,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
* def convertGTback(self, GTdata):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_15 = PyList_New(3); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 594; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
+ __pyx_t_15 = PyList_New(3); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;}
__Pyx_GOTREF(__pyx_t_15);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
PyList_SET_ITEM(__pyx_t_15, 0, ((PyObject *)__pyx_kp_s_9));
@@ -12786,11 +13029,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__pyx_r = ((PyObject *)__pyx_t_15);
__pyx_t_15 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L7_except_return;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
goto __pyx_L5_exception_handled;
@@ -12818,7 +13061,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
__pyx_L1_error:;
- __Pyx_XDECREF(__pyx_t_2);
+ __Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_6);
__Pyx_XDECREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_t_12);
@@ -12840,12 +13083,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_27convertGTback = {__Pyx_NAMESTR
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
CYTHON_UNUSED PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_GTdata = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTdata,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("convertGTback (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__GTdata,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -12859,18 +13101,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTdata);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__GTdata)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "convertGTback") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "convertGTback") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -12883,7 +13123,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("convertGTback", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.convertGTback", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -12894,7 +13134,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_27convertGTback(PyObject *__pyx_self
return __pyx_r;
}
-/* "pysam/cvcf.pyx":596
+/* "pysam/cvcf.pyx":599
* return [".","|","."]
*
* def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
@@ -12913,7 +13153,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObje
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("convertGTback", 0);
- /* "pysam/cvcf.pyx":597
+ /* "pysam/cvcf.pyx":600
*
* def convertGTback(self, GTdata):
* return ''.join(map(str,GTdata)) # <<<<<<<<<<<<<<
@@ -12921,9 +13161,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObje
* def parse_formatdata( self, key, value, formatdict, line ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_1), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)((PyObject*)(&PyString_Type))));
@@ -12931,15 +13171,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObje
__Pyx_INCREF(__pyx_v_GTdata);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_GTdata);
__Pyx_GIVEREF(__pyx_v_GTdata);
- __pyx_t_3 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 600; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -12970,12 +13210,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_s
PyObject *__pyx_v_value = 0;
PyObject *__pyx_v_formatdict = 0;
PyObject *__pyx_v_line = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__formatdict,&__pyx_n_s__line,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_formatdata (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__key,&__pyx_n_s__value,&__pyx_n_s__formatdict,&__pyx_n_s__line,0};
PyObject* values[5] = {0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -12992,36 +13231,31 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_s
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__key)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__value)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__formatdict)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[4])) kw_args--;
+ if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_formatdata") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_formatdata") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 5) {
goto __pyx_L5_argtuple_error;
@@ -13040,7 +13274,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_s
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_formatdata", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -13051,7 +13285,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_29parse_formatdata(PyObject *__pyx_s
return __pyx_r;
}
-/* "pysam/cvcf.pyx":599
+/* "pysam/cvcf.pyx":602
* return ''.join(map(str,GTdata))
*
* def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
@@ -13090,16 +13324,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("parse_formatdata", 0);
- /* "pysam/cvcf.pyx":601
+ /* "pysam/cvcf.pyx":604
* def parse_formatdata( self, key, value, formatdict, line ):
* # To do: check that the right number of values is present
* f = formatdict.get(key,None) # <<<<<<<<<<<<<<
* if f == None:
* self._add_definition(formatdict, key, value, line )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_formatdict, __pyx_n_s__get); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_formatdict, __pyx_n_s__get); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_key);
@@ -13107,36 +13341,35 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_INCREF(Py_None);
PyTuple_SET_ITEM(__pyx_t_2, 1, Py_None);
__Pyx_GIVEREF(Py_None);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 601; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_v_f = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":602
+ /* "pysam/cvcf.pyx":605
* # To do: check that the right number of values is present
* f = formatdict.get(key,None)
* if f == None: # <<<<<<<<<<<<<<
* self._add_definition(formatdict, key, value, line )
* f = formatdict[key]
*/
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_f, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":603
+ /* "pysam/cvcf.pyx":606
* f = formatdict.get(key,None)
* if f == None:
* self._add_definition(formatdict, key, value, line ) # <<<<<<<<<<<<<<
* f = formatdict[key]
* if f.type == "Flag":
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___add_definition); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___add_definition); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_formatdict);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_formatdict);
@@ -13150,20 +13383,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 603; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":604
+ /* "pysam/cvcf.pyx":607
* if f == None:
* self._add_definition(formatdict, key, value, line )
* f = formatdict[key] # <<<<<<<<<<<<<<
* if f.type == "Flag":
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_formatdict, __pyx_v_key); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 604; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_formatdict, __pyx_v_key); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_f);
__pyx_v_f = __pyx_t_1;
@@ -13172,20 +13405,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":605
+ /* "pysam/cvcf.pyx":608
* self._add_definition(formatdict, key, value, line )
* f = formatdict[key]
* if f.type == "Flag": # <<<<<<<<<<<<<<
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
* return []
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 605; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, ((PyObject *)__pyx_n_s__Flag), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- /* "pysam/cvcf.pyx":606
+ /* "pysam/cvcf.pyx":609
* f = formatdict[key]
* if f.type == "Flag":
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE) # <<<<<<<<<<<<<<
@@ -13194,28 +13429,28 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
*/
__pyx_t_4 = (__pyx_v_value != Py_None);
if (__pyx_t_4) {
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_96); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_96); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 606; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1);
+ __Pyx_GIVEREF(__pyx_t_1);
+ __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 609; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L5;
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":607
+ /* "pysam/cvcf.pyx":610
* if f.type == "Flag":
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
* return [] # <<<<<<<<<<<<<<
@@ -13223,42 +13458,46 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
* # deal with trailing data in some early VCF files
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_r = ((PyObject *)__pyx_t_2);
- __pyx_t_2 = 0;
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_r = ((PyObject *)__pyx_t_1);
+ __pyx_t_1 = 0;
goto __pyx_L0;
goto __pyx_L4;
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":608
+ /* "pysam/cvcf.pyx":611
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
* return []
* values = value.split(',') # <<<<<<<<<<<<<<
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_value, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_97), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_values = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":610
+ /* "pysam/cvcf.pyx":613
* values = value.split(',')
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<<
* self.error(line,self.ERROR_TRAILING_DATA,values[-1])
* values[-1] = values[-1].split(';')[0]
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_4 = __Pyx_PyString_Equals(__pyx_t_3, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_4 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (!((int)__pyx_t_4)) {
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_3, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely((__pyx_t_5 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_6 = ((int)__pyx_t_5);
} else {
__pyx_t_6 = ((int)__pyx_t_4);
@@ -13266,22 +13505,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__pyx_t_4 = __pyx_t_6;
if (__pyx_t_4) {
- __pyx_t_7 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = (__pyx_t_7 > 0);
if (__pyx_t_6) {
- __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__find); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_t_3, __pyx_n_s__find); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_98), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_3, __pyx_int_neg_1, Py_GT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, __pyx_int_neg_1, Py_GT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_8 = __pyx_t_5;
} else {
__pyx_t_8 = __pyx_t_6;
@@ -13292,74 +13530,76 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
}
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":611
+ /* "pysam/cvcf.pyx":614
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
* self.error(line,self.ERROR_TRAILING_DATA,values[-1]) # <<<<<<<<<<<<<<
* values[-1] = values[-1].split(';')[0]
* if f.type == "Integer":
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_TRAILING_DATA); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_TRAILING_DATA); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
- PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_1);
- __Pyx_GIVEREF(__pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__pyx_t_3 = 0;
- __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":612
+ /* "pysam/cvcf.pyx":615
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
* self.error(line,self.ERROR_TRAILING_DATA,values[-1])
* values[-1] = values[-1].split(';')[0] # <<<<<<<<<<<<<<
* if f.type == "Integer":
* for idx,v in enumerate(values):
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_values, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_99), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_1, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_t_2, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (__Pyx_SetItemInt(__pyx_v_values, -1, __pyx_t_9, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ if (__Pyx_SetItemInt(__pyx_v_values, -1, __pyx_t_9, sizeof(long), PyInt_FromLong) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L6;
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":613
+ /* "pysam/cvcf.pyx":616
* self.error(line,self.ERROR_TRAILING_DATA,values[-1])
* values[-1] = values[-1].split(';')[0]
* if f.type == "Integer": # <<<<<<<<<<<<<<
* for idx,v in enumerate(values):
* try:
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Integer), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__Integer), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":614
+ /* "pysam/cvcf.pyx":617
* values[-1] = values[-1].split(';')[0]
* if f.type == "Integer":
* for idx,v in enumerate(values): # <<<<<<<<<<<<<<
@@ -13367,46 +13607,54 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
* if v == ".": values[idx] = f.missingvalue
*/
__Pyx_INCREF(__pyx_int_0);
- __pyx_t_9 = __pyx_int_0;
+ __pyx_t_2 = __pyx_int_0;
if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
- __pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_7 = 0;
+ __pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_7 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_10 = Py_TYPE(__pyx_t_1)->tp_iternext;
+ __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_1)) {
- if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_1)) {
- if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_10(__pyx_t_1);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_1 = __pyx_t_10(__pyx_t_9);
+ if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_1);
}
__Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_2;
- __pyx_t_2 = 0;
- __Pyx_INCREF(__pyx_t_9);
+ __pyx_v_v = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __Pyx_INCREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_v_idx);
- __pyx_v_idx = __pyx_t_9;
- __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_9);
- __pyx_t_9 = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_idx = __pyx_t_2;
+ __pyx_t_1 = PyNumber_Add(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_2);
+ __pyx_t_2 = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":615
+ /* "pysam/cvcf.pyx":618
* if f.type == "Integer":
* for idx,v in enumerate(values):
* try: # <<<<<<<<<<<<<<
@@ -13420,39 +13668,41 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_XGOTREF(__pyx_t_13);
/*try:*/ {
- /* "pysam/cvcf.pyx":616
+ /* "pysam/cvcf.pyx":619
* for idx,v in enumerate(values):
* try:
* if v == ".": values[idx] = f.missingvalue # <<<<<<<<<<<<<<
* else: values[idx] = int(v)
* except:
*/
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_6) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 616; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L18;
}
/*else*/ {
- /* "pysam/cvcf.pyx":617
+ /* "pysam/cvcf.pyx":620
* try:
* if v == ".": values[idx] = f.missingvalue
* else: values[idx] = int(v) # <<<<<<<<<<<<<<
* except:
* self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
*/
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_v);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_v);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_v);
__Pyx_GIVEREF(__pyx_v_v);
- __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 617; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L10_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
}
__pyx_L18:;
@@ -13462,10 +13712,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
goto __pyx_L17_try_end;
__pyx_L10_error:;
- __Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":618
+ /* "pysam/cvcf.pyx":621
* if v == ".": values[idx] = f.missingvalue
* else: values[idx] = int(v)
* except: # <<<<<<<<<<<<<<
@@ -13474,31 +13724,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_2, &__pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 618; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ if (__Pyx_GetException(&__pyx_t_3, &__pyx_t_1, &__pyx_t_14) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 621; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_GOTREF(__pyx_t_14);
- /* "pysam/cvcf.pyx":619
+ /* "pysam/cvcf.pyx":622
* else: values[idx] = int(v)
* except:
* self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values))) # <<<<<<<<<<<<<<
* return [0] * len(values)
* return values
*/
- __pyx_t_15 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_15 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_15);
- __pyx_t_16 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_100); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_16 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_100); if (unlikely(!__pyx_t_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_16);
- __pyx_t_17 = PyTuple_New(1); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_17 = PyTuple_New(1); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_17);
__Pyx_INCREF(__pyx_v_values);
PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_v_values);
__Pyx_GIVEREF(__pyx_v_values);
- __pyx_t_18 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_17), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_18 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_17), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_DECREF(((PyObject *)__pyx_t_17)); __pyx_t_17 = 0;
- __pyx_t_17 = PyTuple_New(2); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_17 = PyTuple_New(2); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_17);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_v_key);
@@ -13506,10 +13756,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
PyTuple_SET_ITEM(__pyx_t_17, 1, __pyx_t_18);
__Pyx_GIVEREF(__pyx_t_18);
__pyx_t_18 = 0;
- __pyx_t_18 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_17)); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_18 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_17)); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_18));
__Pyx_DECREF(((PyObject *)__pyx_t_17)); __pyx_t_17 = 0;
- __pyx_t_17 = PyTuple_New(3); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_17 = PyTuple_New(3); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_17);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_17, 0, __pyx_v_line);
@@ -13520,13 +13770,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_GIVEREF(((PyObject *)__pyx_t_18));
__pyx_t_16 = 0;
__pyx_t_18 = 0;
- __pyx_t_18 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_17), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 619; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_18 = PyObject_Call(__pyx_t_15, ((PyObject *)__pyx_t_17), NULL); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_17)); __pyx_t_17 = 0;
__Pyx_DECREF(__pyx_t_18); __pyx_t_18 = 0;
- /* "pysam/cvcf.pyx":620
+ /* "pysam/cvcf.pyx":623
* except:
* self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
* return [0] * len(values) # <<<<<<<<<<<<<<
@@ -13534,8 +13784,8 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
* elif f.type == "String":
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_19 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
- __pyx_t_18 = PyList_New(1 * ((__pyx_t_19<0) ? 0:__pyx_t_19)); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 620; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_19 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 623; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
+ __pyx_t_18 = PyList_New(1 * ((__pyx_t_19<0) ? 0:__pyx_t_19)); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 623; __pyx_clineno = __LINE__; goto __pyx_L12_except_error;}
__Pyx_GOTREF(__pyx_t_18);
{ Py_ssize_t __pyx_temp;
for (__pyx_temp=0; __pyx_temp < __pyx_t_19; __pyx_temp++) {
@@ -13553,7 +13803,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L13_except_return;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L11_exception_handled;
}
@@ -13577,10 +13827,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__pyx_L17_try_end:;
}
}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":621
+ /* "pysam/cvcf.pyx":624
* self.error(line,self.ERROR_FORMAT_NOT_INTEGER,"%s=%s" % (key, str(values)))
* return [0] * len(values)
* return values # <<<<<<<<<<<<<<
@@ -13594,69 +13844,73 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
goto __pyx_L7;
}
- /* "pysam/cvcf.pyx":622
+ /* "pysam/cvcf.pyx":625
* return [0] * len(values)
* return values
* elif f.type == "String": # <<<<<<<<<<<<<<
* self._line = line
* if f.id == "GT": values = list(map( self.convertGT, values ))
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__String), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 622; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__String), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 625; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":623
+ /* "pysam/cvcf.pyx":626
* return values
* elif f.type == "String":
* self._line = line # <<<<<<<<<<<<<<
* if f.id == "GT": values = list(map( self.convertGT, values ))
* return values
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___line, __pyx_v_line) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 623; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___line, __pyx_v_line) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":624
+ /* "pysam/cvcf.pyx":627
* elif f.type == "String":
* self._line = line
* if f.id == "GT": values = list(map( self.convertGT, values )) # <<<<<<<<<<<<<<
* return values
* elif f.type == "Character":
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__id); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__GT), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__GT), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_6) {
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGT); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__convertGT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_values);
- PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_v_values);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_values);
__Pyx_GIVEREF(__pyx_v_values);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 624; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_v_values);
- __pyx_v_values = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_values = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L21;
}
__pyx_L21:;
- /* "pysam/cvcf.pyx":625
+ /* "pysam/cvcf.pyx":628
* self._line = line
* if f.id == "GT": values = list(map( self.convertGT, values ))
* return values # <<<<<<<<<<<<<<
@@ -13670,20 +13924,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
goto __pyx_L7;
}
- /* "pysam/cvcf.pyx":626
+ /* "pysam/cvcf.pyx":629
* if f.id == "GT": values = list(map( self.convertGT, values ))
* return values
* elif f.type == "Character": # <<<<<<<<<<<<<<
* for v in values:
* if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Character), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 626; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_2, ((PyObject *)__pyx_n_s__Character), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 629; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":627
+ /* "pysam/cvcf.pyx":630
* return values
* elif f.type == "Character":
* for v in values: # <<<<<<<<<<<<<<
@@ -13694,58 +13950,66 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
for (;;) {
if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_1 = __pyx_t_10(__pyx_t_9);
- if (unlikely(!__pyx_t_1)) {
+ __pyx_t_2 = __pyx_t_10(__pyx_t_9);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 627; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_1;
- __pyx_t_1 = 0;
+ __pyx_v_v = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":628
+ /* "pysam/cvcf.pyx":631
* elif f.type == "Character":
* for v in values:
* if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR) # <<<<<<<<<<<<<<
* return values
* elif f.type == "Float":
*/
- __pyx_t_19 = PyObject_Length(__pyx_v_v); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = PyObject_Length(__pyx_v_v); if (unlikely(__pyx_t_19 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_6 = (__pyx_t_19 != 1);
if (__pyx_t_6) {
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_101); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_101); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_14);
+ PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_14);
__Pyx_GIVEREF(__pyx_t_14);
__pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 628; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L24;
}
@@ -13753,7 +14017,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":629
+ /* "pysam/cvcf.pyx":632
* for v in values:
* if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
* return values # <<<<<<<<<<<<<<
@@ -13767,20 +14031,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
goto __pyx_L7;
}
- /* "pysam/cvcf.pyx":630
+ /* "pysam/cvcf.pyx":633
* if len(v) != 1: self.error(line,self.ERROR_FORMAT_NOT_CHAR)
* return values
* elif f.type == "Float": # <<<<<<<<<<<<<<
* for idx,v in enumerate(values):
* if v == ".": values[idx] = f.missingvalue
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__type); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__Float), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 630; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__Float), Py_EQ); __Pyx_XGOTREF(__pyx_t_14); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_14); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":631
+ /* "pysam/cvcf.pyx":634
* return values
* elif f.type == "Float":
* for idx,v in enumerate(values): # <<<<<<<<<<<<<<
@@ -13788,66 +14054,76 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
* try: return list(map(float,values))
*/
__Pyx_INCREF(__pyx_int_0);
- __pyx_t_9 = __pyx_int_0;
+ __pyx_t_14 = __pyx_int_0;
if (PyList_CheckExact(__pyx_v_values) || PyTuple_CheckExact(__pyx_v_values)) {
- __pyx_t_14 = __pyx_v_values; __Pyx_INCREF(__pyx_t_14); __pyx_t_7 = 0;
+ __pyx_t_9 = __pyx_v_values; __Pyx_INCREF(__pyx_t_9); __pyx_t_7 = 0;
__pyx_t_10 = NULL;
} else {
- __pyx_t_7 = -1; __pyx_t_14 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __pyx_t_10 = Py_TYPE(__pyx_t_14)->tp_iternext;
+ __pyx_t_7 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_14)) {
- if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_14)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_14, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
- } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_14)) {
- if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_14)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_14, __pyx_t_7); __Pyx_INCREF(__pyx_t_2); __pyx_t_7++;
+ if (!__pyx_t_10 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_10 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_7); __Pyx_INCREF(__pyx_t_1); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_9, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_10(__pyx_t_14);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_1 = __pyx_t_10(__pyx_t_9);
+ if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_1);
}
__Pyx_XDECREF(__pyx_v_v);
- __pyx_v_v = __pyx_t_2;
- __pyx_t_2 = 0;
- __Pyx_INCREF(__pyx_t_9);
- __Pyx_XDECREF(__pyx_v_idx);
- __pyx_v_idx = __pyx_t_9;
- __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 631; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_9);
- __pyx_t_9 = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_v = __pyx_t_1;
+ __pyx_t_1 = 0;
+ __Pyx_INCREF(__pyx_t_14);
+ __Pyx_XDECREF(__pyx_v_idx);
+ __pyx_v_idx = __pyx_t_14;
+ __pyx_t_1 = PyNumber_Add(__pyx_t_14, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __Pyx_DECREF(__pyx_t_14);
+ __pyx_t_14 = __pyx_t_1;
+ __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":632
+ /* "pysam/cvcf.pyx":635
* elif f.type == "Float":
* for idx,v in enumerate(values):
* if v == ".": values[idx] = f.missingvalue # <<<<<<<<<<<<<<
* try: return list(map(float,values))
* except:
*/
- __pyx_t_6 = __Pyx_PyString_Equals(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_v, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_6) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 632; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_f, __pyx_n_s__missingvalue); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ if (PyObject_SetItem(__pyx_v_values, __pyx_v_idx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L27;
}
__pyx_L27:;
}
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
- /* "pysam/cvcf.pyx":633
+ /* "pysam/cvcf.pyx":636
* for idx,v in enumerate(values):
* if v == ".": values[idx] = f.missingvalue
* try: return list(map(float,values)) # <<<<<<<<<<<<<<
@@ -13861,27 +14137,27 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_14 = PyTuple_New(2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __Pyx_GOTREF(__pyx_t_14);
__Pyx_INCREF(((PyObject *)((PyObject*)(&PyFloat_Type))));
- PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)((PyObject*)(&PyFloat_Type))));
+ PyTuple_SET_ITEM(__pyx_t_14, 0, ((PyObject *)((PyObject*)(&PyFloat_Type))));
__Pyx_GIVEREF(((PyObject *)((PyObject*)(&PyFloat_Type))));
__Pyx_INCREF(__pyx_v_values);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_values);
+ PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_v_values);
__Pyx_GIVEREF(__pyx_v_values);
- __pyx_t_14 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
- __Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
__Pyx_GOTREF(__pyx_t_9);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_14);
- __Pyx_GIVEREF(__pyx_t_14);
- __pyx_t_14 = 0;
- __pyx_t_14 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __pyx_t_14 = PyTuple_New(1); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
__Pyx_GOTREF(__pyx_t_14);
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
- __pyx_r = __pyx_t_14;
- __pyx_t_14 = 0;
+ PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyList_Type))), ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
+ __pyx_r = __pyx_t_9;
+ __pyx_t_9 = 0;
goto __pyx_L32_try_return;
}
__Pyx_XDECREF(__pyx_t_13); __pyx_t_13 = 0;
@@ -13900,12 +14176,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_XDECREF(__pyx_t_17); __pyx_t_17 = 0;
__Pyx_XDECREF(__pyx_t_18); __pyx_t_18 = 0;
__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
- __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":634
+ /* "pysam/cvcf.pyx":637
* if v == ".": values[idx] = f.missingvalue
* try: return list(map(float,values))
* except: # <<<<<<<<<<<<<<
@@ -13914,31 +14190,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_formatdata", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_14, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 634; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
- __Pyx_GOTREF(__pyx_t_14);
+ if (__Pyx_GetException(&__pyx_t_9, &__pyx_t_14, &__pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 637; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_GOTREF(__pyx_t_1);
- /* "pysam/cvcf.pyx":635
+ /* "pysam/cvcf.pyx":638
* try: return list(map(float,values))
* except:
* self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values))) # <<<<<<<<<<<<<<
* return [0.0] * len(values)
* else:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_102); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_18 = PyTuple_New(1); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_INCREF(__pyx_v_values);
PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_v_values);
__Pyx_GIVEREF(__pyx_v_values);
- __pyx_t_17 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_17 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_17);
__Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0;
- __pyx_t_18 = PyTuple_New(2); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_18 = PyTuple_New(2); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_INCREF(__pyx_v_key);
PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_v_key);
@@ -13946,10 +14222,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
PyTuple_SET_ITEM(__pyx_t_18, 1, __pyx_t_17);
__Pyx_GIVEREF(__pyx_t_17);
__pyx_t_17 = 0;
- __pyx_t_17 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_18)); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_17 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_59), ((PyObject *)__pyx_t_18)); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_17));
__Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0;
- __pyx_t_18 = PyTuple_New(3); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_18 = PyTuple_New(3); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_18);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_18, 0, __pyx_v_line);
@@ -13960,13 +14236,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_GIVEREF(((PyObject *)__pyx_t_17));
__pyx_t_3 = 0;
__pyx_t_17 = 0;
- __pyx_t_17 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_17 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_18), NULL); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 638; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_17);
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_18)); __pyx_t_18 = 0;
__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
- /* "pysam/cvcf.pyx":636
+ /* "pysam/cvcf.pyx":639
* except:
* self.error(line,self.ERROR_FORMAT_NOT_NUMERICAL,"%s=%s" % (key, str(values)))
* return [0.0] * len(values) # <<<<<<<<<<<<<<
@@ -13974,10 +14250,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
* # can't happen
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_17 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_17 = PyFloat_FromDouble(0.0); if (unlikely(!__pyx_t_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_17);
- __pyx_t_7 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
- __pyx_t_18 = PyList_New(1 * ((__pyx_t_7<0) ? 0:__pyx_t_7)); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 636; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_7 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_7 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_18 = PyList_New(1 * ((__pyx_t_7<0) ? 0:__pyx_t_7)); if (unlikely(!__pyx_t_18)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_18);
{ Py_ssize_t __pyx_temp;
for (__pyx_temp=0; __pyx_temp < __pyx_t_7; __pyx_temp++) {
@@ -13989,13 +14265,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
__Pyx_DECREF(__pyx_t_17); __pyx_t_17 = 0;
__pyx_r = ((PyObject *)__pyx_t_18);
__pyx_t_18 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
goto __pyx_L31_except_return;
- __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L29_exception_handled;
}
__pyx_L30_except_error:;
@@ -14021,30 +14297,30 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyO
}
/*else*/ {
- /* "pysam/cvcf.pyx":639
+ /* "pysam/cvcf.pyx":642
* else:
* # can't happen
* self.error(line,self.ERROR_INFO_STRING) # <<<<<<<<<<<<<<
*
* def inregion(self, chrom, pos):
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_14 = PyTuple_New(2); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_14 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_14);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_14, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_14, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_14), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 639; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_14)); __pyx_t_14 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_14);
+ __Pyx_GIVEREF(__pyx_t_14);
+ __pyx_t_14 = 0;
+ __pyx_t_14 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_14)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_14);
+ __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_14); __pyx_t_14 = 0;
}
__pyx_L7:;
@@ -14079,12 +14355,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyO
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_chrom = 0;
PyObject *__pyx_v_pos = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__chrom,&__pyx_n_s__pos,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("inregion (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__chrom,&__pyx_n_s__pos,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -14099,24 +14374,21 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyO
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "inregion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "inregion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -14131,7 +14403,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyO
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("inregion", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.inregion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -14142,7 +14414,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_31inregion(PyObject *__pyx_self, PyO
return __pyx_r;
}
-/* "pysam/cvcf.pyx":641
+/* "pysam/cvcf.pyx":644
* self.error(line,self.ERROR_INFO_STRING)
*
* def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
@@ -14168,21 +14440,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("inregion", 0);
- /* "pysam/cvcf.pyx":642
+ /* "pysam/cvcf.pyx":645
*
* def inregion(self, chrom, pos):
* if not self._regions: return True # <<<<<<<<<<<<<<
* for r in self._regions:
* if r[0] == chrom and r[1] <= pos < r[2]: return True
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___regions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___regions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (!__pyx_t_2);
if (__pyx_t_3) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 642; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -14191,20 +14463,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":643
+ /* "pysam/cvcf.pyx":646
* def inregion(self, chrom, pos):
* if not self._regions: return True
* for r in self._regions: # <<<<<<<<<<<<<<
* if r[0] == chrom and r[1] <= pos < r[2]: return True
* return False
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___regions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___regions); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyList_CheckExact(__pyx_t_1) || PyTuple_CheckExact(__pyx_t_1)) {
__pyx_t_4 = __pyx_t_1; __Pyx_INCREF(__pyx_t_4); __pyx_t_5 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = -1; __pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext;
}
@@ -14212,16 +14484,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
for (;;) {
if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyList_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_4)) {
if (__pyx_t_5 >= PyTuple_GET_SIZE(__pyx_t_4)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_4, __pyx_t_5); __Pyx_INCREF(__pyx_t_1); __pyx_t_5++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_4, __pyx_t_5); __pyx_t_5++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_1 = __pyx_t_6(__pyx_t_4);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 643; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 646; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -14231,35 +14511,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
__pyx_v_r = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":644
+ /* "pysam/cvcf.pyx":647
* if not self._regions: return True
* for r in self._regions:
* if r[0] == chrom and r[1] <= pos < r[2]: return True # <<<<<<<<<<<<<<
* return False
*
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_r, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_r, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_v_chrom, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
if (__pyx_t_3) {
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_r, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_r, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_7, __pyx_v_pos, Py_LE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__Pyx_PyObject_IsTrue(__pyx_t_1)) {
__Pyx_DECREF(__pyx_t_1);
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_r, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_r, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos, __pyx_t_8, Py_LT); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_9 = __pyx_t_2;
} else {
@@ -14267,7 +14544,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
}
if (__pyx_t_9) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -14279,7 +14556,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":645
+ /* "pysam/cvcf.pyx":648
* for r in self._regions:
* if r[0] == chrom and r[1] <= pos < r[2]: return True
* return False # <<<<<<<<<<<<<<
@@ -14287,7 +14564,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
* def parse_data( self, line, lineparse=False ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 645; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
@@ -14309,7 +14586,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *_
return __pyx_r;
}
-/* "pysam/cvcf.pyx":647
+/* "pysam/cvcf.pyx":650
* return False
*
* def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
@@ -14326,7 +14603,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("__defaults__", 0);
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_self)->__pyx_arg_lineparse);
PyTuple_SET_ITEM(__pyx_t_1, 0, __Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_self)->__pyx_arg_lineparse);
@@ -14354,12 +14631,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, P
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_lineparse = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__lineparse,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse_data (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__lineparse,0};
PyObject* values[3] = {0,0,0};
__pyx_defaults4 *__pyx_dynamic_args = __Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_self);
values[2] = __pyx_dynamic_args->__pyx_arg_lineparse;
@@ -14376,14 +14652,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
if (kw_args > 0) {
@@ -14392,7 +14666,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, P
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_data") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse_data") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -14409,7 +14683,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse_data", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -14421,7 +14695,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_33parse_data(PyObject *__pyx_self, P
}
static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
-/* "pysam/cvcf.pyx":790
+/* "pysam/cvcf.pyx":793
* if alt:
* for i in range(1,min(len(ref),min(map(len,alt)))):
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<<
@@ -14447,7 +14721,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx
__Pyx_INCREF(((PyObject *)__pyx_cur_scope->__pyx_outer_scope));
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_outer_scope);
{
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_cur_scope);
__Pyx_RefNannyFinishContext();
return (PyObject *) gen;
@@ -14484,29 +14758,37 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_Gener
return NULL;
}
__pyx_L3_first_run:;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt)) { __Pyx_RaiseClosureNameError("alt"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt)) { __Pyx_RaiseClosureNameError("alt"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
if (PyList_CheckExact(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt)) {
__pyx_t_1 = __pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
__pyx_t_3 = NULL;
} else {
- __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_cur_scope->__pyx_outer_scope->__pyx_v_alt); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -14517,12 +14799,12 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_Gener
__Pyx_GIVEREF(__pyx_t_4);
__pyx_cur_scope->__pyx_v_allele = __pyx_t_4;
__pyx_t_4 = 0;
- __pyx_t_4 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_allele, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_allele, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_4) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__upper); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__upper); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_r = __pyx_t_4;
@@ -14542,7 +14824,7 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_Gener
__Pyx_XGOTREF(__pyx_t_1);
__pyx_t_2 = __pyx_cur_scope->__pyx_t_1;
__pyx_t_3 = __pyx_cur_scope->__pyx_t_2;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
PyErr_SetNone(PyExc_StopIteration);
@@ -14555,11 +14837,12 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_10parse_data_2generator1(__pyx_Gener
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
__pyx_generator->resume_label = -1;
+ __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
-/* "pysam/cvcf.pyx":647
+/* "pysam/cvcf.pyx":650
* return False
*
* def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
@@ -14648,106 +14931,106 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__Pyx_GOTREF(__pyx_cur_scope);
- /* "pysam/cvcf.pyx":648
+ /* "pysam/cvcf.pyx":651
*
* def parse_data( self, line, lineparse=False ):
* cols = line.split('\t') # <<<<<<<<<<<<<<
* if len(cols) != len(self._samples)+9:
* # gracefully deal with absent FORMAT column
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__split); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_103), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_103), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_v_cols = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":649
+ /* "pysam/cvcf.pyx":652
* def parse_data( self, line, lineparse=False ):
* cols = line.split('\t')
* if len(cols) != len(self._samples)+9: # <<<<<<<<<<<<<<
* # gracefully deal with absent FORMAT column
* # and those missing samples
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 649; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_5 = (__pyx_t_3 != (__pyx_t_4 + 9));
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":652
+ /* "pysam/cvcf.pyx":655
* # gracefully deal with absent FORMAT column
* # and those missing samples
* if len(cols) == 8: # <<<<<<<<<<<<<<
* cols.append("")
* else:
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 652; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_4 == 8);
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":653
+ /* "pysam/cvcf.pyx":656
* # and those missing samples
* if len(cols) == 8:
* cols.append("") # <<<<<<<<<<<<<<
* else:
* self.error(line,
*/
- __pyx_t_2 = __Pyx_PyObject_Append(__pyx_v_cols, ((PyObject *)__pyx_kp_s_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 653; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_Append(__pyx_v_cols, ((PyObject *)__pyx_kp_s_1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L4;
}
/*else*/ {
- /* "pysam/cvcf.pyx":655
+ /* "pysam/cvcf.pyx":658
* cols.append("")
* else:
* self.error(line, # <<<<<<<<<<<<<<
* self.BAD_NUMBER_OF_COLUMNS,
* "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- /* "pysam/cvcf.pyx":656
+ /* "pysam/cvcf.pyx":659
* else:
* self.error(line,
* self.BAD_NUMBER_OF_COLUMNS, # <<<<<<<<<<<<<<
* "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_104); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 656; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_104); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/cvcf.pyx":657
+ /* "pysam/cvcf.pyx":660
* self.error(line,
* self.BAD_NUMBER_OF_COLUMNS,
* "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols))) # <<<<<<<<<<<<<<
*
* chrom = cols[0]
*/
- __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_4 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_t_6); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
- __pyx_t_6 = PyInt_FromSsize_t((__pyx_t_4 + 9)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyInt_FromSsize_t((__pyx_t_4 + 9)); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_4 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_4 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_cols); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
@@ -14761,10 +15044,10 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_7 = 0;
__pyx_t_8 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_105), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 657; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_105), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 660; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
@@ -14775,7 +15058,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(((PyObject *)__pyx_t_9));
__pyx_t_1 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 658; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
@@ -14786,19 +15069,19 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":659
+ /* "pysam/cvcf.pyx":662
* "expected %s for %s samples (%s), got %s" % (len(self._samples)+9, len(self._samples), self._samples, len(cols)))
*
* chrom = cols[0] # <<<<<<<<<<<<<<
*
* # get 0-based position
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 659; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_v_chrom = __pyx_t_9;
__pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":662
+ /* "pysam/cvcf.pyx":665
*
* # get 0-based position
* try: pos = int(cols[1])-1 # <<<<<<<<<<<<<<
@@ -14811,17 +15094,17 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_XGOTREF(__pyx_t_12);
__Pyx_XGOTREF(__pyx_t_13);
/*try:*/ {
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
__Pyx_GOTREF(__pyx_t_10);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Subtract(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 662; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
+ __pyx_t_10 = PyNumber_Subtract(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 665; __pyx_clineno = __LINE__; goto __pyx_L5_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_v_pos = __pyx_t_10;
@@ -14840,7 +15123,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":663
+ /* "pysam/cvcf.pyx":666
* # get 0-based position
* try: pos = int(cols[1])-1
* except: self.error(line,self.POS_NOT_NUMERICAL) # <<<<<<<<<<<<<<
@@ -14849,15 +15132,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_GOTREF(__pyx_t_9);
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__POS_NOT_NUMERICAL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__POS_NOT_NUMERICAL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
@@ -14865,7 +15148,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_8);
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 666; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
@@ -14889,24 +15172,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_L12_try_end:;
}
- /* "pysam/cvcf.pyx":664
+ /* "pysam/cvcf.pyx":667
* try: pos = int(cols[1])-1
* except: self.error(line,self.POS_NOT_NUMERICAL)
* if pos < 0: self.error(line,self.POS_NOT_POSITIVE) # <<<<<<<<<<<<<<
*
* # implement filtering
*/
- if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_v_pos)) { __Pyx_RaiseUnboundLocalError("pos"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_5) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__POS_NOT_POSITIVE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__POS_NOT_POSITIVE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
@@ -14914,7 +15196,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 664; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
@@ -14923,16 +15205,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L15:;
- /* "pysam/cvcf.pyx":667
+ /* "pysam/cvcf.pyx":670
*
* # implement filtering
* if not self.inregion(chrom,pos): return None # <<<<<<<<<<<<<<
*
* # end of first-pass parse for sortedVCF
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__inregion); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__inregion); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_chrom);
@@ -14940,11 +15222,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_INCREF(__pyx_v_pos);
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_pos);
__Pyx_GIVEREF(__pyx_v_pos);
- __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 667; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_14 = (!__pyx_t_5);
if (__pyx_t_14) {
@@ -14956,17 +15238,17 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L16:;
- /* "pysam/cvcf.pyx":670
+ /* "pysam/cvcf.pyx":673
*
* # end of first-pass parse for sortedVCF
* if lineparse: return chrom, pos, line # <<<<<<<<<<<<<<
*
* id = cols[2]
*/
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_lineparse); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_v_lineparse); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 670; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_chrom);
@@ -14984,58 +15266,60 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L17:;
- /* "pysam/cvcf.pyx":672
+ /* "pysam/cvcf.pyx":675
* if lineparse: return chrom, pos, line
*
* id = cols[2] # <<<<<<<<<<<<<<
*
* ref = cols[3].upper()
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 672; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 2, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_v_id = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":674
+ /* "pysam/cvcf.pyx":677
* id = cols[2]
*
* ref = cols[3].upper() # <<<<<<<<<<<<<<
* if ref == ".":
* self.error(line,self.MISSING_REF)
*/
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 3, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_cols, 3, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 674; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_v_ref = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":675
+ /* "pysam/cvcf.pyx":678
*
* ref = cols[3].upper()
* if ref == ".": # <<<<<<<<<<<<<<
* self.error(line,self.MISSING_REF)
* if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
*/
- __pyx_t_14 = __Pyx_PyString_Equals(__pyx_v_ref, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 675; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_ref, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 678; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":676
+ /* "pysam/cvcf.pyx":679
* ref = cols[3].upper()
* if ref == ".":
* self.error(line,self.MISSING_REF) # <<<<<<<<<<<<<<
* if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
* else: ref = ""
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__MISSING_REF); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__MISSING_REF); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
@@ -15043,34 +15327,33 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 676; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 679; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":677
+ /* "pysam/cvcf.pyx":680
* if ref == ".":
* self.error(line,self.MISSING_REF)
* if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference) # <<<<<<<<<<<<<<
* else: ref = ""
* else:
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_14) {
- __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_chrom);
@@ -15084,7 +15367,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_10 = 0;
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 677; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
@@ -15095,7 +15378,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":678
+ /* "pysam/cvcf.pyx":681
* self.error(line,self.MISSING_REF)
* if self._version == 33: ref = get_sequence(chrom,pos,pos+1,self._reference)
* else: ref = "" # <<<<<<<<<<<<<<
@@ -15111,7 +15394,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":680
+ /* "pysam/cvcf.pyx":683
* else: ref = ""
* else:
* for c in ref: # <<<<<<<<<<<<<<
@@ -15122,23 +15405,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_2 = __pyx_v_ref; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_ref); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_v_ref); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_8 = __pyx_t_15(__pyx_t_2);
if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 683; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -15148,20 +15439,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_v_c = __pyx_t_8;
__pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":681
+ /* "pysam/cvcf.pyx":684
* else:
* for c in ref:
* if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF) # <<<<<<<<<<<<<<
* if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
*
*/
- __pyx_t_14 = (__Pyx_NegateNonNeg(PySequence_Contains(((PyObject *)__pyx_n_s__ACGTN), __pyx_v_c))); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = (__Pyx_PySequence_Contains(__pyx_v_c, ((PyObject *)__pyx_n_s__ACGTN), Py_NE)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__UNKNOWN_CHAR_IN_REF); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__UNKNOWN_CHAR_IN_REF); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
@@ -15169,7 +15460,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 684; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
@@ -15180,26 +15471,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":682
+ /* "pysam/cvcf.pyx":685
* for c in ref:
* if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
* if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference) # <<<<<<<<<<<<<<
*
* # make sure reference is sane
*/
- __pyx_t_14 = ((PySequence_Contains(__pyx_v_ref, ((PyObject *)__pyx_n_s__N)))); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__N), __pyx_v_ref, Py_EQ)); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_14) {
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyTuple_New(4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_chrom);
@@ -15213,7 +15504,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_9);
__pyx_t_10 = 0;
__pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 682; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
@@ -15226,68 +15517,69 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L18:;
- /* "pysam/cvcf.pyx":685
+ /* "pysam/cvcf.pyx":688
*
* # make sure reference is sane
* if self._reference: # <<<<<<<<<<<<<<
* left = max(0,pos-100)
* faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 685; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":686
+ /* "pysam/cvcf.pyx":689
* # make sure reference is sane
* if self._reference:
* left = max(0,pos-100) # <<<<<<<<<<<<<<
* faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
* faref = faref_leftflank[pos-left:]
*/
- __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_100); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_100); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_t_16 = 0;
- __pyx_t_2 = PyInt_FromLong(__pyx_t_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromLong(__pyx_t_16); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_14) {
__Pyx_INCREF(__pyx_t_9);
__pyx_t_8 = __pyx_t_9;
} else {
- __pyx_t_10 = PyInt_FromLong(__pyx_t_16); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyInt_FromLong(__pyx_t_16); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__pyx_t_8 = __pyx_t_10;
__pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_INCREF(__pyx_t_8);
- __pyx_v_left = __pyx_t_8;
+ __pyx_t_9 = __pyx_t_8;
+ __Pyx_INCREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_left = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":687
+ /* "pysam/cvcf.pyx":690
* if self._reference:
* left = max(0,pos-100)
* faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference) # <<<<<<<<<<<<<<
* faref = faref_leftflank[pos-left:]
* if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_chrom);
@@ -15297,81 +15589,80 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_v_left);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_10);
__Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
__pyx_t_10 = 0;
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 687; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 690; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_v_faref_leftflank = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_faref_leftflank = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":688
+ /* "pysam/cvcf.pyx":691
* left = max(0,pos-100)
* faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
* faref = faref_leftflank[pos-left:] # <<<<<<<<<<<<<<
* if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
* ref = faref
*/
- __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_9); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_faref_leftflank, __pyx_t_4, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 688; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_v_faref = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_t_8 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_4 = __Pyx_PyIndex_AsSsize_t(__pyx_t_8); if (unlikely((__pyx_t_4 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_faref_leftflank, __pyx_t_4, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 691; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_v_faref = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":689
+ /* "pysam/cvcf.pyx":692
* faref_leftflank = get_sequence(chrom,left,pos+len(ref),self._reference)
* faref = faref_leftflank[pos-left:]
* if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref)) # <<<<<<<<<<<<<<
* ref = faref
*
*/
- __pyx_t_9 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_faref, __pyx_v_ref, Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_14) {
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__WRONG_REF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__WRONG_REF); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_faref);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_faref);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_faref);
__Pyx_GIVEREF(__pyx_v_faref);
__Pyx_INCREF(__pyx_v_ref);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_v_ref);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_v_ref);
__Pyx_GIVEREF(__pyx_v_ref);
- __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_106), ((PyObject *)__pyx_t_9)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_8, 2, ((PyObject *)__pyx_t_10));
+ PyTuple_SET_ITEM(__pyx_t_9, 2, ((PyObject *)__pyx_t_10));
__Pyx_GIVEREF(((PyObject *)__pyx_t_10));
__pyx_t_2 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 692; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L25;
}
__pyx_L25:;
- /* "pysam/cvcf.pyx":690
+ /* "pysam/cvcf.pyx":693
* faref = faref_leftflank[pos-left:]
* if faref != ref: self.error(line,self.WRONG_REF,"(reference is %s, VCF says %s)" % (faref,ref))
* ref = faref # <<<<<<<<<<<<<<
@@ -15385,64 +15676,68 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L24:;
- /* "pysam/cvcf.pyx":693
+ /* "pysam/cvcf.pyx":696
*
* # convert v3.3 to v4.0 alleles below
* if cols[4] == ".": alt = [] # <<<<<<<<<<<<<<
* else: alt = cols[4].upper().split(',')
*
*/
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_14) {
- __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 693; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
- __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_10);
- __pyx_t_10 = 0;
+ __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
+ __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_9);
+ __pyx_t_9 = 0;
goto __pyx_L26;
}
/*else*/ {
- /* "pysam/cvcf.pyx":694
+ /* "pysam/cvcf.pyx":697
* # convert v3.3 to v4.0 alleles below
* if cols[4] == ".": alt = []
* else: alt = cols[4].upper().split(',') # <<<<<<<<<<<<<<
*
* if cols[5] == ".": qual = -1
*/
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 4, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_107), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_10;
- __pyx_t_10 = 0;
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_9;
+ __pyx_t_9 = 0;
}
__pyx_L26:;
- /* "pysam/cvcf.pyx":696
+ /* "pysam/cvcf.pyx":699
* else: alt = cols[4].upper().split(',')
*
* if cols[5] == ".": qual = -1 # <<<<<<<<<<<<<<
* else:
* try: qual = float(cols[5])
*/
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_10, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 696; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_14) {
__pyx_v_qual = -1.0;
@@ -15450,7 +15745,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":698
+ /* "pysam/cvcf.pyx":701
* if cols[5] == ".": qual = -1
* else:
* try: qual = float(cols[5]) # <<<<<<<<<<<<<<
@@ -15463,9 +15758,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_XGOTREF(__pyx_t_12);
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 5, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_17 = __Pyx_PyObject_AsDouble(__pyx_t_10); if (unlikely(__pyx_t_17 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
+ __pyx_t_17 = __Pyx_PyObject_AsDouble(__pyx_t_10); if (unlikely(__pyx_t_17 == ((double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 701; __pyx_clineno = __LINE__; goto __pyx_L28_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_v_qual = __pyx_t_17;
}
@@ -15478,11 +15773,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":699
+ /* "pysam/cvcf.pyx":702
* else:
* try: qual = float(cols[5])
* except: self.error(line,self.QUAL_NOT_NUMERICAL) # <<<<<<<<<<<<<<
@@ -15491,15 +15786,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*/
/*except:*/ {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_8, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_GOTREF(__pyx_t_8);
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__QUAL_NOT_NUMERICAL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_line);
@@ -15507,14 +15802,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_1, 1, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 699; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L30_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L29_exception_handled;
}
__pyx_L30_except_error:;
@@ -15533,26 +15828,32 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L27:;
- /* "pysam/cvcf.pyx":702
+ /* "pysam/cvcf.pyx":705
*
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = [] # <<<<<<<<<<<<<<
* else: filter = cols[6].split(';')
*
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_14 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_EQ); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_kp_s_9), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (!__pyx_t_14) {
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_n_s__PASS), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_n_s__PASS), Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (!__pyx_t_5) {
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_18 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s__0), Py_EQ); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, ((PyObject *)__pyx_kp_s__0), Py_EQ); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_18 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_18 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_19 = __pyx_t_18;
} else {
@@ -15563,7 +15864,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_5 = __pyx_t_14;
}
if (__pyx_t_5) {
- __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__pyx_v_filter = ((PyObject *)__pyx_t_9);
__pyx_t_9 = 0;
@@ -15571,19 +15872,19 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":703
+ /* "pysam/cvcf.pyx":706
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
* else: filter = cols[6].split(';') # <<<<<<<<<<<<<<
*
* # dictionary of keys, and list of values
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 6, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_108), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_108), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_v_filter = __pyx_t_9;
@@ -15591,101 +15892,111 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L38:;
- /* "pysam/cvcf.pyx":706
+ /* "pysam/cvcf.pyx":709
*
* # dictionary of keys, and list of values
* info = {} # <<<<<<<<<<<<<<
* if cols[7] != ".":
* for blurp in cols[7].split(';'):
*/
- __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_9));
- __pyx_v_info = __pyx_t_9;
+ __pyx_v_info = ((PyObject*)__pyx_t_9);
__pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":707
+ /* "pysam/cvcf.pyx":710
* # dictionary of keys, and list of values
* info = {}
* if cols[7] != ".": # <<<<<<<<<<<<<<
* for blurp in cols[7].split(';'):
* elts = blurp.split('=')
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_NE); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_9), Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":708
+ /* "pysam/cvcf.pyx":711
* info = {}
* if cols[7] != ".":
* for blurp in cols[7].split(';'): # <<<<<<<<<<<<<<
* elts = blurp.split('=')
* if len(elts) == 1: v = None
*/
- __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 7, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
- __pyx_t_8 = __pyx_t_9; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_109), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
+ __pyx_t_9 = __pyx_t_8; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_9 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_9)) {
+ __pyx_t_8 = __pyx_t_15(__pyx_t_9);
+ if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_GOTREF(__pyx_t_8);
}
__Pyx_XDECREF(__pyx_v_blurp);
- __pyx_v_blurp = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_blurp = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":709
+ /* "pysam/cvcf.pyx":712
* if cols[7] != ".":
* for blurp in cols[7].split(';'):
* elts = blurp.split('=') # <<<<<<<<<<<<<<
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_blurp, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_110), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_elts);
__pyx_v_elts = __pyx_t_10;
__pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":710
+ /* "pysam/cvcf.pyx":713
* for blurp in cols[7].split(';'):
* elts = blurp.split('=')
* if len(elts) == 1: v = None # <<<<<<<<<<<<<<
* elif len(elts) == 2: v = elts[1]
* else: self.error(line,self.ERROR_INFO_STRING)
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_3 == 1);
if (__pyx_t_5) {
__Pyx_INCREF(Py_None);
@@ -15694,17 +16005,17 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
goto __pyx_L42;
}
- /* "pysam/cvcf.pyx":711
+ /* "pysam/cvcf.pyx":714
* elts = blurp.split('=')
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1] # <<<<<<<<<<<<<<
* else: self.error(line,self.ERROR_INFO_STRING)
* info[elts[0]] = self.parse_formatdata(elts[0],
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_elts); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_3 == 2);
if (__pyx_t_5) {
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_elts, 1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 714; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_v_v);
__pyx_v_v = __pyx_t_10;
@@ -15713,72 +16024,72 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":712
+ /* "pysam/cvcf.pyx":715
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
* else: self.error(line,self.ERROR_INFO_STRING) # <<<<<<<<<<<<<<
* info[elts[0]] = self.parse_formatdata(elts[0],
* v,
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ERROR_INFO_STRING); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__pyx_L42:;
- /* "pysam/cvcf.pyx":713
+ /* "pysam/cvcf.pyx":716
* elif len(elts) == 2: v = elts[1]
* else: self.error(line,self.ERROR_INFO_STRING)
* info[elts[0]] = self.parse_formatdata(elts[0], # <<<<<<<<<<<<<<
* v,
* self._info,
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/cvcf.pyx":714
+ /* "pysam/cvcf.pyx":717
* else: self.error(line,self.ERROR_INFO_STRING)
* info[elts[0]] = self.parse_formatdata(elts[0],
* v, # <<<<<<<<<<<<<<
* self._info,
* line)
*/
- if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 714; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (unlikely(!__pyx_v_v)) { __Pyx_RaiseUnboundLocalError("v"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- /* "pysam/cvcf.pyx":715
+ /* "pysam/cvcf.pyx":718
* info[elts[0]] = self.parse_formatdata(elts[0],
* v,
* self._info, # <<<<<<<<<<<<<<
* line)
*
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 715; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- /* "pysam/cvcf.pyx":716
+ /* "pysam/cvcf.pyx":719
* v,
* self._info,
* line) # <<<<<<<<<<<<<<
*
* # Gracefully deal with absent FORMAT column
*/
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
@@ -15792,70 +16103,72 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_v_line);
__pyx_t_7 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":713
+ /* "pysam/cvcf.pyx":716
* elif len(elts) == 2: v = elts[1]
* else: self.error(line,self.ERROR_INFO_STRING)
* info[elts[0]] = self.parse_formatdata(elts[0], # <<<<<<<<<<<<<<
* v,
* self._info,
*/
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_elts, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyDict_SetItem(((PyObject *)__pyx_v_info), __pyx_t_1, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 713; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_info), __pyx_t_1, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 716; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L39;
}
__pyx_L39:;
- /* "pysam/cvcf.pyx":719
+ /* "pysam/cvcf.pyx":722
*
* # Gracefully deal with absent FORMAT column
* if cols[8] == "": format = [] # <<<<<<<<<<<<<<
* else: format = cols[8].split(':')
*
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_t_8, ((PyObject *)__pyx_kp_s_1), Py_EQ); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, ((PyObject *)__pyx_kp_s_1), Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_v_format = ((PyObject *)__pyx_t_8);
- __pyx_t_8 = 0;
+ __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_v_format = ((PyObject *)__pyx_t_10);
+ __pyx_t_10 = 0;
goto __pyx_L43;
}
/*else*/ {
- /* "pysam/cvcf.pyx":720
+ /* "pysam/cvcf.pyx":723
* # Gracefully deal with absent FORMAT column
* if cols[8] == "": format = []
* else: format = cols[8].split(':') # <<<<<<<<<<<<<<
*
* # check: all filters are defined
*/
- __pyx_t_8 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_8, __pyx_n_s__split); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_cols, 8, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_111), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__split); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_v_format = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_111), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_v_format = __pyx_t_10;
+ __pyx_t_10 = 0;
}
__pyx_L43:;
- /* "pysam/cvcf.pyx":723
+ /* "pysam/cvcf.pyx":726
*
* # check: all filters are defined
* for f in filter: # <<<<<<<<<<<<<<
@@ -15863,87 +16176,95 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*
*/
if (PyList_CheckExact(__pyx_v_filter) || PyTuple_CheckExact(__pyx_v_filter)) {
- __pyx_t_8 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_10 = __pyx_v_filter; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_v_filter); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_9 = __pyx_t_15(__pyx_t_10);
+ if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_9);
}
__Pyx_XDECREF(__pyx_v_f);
- __pyx_v_f = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_f = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":724
+ /* "pysam/cvcf.pyx":727
* # check: all filters are defined
* for f in filter:
* if f not in self._filter: self.error(line,self.FILTER_NOT_DEFINED, f) # <<<<<<<<<<<<<<
*
* # check: format fields are defined
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_10, __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_9, Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_5) {
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FILTER_NOT_DEFINED); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FILTER_NOT_DEFINED); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_8 = PyTuple_New(3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_1);
+ PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
goto __pyx_L46;
}
__pyx_L46:;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":727
+ /* "pysam/cvcf.pyx":730
*
* # check: format fields are defined
* if self._format: # <<<<<<<<<<<<<<
* for f in format:
* if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f)
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":728
+ /* "pysam/cvcf.pyx":731
* # check: format fields are defined
* if self._format:
* for f in format: # <<<<<<<<<<<<<<
@@ -15951,26 +16272,34 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*
*/
if (PyList_CheckExact(__pyx_v_format) || PyTuple_CheckExact(__pyx_v_format)) {
- __pyx_t_8 = __pyx_v_format; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_10 = __pyx_v_format; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_v_format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_1 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_1 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_1); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_1 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_1 = __pyx_t_15(__pyx_t_8);
+ __pyx_t_1 = __pyx_t_15(__pyx_t_10);
if (unlikely(!__pyx_t_1)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 728; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -15980,107 +16309,106 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_v_f = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":729
+ /* "pysam/cvcf.pyx":732
* if self._format:
* for f in format:
* if f not in self._format: self.error(line,self.FORMAT_NOT_DEFINED, f) # <<<<<<<<<<<<<<
*
* # convert v3.3 alleles
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_1, __pyx_v_f))); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = (__Pyx_PySequence_Contains(__pyx_v_f, __pyx_t_1, Py_NE)); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_5) {
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__FORMAT_NOT_DEFINED); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyTuple_New(3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
__Pyx_INCREF(__pyx_v_f);
- PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_f);
+ PyTuple_SET_ITEM(__pyx_t_9, 2, __pyx_v_f);
__Pyx_GIVEREF(__pyx_v_f);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 729; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L50;
}
__pyx_L50:;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L47;
}
__pyx_L47:;
- /* "pysam/cvcf.pyx":732
+ /* "pysam/cvcf.pyx":735
*
* # convert v3.3 alleles
* if self._version == 33: # <<<<<<<<<<<<<<
* if len(ref) != 1: self.error(line,self.V33_BAD_REF)
* newalts = []
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_10, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":733
+ /* "pysam/cvcf.pyx":736
* # convert v3.3 alleles
* if self._version == 33:
* if len(ref) != 1: self.error(line,self.V33_BAD_REF) # <<<<<<<<<<<<<<
* newalts = []
* have_deletions = False
*/
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_4 != 1);
if (__pyx_t_5) {
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_REF); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_REF); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L52;
}
__pyx_L52:;
- /* "pysam/cvcf.pyx":734
+ /* "pysam/cvcf.pyx":737
* if self._version == 33:
* if len(ref) != 1: self.error(line,self.V33_BAD_REF)
* newalts = [] # <<<<<<<<<<<<<<
* have_deletions = False
* for a in alt:
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_v_newalts = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_v_newalts = ((PyObject*)__pyx_t_10);
+ __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":735
+ /* "pysam/cvcf.pyx":738
* if len(ref) != 1: self.error(line,self.V33_BAD_REF)
* newalts = []
* have_deletions = False # <<<<<<<<<<<<<<
@@ -16089,7 +16417,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*/
__pyx_v_have_deletions = 0;
- /* "pysam/cvcf.pyx":736
+ /* "pysam/cvcf.pyx":739
* newalts = []
* have_deletions = False
* for a in alt: # <<<<<<<<<<<<<<
@@ -16097,108 +16425,116 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_10 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_10); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_10 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_15 = Py_TYPE(__pyx_t_10)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_10)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_10)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_10)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_10)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_10, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_10, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_9 = __pyx_t_15(__pyx_t_10);
+ if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_9);
}
__Pyx_XDECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_a = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":737
+ /* "pysam/cvcf.pyx":740
* have_deletions = False
* for a in alt:
* if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference # <<<<<<<<<<<<<<
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
* elif a.startswith('D'): # allow D<seq> and D<num>
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_a); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_5 = (__pyx_t_3 == 1);
if (__pyx_t_5) {
- __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyNumber_Add(__pyx_v_a, __pyx_t_10); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_8 = PyNumber_Add(__pyx_v_a, __pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_a = __pyx_t_8;
+ __pyx_t_8 = 0;
goto __pyx_L55;
}
- /* "pysam/cvcf.pyx":738
+ /* "pysam/cvcf.pyx":741
* for a in alt:
* if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference # <<<<<<<<<<<<<<
* elif a.startswith('D'): # allow D<seq> and D<num>
* have_deletions = True
*/
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_112), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyNumber_Add(__pyx_t_10, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_1 = PyNumber_Add(__pyx_t_9, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyNumber_Add(__pyx_t_1, __pyx_t_8); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyNumber_Add(__pyx_t_1, __pyx_t_9); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(__pyx_v_a);
- __pyx_v_a = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_a = __pyx_t_9;
+ __pyx_t_9 = 0;
goto __pyx_L55;
}
- /* "pysam/cvcf.pyx":739
+ /* "pysam/cvcf.pyx":742
* if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
* elif a.startswith('D'): # allow D<seq> and D<num> # <<<<<<<<<<<<<<
* have_deletions = True
* try:
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_k_tuple_113), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_a, __pyx_n_s__startswith); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_k_tuple_113), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":740
+ /* "pysam/cvcf.pyx":743
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
* elif a.startswith('D'): # allow D<seq> and D<num>
* have_deletions = True # <<<<<<<<<<<<<<
@@ -16207,7 +16543,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*/
__pyx_v_have_deletions = 1;
- /* "pysam/cvcf.pyx":741
+ /* "pysam/cvcf.pyx":744
* elif a.startswith('D'): # allow D<seq> and D<num>
* have_deletions = True
* try: # <<<<<<<<<<<<<<
@@ -16221,99 +16557,98 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_XGOTREF(__pyx_t_13);
/*try:*/ {
- /* "pysam/cvcf.pyx":742
+ /* "pysam/cvcf.pyx":745
* have_deletions = True
* try:
* l = int(a[1:]) # throws ValueError if sequence # <<<<<<<<<<<<<<
* if len(ref) < l: # add to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
*/
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
- __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_9);
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(((PyObject *)((PyObject*)(&PyInt_Type))), ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_v_l);
- __pyx_v_l = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_l = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":743
+ /* "pysam/cvcf.pyx":746
* try:
* l = int(a[1:]) # throws ValueError if sequence
* if len(ref) < l: # add to reference if necessary # <<<<<<<<<<<<<<
* addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
* ref += addns
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_9, __pyx_v_l, Py_LT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_8, __pyx_v_l, Py_LT); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":744
+ /* "pysam/cvcf.pyx":747
* l = int(a[1:]) # throws ValueError if sequence
* if len(ref) < l: # add to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference) # <<<<<<<<<<<<<<
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns
*/
- __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_1 = PyNumber_Add(__pyx_v_pos, __pyx_t_9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_1 = PyNumber_Add(__pyx_v_pos, __pyx_t_8); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyNumber_Add(__pyx_v_pos, __pyx_v_l); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_1 = 0;
- __pyx_t_9 = 0;
+ __pyx_t_8 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_addns);
__pyx_v_addns = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":745
+ /* "pysam/cvcf.pyx":748
* if len(ref) < l: # add to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
* ref += addns # <<<<<<<<<<<<<<
* for i,na in enumerate(newalts): newalts[i] = na+addns
* a = ref[l:] # new deletion, deleting pos...pos+l
*/
- __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addns); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_7 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addns); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":746
+ /* "pysam/cvcf.pyx":749
* addns = get_sequence(chrom,pos+len(ref),pos+l,self._reference)
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns # <<<<<<<<<<<<<<
@@ -16325,22 +16660,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_2 = ((PyObject *)__pyx_v_newalts); __Pyx_INCREF(__pyx_t_2); __pyx_t_3 = 0;
for (;;) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_10); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_3); __Pyx_INCREF(__pyx_t_9); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ #endif
__Pyx_XDECREF(__pyx_v_na);
- __pyx_v_na = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_na = __pyx_t_9;
+ __pyx_t_9 = 0;
__Pyx_INCREF(__pyx_t_7);
__Pyx_XDECREF(__pyx_v_i);
__pyx_v_i = __pyx_t_7;
- __pyx_t_10 = PyNumber_Add(__pyx_t_7, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyNumber_Add(__pyx_t_7, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_7);
- __pyx_t_7 = __pyx_t_10;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 746; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_7 = __pyx_t_9;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
@@ -16348,15 +16687,15 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L64:;
- /* "pysam/cvcf.pyx":747
+ /* "pysam/cvcf.pyx":750
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns
* a = ref[l:] # new deletion, deleting pos...pos+l # <<<<<<<<<<<<<<
* except ValueError:
* s = a[1:]
*/
- __pyx_t_3 = __Pyx_PyIndex_AsSsize_t(__pyx_v_l); if (unlikely((__pyx_t_3 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
- __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_ref, __pyx_t_3, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_3 = __Pyx_PyIndex_AsSsize_t(__pyx_v_l); if (unlikely((__pyx_t_3 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
+ __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_ref, __pyx_t_3, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_v_a);
__pyx_v_a = __pyx_t_7;
@@ -16369,12 +16708,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_L56_error:;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
+ __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_t_9); __pyx_t_9 = 0;
- __Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":748
+ /* "pysam/cvcf.pyx":751
* for i,na in enumerate(newalts): newalts[i] = na+addns
* a = ref[l:] # new deletion, deleting pos...pos+l
* except ValueError: # <<<<<<<<<<<<<<
@@ -16384,60 +16723,60 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_20 = PyErr_ExceptionMatches(__pyx_builtin_ValueError);
if (__pyx_t_20) {
__Pyx_AddTraceback("pysam.cvcf.VCF.parse_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_2, &__pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_9);
- /* "pysam/cvcf.pyx":749
+ /* "pysam/cvcf.pyx":752
* a = ref[l:] # new deletion, deleting pos...pos+l
* except ValueError:
* s = a[1:] # <<<<<<<<<<<<<<
* if len(ref) < len(s): # add Ns to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
*/
- __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 749; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_a, 1, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_XDECREF(__pyx_v_s);
- __pyx_v_s = __pyx_t_9;
- __pyx_t_9 = 0;
+ __pyx_v_s = __pyx_t_8;
+ __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":750
+ /* "pysam/cvcf.pyx":753
* except ValueError:
* s = a[1:]
* if len(ref) < len(s): # add Ns to reference if necessary # <<<<<<<<<<<<<<
* addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
* if not s.endswith(addns) and addns != 'N'*len(addns):
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__pyx_t_5 = (__pyx_t_3 < __pyx_t_21);
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":751
+ /* "pysam/cvcf.pyx":754
* s = a[1:]
* if len(ref) < len(s): # add Ns to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference) # <<<<<<<<<<<<<<
* if not s.endswith(addns) and addns != 'N'*len(addns):
* self.error(line,self.V33_UNMATCHED_DELETION,
*/
- __pyx_t_9 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_21 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_21 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_6 = PyNumber_Add(__pyx_v_pos, __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_6 = PyNumber_Add(__pyx_v_pos, __pyx_t_1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_22 = PyNumber_Add(__pyx_v_pos, __pyx_t_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyNumber_Add(__pyx_v_pos, __pyx_t_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_23 = PyTuple_New(4); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_23 = PyTuple_New(4); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_23);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_23, 0, __pyx_v_chrom);
@@ -16451,80 +16790,82 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_6 = 0;
__pyx_t_22 = 0;
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 751; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0;
__Pyx_XDECREF(__pyx_v_addns);
__pyx_v_addns = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":752
+ /* "pysam/cvcf.pyx":755
* if len(ref) < len(s): # add Ns to reference if necessary
* addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
* if not s.endswith(addns) and addns != 'N'*len(addns): # <<<<<<<<<<<<<<
* self.error(line,self.V33_UNMATCHED_DELETION,
* "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_s, __pyx_n_s__endswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_s, __pyx_n_s__endswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_23 = PyTuple_New(1); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_23 = PyTuple_New(1); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_23);
__Pyx_INCREF(__pyx_v_addns);
PyTuple_SET_ITEM(__pyx_t_23, 0, __pyx_v_addns);
__Pyx_GIVEREF(__pyx_v_addns);
- __pyx_t_9 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_8 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_23), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_14 = (!__pyx_t_5);
if (__pyx_t_14) {
- __pyx_t_21 = PyObject_Length(__pyx_v_addns); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_9 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_9);
- __pyx_t_23 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_9); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_addns); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_23 = PyNumber_Multiply(((PyObject *)__pyx_n_s__N), __pyx_t_8); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_23));
- __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_5 = __Pyx_PyString_Equals(__pyx_v_addns, ((PyObject *)__pyx_t_23), Py_NE); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_RichCompare(__pyx_v_addns, ((PyObject *)__pyx_t_23), Py_NE); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_23)); __pyx_t_23 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__pyx_t_19 = __pyx_t_5;
} else {
__pyx_t_19 = __pyx_t_14;
}
if (__pyx_t_19) {
- /* "pysam/cvcf.pyx":753
+ /* "pysam/cvcf.pyx":756
* addns = get_sequence(chrom,pos+len(ref),pos+len(s),self._reference)
* if not s.endswith(addns) and addns != 'N'*len(addns):
* self.error(line,self.V33_UNMATCHED_DELETION, # <<<<<<<<<<<<<<
* "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
* ref += addns
*/
- __pyx_t_23 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_23 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_114); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_23);
- __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_114); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_9);
- /* "pysam/cvcf.pyx":754
+ /* "pysam/cvcf.pyx":757
* if not s.endswith(addns) and addns != 'N'*len(addns):
* self.error(line,self.V33_UNMATCHED_DELETION,
* "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference))) # <<<<<<<<<<<<<<
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_6 = PyNumber_Add(__pyx_v_pos, __pyx_t_22); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_6 = PyNumber_Add(__pyx_v_pos, __pyx_t_22); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_24 = PyTuple_New(4); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_24 = PyTuple_New(4); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_24);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_chrom);
@@ -16538,11 +16879,11 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_22);
__pyx_t_6 = 0;
__pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
- __pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_24);
__Pyx_INCREF(__pyx_v_a);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_a);
@@ -16550,43 +16891,43 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_22);
__Pyx_GIVEREF(__pyx_t_22);
__pyx_t_22 = 0;
- __pyx_t_22 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_115), ((PyObject *)__pyx_t_24)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_115), ((PyObject *)__pyx_t_24)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_22));
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
- __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_24);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_9);
- __Pyx_GIVEREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_23);
+ __Pyx_GIVEREF(__pyx_t_23);
PyTuple_SET_ITEM(__pyx_t_24, 2, ((PyObject *)__pyx_t_22));
__Pyx_GIVEREF(((PyObject *)__pyx_t_22));
- __pyx_t_9 = 0;
+ __pyx_t_23 = 0;
__pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_23, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 753; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
goto __pyx_L70;
}
__pyx_L70:;
- /* "pysam/cvcf.pyx":755
+ /* "pysam/cvcf.pyx":758
* self.error(line,self.V33_UNMATCHED_DELETION,
* "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
* ref += addns # <<<<<<<<<<<<<<
* for i,na in enumerate(newalts): newalts[i] = na+addns
* a = ref[len(s):] # new deletion, deleting from pos
*/
- __pyx_t_22 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addns); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addns); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 758; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_22;
__pyx_t_22 = 0;
- /* "pysam/cvcf.pyx":756
+ /* "pysam/cvcf.pyx":759
* "(deletion is %s, reference is %s)" % (a,get_sequence(chrom,pos,pos+len(s),self._reference)))
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns # <<<<<<<<<<<<<<
@@ -16598,22 +16939,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_24 = ((PyObject *)__pyx_v_newalts); __Pyx_INCREF(__pyx_t_24); __pyx_t_21 = 0;
for (;;) {
if (__pyx_t_21 >= PyList_GET_SIZE(__pyx_t_24)) break;
- __pyx_t_23 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_21); __Pyx_INCREF(__pyx_t_23); __pyx_t_21++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_21); __Pyx_INCREF(__pyx_t_8); __pyx_t_21++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_24, __pyx_t_21); __pyx_t_21++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ #endif
__Pyx_XDECREF(__pyx_v_na);
- __pyx_v_na = __pyx_t_23;
- __pyx_t_23 = 0;
+ __pyx_v_na = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_INCREF(__pyx_t_22);
__Pyx_XDECREF(__pyx_v_i);
__pyx_v_i = __pyx_t_22;
- __pyx_t_23 = PyNumber_Add(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_8 = PyNumber_Add(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_22);
- __pyx_t_22 = __pyx_t_23;
- __pyx_t_23 = 0;
- __pyx_t_23 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_GOTREF(__pyx_t_23);
- if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_23) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 756; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
+ __pyx_t_22 = __pyx_t_8;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyNumber_Add(__pyx_v_na, __pyx_v_addns); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ if (PyObject_SetItem(((PyObject *)__pyx_v_newalts), __pyx_v_i, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
}
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
@@ -16621,22 +16966,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L69:;
- /* "pysam/cvcf.pyx":757
+ /* "pysam/cvcf.pyx":760
* ref += addns
* for i,na in enumerate(newalts): newalts[i] = na+addns
* a = ref[len(s):] # new deletion, deleting from pos # <<<<<<<<<<<<<<
* else:
* self.error(line,self.V33_BAD_ALLELE)
*/
- __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
- __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_ref, __pyx_t_21, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_s); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
+ __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_ref, __pyx_t_21, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L58_except_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_v_a);
__pyx_v_a = __pyx_t_22;
__pyx_t_22 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L57_exception_handled;
}
__pyx_L58_except_error:;
@@ -16656,18 +17001,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":759
+ /* "pysam/cvcf.pyx":762
* a = ref[len(s):] # new deletion, deleting from pos
* else:
* self.error(line,self.V33_BAD_ALLELE) # <<<<<<<<<<<<<<
* newalts.append(a)
* alt = newalts
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V33_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
@@ -16675,26 +17020,26 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 759; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 762; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_L55:;
- /* "pysam/cvcf.pyx":760
+ /* "pysam/cvcf.pyx":763
* else:
* self.error(line,self.V33_BAD_ALLELE)
* newalts.append(a) # <<<<<<<<<<<<<<
* alt = newalts
* # deletion alleles exist, add dummy 1st reference allele, and account for leading base
*/
- __pyx_t_25 = PyList_Append(__pyx_v_newalts, __pyx_v_a); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_25 = PyList_Append(__pyx_v_newalts, __pyx_v_a); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":761
+ /* "pysam/cvcf.pyx":764
* self.error(line,self.V33_BAD_ALLELE)
* newalts.append(a)
* alt = newalts # <<<<<<<<<<<<<<
@@ -16707,7 +17052,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(((PyObject *)__pyx_v_newalts));
__pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_v_newalts);
- /* "pysam/cvcf.pyx":763
+ /* "pysam/cvcf.pyx":766
* alt = newalts
* # deletion alleles exist, add dummy 1st reference allele, and account for leading base
* if have_deletions: # <<<<<<<<<<<<<<
@@ -16716,46 +17061,45 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*/
if (__pyx_v_have_deletions) {
- /* "pysam/cvcf.pyx":764
+ /* "pysam/cvcf.pyx":767
* # deletion alleles exist, add dummy 1st reference allele, and account for leading base
* if have_deletions:
* if pos == 0: # <<<<<<<<<<<<<<
* # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
* addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
*/
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_10 = PyObject_RichCompare(__pyx_v_pos, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_19) {
- /* "pysam/cvcf.pyx":766
+ /* "pysam/cvcf.pyx":769
* if pos == 0:
* # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
* addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference) # <<<<<<<<<<<<<<
* ref += addn
* alt = [allele+addn for allele in alt]
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyNumber_Add(__pyx_v_pos, __pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Add(__pyx_t_10, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_9, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_chrom);
@@ -16764,195 +17108,215 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
__pyx_t_7 = 0;
__pyx_t_2 = 0;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 769; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __pyx_v_addn = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_addn = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":767
+ /* "pysam/cvcf.pyx":770
* # Petr Danacek's: we can't have a leading nucleotide at (1-based) position 1
* addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
* ref += addn # <<<<<<<<<<<<<<
* alt = [allele+addn for allele in alt]
* else:
*/
- __pyx_t_10 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 767; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyNumber_InPlaceAdd(__pyx_v_ref, __pyx_v_addn); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_ref = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":768
+ /* "pysam/cvcf.pyx":771
* addn = get_sequence(chrom,pos+len(ref),pos+len(ref)+1,self._reference)
* ref += addn
* alt = [allele+addn for allele in alt] # <<<<<<<<<<<<<<
* else:
* addn = get_sequence(chrom,pos-1,pos,self._reference)
*/
- __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
__pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
}
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_22, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_22, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_8 = __pyx_t_15(__pyx_t_22);
- if (unlikely(!__pyx_t_8)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_22);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_8;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Add(__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- if (unlikely(PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_8))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyNumber_Add(__pyx_v_allele, __pyx_v_addn); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_10));
+ __pyx_t_22 = ((PyObject *)__pyx_t_9);
+ __Pyx_INCREF(__pyx_t_22);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(((PyObject *)__pyx_t_10));
- __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_10);
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_GIVEREF(__pyx_t_22);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_22;
+ __pyx_t_22 = 0;
goto __pyx_L74;
}
/*else*/ {
- /* "pysam/cvcf.pyx":770
+ /* "pysam/cvcf.pyx":773
* alt = [allele+addn for allele in alt]
* else:
* addn = get_sequence(chrom,pos-1,pos,self._reference) # <<<<<<<<<<<<<<
* ref = addn + ref
* alt = [addn + allele for allele in alt]
*/
- __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_GetName(__pyx_m, __pyx_n_s__get_sequence); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyNumber_Subtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_2 = PyTuple_New(4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_chrom);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_chrom);
__Pyx_GIVEREF(__pyx_v_chrom);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_pos);
PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_v_pos);
__Pyx_GIVEREF(__pyx_v_pos);
- PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_22 = 0;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 770; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ PyTuple_SET_ITEM(__pyx_t_2, 3, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ __pyx_t_9 = 0;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_v_addn = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_addn = __pyx_t_10;
+ __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":771
+ /* "pysam/cvcf.pyx":774
* else:
* addn = get_sequence(chrom,pos-1,pos,self._reference)
* ref = addn + ref # <<<<<<<<<<<<<<
* alt = [addn + allele for allele in alt]
* pos -= 1
*/
- __pyx_t_8 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyNumber_Add(__pyx_v_addn, __pyx_v_ref); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_ref = __pyx_t_10;
+ __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":772
+ /* "pysam/cvcf.pyx":775
* addn = get_sequence(chrom,pos-1,pos,self._reference)
* ref = addn + ref
* alt = [addn + allele for allele in alt] # <<<<<<<<<<<<<<
* pos -= 1
* else:
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
__pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_22 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_22 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
- __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_22 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_10 = __pyx_t_15(__pyx_t_2);
- if (unlikely(!__pyx_t_10)) {
+ __pyx_t_22 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_22)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_GOTREF(__pyx_t_22);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_10;
- __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Add(__pyx_v_addn, __pyx_v_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_v_allele = __pyx_t_22;
+ __pyx_t_22 = 0;
+ __pyx_t_22 = PyNumber_Add(__pyx_v_addn, __pyx_v_allele); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_22))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 775; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_8));
+ __pyx_t_2 = ((PyObject *)__pyx_t_10);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":773
+ /* "pysam/cvcf.pyx":776
* ref = addn + ref
* alt = [addn + allele for allele in alt]
* pos -= 1 # <<<<<<<<<<<<<<
* else:
* # format v4.0 -- just check for nucleotides
*/
- __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 773; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_pos);
- __pyx_v_pos = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_pos = __pyx_t_2;
+ __pyx_t_2 = 0;
}
__pyx_L74:;
goto __pyx_L73;
@@ -16962,7 +17326,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":776
+ /* "pysam/cvcf.pyx":779
* else:
* # format v4.0 -- just check for nucleotides
* for allele in alt: # <<<<<<<<<<<<<<
@@ -16970,97 +17334,105 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
* self.error(line,self.V40_BAD_ALLELE,allele)
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 779; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":777
+ /* "pysam/cvcf.pyx":780
* # format v4.0 -- just check for nucleotides
* for allele in alt:
* if not alleleRegEx.match(allele): # <<<<<<<<<<<<<<
* self.error(line,self.V40_BAD_ALLELE,allele)
*
*/
- __pyx_t_2 = __Pyx_GetName(__pyx_m, __pyx_n_s__alleleRegEx); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__match); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetName(__pyx_m, __pyx_n_s__alleleRegEx); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_INCREF(__pyx_v_allele);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_allele);
- __Pyx_GIVEREF(__pyx_v_allele);
- __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__match); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_INCREF(__pyx_v_allele);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_allele);
+ __Pyx_GIVEREF(__pyx_v_allele);
+ __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_14 = (!__pyx_t_19);
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":778
+ /* "pysam/cvcf.pyx":781
* for allele in alt:
* if not alleleRegEx.match(allele):
* self.error(line,self.V40_BAD_ALLELE,allele) # <<<<<<<<<<<<<<
*
* # check for leading nucleotide in indel calls
*/
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V40_BAD_ALLELE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__V40_BAD_ALLELE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_allele);
- PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_v_allele);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_v_allele);
__Pyx_GIVEREF(__pyx_v_allele);
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
goto __pyx_L81;
}
__pyx_L81:;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
}
__pyx_L51:;
- /* "pysam/cvcf.pyx":781
+ /* "pysam/cvcf.pyx":784
*
* # check for leading nucleotide in indel calls
* for allele in alt: # <<<<<<<<<<<<<<
@@ -17068,154 +17440,161 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
* if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 781; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":782
+ /* "pysam/cvcf.pyx":785
* # check for leading nucleotide in indel calls
* for allele in alt:
* if len(allele) != len(ref): # <<<<<<<<<<<<<<
* if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
* if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
*/
- __pyx_t_21 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_21 != __pyx_t_3);
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":783
+ /* "pysam/cvcf.pyx":786
* for allele in alt:
* if len(allele) != len(ref):
* if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE) # <<<<<<<<<<<<<<
* if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
* self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_3 == 0);
if (__pyx_t_14) {
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyTuple_New(2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__ZERO_LENGTH_ALLELE); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 783; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
+ __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
goto __pyx_L85;
}
__pyx_L85:;
- /* "pysam/cvcf.pyx":784
+ /* "pysam/cvcf.pyx":787
* if len(allele) != len(ref):
* if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
* if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper(): # <<<<<<<<<<<<<<
* self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE)
*
*/
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_10, __pyx_t_22, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_9, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_14) {
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyNumber_Add(__pyx_t_2, __pyx_t_22); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_ref, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_allele, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyNumber_Add(__pyx_t_10, __pyx_t_9); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_19 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_n_s__N), __pyx_t_22, Py_NE)); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 787; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_19 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_t_10, ((PyObject *)__pyx_n_s__N)))); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 784; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__pyx_t_5 = __pyx_t_19;
} else {
__pyx_t_5 = __pyx_t_14;
}
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":785
+ /* "pysam/cvcf.pyx":788
* if len(allele) == 0: self.error(line,self.ZERO_LENGTH_ALLELE)
* if ref[0].upper() != allele[0].upper() and "N" not in (ref[0]+allele[0]).upper():
* self.error(line,self.MISSING_INDEL_ALLELE_REF_BASE) # <<<<<<<<<<<<<<
*
* # trim trailing bases in alleles
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_116); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_116); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_10 = PyTuple_New(2); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
- __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
goto __pyx_L86;
}
__pyx_L86:;
@@ -17223,160 +17602,166 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L84:;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":788
+ /* "pysam/cvcf.pyx":791
*
* # trim trailing bases in alleles
* if alt: # <<<<<<<<<<<<<<
* for i in range(1,min(len(ref),min(map(len,alt)))):
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
*/
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_alt); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_alt); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 791; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":789
+ /* "pysam/cvcf.pyx":792
* # trim trailing bases in alleles
* if alt:
* for i in range(1,min(len(ref),min(map(len,alt)))): # <<<<<<<<<<<<<<
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
* break
*/
- __pyx_t_8 = __Pyx_GetName(__pyx_b, __pyx_n_s__len); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_22 = PyTuple_New(2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_2 = __Pyx_GetName(__pyx_b, __pyx_n_s__len); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyTuple_New(2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_alt);
- PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_cur_scope->__pyx_v_alt);
+ PyTuple_SET_ITEM(__pyx_t_9, 1, __pyx_cur_scope->__pyx_v_alt);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_alt);
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_map, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_8, __pyx_t_2, Py_LT); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_RichCompare(__pyx_t_2, __pyx_t_10, Py_LT); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
if (__pyx_t_5) {
- __Pyx_INCREF(__pyx_t_8);
- __pyx_t_22 = __pyx_t_8;
+ __Pyx_INCREF(__pyx_t_2);
+ __pyx_t_9 = __pyx_t_2;
} else {
- __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_22 = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_9 = __pyx_t_22;
+ __pyx_t_22 = 0;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyTuple_New(2); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_int_1);
- PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_int_1);
+ PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_int_1);
__Pyx_GIVEREF(__pyx_int_1);
- __Pyx_INCREF(__pyx_t_22);
- PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- if (PyList_CheckExact(__pyx_t_22) || PyTuple_CheckExact(__pyx_t_22)) {
- __pyx_t_8 = __pyx_t_22; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __Pyx_INCREF(__pyx_t_9);
+ PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
+ __pyx_t_2 = __pyx_t_9; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_22 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_22 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_22)) {
+ __pyx_t_9 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_GOTREF(__pyx_t_9);
}
__Pyx_XDECREF(__pyx_v_i);
- __pyx_v_i = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_i = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":790
+ /* "pysam/cvcf.pyx":793
* if alt:
* for i in range(1,min(len(ref),min(map(len,alt)))):
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<<
* break
* ref, alt = ref[:-1], [allele[:-1] for allele in alt]
*/
- __pyx_t_22 = __pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyTuple_New(1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
- __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(((PyObject *)((PyObject*)(&PySet_Type))), ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(((PyObject*)__pyx_cur_scope)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- __pyx_t_3 = PySet_Size(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(((PyObject *)((PyObject*)(&PySet_Type))), ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
+ __pyx_t_3 = PySet_Size(__pyx_t_9); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__pyx_t_5 = (__pyx_t_3 > 1);
if (!__pyx_t_5) {
- __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_ref, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_GetItemInt(__pyx_v_ref, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_alt, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_cur_scope->__pyx_v_alt, 0, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_10, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_22, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_RichCompare(__pyx_t_9, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__pyx_t_19 = __pyx_t_14;
} else {
__pyx_t_19 = __pyx_t_5;
}
if (__pyx_t_19) {
- /* "pysam/cvcf.pyx":791
+ /* "pysam/cvcf.pyx":794
* for i in range(1,min(len(ref),min(map(len,alt)))):
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
* break # <<<<<<<<<<<<<<
@@ -17388,38 +17773,46 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L90:;
- /* "pysam/cvcf.pyx":792
+ /* "pysam/cvcf.pyx":795
* if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper():
* break
* ref, alt = ref[:-1], [allele[:-1] for allele in alt] # <<<<<<<<<<<<<<
*
* # left-align alleles, if a reference is available
*/
- __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_10 = PyList_New(0); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_3 = 0;
+ __pyx_t_9 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_9); __pyx_t_3 = 0;
__pyx_t_26 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_26 = Py_TYPE(__pyx_t_22)->tp_iternext;
+ __pyx_t_3 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_26 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_22)) {
- if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
- } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_22)) {
- if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_9, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_9, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_7 = __pyx_t_26(__pyx_t_22);
+ __pyx_t_7 = __pyx_t_26(__pyx_t_9);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -17428,53 +17821,53 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__Pyx_XDECREF(__pyx_v_allele);
__pyx_v_allele = __pyx_t_7;
__pyx_t_7 = 0;
- __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- if (unlikely(PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_10, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = ((PyObject *)__pyx_t_2);
- __Pyx_INCREF(__pyx_t_22);
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = ((PyObject *)__pyx_t_10);
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_ref = __pyx_t_22;
+ __pyx_t_22 = 0;
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(__pyx_t_22);
- __pyx_cur_scope->__pyx_v_alt = __pyx_t_22;
- __pyx_t_22 = 0;
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_9;
+ __pyx_t_9 = 0;
}
__pyx_L89_break:;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L87;
}
__pyx_L87:;
- /* "pysam/cvcf.pyx":795
+ /* "pysam/cvcf.pyx":798
*
* # left-align alleles, if a reference is available
* if self._leftalign and self._reference: # <<<<<<<<<<<<<<
* while left < pos:
* movable = True
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___leftalign); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_19) {
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___reference); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_14 = __pyx_t_5;
} else {
__pyx_t_14 = __pyx_t_19;
}
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":796
+ /* "pysam/cvcf.pyx":799
* # left-align alleles, if a reference is available
* if self._leftalign and self._reference:
* while left < pos: # <<<<<<<<<<<<<<
@@ -17482,14 +17875,13 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
* for allele in alt:
*/
while (1) {
- if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_8 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ if (unlikely(!__pyx_v_left)) { __Pyx_RaiseUnboundLocalError("left"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_2 = PyObject_RichCompare(__pyx_v_left, __pyx_v_pos, Py_LT); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!__pyx_t_14) break;
- /* "pysam/cvcf.pyx":797
+ /* "pysam/cvcf.pyx":800
* if self._leftalign and self._reference:
* while left < pos:
* movable = True # <<<<<<<<<<<<<<
@@ -17498,7 +17890,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
*/
__pyx_v_movable = 1;
- /* "pysam/cvcf.pyx":798
+ /* "pysam/cvcf.pyx":801
* while left < pos:
* movable = True
* for allele in alt: # <<<<<<<<<<<<<<
@@ -17506,126 +17898,133 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
* longest, shortest = allele, ref
*/
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_8 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_8); __pyx_t_4 = 0;
+ __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_15 = Py_TYPE(__pyx_t_8)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_22 = PyList_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_8)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
- __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_8, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_22 = __pyx_t_15(__pyx_t_8);
- if (unlikely(!__pyx_t_22)) {
+ __pyx_t_9 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 798; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 801; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_GOTREF(__pyx_t_9);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_allele = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":799
+ /* "pysam/cvcf.pyx":802
* movable = True
* for allele in alt:
* if len(allele) > len(ref): # <<<<<<<<<<<<<<
* longest, shortest = allele, ref
* else:
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_21 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_3 > __pyx_t_21);
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":800
+ /* "pysam/cvcf.pyx":803
* for allele in alt:
* if len(allele) > len(ref):
* longest, shortest = allele, ref # <<<<<<<<<<<<<<
* else:
* longest, shortest = ref, allele
*/
- __pyx_t_22 = __pyx_v_allele;
+ __pyx_t_9 = __pyx_v_allele;
+ __Pyx_INCREF(__pyx_t_9);
+ __pyx_t_22 = __pyx_v_ref;
__Pyx_INCREF(__pyx_t_22);
- __pyx_t_10 = __pyx_v_ref;
- __Pyx_INCREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_v_longest);
- __pyx_v_longest = __pyx_t_22;
- __pyx_t_22 = 0;
+ __pyx_v_longest = __pyx_t_9;
+ __pyx_t_9 = 0;
__Pyx_XDECREF(__pyx_v_shortest);
- __pyx_v_shortest = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_shortest = __pyx_t_22;
+ __pyx_t_22 = 0;
goto __pyx_L98;
}
/*else*/ {
- /* "pysam/cvcf.pyx":802
+ /* "pysam/cvcf.pyx":805
* longest, shortest = allele, ref
* else:
* longest, shortest = ref, allele # <<<<<<<<<<<<<<
* if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
* movable = False
*/
- __pyx_t_10 = __pyx_v_ref;
- __Pyx_INCREF(__pyx_t_10);
- __pyx_t_22 = __pyx_v_allele;
+ __pyx_t_22 = __pyx_v_ref;
__Pyx_INCREF(__pyx_t_22);
+ __pyx_t_9 = __pyx_v_allele;
+ __Pyx_INCREF(__pyx_t_9);
__Pyx_XDECREF(__pyx_v_longest);
- __pyx_v_longest = __pyx_t_10;
- __pyx_t_10 = 0;
- __Pyx_XDECREF(__pyx_v_shortest);
- __pyx_v_shortest = __pyx_t_22;
+ __pyx_v_longest = __pyx_t_22;
__pyx_t_22 = 0;
+ __Pyx_XDECREF(__pyx_v_shortest);
+ __pyx_v_shortest = __pyx_t_9;
+ __pyx_t_9 = 0;
}
__pyx_L98:;
- /* "pysam/cvcf.pyx":803
+ /* "pysam/cvcf.pyx":806
* else:
* longest, shortest = ref, allele
* if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper(): # <<<<<<<<<<<<<<
* movable = False
* if longest[-1].upper() != longest[len(shortest)-1].upper():
*/
- __pyx_t_21 = PyObject_Length(__pyx_v_longest); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_longest); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_21 == __pyx_t_3);
if (!__pyx_t_14) {
- __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_22 = __Pyx_PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PySequence_GetSlice(__pyx_v_longest, 0, __pyx_t_3); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_t_9, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_shortest, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_shortest, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_RichCompare(__pyx_t_9, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_22); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__pyx_t_5 = __pyx_t_19;
} else {
__pyx_t_5 = __pyx_t_14;
}
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":804
+ /* "pysam/cvcf.pyx":807
* longest, shortest = ref, allele
* if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
* movable = False # <<<<<<<<<<<<<<
@@ -17637,40 +18036,39 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L99:;
- /* "pysam/cvcf.pyx":805
+ /* "pysam/cvcf.pyx":808
* if len(longest) == len(shortest) or longest[:len(shortest)].upper() != shortest.upper():
* movable = False
* if longest[-1].upper() != longest[len(shortest)-1].upper(): # <<<<<<<<<<<<<<
* movable = False
* if not movable:
*/
- __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_longest, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_21 = (__pyx_t_3 - 1);
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_21, sizeof(Py_ssize_t), PyInt_FromSsize_t); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_22 = PyObject_GetAttr(__pyx_t_2, __pyx_n_s__upper); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_GetItemInt(__pyx_v_longest, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_t_22, __pyx_n_s__upper); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_RichCompare(__pyx_t_10, __pyx_t_2, Py_NE); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 805; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_shortest); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = (__pyx_t_3 - 1);
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_v_longest, __pyx_t_21, sizeof(Py_ssize_t), PyInt_FromSsize_t); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_9 = PyObject_GetAttr(__pyx_t_10, __pyx_n_s__upper); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_RichCompare(__pyx_t_22, __pyx_t_10, Py_NE); __Pyx_XGOTREF(__pyx_t_9); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_9); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":806
+ /* "pysam/cvcf.pyx":809
* movable = False
* if longest[-1].upper() != longest[len(shortest)-1].upper():
* movable = False # <<<<<<<<<<<<<<
@@ -17682,9 +18080,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L100:;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":807
+ /* "pysam/cvcf.pyx":810
* if longest[-1].upper() != longest[len(shortest)-1].upper():
* movable = False
* if not movable: # <<<<<<<<<<<<<<
@@ -17694,7 +18092,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_t_5 = (!__pyx_v_movable);
if (__pyx_t_5) {
- /* "pysam/cvcf.pyx":808
+ /* "pysam/cvcf.pyx":811
* movable = False
* if not movable:
* break # <<<<<<<<<<<<<<
@@ -17706,131 +18104,148 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L101:;
- /* "pysam/cvcf.pyx":809
+ /* "pysam/cvcf.pyx":812
* if not movable:
* break
* ref = ref[:-1] # <<<<<<<<<<<<<<
* alt = [allele[:-1] for allele in alt]
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
*/
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 809; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_ref, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_ref = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":810
+ /* "pysam/cvcf.pyx":813
* break
* ref = ref[:-1]
* alt = [allele[:-1] for allele in alt] # <<<<<<<<<<<<<<
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
* ref = faref_leftflank[pos-left-1] + ref
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
+ __pyx_t_9 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_15(__pyx_t_22);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_9);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_2;
- __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_2))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = __Pyx_PySequence_GetSlice(__pyx_v_allele, 0, -1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_2, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_8));
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = ((PyObject *)__pyx_t_2);
+ __Pyx_INCREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_GIVEREF(__pyx_t_9);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":811
+ /* "pysam/cvcf.pyx":814
* ref = ref[:-1]
* alt = [allele[:-1] for allele in alt]
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0: # <<<<<<<<<<<<<<
* ref = faref_leftflank[pos-left-1] + ref
* alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
+ __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_15(__pyx_t_22);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_2;
- __pyx_t_2 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_2))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_21 = PyObject_Length(__pyx_v_allele); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyTuple_New(1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_INCREF(((PyObject *)__pyx_t_8));
- PyTuple_SET_ITEM(__pyx_t_22, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_RichCompare(__pyx_t_8, __pyx_int_0, Py_EQ); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_22); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_INCREF(((PyObject *)__pyx_t_9));
+ PyTuple_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_t_9));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_9));
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_min, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_9, __pyx_int_0, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (!__pyx_t_5) {
- __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_v_ref); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_14 = (__pyx_t_4 == 0);
__pyx_t_19 = __pyx_t_14;
} else {
@@ -17838,101 +18253,111 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
if (__pyx_t_19) {
- /* "pysam/cvcf.pyx":812
+ /* "pysam/cvcf.pyx":815
* alt = [allele[:-1] for allele in alt]
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
* ref = faref_leftflank[pos-left-1] + ref # <<<<<<<<<<<<<<
* alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
* pos -= 1
*/
- if (unlikely(!__pyx_v_faref_leftflank)) { __Pyx_RaiseUnboundLocalError("faref_leftflank"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
- __pyx_t_22 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_8 = PyNumber_Subtract(__pyx_t_22, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_8); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyNumber_Add(__pyx_t_22, __pyx_v_ref); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 812; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ if (unlikely(!__pyx_v_faref_leftflank)) { __Pyx_RaiseUnboundLocalError("faref_leftflank"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ __pyx_t_2 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_9 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_9); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_9 = PyNumber_Add(__pyx_t_2, __pyx_v_ref); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_v_ref);
- __pyx_v_ref = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_ref = __pyx_t_9;
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":813
+ /* "pysam/cvcf.pyx":816
* if min([len(allele) for allele in alt]) == 0 or len(ref) == 0:
* ref = faref_leftflank[pos-left-1] + ref
* alt = [faref_leftflank[pos-left-1] + allele for allele in alt] # <<<<<<<<<<<<<<
* pos -= 1
*
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_9 = PyList_New(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
if (PyList_CheckExact(__pyx_cur_scope->__pyx_v_alt) || PyTuple_CheckExact(__pyx_cur_scope->__pyx_v_alt)) {
- __pyx_t_22 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
+ __pyx_t_2 = __pyx_cur_scope->__pyx_v_alt; __Pyx_INCREF(__pyx_t_2); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_2 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_alt); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_15 = Py_TYPE(__pyx_t_2)->tp_iternext;
}
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_2)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_2)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_10 = PyTuple_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_10); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_10 = PySequence_ITEM(__pyx_t_2, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_2 = __pyx_t_15(__pyx_t_22);
- if (unlikely(!__pyx_t_2)) {
+ __pyx_t_10 = __pyx_t_15(__pyx_t_2);
+ if (unlikely(!__pyx_t_10)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_GOTREF(__pyx_t_10);
}
__Pyx_XDECREF(__pyx_v_allele);
- __pyx_v_allele = __pyx_t_2;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyNumber_Subtract(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_allele = __pyx_t_10;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyNumber_Subtract(__pyx_v_pos, __pyx_v_left); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_10); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_22 = PyNumber_Subtract(__pyx_t_10, __pyx_int_1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_Add(__pyx_t_2, __pyx_v_allele); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_faref_leftflank, __pyx_t_22); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (unlikely(PyList_Append(__pyx_t_8, (PyObject*)__pyx_t_10))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 813; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyNumber_Add(__pyx_t_10, __pyx_v_allele); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ if (unlikely(__Pyx_PyList_Append(__pyx_t_9, (PyObject*)__pyx_t_22))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __Pyx_INCREF(((PyObject *)__pyx_t_8));
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = ((PyObject *)__pyx_t_9);
+ __Pyx_INCREF(__pyx_t_2);
+ __Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_GOTREF(__pyx_cur_scope->__pyx_v_alt);
__Pyx_DECREF(__pyx_cur_scope->__pyx_v_alt);
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_cur_scope->__pyx_v_alt = ((PyObject *)__pyx_t_8);
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
+ __Pyx_GIVEREF(__pyx_t_2);
+ __pyx_cur_scope->__pyx_v_alt = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":814
+ /* "pysam/cvcf.pyx":817
* ref = faref_leftflank[pos-left-1] + ref
* alt = [faref_leftflank[pos-left-1] + allele for allele in alt]
* pos -= 1 # <<<<<<<<<<<<<<
*
* # parse sample columns
*/
- __pyx_t_8 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_2 = PyNumber_InPlaceSubtract(__pyx_v_pos, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_pos);
- __pyx_v_pos = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_pos = __pyx_t_2;
+ __pyx_t_2 = 0;
goto __pyx_L104;
}
__pyx_L104:;
@@ -17942,173 +18367,181 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
__pyx_L93:;
- /* "pysam/cvcf.pyx":817
+ /* "pysam/cvcf.pyx":820
*
* # parse sample columns
* samples = [] # <<<<<<<<<<<<<<
* for sample in cols[9:]:
* dict = {}
*/
- __pyx_t_8 = PyList_New(0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_v_samples = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_v_samples = ((PyObject*)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":818
+ /* "pysam/cvcf.pyx":821
* # parse sample columns
* samples = []
* for sample in cols[9:]: # <<<<<<<<<<<<<<
* dict = {}
* values = sample.split(':')
*/
- __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_v_cols, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
- __pyx_t_22 = __pyx_t_8; __Pyx_INCREF(__pyx_t_22); __pyx_t_4 = 0;
+ __pyx_t_2 = __Pyx_PySequence_GetSlice(__pyx_v_cols, 9, PY_SSIZE_T_MAX); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ if (PyList_CheckExact(__pyx_t_2) || PyTuple_CheckExact(__pyx_t_2)) {
+ __pyx_t_9 = __pyx_t_2; __Pyx_INCREF(__pyx_t_9); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_22 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_15 = Py_TYPE(__pyx_t_22)->tp_iternext;
+ __pyx_t_4 = -1; __pyx_t_9 = PyObject_GetIter(__pyx_t_2); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_15 = Py_TYPE(__pyx_t_9)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
for (;;) {
- if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
- } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_22)) {
- if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_22)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_22, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
+ } else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_9)) {
+ if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_9)) break;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_9, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_9, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_8 = __pyx_t_15(__pyx_t_22);
- if (unlikely(!__pyx_t_8)) {
+ __pyx_t_2 = __pyx_t_15(__pyx_t_9);
+ if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_GOTREF(__pyx_t_2);
}
__Pyx_XDECREF(__pyx_v_sample);
- __pyx_v_sample = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_sample = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":819
+ /* "pysam/cvcf.pyx":822
* samples = []
* for sample in cols[9:]:
* dict = {} # <<<<<<<<<<<<<<
* values = sample.split(':')
* if len(values) > len(format):
*/
- __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 819; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_8));
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_XDECREF(((PyObject *)__pyx_v_dict));
- __pyx_v_dict = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_dict = ((PyObject*)__pyx_t_2);
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":820
+ /* "pysam/cvcf.pyx":823
* for sample in cols[9:]:
* dict = {}
* values = sample.split(':') # <<<<<<<<<<<<<<
* if len(values) > len(format):
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_sample, __pyx_n_s__split); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_sample, __pyx_n_s__split); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_22 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_117), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_XDECREF(__pyx_v_values);
- __pyx_v_values = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_values = __pyx_t_22;
+ __pyx_t_22 = 0;
- /* "pysam/cvcf.pyx":821
+ /* "pysam/cvcf.pyx":824
* dict = {}
* values = sample.split(':')
* if len(values) > len(format): # <<<<<<<<<<<<<<
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
* for idx in range(len(format)):
*/
- __pyx_t_21 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 821; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_19 = (__pyx_t_21 > __pyx_t_3);
if (__pyx_t_19) {
- /* "pysam/cvcf.pyx":822
+ /* "pysam/cvcf.pyx":825
* values = sample.split(':')
* if len(values) > len(format):
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format))) # <<<<<<<<<<<<<<
* for idx in range(len(format)):
* expected = self.get_expected(format[idx], self._format, alt)
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_18); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_18); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
- PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_sample);
PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_v_sample);
__Pyx_GIVEREF(__pyx_v_sample);
PyTuple_SET_ITEM(__pyx_t_24, 2, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
- __pyx_t_2 = 0;
+ __pyx_t_10 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_24)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_19), ((PyObject *)__pyx_t_24)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
- __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_24 = PyTuple_New(3); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_24, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_24, 2, ((PyObject *)__pyx_t_7));
__Pyx_GIVEREF(((PyObject *)__pyx_t_7));
- __pyx_t_8 = 0;
+ __pyx_t_2 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_22, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
goto __pyx_L111;
}
__pyx_L111:;
- /* "pysam/cvcf.pyx":823
+ /* "pysam/cvcf.pyx":826
* if len(values) > len(format):
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
* for idx in range(len(format)): # <<<<<<<<<<<<<<
* expected = self.get_expected(format[idx], self._format, alt)
* if idx < len(values): value = values[idx]
*/
- __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_format); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_24 = PyTuple_New(1); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_24 = PyTuple_New(1); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_builtin_range, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
if (PyList_CheckExact(__pyx_t_7) || PyTuple_CheckExact(__pyx_t_7)) {
__pyx_t_24 = __pyx_t_7; __Pyx_INCREF(__pyx_t_24); __pyx_t_3 = 0;
__pyx_t_26 = NULL;
} else {
- __pyx_t_3 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_7); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
__pyx_t_26 = Py_TYPE(__pyx_t_24)->tp_iternext;
}
@@ -18116,16 +18549,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
for (;;) {
if (!__pyx_t_26 && PyList_CheckExact(__pyx_t_24)) {
if (__pyx_t_3 >= PyList_GET_SIZE(__pyx_t_24)) break;
- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_24, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_26 && PyTuple_CheckExact(__pyx_t_24)) {
if (__pyx_t_3 >= PyTuple_GET_SIZE(__pyx_t_24)) break;
- __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_7 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_3); __Pyx_INCREF(__pyx_t_7); __pyx_t_3++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_7 = PySequence_ITEM(__pyx_t_24, __pyx_t_3); __pyx_t_3++; if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_7 = __pyx_t_26(__pyx_t_24);
if (unlikely(!__pyx_t_7)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -18135,74 +18576,72 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
__pyx_v_idx = __pyx_t_7;
__pyx_t_7 = 0;
- /* "pysam/cvcf.pyx":824
+ /* "pysam/cvcf.pyx":827
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
* for idx in range(len(format)):
* expected = self.get_expected(format[idx], self._format, alt) # <<<<<<<<<<<<<<
* if idx < len(values): value = values[idx]
* else:
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__get_expected); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__get_expected); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_2 = PyTuple_New(3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_10 = PyTuple_New(3); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_alt);
- PyTuple_SET_ITEM(__pyx_t_2, 2, __pyx_cur_scope->__pyx_v_alt);
+ PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_cur_scope->__pyx_v_alt);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_alt);
- __pyx_t_10 = 0;
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_22 = 0;
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
__Pyx_XDECREF(__pyx_v_expected);
- __pyx_v_expected = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_expected = __pyx_t_2;
+ __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":825
+ /* "pysam/cvcf.pyx":828
* for idx in range(len(format)):
* expected = self.get_expected(format[idx], self._format, alt)
* if idx < len(values): value = values[idx] # <<<<<<<<<<<<<<
* else:
* if expected == -1: value = "."
*/
- __pyx_t_21 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_8, Py_LT); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_21 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_RichCompare(__pyx_v_idx, __pyx_t_2, Py_LT); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_19) {
- __pyx_t_2 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 825; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_values, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_2;
- __pyx_t_2 = 0;
+ __pyx_v_value = __pyx_t_10;
+ __pyx_t_10 = 0;
goto __pyx_L114;
}
/*else*/ {
- /* "pysam/cvcf.pyx":827
+ /* "pysam/cvcf.pyx":830
* if idx < len(values): value = values[idx]
* else:
* if expected == -1: value = "." # <<<<<<<<<<<<<<
* else: value = ",".join(["."]*expected)
*
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_10 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_19) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
__Pyx_XDECREF(__pyx_v_value);
@@ -18211,494 +18650,508 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":828
+ /* "pysam/cvcf.pyx":831
* else:
* if expected == -1: value = "."
* else: value = ",".join(["."]*expected) # <<<<<<<<<<<<<<
*
* dict[format[idx]] = self.parse_formatdata(format[idx],
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_8 = PyList_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
- PyList_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_kp_s_9));
+ PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
- { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_8, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_v_expected); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_temp);
- __Pyx_DECREF(__pyx_t_8);
- __pyx_t_8 = __pyx_temp;
+ __Pyx_DECREF(__pyx_t_2);
+ __pyx_t_2 = __pyx_temp;
}
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_8));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
- __pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_2));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_2));
+ __pyx_t_2 = 0;
+ __pyx_t_2 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_8;
- __pyx_t_8 = 0;
+ __pyx_v_value = __pyx_t_2;
+ __pyx_t_2 = 0;
}
__pyx_L115:;
}
__pyx_L114:;
- /* "pysam/cvcf.pyx":830
+ /* "pysam/cvcf.pyx":833
* else: value = ",".join(["."]*expected)
*
* dict[format[idx]] = self.parse_formatdata(format[idx], # <<<<<<<<<<<<<<
* value,
* self._format,
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_formatdata); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/cvcf.pyx":832
+ /* "pysam/cvcf.pyx":835
* dict[format[idx]] = self.parse_formatdata(format[idx],
* value,
* self._format, # <<<<<<<<<<<<<<
* line)
* if expected != -1 and len(dict[format[idx]]) != expected:
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
- /* "pysam/cvcf.pyx":833
+ /* "pysam/cvcf.pyx":836
* value,
* self._format,
* line) # <<<<<<<<<<<<<<
* if expected != -1 and len(dict[format[idx]]) != expected:
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
*/
- __pyx_t_10 = PyTuple_New(4); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_10, 0, __pyx_t_7);
+ __pyx_t_22 = PyTuple_New(4); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_10, 1, __pyx_v_value);
+ PyTuple_SET_ITEM(__pyx_t_22, 1, __pyx_v_value);
__Pyx_GIVEREF(__pyx_v_value);
- PyTuple_SET_ITEM(__pyx_t_10, 2, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
+ PyTuple_SET_ITEM(__pyx_t_22, 2, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
__Pyx_INCREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_10, 3, __pyx_v_line);
+ PyTuple_SET_ITEM(__pyx_t_22, 3, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
__pyx_t_7 = 0;
- __pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_10), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
+ __pyx_t_10 = 0;
+ __pyx_t_10 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_22), NULL); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_10);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_22)); __pyx_t_22 = 0;
- /* "pysam/cvcf.pyx":830
+ /* "pysam/cvcf.pyx":833
* else: value = ",".join(["."]*expected)
*
* dict[format[idx]] = self.parse_formatdata(format[idx], # <<<<<<<<<<<<<<
* value,
* self._format,
*/
- __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_10, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_22, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":834
+ /* "pysam/cvcf.pyx":837
* self._format,
* line)
* if expected != -1 and len(dict[format[idx]]) != expected: # <<<<<<<<<<<<<<
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
*/
- __pyx_t_2 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_10 = PyObject_RichCompare(__pyx_v_expected, __pyx_int_neg_1, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_19 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_19 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
if (__pyx_t_19) {
- __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_2); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_t_10); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_10, __pyx_v_expected, Py_NE); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_21 = PyObject_Length(__pyx_t_22); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_10 = PyObject_RichCompare(__pyx_t_22, __pyx_v_expected, Py_NE); __Pyx_XGOTREF(__pyx_t_10); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_10); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_5 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 834; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_14 = __pyx_t_5;
} else {
__pyx_t_14 = __pyx_t_19;
}
if (__pyx_t_14) {
- /* "pysam/cvcf.pyx":835
+ /* "pysam/cvcf.pyx":838
* line)
* if expected != -1 and len(dict[format[idx]]) != expected:
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS, # <<<<<<<<<<<<<<
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_20); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__error); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_20); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
- /* "pysam/cvcf.pyx":836
+ /* "pysam/cvcf.pyx":839
* if expected != -1 and len(dict[format[idx]]) != expected:
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]])) # <<<<<<<<<<<<<<
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
* dict[format[idx]] = dict[format[idx]][:expected]
*/
- __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_23 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_7); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_7); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_8);
- __Pyx_GIVEREF(__pyx_t_8);
+ PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
+ __Pyx_GIVEREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_expected);
PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_v_expected);
__Pyx_GIVEREF(__pyx_v_expected);
- PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_23);
- __Pyx_GIVEREF(__pyx_t_23);
+ PyTuple_SET_ITEM(__pyx_t_7, 2, __pyx_t_8);
+ __Pyx_GIVEREF(__pyx_t_8);
+ __pyx_t_2 = 0;
__pyx_t_8 = 0;
- __pyx_t_23 = 0;
- __pyx_t_23 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_23));
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_21), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(3); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(__pyx_v_line);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_line);
__Pyx_GIVEREF(__pyx_v_line);
- PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_10);
- __Pyx_GIVEREF(__pyx_t_10);
- PyTuple_SET_ITEM(__pyx_t_7, 2, ((PyObject *)__pyx_t_23));
- __Pyx_GIVEREF(((PyObject *)__pyx_t_23));
- __pyx_t_10 = 0;
- __pyx_t_23 = 0;
- __pyx_t_23 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ PyTuple_SET_ITEM(__pyx_t_7, 1, __pyx_t_22);
+ __Pyx_GIVEREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_7, 2, ((PyObject *)__pyx_t_8));
+ __Pyx_GIVEREF(((PyObject *)__pyx_t_8));
+ __pyx_t_22 = 0;
+ __pyx_t_8 = 0;
+ __pyx_t_8 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":837
+ /* "pysam/cvcf.pyx":840
* self.error(line,self.BAD_NUMBER_OF_PARAMETERS,
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]])) # <<<<<<<<<<<<<<
* dict[format[idx]] = dict[format[idx]][:expected]
* samples.append( dict )
*/
- __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_21 = PyObject_Length(__pyx_t_7); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_23 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_LT); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
+ __pyx_t_8 = PyObject_RichCompare(__pyx_t_7, __pyx_v_expected, Py_LT); __Pyx_XGOTREF(__pyx_t_8); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_23); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
+ __pyx_t_14 = __Pyx_PyObject_IsTrue(__pyx_t_8); if (unlikely(__pyx_t_14 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
if (__pyx_t_14) {
- __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
- __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_7 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_2); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = __Pyx_GetItemInt(__pyx_t_10, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_8 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_10); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_21 = PyObject_Length(__pyx_t_8); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- __pyx_t_10 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_8); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = __Pyx_GetItemInt(__pyx_t_22, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- __pyx_t_8 = PyList_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_8);
- PyList_SET_ITEM(__pyx_t_8, 0, __pyx_t_2);
- __Pyx_GIVEREF(__pyx_t_2);
- { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_8, __pyx_t_10); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_2 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_22); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_21 = PyObject_Length(__pyx_t_2); if (unlikely(__pyx_t_21 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyInt_FromSsize_t(__pyx_t_21); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_22 = PyNumber_Subtract(__pyx_v_expected, __pyx_t_2); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_2 = PyList_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ PyList_SET_ITEM(__pyx_t_2, 0, __pyx_t_10);
+ __Pyx_GIVEREF(__pyx_t_10);
+ { PyObject* __pyx_temp = PyNumber_InPlaceMultiply(__pyx_t_2, __pyx_t_22); if (unlikely(!__pyx_temp)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_temp);
- __Pyx_DECREF(__pyx_t_8);
- __pyx_t_8 = __pyx_temp;
+ __Pyx_DECREF(__pyx_t_2);
+ __pyx_t_2 = __pyx_temp;
}
- __pyx_t_2 = 0;
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyNumber_InPlaceAdd(__pyx_t_7, ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
+ __pyx_t_10 = 0;
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyNumber_InPlaceAdd(__pyx_t_7, ((PyObject *)__pyx_t_2)); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_23, __pyx_t_10) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
+ __Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
+ if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_8, __pyx_t_22) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L117;
}
__pyx_L117:;
- /* "pysam/cvcf.pyx":838
+ /* "pysam/cvcf.pyx":841
* "id=%s, expected %s parameters, got %s" % (format[idx],expected,dict[format[idx]]))
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
* dict[format[idx]] = dict[format[idx]][:expected] # <<<<<<<<<<<<<<
* samples.append( dict )
*
*/
- __pyx_t_23 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_23) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
- __pyx_t_10 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_23); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
- __pyx_t_21 = __Pyx_PyIndex_AsSsize_t(__pyx_v_expected); if (unlikely((__pyx_t_21 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_23 = __Pyx_PySequence_GetSlice(__pyx_t_10, 0, __pyx_t_21); if (unlikely(!__pyx_t_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_23);
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __pyx_t_10 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_10) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_10);
- if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_10, __pyx_t_23) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 838; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
- __Pyx_DECREF(__pyx_t_23); __pyx_t_23 = 0;
+ __pyx_t_8 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_8) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_22 = __Pyx_PyDict_GetItem(((PyObject *)__pyx_v_dict), __pyx_t_8); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ __pyx_t_21 = __Pyx_PyIndex_AsSsize_t(__pyx_v_expected); if (unlikely((__pyx_t_21 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PySequence_GetSlice(__pyx_t_22, 0, __pyx_t_21); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __pyx_t_22 = PyObject_GetItem(__pyx_v_format, __pyx_v_idx); if (!__pyx_t_22) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ if (PyDict_SetItem(((PyObject *)__pyx_v_dict), __pyx_t_22, __pyx_t_8) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 841; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
goto __pyx_L116;
}
__pyx_L116:;
}
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
- /* "pysam/cvcf.pyx":839
+ /* "pysam/cvcf.pyx":842
* if len(dict[format[idx]] ) < expected: dict[format[idx]] += [dict[format[idx]][-1]]*(expected-len(dict[format[idx]]))
* dict[format[idx]] = dict[format[idx]][:expected]
* samples.append( dict ) # <<<<<<<<<<<<<<
*
* # done
*/
- __pyx_t_25 = PyList_Append(__pyx_v_samples, ((PyObject *)__pyx_v_dict)); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_25 = PyList_Append(__pyx_v_samples, ((PyObject *)__pyx_v_dict)); if (unlikely(__pyx_t_25 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":842
+ /* "pysam/cvcf.pyx":845
*
* # done
* d = {'chrom':chrom, # <<<<<<<<<<<<<<
* 'pos':pos, # return 0-based position
* 'id':id,
*/
- __pyx_t_22 = PyDict_New(); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(((PyObject *)__pyx_t_22));
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__chrom), __pyx_v_chrom) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(((PyObject *)__pyx_t_9));
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__chrom), __pyx_v_chrom) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":843
+ /* "pysam/cvcf.pyx":846
* # done
* d = {'chrom':chrom,
* 'pos':pos, # return 0-based position # <<<<<<<<<<<<<<
* 'id':id,
* 'ref':ref,
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__pos), __pyx_v_pos) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__pos), __pyx_v_pos) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":844
+ /* "pysam/cvcf.pyx":847
* d = {'chrom':chrom,
* 'pos':pos, # return 0-based position
* 'id':id, # <<<<<<<<<<<<<<
* 'ref':ref,
* 'alt':alt,
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__id), __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__id), __pyx_v_id) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":845
+ /* "pysam/cvcf.pyx":848
* 'pos':pos, # return 0-based position
* 'id':id,
* 'ref':ref, # <<<<<<<<<<<<<<
* 'alt':alt,
* 'qual':qual,
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__ref), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__ref), __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":846
+ /* "pysam/cvcf.pyx":849
* 'id':id,
* 'ref':ref,
* 'alt':alt, # <<<<<<<<<<<<<<
* 'qual':qual,
* 'filter':filter,
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__alt), __pyx_cur_scope->__pyx_v_alt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__alt), __pyx_cur_scope->__pyx_v_alt) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":847
+ /* "pysam/cvcf.pyx":850
* 'ref':ref,
* 'alt':alt,
* 'qual':qual, # <<<<<<<<<<<<<<
* 'filter':filter,
* 'info':info,
*/
- __pyx_t_24 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 847; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_24 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 850; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__qual), __pyx_t_24) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__qual), __pyx_t_24) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
- /* "pysam/cvcf.pyx":848
+ /* "pysam/cvcf.pyx":851
* 'alt':alt,
* 'qual':qual,
* 'filter':filter, # <<<<<<<<<<<<<<
* 'info':info,
* 'format':format}
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__filter), __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__filter), __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":849
+ /* "pysam/cvcf.pyx":852
* 'qual':qual,
* 'filter':filter,
* 'info':info, # <<<<<<<<<<<<<<
* 'format':format}
* for key,value in zip(self._samples,samples):
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_v_info)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__info), ((PyObject *)__pyx_v_info)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":850
+ /* "pysam/cvcf.pyx":853
* 'filter':filter,
* 'info':info,
* 'format':format} # <<<<<<<<<<<<<<
* for key,value in zip(self._samples,samples):
* d[key] = value
*/
- if (PyDict_SetItem(__pyx_t_22, ((PyObject *)__pyx_n_s__format), __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 842; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_v_d = __pyx_t_22;
- __pyx_t_22 = 0;
+ if (PyDict_SetItem(__pyx_t_9, ((PyObject *)__pyx_n_s__format), __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 845; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_d = ((PyObject*)__pyx_t_9);
+ __pyx_t_9 = 0;
- /* "pysam/cvcf.pyx":851
+ /* "pysam/cvcf.pyx":854
* 'info':info,
* 'format':format}
* for key,value in zip(self._samples,samples): # <<<<<<<<<<<<<<
* d[key] = value
*
*/
- __pyx_t_22 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
- __pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
+ __pyx_t_24 = PyTuple_New(2); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
- PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_22);
- __Pyx_GIVEREF(__pyx_t_22);
+ PyTuple_SET_ITEM(__pyx_t_24, 0, __pyx_t_9);
+ __Pyx_GIVEREF(__pyx_t_9);
__Pyx_INCREF(((PyObject *)__pyx_v_samples));
PyTuple_SET_ITEM(__pyx_t_24, 1, ((PyObject *)__pyx_v_samples));
__Pyx_GIVEREF(((PyObject *)__pyx_v_samples));
- __pyx_t_22 = 0;
- __pyx_t_22 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_22);
+ __pyx_t_9 = 0;
+ __pyx_t_9 = PyObject_Call(__pyx_builtin_zip, ((PyObject *)__pyx_t_24), NULL); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(((PyObject *)__pyx_t_24)); __pyx_t_24 = 0;
- if (PyList_CheckExact(__pyx_t_22) || PyTuple_CheckExact(__pyx_t_22)) {
- __pyx_t_24 = __pyx_t_22; __Pyx_INCREF(__pyx_t_24); __pyx_t_4 = 0;
+ if (PyList_CheckExact(__pyx_t_9) || PyTuple_CheckExact(__pyx_t_9)) {
+ __pyx_t_24 = __pyx_t_9; __Pyx_INCREF(__pyx_t_24); __pyx_t_4 = 0;
__pyx_t_15 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_24 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_24)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_24);
__pyx_t_15 = Py_TYPE(__pyx_t_24)->tp_iternext;
}
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
for (;;) {
if (!__pyx_t_15 && PyList_CheckExact(__pyx_t_24)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_24)) break;
- __pyx_t_22 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyList_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_24, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_15 && PyTuple_CheckExact(__pyx_t_24)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_24)) break;
- __pyx_t_22 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_22); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_24, __pyx_t_4); __Pyx_INCREF(__pyx_t_9); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_9 = PySequence_ITEM(__pyx_t_24, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
- __pyx_t_22 = __pyx_t_15(__pyx_t_24);
- if (unlikely(!__pyx_t_22)) {
+ __pyx_t_9 = __pyx_t_15(__pyx_t_24);
+ if (unlikely(!__pyx_t_9)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
- __Pyx_GOTREF(__pyx_t_22);
+ __Pyx_GOTREF(__pyx_t_9);
}
- if ((likely(PyTuple_CheckExact(__pyx_t_22))) || (PyList_CheckExact(__pyx_t_22))) {
- PyObject* sequence = __pyx_t_22;
+ if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
+ PyObject* sequence = __pyx_t_9;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
+ if (unlikely(size != 2)) {
+ if (size > 2) __Pyx_RaiseTooManyValuesError(2);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 2)) {
- if (PyTuple_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_23 = PyTuple_GET_ITEM(sequence, 0);
- __pyx_t_10 = PyTuple_GET_ITEM(sequence, 1);
+ __pyx_t_8 = PyTuple_GET_ITEM(sequence, 0);
+ __pyx_t_22 = PyTuple_GET_ITEM(sequence, 1);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 2)) {
- if (PyList_GET_SIZE(sequence) > 2) __Pyx_RaiseTooManyValuesError(2);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
- __pyx_t_23 = PyList_GET_ITEM(sequence, 0);
- __pyx_t_10 = PyList_GET_ITEM(sequence, 1);
+ __pyx_t_8 = PyList_GET_ITEM(sequence, 0);
+ __pyx_t_22 = PyList_GET_ITEM(sequence, 1);
}
- __Pyx_INCREF(__pyx_t_23);
- __Pyx_INCREF(__pyx_t_10);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- } else {
+ __Pyx_INCREF(__pyx_t_8);
+ __Pyx_INCREF(__pyx_t_22);
+ #else
+ __pyx_t_8 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_8);
+ __pyx_t_22 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_22);
+ #endif
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ } else
+ {
Py_ssize_t index = -1;
- __pyx_t_8 = PyObject_GetIter(__pyx_t_22); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_t_2);
+ __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
+ __pyx_t_27 = Py_TYPE(__pyx_t_2)->tp_iternext;
+ index = 0; __pyx_t_8 = __pyx_t_27(__pyx_t_2); if (unlikely(!__pyx_t_8)) goto __pyx_L120_unpacking_failed;
__Pyx_GOTREF(__pyx_t_8);
- __Pyx_DECREF(__pyx_t_22); __pyx_t_22 = 0;
- __pyx_t_27 = Py_TYPE(__pyx_t_8)->tp_iternext;
- index = 0; __pyx_t_23 = __pyx_t_27(__pyx_t_8); if (unlikely(!__pyx_t_23)) goto __pyx_L120_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_23);
- index = 1; __pyx_t_10 = __pyx_t_27(__pyx_t_8); if (unlikely(!__pyx_t_10)) goto __pyx_L120_unpacking_failed;
- __Pyx_GOTREF(__pyx_t_10);
- if (__Pyx_IternextUnpackEndCheck(__pyx_t_27(__pyx_t_8), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
+ index = 1; __pyx_t_22 = __pyx_t_27(__pyx_t_2); if (unlikely(!__pyx_t_22)) goto __pyx_L120_unpacking_failed;
+ __Pyx_GOTREF(__pyx_t_22);
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_27(__pyx_t_2), 2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_27 = NULL;
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
goto __pyx_L121_unpacking_done;
__pyx_L120_unpacking_failed:;
- __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
+ __pyx_t_27 = NULL;
+ if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_L121_unpacking_done:;
}
__Pyx_XDECREF(__pyx_v_key);
- __pyx_v_key = __pyx_t_23;
- __pyx_t_23 = 0;
+ __pyx_v_key = __pyx_t_8;
+ __pyx_t_8 = 0;
__Pyx_XDECREF(__pyx_v_value);
- __pyx_v_value = __pyx_t_10;
- __pyx_t_10 = 0;
+ __pyx_v_value = __pyx_t_22;
+ __pyx_t_22 = 0;
- /* "pysam/cvcf.pyx":852
+ /* "pysam/cvcf.pyx":855
* 'format':format}
* for key,value in zip(self._samples,samples):
* d[key] = value # <<<<<<<<<<<<<<
*
* return d
*/
- if (PyDict_SetItem(((PyObject *)__pyx_v_d), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 852; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(((PyObject *)__pyx_v_d), __pyx_v_key, __pyx_v_value) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 855; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
__Pyx_DECREF(__pyx_t_24); __pyx_t_24 = 0;
- /* "pysam/cvcf.pyx":854
+ /* "pysam/cvcf.pyx":857
* d[key] = value
*
* return d # <<<<<<<<<<<<<<
@@ -18775,12 +19228,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_35write_data(PyObject *__pyx_self, P
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
PyObject *__pyx_v_data = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__data,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write_data (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__data,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -18795,24 +19247,21 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_35write_data(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__data)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write_data") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write_data") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -18827,7 +19276,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_35write_data(PyObject *__pyx_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write_data", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.write_data", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -18838,7 +19287,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_35write_data(PyObject *__pyx_self, P
return __pyx_r;
}
-/* "pysam/cvcf.pyx":857
+/* "pysam/cvcf.pyx":860
*
*
* def write_data(self, stream, data): # <<<<<<<<<<<<<<
@@ -18874,14 +19323,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("write_data", 0);
- /* "pysam/cvcf.pyx":858
+ /* "pysam/cvcf.pyx":861
*
* def write_data(self, stream, data):
* required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples # <<<<<<<<<<<<<<
* for k in required:
* if k not in data: raise ValueError("Required key %s not found in data" % str(k))
*/
- __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__chrom));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__chrom));
@@ -18910,16 +19359,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__Pyx_INCREF(((PyObject *)__pyx_n_s__format));
PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__format));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_1), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyNumber_Add(((PyObject *)__pyx_t_1), __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_v_required = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":859
+ /* "pysam/cvcf.pyx":862
* def write_data(self, stream, data):
* required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
* for k in required: # <<<<<<<<<<<<<<
@@ -18930,23 +19379,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__pyx_t_3 = __pyx_v_required; __Pyx_INCREF(__pyx_t_3); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_required); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_required); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_t_5 = Py_TYPE(__pyx_t_3)->tp_iternext;
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_3)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_3)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_3)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_3, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_3);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 859; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -18956,59 +19413,58 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__pyx_v_k = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":860
+ /* "pysam/cvcf.pyx":863
* required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
* for k in required:
* if k not in data: raise ValueError("Required key %s not found in data" % str(k)) # <<<<<<<<<<<<<<
* if data['alt'] == []: alt = "."
* else: alt = ",".join(data['alt'])
*/
- __pyx_t_6 = (__Pyx_NegateNonNeg(PySequence_Contains(__pyx_v_data, __pyx_v_k))); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = (__Pyx_PySequence_Contains(__pyx_v_k, __pyx_v_data, Py_NE)); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_6) {
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_k);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_k);
__Pyx_GIVEREF(__pyx_v_k);
- __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_118), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_118), __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_t_2));
__Pyx_GIVEREF(((PyObject *)__pyx_t_2));
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_Raise(__pyx_t_2, 0, 0, 0);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
}
__pyx_L5:;
}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":861
+ /* "pysam/cvcf.pyx":864
* for k in required:
* if k not in data: raise ValueError("Required key %s not found in data" % str(k))
* if data['alt'] == []: alt = "." # <<<<<<<<<<<<<<
* else: alt = ",".join(data['alt'])
* if data['filter'] == None: filter = "."
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__alt)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__alt)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_6) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
@@ -19017,23 +19473,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":862
+ /* "pysam/cvcf.pyx":865
* if k not in data: raise ValueError("Required key %s not found in data" % str(k))
* if data['alt'] == []: alt = "."
* else: alt = ",".join(data['alt']) # <<<<<<<<<<<<<<
* if data['filter'] == None: filter = "."
* elif data['filter'] == []:
*/
- __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_2), __pyx_n_s__join); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__alt)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__alt)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 862; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -19042,19 +19498,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
__pyx_L6:;
- /* "pysam/cvcf.pyx":863
+ /* "pysam/cvcf.pyx":866
* if data['alt'] == []: alt = "."
* else: alt = ",".join(data['alt'])
* if data['filter'] == None: filter = "." # <<<<<<<<<<<<<<
* elif data['filter'] == []:
* if self._version == 33: filter = "0"
*/
- __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_2, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 863; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 866; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_6) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
@@ -19062,38 +19517,36 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
goto __pyx_L7;
}
- /* "pysam/cvcf.pyx":864
+ /* "pysam/cvcf.pyx":867
* else: alt = ",".join(data['alt'])
* if data['filter'] == None: filter = "."
* elif data['filter'] == []: # <<<<<<<<<<<<<<
* if self._version == 33: filter = "0"
* else: filter = "PASS"
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_3, ((PyObject *)__pyx_t_2), Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":865
+ /* "pysam/cvcf.pyx":868
* if data['filter'] == None: filter = "."
* elif data['filter'] == []:
* if self._version == 33: filter = "0" # <<<<<<<<<<<<<<
* else: filter = "PASS"
* else: filter = ';'.join(data['filter'])
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___version); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_2);
+ __pyx_t_2 = PyObject_RichCompare(__pyx_t_1, __pyx_int_33, Py_EQ); __Pyx_XGOTREF(__pyx_t_2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 865; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_6) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s__0));
@@ -19102,7 +19555,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":866
+ /* "pysam/cvcf.pyx":869
* elif data['filter'] == []:
* if self._version == 33: filter = "0"
* else: filter = "PASS" # <<<<<<<<<<<<<<
@@ -19117,23 +19570,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":867
+ /* "pysam/cvcf.pyx":870
* if self._version == 33: filter = "0"
* else: filter = "PASS"
* else: filter = ';'.join(data['filter']) # <<<<<<<<<<<<<<
* if data['qual'] == -1: qual = "."
* else: qual = str(data['qual'])
*/
- __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_11), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_11), __pyx_n_s__join); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__filter)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -19142,19 +19595,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
__pyx_L7:;
- /* "pysam/cvcf.pyx":868
+ /* "pysam/cvcf.pyx":871
* else: filter = "PASS"
* else: filter = ';'.join(data['filter'])
* if data['qual'] == -1: qual = "." # <<<<<<<<<<<<<<
* else: qual = str(data['qual'])
*
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__qual)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__qual)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_neg_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 868; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (__pyx_t_6) {
__Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
@@ -19163,21 +19615,21 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
/*else*/ {
- /* "pysam/cvcf.pyx":869
+ /* "pysam/cvcf.pyx":872
* else: filter = ';'.join(data['filter'])
* if data['qual'] == -1: qual = "."
* else: qual = str(data['qual']) # <<<<<<<<<<<<<<
*
* output = [data['chrom'],
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__qual)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__qual)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 869; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__pyx_v_qual = __pyx_t_3;
@@ -19185,71 +19637,71 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
}
__pyx_L9:;
- /* "pysam/cvcf.pyx":871
+ /* "pysam/cvcf.pyx":874
* else: qual = str(data['qual'])
*
* output = [data['chrom'], # <<<<<<<<<<<<<<
* str(data['pos']+1), # change to 1-based position
* data['id'],
*/
- __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__chrom)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__chrom)); if (!__pyx_t_3) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- /* "pysam/cvcf.pyx":872
+ /* "pysam/cvcf.pyx":875
*
* output = [data['chrom'],
* str(data['pos']+1), # change to 1-based position # <<<<<<<<<<<<<<
* data['id'],
* data['ref'],
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__pos)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__pos)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyNumber_Add(__pyx_t_1, __pyx_int_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(((PyObject *)((PyObject*)(&PyString_Type))), ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":873
+ /* "pysam/cvcf.pyx":876
* output = [data['chrom'],
* str(data['pos']+1), # change to 1-based position
* data['id'], # <<<<<<<<<<<<<<
* data['ref'],
* alt,
*/
- __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 873; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__id)); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 876; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- /* "pysam/cvcf.pyx":874
+ /* "pysam/cvcf.pyx":877
* str(data['pos']+1), # change to 1-based position
* data['id'],
* data['ref'], # <<<<<<<<<<<<<<
* alt,
* qual,
*/
- __pyx_t_7 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__ref)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__ref)); if (!__pyx_t_7) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- /* "pysam/cvcf.pyx":878
+ /* "pysam/cvcf.pyx":881
* qual,
* filter,
* self.format_formatdata( data['info'], self._info, separator=";" ), # <<<<<<<<<<<<<<
* self.format_formatdata( data['format'], self._format, value=False ) ]
*
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__info)); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__info)); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_11 = PyTuple_New(2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyTuple_New(2); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
PyTuple_SET_ITEM(__pyx_t_11, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
@@ -19257,29 +19709,29 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_10);
__pyx_t_9 = 0;
__pyx_t_10 = 0;
- __pyx_t_10 = PyDict_New(); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyDict_New(); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_10));
- if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__separator), ((PyObject *)__pyx_kp_s_11)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_11), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 878; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_10, ((PyObject *)__pyx_n_s__separator), ((PyObject *)__pyx_kp_s_11)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_11), ((PyObject *)__pyx_t_10)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_11)); __pyx_t_11 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_10)); __pyx_t_10 = 0;
- /* "pysam/cvcf.pyx":879
+ /* "pysam/cvcf.pyx":882
* filter,
* self.format_formatdata( data['info'], self._info, separator=";" ),
* self.format_formatdata( data['format'], self._format, value=False ) ] # <<<<<<<<<<<<<<
*
* for s in self._samples:
*/
- __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_formatdata); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_10 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_formatdata); if (unlikely(!__pyx_t_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_10);
- __pyx_t_11 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__format)); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetItem(__pyx_v_data, ((PyObject *)__pyx_n_s__format)); if (!__pyx_t_11) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_12 = PyTuple_New(2); if (unlikely(!__pyx_t_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_12);
PyTuple_SET_ITEM(__pyx_t_12, 0, __pyx_t_11);
__Pyx_GIVEREF(__pyx_t_11);
@@ -19287,18 +19739,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_8);
__pyx_t_11 = 0;
__pyx_t_8 = 0;
- __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyDict_New(); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_11 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__value), __pyx_t_11) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_8, ((PyObject *)__pyx_n_s__value), __pyx_t_11) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- __pyx_t_11 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_12), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_Call(__pyx_t_10, ((PyObject *)__pyx_t_12), ((PyObject *)__pyx_t_8)); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_12)); __pyx_t_12 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
- __pyx_t_8 = PyList_New(9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 871; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyList_New(9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyList_SET_ITEM(__pyx_t_8, 0, __pyx_t_3);
__Pyx_GIVEREF(__pyx_t_3);
@@ -19327,23 +19779,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__pyx_t_7 = 0;
__pyx_t_9 = 0;
__pyx_t_11 = 0;
- __pyx_v_output = __pyx_t_8;
+ __pyx_v_output = ((PyObject*)__pyx_t_8);
__pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":881
+ /* "pysam/cvcf.pyx":884
* self.format_formatdata( data['format'], self._format, value=False ) ]
*
* for s in self._samples: # <<<<<<<<<<<<<<
* output.append( self.format_formatdata( data[s], self._format, key=False ) )
*
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
if (PyList_CheckExact(__pyx_t_8) || PyTuple_CheckExact(__pyx_t_8)) {
__pyx_t_11 = __pyx_t_8; __Pyx_INCREF(__pyx_t_11); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_11 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
__pyx_t_5 = Py_TYPE(__pyx_t_11)->tp_iternext;
}
@@ -19351,16 +19803,24 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_11)) break;
- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyList_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_11)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_11)) break;
- __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_8 = PyTuple_GET_ITEM(__pyx_t_11, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_8 = PySequence_ITEM(__pyx_t_11, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_8 = __pyx_t_5(__pyx_t_11);
if (unlikely(!__pyx_t_8)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -19370,20 +19830,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__pyx_v_s = __pyx_t_8;
__pyx_t_8 = 0;
- /* "pysam/cvcf.pyx":882
+ /* "pysam/cvcf.pyx":885
*
* for s in self._samples:
* output.append( self.format_formatdata( data[s], self._format, key=False ) ) # <<<<<<<<<<<<<<
*
* stream.write( "\t".join(output) + "\n" )
*/
- __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__format_formatdata); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
- __pyx_t_9 = PyObject_GetItem(__pyx_v_data, __pyx_v_s); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetItem(__pyx_v_data, __pyx_v_s); if (!__pyx_t_9) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_9);
__Pyx_GIVEREF(__pyx_t_9);
@@ -19391,51 +19851,51 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_9 = 0;
__pyx_t_7 = 0;
- __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyDict_New(); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_7));
- __pyx_t_9 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__key), __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_7, ((PyObject *)__pyx_n_s__key), __pyx_t_9) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
- __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_Call(__pyx_t_8, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_7)); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_13 = PyList_Append(__pyx_v_output, __pyx_t_9); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 882; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_13 = PyList_Append(__pyx_v_output, __pyx_t_9); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
}
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
- /* "pysam/cvcf.pyx":884
+ /* "pysam/cvcf.pyx":887
* output.append( self.format_formatdata( data[s], self._format, key=False ) )
*
* stream.write( "\t".join(output) + "\n" ) # <<<<<<<<<<<<<<
*
* def _parse_header(self, stream):
*/
- __pyx_t_11 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_11 = PyObject_GetAttr(__pyx_v_stream, __pyx_n_s__write); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_11);
- __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_88), __pyx_n_s__join); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = PyObject_GetAttr(((PyObject *)__pyx_kp_s_88), __pyx_n_s__join); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_9);
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_INCREF(((PyObject *)__pyx_v_output));
PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_v_output));
__Pyx_GIVEREF(((PyObject *)__pyx_v_output));
- __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_9, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
- __pyx_t_7 = PyNumber_Add(__pyx_t_1, ((PyObject *)__pyx_kp_s_94)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyNumber_Add(__pyx_t_1, ((PyObject *)__pyx_kp_s_94)); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 884; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_11, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_11); __pyx_t_11 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -19474,12 +19934,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_37_parse_header = {__Pyx_NAMESTR
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_parse_header (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -19493,18 +19952,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parse_header") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parse_header") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -19517,7 +19974,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parse_header", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF._parse_header", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -19528,7 +19985,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_37_parse_header(PyObject *__pyx_self
return __pyx_r;
}
-/* "pysam/cvcf.pyx":886
+/* "pysam/cvcf.pyx":889
* stream.write( "\t".join(output) + "\n" )
*
* def _parse_header(self, stream): # <<<<<<<<<<<<<<
@@ -19552,16 +20009,16 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_parse_header", 0);
- /* "pysam/cvcf.pyx":887
+ /* "pysam/cvcf.pyx":890
*
* def _parse_header(self, stream):
* self._lineno = 0 # <<<<<<<<<<<<<<
* for line in stream:
* self._lineno += 1
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lineno, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 887; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lineno, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":888
+ /* "pysam/cvcf.pyx":891
* def _parse_header(self, stream):
* self._lineno = 0
* for line in stream: # <<<<<<<<<<<<<<
@@ -19572,23 +20029,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
__pyx_t_1 = __pyx_v_stream; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0;
__pyx_t_3 = NULL;
} else {
- __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_stream); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_stream); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_3 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
if (!__pyx_t_3 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_3 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_2 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_4 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_2); __Pyx_INCREF(__pyx_t_4); __pyx_t_2++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_4 = PySequence_ITEM(__pyx_t_1, __pyx_t_2); __pyx_t_2++; if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_4 = __pyx_t_3(__pyx_t_1);
if (unlikely(!__pyx_t_4)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -19598,57 +20063,57 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
__pyx_v_line = __pyx_t_4;
__pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":889
+ /* "pysam/cvcf.pyx":892
* self._lineno = 0
* for line in stream:
* self._lineno += 1 # <<<<<<<<<<<<<<
* if line.startswith('##'):
* self.parse_header( line.strip() )
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyNumber_InPlaceAdd(__pyx_t_4, __pyx_int_1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lineno, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___lineno, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":890
+ /* "pysam/cvcf.pyx":893
* for line in stream:
* self._lineno += 1
* if line.startswith('##'): # <<<<<<<<<<<<<<
* self.parse_header( line.strip() )
* elif line.startswith('#'):
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_119), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_119), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_4); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":891
+ /* "pysam/cvcf.pyx":894
* self._lineno += 1
* if line.startswith('##'):
* self.parse_header( line.strip() ) # <<<<<<<<<<<<<<
* elif line.startswith('#'):
* self.parse_heading( line.strip() )
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_header); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_header); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyTuple_New(1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_7);
__Pyx_GIVEREF(__pyx_t_7);
__pyx_t_7 = 0;
- __pyx_t_7 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 891; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_5)); __pyx_t_5 = 0;
@@ -19656,57 +20121,57 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
goto __pyx_L5;
}
- /* "pysam/cvcf.pyx":892
+ /* "pysam/cvcf.pyx":895
* if line.startswith('##'):
* self.parse_header( line.strip() )
* elif line.startswith('#'): # <<<<<<<<<<<<<<
* self.parse_heading( line.strip() )
* self.enter_default_format()
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_120), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_k_tuple_120), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_6 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_6) {
- /* "pysam/cvcf.pyx":893
+ /* "pysam/cvcf.pyx":896
* self.parse_header( line.strip() )
* elif line.startswith('#'):
* self.parse_heading( line.strip() ) # <<<<<<<<<<<<<<
* self.enter_default_format()
* else:
*/
- __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_heading); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__parse_heading); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_4 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
- __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_4);
__Pyx_GIVEREF(__pyx_t_4);
__pyx_t_4 = 0;
- __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_7), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- /* "pysam/cvcf.pyx":894
+ /* "pysam/cvcf.pyx":897
* elif line.startswith('#'):
* self.parse_heading( line.strip() )
* self.enter_default_format() # <<<<<<<<<<<<<<
* else:
* break
*/
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_121); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s_121); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_7 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 894; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
@@ -19714,7 +20179,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
}
/*else*/ {
- /* "pysam/cvcf.pyx":896
+ /* "pysam/cvcf.pyx":899
* self.enter_default_format()
* else:
* break # <<<<<<<<<<<<<<
@@ -19728,7 +20193,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
__pyx_L4_break:;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":897
+ /* "pysam/cvcf.pyx":900
* else:
* break
* return line # <<<<<<<<<<<<<<
@@ -19736,7 +20201,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObje
* def _parse(self, line, stream):
*/
__Pyx_XDECREF(__pyx_r);
- if (unlikely(!__pyx_v_line)) { __Pyx_RaiseUnboundLocalError("line"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 897; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
+ if (unlikely(!__pyx_v_line)) { __Pyx_RaiseUnboundLocalError("line"); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 900; __pyx_clineno = __LINE__; goto __pyx_L1_error;} }
__Pyx_INCREF(__pyx_v_line);
__pyx_r = __pyx_v_line;
goto __pyx_L0;
@@ -19765,12 +20230,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObj
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_line = 0;
PyObject *__pyx_v_stream = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("_parse (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__line,&__pyx_n_s__stream,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -19785,24 +20249,21 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObj
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__line)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parse") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_parse") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -19817,7 +20278,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObj
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("_parse", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF._parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -19828,7 +20289,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_39_parse(PyObject *__pyx_self, PyObj
return __pyx_r;
}
-/* "pysam/cvcf.pyx":899
+/* "pysam/cvcf.pyx":902
* return line
*
* def _parse(self, line, stream): # <<<<<<<<<<<<<<
@@ -19860,7 +20321,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__p
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_stream);
__Pyx_GIVEREF(__pyx_cur_scope->__pyx_v_stream);
{
- __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_4cvcf_3VCF_40generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_GeneratorObject *gen = __Pyx_Generator_New((__pyx_generator_body_t) __pyx_gb_5pysam_4cvcf_3VCF_40generator, (PyObject *) __pyx_cur_scope); if (unlikely(!gen)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_cur_scope);
__Pyx_RefNannyFinishContext();
return (PyObject *) gen;
@@ -19902,21 +20363,21 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
return NULL;
}
__pyx_L3_first_run:;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":901
+ /* "pysam/cvcf.pyx":904
* def _parse(self, line, stream):
* # deal with files with header only
* if line.startswith("##"): return # <<<<<<<<<<<<<<
* if len(line.strip()) > 0:
* d = self.parse_data( line.strip() )
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__startswith); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_122), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_2); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_3) {
__Pyx_XDECREF(__pyx_r);
@@ -19926,43 +20387,43 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
}
__pyx_L4:;
- /* "pysam/cvcf.pyx":902
+ /* "pysam/cvcf.pyx":905
* # deal with files with header only
* if line.startswith("##"): return
* if len(line.strip()) > 0: # <<<<<<<<<<<<<<
* d = self.parse_data( line.strip() )
* if d: yield d
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_4 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyObject_Length(__pyx_t_1); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_3 = (__pyx_t_4 > 0);
if (__pyx_t_3) {
- /* "pysam/cvcf.pyx":903
+ /* "pysam/cvcf.pyx":906
* if line.startswith("##"): return
* if len(line.strip()) > 0:
* d = self.parse_data( line.strip() ) # <<<<<<<<<<<<<<
* if d: yield d
* for line in stream:
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s__parse_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s__parse_data); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_5);
__Pyx_GIVEREF(__pyx_t_5);
__pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 903; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -19970,14 +20431,14 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_cur_scope->__pyx_v_d = __pyx_t_5;
__pyx_t_5 = 0;
- /* "pysam/cvcf.pyx":904
+ /* "pysam/cvcf.pyx":907
* if len(line.strip()) > 0:
* d = self.parse_data( line.strip() )
* if d: yield d # <<<<<<<<<<<<<<
* for line in stream:
* self._lineno += 1
*/
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_d); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_d); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_d);
__pyx_r = __pyx_cur_scope->__pyx_v_d;
@@ -19987,7 +20448,7 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_generator->resume_label = 1;
return __pyx_r;
__pyx_L7_resume_from_yield:;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L6;
}
__pyx_L6:;
@@ -19995,7 +20456,7 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
}
__pyx_L5:;
- /* "pysam/cvcf.pyx":905
+ /* "pysam/cvcf.pyx":908
* d = self.parse_data( line.strip() )
* if d: yield d
* for line in stream: # <<<<<<<<<<<<<<
@@ -20006,23 +20467,31 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_t_5 = __pyx_cur_scope->__pyx_v_stream; __Pyx_INCREF(__pyx_t_5); __pyx_t_4 = 0;
__pyx_t_6 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_stream); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_5 = PyObject_GetIter(__pyx_cur_scope->__pyx_v_stream); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__pyx_t_6 = Py_TYPE(__pyx_t_5)->tp_iternext;
}
for (;;) {
if (!__pyx_t_6 && PyList_CheckExact(__pyx_t_5)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_5)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_5)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_5)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_5, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_5, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_5);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 905; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -20034,42 +20503,41 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_cur_scope->__pyx_v_line = __pyx_t_2;
__pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":906
+ /* "pysam/cvcf.pyx":909
* if d: yield d
* for line in stream:
* self._lineno += 1 # <<<<<<<<<<<<<<
* if self._lines and self._lineno > self._lines: raise StopIteration
* d = self.parse_data( line.strip() )
*/
- __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyNumber_InPlaceAdd(__pyx_t_2, __pyx_int_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 906; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":907
+ /* "pysam/cvcf.pyx":910
* for line in stream:
* self._lineno += 1
* if self._lines and self._lineno > self._lines: raise StopIteration # <<<<<<<<<<<<<<
* d = self.parse_data( line.strip() )
* if d: yield d
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lines); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lines); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_3) {
- __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lineno); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s___lines); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_GT); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_1, __pyx_t_2, Py_GT); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_9 = __pyx_t_8;
} else {
@@ -20077,31 +20545,31 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
}
if (__pyx_t_9) {
__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L10;
}
__pyx_L10:;
- /* "pysam/cvcf.pyx":908
+ /* "pysam/cvcf.pyx":911
* self._lineno += 1
* if self._lines and self._lineno > self._lines: raise StopIteration
* d = self.parse_data( line.strip() ) # <<<<<<<<<<<<<<
* if d: yield d
*
*/
- __pyx_t_7 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s__parse_data); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_self, __pyx_n_s__parse_data); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
- __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_cur_scope->__pyx_v_line, __pyx_n_s__strip); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_1);
__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 908; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_7, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 911; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -20111,14 +20579,14 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_cur_scope->__pyx_v_d = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":909
+ /* "pysam/cvcf.pyx":912
* if self._lines and self._lineno > self._lines: raise StopIteration
* d = self.parse_data( line.strip() )
* if d: yield d # <<<<<<<<<<<<<<
*
* ######################################################################################################
*/
- __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_d); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_9 = __Pyx_PyObject_IsTrue(__pyx_cur_scope->__pyx_v_d); if (unlikely(__pyx_t_9 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_9) {
__Pyx_INCREF(__pyx_cur_scope->__pyx_v_d);
__pyx_r = __pyx_cur_scope->__pyx_v_d;
@@ -20137,7 +20605,7 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_cur_scope->__pyx_t_1 = 0;
__Pyx_XGOTREF(__pyx_t_5);
__pyx_t_6 = __pyx_cur_scope->__pyx_t_2;
- if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 909; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 912; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L11;
}
__pyx_L11:;
@@ -20154,6 +20622,7 @@ static PyObject *__pyx_gb_5pysam_4cvcf_3VCF_40generator(__pyx_GeneratorObject *_
__pyx_L0:;
__Pyx_XDECREF(__pyx_r);
__pyx_generator->resume_label = -1;
+ __Pyx_Generator_clear((PyObject*)__pyx_generator);
__Pyx_RefNannyFinishContext();
return NULL;
}
@@ -20166,13 +20635,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_42getsamples(PyObject *__pyx_self, P
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getsamples (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_41getsamples(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":917
+/* "pysam/cvcf.pyx":920
* ######################################################################################################
*
* def getsamples(self): # <<<<<<<<<<<<<<
@@ -20189,7 +20657,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("getsamples", 0);
- /* "pysam/cvcf.pyx":919
+ /* "pysam/cvcf.pyx":922
* def getsamples(self):
* """ List of samples in VCF file """
* return self._samples # <<<<<<<<<<<<<<
@@ -20197,7 +20665,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject
* def setsamples(self,samples):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 919; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___samples); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -20222,12 +20690,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_44setsamples = {__Pyx_NAMESTR("s
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_samples = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__samples,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setsamples (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__samples,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -20241,18 +20708,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samples);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__samples)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setsamples") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setsamples") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -20265,7 +20730,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setsamples", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setsamples", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -20276,7 +20741,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_44setsamples(PyObject *__pyx_self, P
return __pyx_r;
}
-/* "pysam/cvcf.pyx":921
+/* "pysam/cvcf.pyx":924
* return self._samples
*
* def setsamples(self,samples): # <<<<<<<<<<<<<<
@@ -20292,14 +20757,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setsamples", 0);
- /* "pysam/cvcf.pyx":923
+ /* "pysam/cvcf.pyx":926
* def setsamples(self,samples):
* """ List of samples in VCF file """
* self._samples = samples # <<<<<<<<<<<<<<
*
* def getheader(self):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_v_samples) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___samples, __pyx_v_samples) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 926; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -20320,13 +20785,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_46getheader(PyObject *__pyx_self, Py
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getheader (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_45getheader(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":925
+/* "pysam/cvcf.pyx":928
* self._samples = samples
*
* def getheader(self): # <<<<<<<<<<<<<<
@@ -20343,7 +20807,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("getheader", 0);
- /* "pysam/cvcf.pyx":927
+ /* "pysam/cvcf.pyx":930
* def getheader(self):
* """ List of header key-value pairs (strings) """
* return self._header # <<<<<<<<<<<<<<
@@ -20351,7 +20815,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *
* def setheader(self,header):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 927; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 930; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -20376,12 +20840,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_48setheader = {__Pyx_NAMESTR("se
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_header = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__header,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setheader (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__header,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -20395,18 +20858,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, Py
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__header)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setheader") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setheader") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -20419,7 +20880,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setheader", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -20430,7 +20891,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_48setheader(PyObject *__pyx_self, Py
return __pyx_r;
}
-/* "pysam/cvcf.pyx":929
+/* "pysam/cvcf.pyx":932
* return self._header
*
* def setheader(self,header): # <<<<<<<<<<<<<<
@@ -20446,14 +20907,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setheader", 0);
- /* "pysam/cvcf.pyx":931
+ /* "pysam/cvcf.pyx":934
* def setheader(self,header):
* """ List of header key-value pairs (strings) """
* self._header = header # <<<<<<<<<<<<<<
*
* def getinfo(self):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___header, __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 931; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___header, __pyx_v_header) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 934; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -20474,13 +20935,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_50getinfo(PyObject *__pyx_self, PyOb
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getinfo (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_49getinfo(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":933
+/* "pysam/cvcf.pyx":936
* self._header = header
*
* def getinfo(self): # <<<<<<<<<<<<<<
@@ -20497,7 +20957,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("getinfo", 0);
- /* "pysam/cvcf.pyx":935
+ /* "pysam/cvcf.pyx":938
* def getinfo(self):
* """ Dictionary of ##INFO tags, as VCF.FORMAT values """
* return self._info # <<<<<<<<<<<<<<
@@ -20505,7 +20965,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__
* def setinfo(self,info):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 935; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___info); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 938; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -20530,12 +20990,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_52setinfo = {__Pyx_NAMESTR("seti
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_info = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__info,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setinfo (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__info,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -20549,18 +21008,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyOb
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__info);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__info)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setinfo") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setinfo") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -20573,7 +21030,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyOb
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setinfo", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setinfo", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -20584,7 +21041,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_52setinfo(PyObject *__pyx_self, PyOb
return __pyx_r;
}
-/* "pysam/cvcf.pyx":937
+/* "pysam/cvcf.pyx":940
* return self._info
*
* def setinfo(self,info): # <<<<<<<<<<<<<<
@@ -20600,14 +21057,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setinfo", 0);
- /* "pysam/cvcf.pyx":939
+ /* "pysam/cvcf.pyx":942
* def setinfo(self,info):
* """ Dictionary of ##INFO tags, as VCF.FORMAT values """
* self._info = info # <<<<<<<<<<<<<<
*
* def getformat(self):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___info, __pyx_v_info) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 939; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___info, __pyx_v_info) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 942; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -20628,13 +21085,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_54getformat(PyObject *__pyx_self, Py
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getformat (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_53getformat(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":941
+/* "pysam/cvcf.pyx":944
* self._info = info
*
* def getformat(self): # <<<<<<<<<<<<<<
@@ -20651,7 +21107,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("getformat", 0);
- /* "pysam/cvcf.pyx":943
+ /* "pysam/cvcf.pyx":946
* def getformat(self):
* """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
* return self._format # <<<<<<<<<<<<<<
@@ -20659,7 +21115,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *
* def setformat(self,format):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 943; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___format); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 946; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -20684,12 +21140,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_56setformat = {__Pyx_NAMESTR("se
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_format = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setformat (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__format,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -20703,18 +21158,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, Py
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__format)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setformat") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setformat") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -20727,7 +21180,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setformat", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setformat", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -20738,7 +21191,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_56setformat(PyObject *__pyx_self, Py
return __pyx_r;
}
-/* "pysam/cvcf.pyx":945
+/* "pysam/cvcf.pyx":948
* return self._format
*
* def setformat(self,format): # <<<<<<<<<<<<<<
@@ -20754,14 +21207,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setformat", 0);
- /* "pysam/cvcf.pyx":947
+ /* "pysam/cvcf.pyx":950
* def setformat(self,format):
* """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
* self._format = format # <<<<<<<<<<<<<<
*
* def getfilter(self):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___format, __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 947; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___format, __pyx_v_format) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 950; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -20782,13 +21235,12 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_58getfilter(PyObject *__pyx_self, Py
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("getfilter (wrapper)", 0);
- __pyx_self = __pyx_self;
__pyx_r = __pyx_pf_5pysam_4cvcf_3VCF_57getfilter(__pyx_self, ((PyObject *)__pyx_v_self));
__Pyx_RefNannyFinishContext();
return __pyx_r;
}
-/* "pysam/cvcf.pyx":949
+/* "pysam/cvcf.pyx":952
* self._format = format
*
* def getfilter(self): # <<<<<<<<<<<<<<
@@ -20805,7 +21257,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("getfilter", 0);
- /* "pysam/cvcf.pyx":951
+ /* "pysam/cvcf.pyx":954
* def getfilter(self):
* """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
* return self._filter # <<<<<<<<<<<<<<
@@ -20813,7 +21265,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *
* def setfilter(self,filter):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 951; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___filter); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 954; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -20838,12 +21290,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_60setfilter = {__Pyx_NAMESTR("se
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filter = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filter,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setfilter (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filter,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -20857,18 +21308,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, Py
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filter);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filter)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfilter") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setfilter") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -20881,7 +21330,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setfilter", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setfilter", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -20892,7 +21341,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_60setfilter(PyObject *__pyx_self, Py
return __pyx_r;
}
-/* "pysam/cvcf.pyx":953
+/* "pysam/cvcf.pyx":956
* return self._filter
*
* def setfilter(self,filter): # <<<<<<<<<<<<<<
@@ -20908,14 +21357,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setfilter", 0);
- /* "pysam/cvcf.pyx":955
+ /* "pysam/cvcf.pyx":958
* def setfilter(self,filter):
* """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
* self._filter = filter # <<<<<<<<<<<<<<
*
* def setversion(self, version):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___filter, __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 955; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___filter, __pyx_v_filter) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -20934,12 +21383,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_62setversion = {__Pyx_NAMESTR("s
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_version = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setversion (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__version,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -20953,18 +21401,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__version);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__version)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setversion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setversion") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -20977,7 +21423,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setversion", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setversion", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -20988,7 +21434,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_62setversion(PyObject *__pyx_self, P
return __pyx_r;
}
-/* "pysam/cvcf.pyx":957
+/* "pysam/cvcf.pyx":960
* self._filter = filter
*
* def setversion(self, version): # <<<<<<<<<<<<<<
@@ -21008,44 +21454,42 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setversion", 0);
- /* "pysam/cvcf.pyx":958
+ /* "pysam/cvcf.pyx":961
*
* def setversion(self, version):
* if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<<
* self._version = version
*
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_33, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_33, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_40, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_version, __pyx_int_40, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_4 = __pyx_t_3;
} else {
__pyx_t_4 = __pyx_t_2;
}
if (__pyx_t_4) {
- __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_124), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_124), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L3;
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":959
+ /* "pysam/cvcf.pyx":962
* def setversion(self, version):
* if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
* self._version = version # <<<<<<<<<<<<<<
*
* def setregions(self, regions):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_v_version) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 959; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___version, __pyx_v_version) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -21065,12 +21509,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_64setregions = {__Pyx_NAMESTR("s
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_regions = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__regions,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setregions (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__regions,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -21084,18 +21527,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, P
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__regions);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__regions)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setregions") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setregions") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -21108,7 +21549,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, P
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setregions", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setregions", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -21119,7 +21560,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_64setregions(PyObject *__pyx_self, P
return __pyx_r;
}
-/* "pysam/cvcf.pyx":961
+/* "pysam/cvcf.pyx":964
* self._version = version
*
* def setregions(self, regions): # <<<<<<<<<<<<<<
@@ -21135,14 +21576,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setregions", 0);
- /* "pysam/cvcf.pyx":962
+ /* "pysam/cvcf.pyx":965
*
* def setregions(self, regions):
* self._regions = regions # <<<<<<<<<<<<<<
*
* def setreference(self, ref):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___regions, __pyx_v_regions) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 962; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___regions, __pyx_v_regions) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 965; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -21162,12 +21603,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_66setreference = {__Pyx_NAMESTR(
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_ref = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__ref,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("setreference (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__ref,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -21181,18 +21621,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setreference") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "setreference") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -21205,7 +21643,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("setreference", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.setreference", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -21216,7 +21654,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_66setreference(PyObject *__pyx_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":964
+/* "pysam/cvcf.pyx":967
* self._regions = regions
*
* def setreference(self, ref): # <<<<<<<<<<<<<<
@@ -21232,14 +21670,14 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObjec
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("setreference", 0);
- /* "pysam/cvcf.pyx":966
+ /* "pysam/cvcf.pyx":969
* def setreference(self, ref):
* """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
* self._reference = ref # <<<<<<<<<<<<<<
*
* def ignoreerror(self, errorstring):
*/
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 966; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s___reference, __pyx_v_ref) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -21258,12 +21696,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_68ignoreerror = {__Pyx_NAMESTR("
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_errorstring = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("ignoreerror (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -21277,18 +21714,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ignoreerror") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "ignoreerror") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -21301,7 +21736,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("ignoreerror", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -21312,7 +21747,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_68ignoreerror(PyObject *__pyx_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":968
+/* "pysam/cvcf.pyx":971
* self._reference = ref
*
* def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
@@ -21337,7 +21772,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("ignoreerror", 0);
- /* "pysam/cvcf.pyx":969
+ /* "pysam/cvcf.pyx":972
*
* def ignoreerror(self, errorstring):
* try: self._ignored_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<<
@@ -21350,22 +21785,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject
__Pyx_XGOTREF(__pyx_t_2);
__Pyx_XGOTREF(__pyx_t_3);
/*try:*/ {
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___ignored_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__add); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__add); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyObject_GetItem(__pyx_t_4, __pyx_v_errorstring); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_4, __pyx_v_errorstring); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 969; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
@@ -21380,7 +21815,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":970
+ /* "pysam/cvcf.pyx":973
* def ignoreerror(self, errorstring):
* try: self._ignored_errors.add(self.__dict__[errorstring])
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<<
@@ -21390,23 +21825,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_7) {
__Pyx_AddTraceback("pysam.cvcf.VCF.ignoreerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_4, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_4, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_125), __pyx_v_errorstring); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_125), __pyx_v_errorstring); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -21448,12 +21883,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_70warnerror = {__Pyx_NAMESTR("wa
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_errorstring = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("warnerror (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__errorstring,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -21467,18 +21901,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, Py
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__errorstring)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "warnerror") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "warnerror") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -21491,7 +21923,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, Py
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("warnerror", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -21502,7 +21934,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_70warnerror(PyObject *__pyx_self, Py
return __pyx_r;
}
-/* "pysam/cvcf.pyx":972
+/* "pysam/cvcf.pyx":975
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def warnerror(self, errorstring): # <<<<<<<<<<<<<<
@@ -21527,7 +21959,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("warnerror", 0);
- /* "pysam/cvcf.pyx":973
+ /* "pysam/cvcf.pyx":976
*
* def warnerror(self, errorstring):
* try: self._warn_errors.add(self.__dict__[errorstring]) # <<<<<<<<<<<<<<
@@ -21540,22 +21972,22 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *
__Pyx_XGOTREF(__pyx_t_2);
__Pyx_XGOTREF(__pyx_t_3);
/*try:*/ {
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___warn_errors); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_5 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__add); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_5 = PyObject_GetAttr(__pyx_t_4, __pyx_n_s__add); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s____dict__); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
- __pyx_t_6 = PyObject_GetItem(__pyx_t_4, __pyx_v_errorstring); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_6 = PyObject_GetItem(__pyx_t_4, __pyx_v_errorstring); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_4);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_6);
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_6 = 0;
- __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
@@ -21570,7 +22002,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *
__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_6); __pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":974
+ /* "pysam/cvcf.pyx":977
* def warnerror(self, errorstring):
* try: self._warn_errors.add(self.__dict__[errorstring])
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring) # <<<<<<<<<<<<<<
@@ -21580,23 +22012,23 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *
__pyx_t_7 = PyErr_ExceptionMatches(__pyx_builtin_KeyError);
if (__pyx_t_7) {
__Pyx_AddTraceback("pysam.cvcf.VCF.warnerror", __pyx_clineno, __pyx_lineno, __pyx_filename);
- if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_4, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ if (__Pyx_GetException(&__pyx_t_6, &__pyx_t_4, &__pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_125), __pyx_v_errorstring); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __pyx_t_8 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_125), __pyx_v_errorstring); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_8));
- __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __pyx_t_9 = PyTuple_New(1); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_9);
PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
__pyx_t_8 = 0;
- __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ __pyx_t_8 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_9), NULL); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
__Pyx_Raise(__pyx_t_8, 0, 0, 0);
__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 974; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 977; __pyx_clineno = __LINE__; goto __pyx_L5_except_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -21639,12 +22071,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_72parse = {__Pyx_NAMESTR("parse"
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("parse (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -21658,18 +22089,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObje
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "parse") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -21682,7 +22111,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("parse", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.parse", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -21693,7 +22122,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_72parse(PyObject *__pyx_self, PyObje
return __pyx_r;
}
-/* "pysam/cvcf.pyx":976
+/* "pysam/cvcf.pyx":979
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def parse(self, stream): # <<<<<<<<<<<<<<
@@ -21713,28 +22142,28 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__py
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("parse", 0);
- /* "pysam/cvcf.pyx":978
+ /* "pysam/cvcf.pyx":981
* def parse(self, stream):
* """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
* last_line = self._parse_header(stream) # <<<<<<<<<<<<<<
* # now return a generator that does the actual work. In this way the pre-processing is done
* # before the first piece of data is yielded
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
__Pyx_GIVEREF(__pyx_v_stream);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 978; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__pyx_v_last_line = __pyx_t_3;
__pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":981
+ /* "pysam/cvcf.pyx":984
* # now return a generator that does the actual work. In this way the pre-processing is done
* # before the first piece of data is yielded
* return self._parse(last_line, stream) # <<<<<<<<<<<<<<
@@ -21742,9 +22171,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__py
* def write(self, stream, datagenerator):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_last_line);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_last_line);
@@ -21752,7 +22181,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__py
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_2, 1, __pyx_v_stream);
__Pyx_GIVEREF(__pyx_v_stream);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 981; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 984; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -21783,12 +22212,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObje
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
PyObject *__pyx_v_datagenerator = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__datagenerator,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("write (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,&__pyx_n_s__datagenerator,0};
PyObject* values[3] = {0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -21803,24 +22231,21 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObje
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__datagenerator);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__datagenerator)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "write") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 3) {
goto __pyx_L5_argtuple_error;
@@ -21835,7 +22260,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("write", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.write", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -21846,7 +22271,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_74write(PyObject *__pyx_self, PyObje
return __pyx_r;
}
-/* "pysam/cvcf.pyx":983
+/* "pysam/cvcf.pyx":986
* return self._parse(last_line, stream)
*
* def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
@@ -21869,47 +22294,47 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__py
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("write", 0);
- /* "pysam/cvcf.pyx":985
+ /* "pysam/cvcf.pyx":988
* def write(self, stream, datagenerator):
* """ Writes a VCF file to a stream, using a data generator (or list) """
* self.write_header(stream) # <<<<<<<<<<<<<<
* self.write_heading(stream)
* for data in datagenerator: self.write_data(stream,data)
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
__Pyx_GIVEREF(__pyx_v_stream);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 985; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 988; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":986
+ /* "pysam/cvcf.pyx":989
* """ Writes a VCF file to a stream, using a data generator (or list) """
* self.write_header(stream)
* self.write_heading(stream) # <<<<<<<<<<<<<<
* for data in datagenerator: self.write_data(stream,data)
*
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_heading); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_heading); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
__Pyx_GIVEREF(__pyx_v_stream);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":987
+ /* "pysam/cvcf.pyx":990
* self.write_header(stream)
* self.write_heading(stream)
* for data in datagenerator: self.write_data(stream,data) # <<<<<<<<<<<<<<
@@ -21920,23 +22345,31 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__py
__pyx_t_1 = __pyx_v_datagenerator; __Pyx_INCREF(__pyx_t_1); __pyx_t_4 = 0;
__pyx_t_5 = NULL;
} else {
- __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_datagenerator); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_datagenerator); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_5 = Py_TYPE(__pyx_t_1)->tp_iternext;
}
for (;;) {
if (!__pyx_t_5 && PyList_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyList_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #else
+ __pyx_t_2 = PySequence_ITEM(__pyx_t_1, __pyx_t_4); __pyx_t_4++; if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
break;
}
@@ -21945,9 +22378,9 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__py
__Pyx_XDECREF(__pyx_v_data);
__pyx_v_data = __pyx_t_2;
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_data); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_data); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
- __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stream);
@@ -21955,7 +22388,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__py
__Pyx_INCREF(__pyx_v_data);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_data);
__Pyx_GIVEREF(__pyx_v_data);
- __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 987; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 990; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
@@ -21986,12 +22419,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_76writeheader = {__Pyx_NAMESTR("
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_stream = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("writeheader (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__stream,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -22005,18 +22437,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self,
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__stream)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "writeheader") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "writeheader") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -22029,7 +22459,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self,
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("writeheader", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.writeheader", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -22040,7 +22470,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_76writeheader(PyObject *__pyx_self,
return __pyx_r;
}
-/* "pysam/cvcf.pyx":989
+/* "pysam/cvcf.pyx":992
* for data in datagenerator: self.write_data(stream,data)
*
* def writeheader(self, stream): # <<<<<<<<<<<<<<
@@ -22059,41 +22489,41 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("writeheader", 0);
- /* "pysam/cvcf.pyx":991
+ /* "pysam/cvcf.pyx":994
* def writeheader(self, stream):
* """ Writes a VCF header """
* self.write_header(stream) # <<<<<<<<<<<<<<
* self.write_heading(stream)
*
*/
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_header); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
__Pyx_GIVEREF(__pyx_v_stream);
- __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 991; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":992
+ /* "pysam/cvcf.pyx":995
* """ Writes a VCF header """
* self.write_header(stream)
* self.write_heading(stream) # <<<<<<<<<<<<<<
*
* def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2):
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_heading); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__write_heading); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyTuple_New(1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(__pyx_v_stream);
PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_v_stream);
__Pyx_GIVEREF(__pyx_v_stream);
- __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_2), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
@@ -22125,12 +22555,11 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self
PyObject *__pyx_v_pos2 = 0;
PyObject *__pyx_v_ref2 = 0;
PyObject *__pyx_v_alt2 = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("compare_calls (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__pos1,&__pyx_n_s__ref1,&__pyx_n_s__alt1,&__pyx_n_s__pos2,&__pyx_n_s__ref2,&__pyx_n_s__alt2,0};
PyObject* values[7] = {0,0,0,0,0,0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -22149,48 +22578,41 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos1)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1);
- if (likely(values[2])) kw_args--;
+ if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref1)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 3:
- values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1);
- if (likely(values[3])) kw_args--;
+ if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt1)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 4:
- values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2);
- if (likely(values[4])) kw_args--;
+ if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__pos2)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 5:
- values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2);
- if (likely(values[5])) kw_args--;
+ if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__ref2)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
case 6:
- values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2);
- if (likely(values[6])) kw_args--;
+ if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__alt2)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compare_calls") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "compare_calls") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 7) {
goto __pyx_L5_argtuple_error;
@@ -22213,7 +22635,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("compare_calls", 1, 7, 7, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.compare_calls", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -22224,7 +22646,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_78compare_calls(PyObject *__pyx_self
return __pyx_r;
}
-/* "pysam/cvcf.pyx":994
+/* "pysam/cvcf.pyx":997
* self.write_heading(stream)
*
* def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
@@ -22252,20 +22674,19 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
__Pyx_INCREF(__pyx_v_ref2);
__Pyx_INCREF(__pyx_v_alt2);
- /* "pysam/cvcf.pyx":999
+ /* "pysam/cvcf.pyx":1002
* # the leftmost position of the alignment gap. If this rule is implemented
* # correctly, the two positions must be equal for the calls to be identical.
* if pos1 != pos2: return False # <<<<<<<<<<<<<<
* # from both calls, trim rightmost bases when identical. Do this safely, i.e.
* # only when the reference bases are not Ns
*/
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_pos1, __pyx_v_pos2, Py_NE); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_2 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 999; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
@@ -22274,7 +22695,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
}
__pyx_L3:;
- /* "pysam/cvcf.pyx":1002
+ /* "pysam/cvcf.pyx":1005
* # from both calls, trim rightmost bases when identical. Do this safely, i.e.
* # only when the reference bases are not Ns
* while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]: # <<<<<<<<<<<<<<
@@ -22282,21 +22703,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
* alt1 = alt1[:-1]
*/
while (1) {
- __pyx_t_3 = PyObject_Length(__pyx_v_ref1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_ref1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = (__pyx_t_3 > 0);
if (__pyx_t_2) {
- __pyx_t_3 = PyObject_Length(__pyx_v_alt1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_alt1); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 > 0);
if (__pyx_t_4) {
- __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_ref1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetItemInt(__pyx_v_ref1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_1) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt1, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_6);
+ __pyx_t_6 = PyObject_RichCompare(__pyx_t_1, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_6); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1002; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_6); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__pyx_t_8 = __pyx_t_7;
} else {
@@ -22308,34 +22728,34 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
}
if (!__pyx_t_4) break;
- /* "pysam/cvcf.pyx":1003
+ /* "pysam/cvcf.pyx":1006
* # only when the reference bases are not Ns
* while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
* ref1 = ref1[:-1] # <<<<<<<<<<<<<<
* alt1 = alt1[:-1]
* while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
*/
- __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_ref1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1003; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_ref1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_v_ref1);
__pyx_v_ref1 = __pyx_t_6;
__pyx_t_6 = 0;
- /* "pysam/cvcf.pyx":1004
+ /* "pysam/cvcf.pyx":1007
* while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
* ref1 = ref1[:-1]
* alt1 = alt1[:-1] # <<<<<<<<<<<<<<
* while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
* ref2 = ref2[:-1]
*/
- __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_alt1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1004; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_PySequence_GetSlice(__pyx_v_alt1, 0, -1); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
__Pyx_DECREF(__pyx_v_alt1);
__pyx_v_alt1 = __pyx_t_6;
__pyx_t_6 = 0;
}
- /* "pysam/cvcf.pyx":1005
+ /* "pysam/cvcf.pyx":1008
* ref1 = ref1[:-1]
* alt1 = alt1[:-1]
* while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]: # <<<<<<<<<<<<<<
@@ -22343,21 +22763,20 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
* alt2 = alt2[:-1]
*/
while (1) {
- __pyx_t_3 = PyObject_Length(__pyx_v_ref2); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_ref2); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 > 0);
if (__pyx_t_4) {
- __pyx_t_3 = PyObject_Length(__pyx_v_alt2); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Length(__pyx_v_alt2); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_2 = (__pyx_t_3 > 0);
if (__pyx_t_2) {
- __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ref2, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_6 = __Pyx_GetItemInt(__pyx_v_ref2, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_6) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_6);
- __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt2, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = __Pyx_GetItemInt(__pyx_v_alt2, -1, sizeof(long), PyInt_FromLong); if (!__pyx_t_5) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_t_6, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1005; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1008; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
__pyx_t_7 = __pyx_t_8;
} else {
@@ -22369,34 +22788,34 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
}
if (!__pyx_t_2) break;
- /* "pysam/cvcf.pyx":1006
+ /* "pysam/cvcf.pyx":1009
* alt1 = alt1[:-1]
* while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
* ref2 = ref2[:-1] # <<<<<<<<<<<<<<
* alt2 = alt2[:-1]
* # now, the alternative alleles must be identical
*/
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_ref2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1006; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_ref2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_ref2);
__pyx_v_ref2 = __pyx_t_1;
__pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":1007
+ /* "pysam/cvcf.pyx":1010
* while len(ref2)>0 and len(alt2)>0 and ref2[-1] == alt2[-1]:
* ref2 = ref2[:-1]
* alt2 = alt2[:-1] # <<<<<<<<<<<<<<
* # now, the alternative alleles must be identical
* return alt1 == alt2
*/
- __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_alt2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1007; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PySequence_GetSlice(__pyx_v_alt2, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1010; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_v_alt2);
__pyx_v_alt2 = __pyx_t_1;
__pyx_t_1 = 0;
}
- /* "pysam/cvcf.pyx":1009
+ /* "pysam/cvcf.pyx":1012
* alt2 = alt2[:-1]
* # now, the alternative alleles must be identical
* return alt1 == alt2 # <<<<<<<<<<<<<<
@@ -22404,8 +22823,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObje
* ###########################################################################################################
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_1);
+ __pyx_t_1 = PyObject_RichCompare(__pyx_v_alt1, __pyx_v_alt2, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1012; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = __pyx_t_1;
__pyx_t_1 = 0;
goto __pyx_L0;
@@ -22435,12 +22853,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_80connect = {__Pyx_NAMESTR("conn
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_self = 0;
PyObject *__pyx_v_filename = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("connect (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__filename,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -22454,18 +22871,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyOb
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "connect") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "connect") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -22478,7 +22893,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyOb
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("connect", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.connect", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -22489,7 +22904,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_80connect(PyObject *__pyx_self, PyOb
return __pyx_r;
}
-/* "pysam/cvcf.pyx":1016
+/* "pysam/cvcf.pyx":1019
* ###########################################################################################################
*
* def connect( self, filename ): # <<<<<<<<<<<<<<
@@ -22508,50 +22923,50 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("connect", 0);
- /* "pysam/cvcf.pyx":1018
+ /* "pysam/cvcf.pyx":1021
* def connect( self, filename ):
* '''connect to tabix file.'''
* self.tabixfile = pysam.Tabixfile( filename ) # <<<<<<<<<<<<<<
* self._parse_header(self.tabixfile.header)
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__pysam); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__pysam); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__Tabixfile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__Tabixfile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_filename);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_filename);
__Pyx_GIVEREF(__pyx_v_filename);
- __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__tabixfile, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1018; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_v_self, __pyx_n_s__tabixfile, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
- /* "pysam/cvcf.pyx":1019
+ /* "pysam/cvcf.pyx":1022
* '''connect to tabix file.'''
* self.tabixfile = pysam.Tabixfile( filename )
* self._parse_header(self.tabixfile.header) # <<<<<<<<<<<<<<
*
* def fetch(self,
*/
- __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse_header); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s___parse_header); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tabixfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tabixfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__header); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__header); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__pyx_t_2 = 0;
- __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_3, ((PyObject *)__pyx_t_1), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1022; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -22581,15 +22996,14 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("fetch (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__reference,&__pyx_n_s__start,&__pyx_n_s__end,&__pyx_n_s__region,0};
PyObject* values[5] = {0,0,0,0,0};
- /* "pysam/cvcf.pyx":1022
+ /* "pysam/cvcf.pyx":1025
*
* def fetch(self,
* reference = None, # <<<<<<<<<<<<<<
@@ -22598,7 +23012,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
*/
values[1] = ((PyObject *)((PyObject *)Py_None));
- /* "pysam/cvcf.pyx":1023
+ /* "pysam/cvcf.pyx":1026
* def fetch(self,
* reference = None,
* start = None, # <<<<<<<<<<<<<<
@@ -22607,7 +23021,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
*/
values[2] = ((PyObject *)((PyObject *)Py_None));
- /* "pysam/cvcf.pyx":1024
+ /* "pysam/cvcf.pyx":1027
* reference = None,
* start = None,
* end = None, # <<<<<<<<<<<<<<
@@ -22616,7 +23030,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
*/
values[3] = ((PyObject *)((PyObject *)Py_None));
- /* "pysam/cvcf.pyx":1025
+ /* "pysam/cvcf.pyx":1028
* start = None,
* end = None,
* region = None ): # <<<<<<<<<<<<<<
@@ -22639,8 +23053,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -22664,7 +23077,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "fetch") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else {
switch (PyTuple_GET_SIZE(__pyx_args)) {
@@ -22685,7 +23098,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("fetch", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("fetch", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.fetch", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -22696,7 +23109,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_82fetch(PyObject *__pyx_self, PyObje
return __pyx_r;
}
-/* "pysam/cvcf.pyx":1021
+/* "pysam/cvcf.pyx":1024
* self._parse_header(self.tabixfile.header)
*
* def fetch(self, # <<<<<<<<<<<<<<
@@ -22717,7 +23130,7 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__py
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("fetch", 0);
- /* "pysam/cvcf.pyx":1028
+ /* "pysam/cvcf.pyx":1031
* """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
*
* return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) ) # <<<<<<<<<<<<<<
@@ -22725,12 +23138,12 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__py
* def validate( self, record ):
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tabixfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_GetAttr(__pyx_v_self, __pyx_n_s__tabixfile); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fetch); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__fetch); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_v_reference);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
@@ -22744,19 +23157,19 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__py
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
- __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_3));
- __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_INCREF(__pyx_v_self);
PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_self);
__Pyx_GIVEREF(__pyx_v_self);
- __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_4cvcf_asVCFRecord)), ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_4cvcf_asVCFRecord)), ((PyObject *)__pyx_t_4), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_4)); __pyx_t_4 = 0;
- if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__parser), __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_3, ((PyObject *)__pyx_n_s__parser), __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1028; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_5 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_3)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1031; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -22788,12 +23201,11 @@ static PyMethodDef __pyx_mdef_5pysam_4cvcf_3VCF_84validate = {__Pyx_NAMESTR("val
static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
CYTHON_UNUSED PyObject *__pyx_v_self = 0;
CYTHON_UNUSED PyObject *__pyx_v_record = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("validate (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__self,&__pyx_n_s__record,0};
PyObject* values[2] = {0,0};
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
@@ -22807,18 +23219,16 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyO
kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__self)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
- values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record);
- if (likely(values[1])) kw_args--;
+ if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__record)) != 0)) kw_args--;
else {
- __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
}
if (unlikely(kw_args > 0)) {
- if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "validate") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "validate") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 2) {
goto __pyx_L5_argtuple_error;
@@ -22831,7 +23241,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyO
}
goto __pyx_L4_argument_unpacking_done;
__pyx_L5_argtuple_error:;
- __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
+ __Pyx_RaiseArgtupleInvalid("validate", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_AddTraceback("pysam.cvcf.VCF.validate", __pyx_clineno, __pyx_lineno, __pyx_filename);
__Pyx_RefNannyFinishContext();
@@ -22842,7 +23252,7 @@ static PyObject *__pyx_pw_5pysam_4cvcf_3VCF_84validate(PyObject *__pyx_self, PyO
return __pyx_r;
}
-/* "pysam/cvcf.pyx":1030
+/* "pysam/cvcf.pyx":1033
* return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) )
*
* def validate( self, record ): # <<<<<<<<<<<<<<
@@ -22859,18 +23269,18 @@ static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *_
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("validate", 0);
- /* "pysam/cvcf.pyx":1036
+ /* "pysam/cvcf.pyx":1039
* '''
*
* raise NotImplementedError( "needs to be checked" ) # <<<<<<<<<<<<<<
*
* chrom, pos = record.chrom, record.pos
*/
- __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_127), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_127), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1039; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_Raise(__pyx_t_1, 0, 0, 0);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1039; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_r = Py_None; __Pyx_INCREF(Py_None);
goto __pyx_L0;
@@ -22900,16 +23310,16 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf_VCFRecord(PyTypeObject *t, PyObject *
static void __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
- Py_XDECREF(p->vcf);
- __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o);
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->vcf);
+ PyObject_GC_Track(o);
+ if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord);
}
static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
- if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) {
- e = __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a); if (e) return e;
- }
+ e = ((likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) ? ((__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse) ? __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_VCFRecord)); if (e) return e;
if (p->vcf) {
e = (*v)(p->vcf, a); if (e) return e;
}
@@ -22919,9 +23329,7 @@ static int __pyx_tp_traverse_5pysam_4cvcf_VCFRecord(PyObject *o, visitproc v, vo
static int __pyx_tp_clear_5pysam_4cvcf_VCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_VCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_VCFRecord *)o;
PyObject* tmp;
- if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) {
- __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o);
- }
+ if (likely(__pyx_ptype_5pysam_10TabProxies_TupleProxy)) { if (__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear) __pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_VCFRecord);
tmp = ((PyObject*)p->vcf);
p->vcf = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -22935,43 +23343,43 @@ static PyObject *__pyx_sq_item_5pysam_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i)
return r;
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o);
}
-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, void *x) {
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) {
return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o);
}
@@ -23159,16 +23567,16 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject
static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
- Py_XDECREF(p->vcffile);
- __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o);
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->vcffile);
+ PyObject_GC_Track(o);
+ if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord);
}
static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
int e;
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
- if (__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) {
- e = __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e;
- }
+ e = ((likely(__pyx_ptype_5pysam_6ctabix_Parser)) ? ((__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord)); if (e) return e;
if (p->vcffile) {
e = (*v)(p->vcffile, a); if (e) return e;
}
@@ -23178,9 +23586,7 @@ static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v,
static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
PyObject* tmp;
- if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) {
- __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o);
- }
+ if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) { if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_asVCFRecord);
tmp = ((PyObject*)p->vcffile);
p->vcffile = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
@@ -23345,7 +23751,7 @@ static PyTypeObject __pyx_type_5pysam_4cvcf_asVCFRecord = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -23356,7 +23762,9 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyType
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o;
- Py_XDECREF(p->__pyx_v_alt);
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_alt);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -23536,7 +23944,7 @@ static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -23549,9 +23957,11 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeOb
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o;
- Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
- Py_XDECREF(p->__pyx_v_allele);
- Py_XDECREF(p->__pyx_t_0);
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_outer_scope);
+ Py_CLEAR(p->__pyx_v_allele);
+ Py_CLEAR(p->__pyx_t_0);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -23743,7 +24153,7 @@ static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
@@ -23758,11 +24168,13 @@ static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObj
static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o;
- Py_XDECREF(p->__pyx_v_d);
- Py_XDECREF(p->__pyx_v_line);
- Py_XDECREF(p->__pyx_v_self);
- Py_XDECREF(p->__pyx_v_stream);
- Py_XDECREF(p->__pyx_t_1);
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_d);
+ Py_CLEAR(p->__pyx_v_line);
+ Py_CLEAR(p->__pyx_v_self);
+ Py_CLEAR(p->__pyx_v_stream);
+ Py_CLEAR(p->__pyx_t_1);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
@@ -23972,7 +24384,11 @@ static PyMethodDef __pyx_methods[] = {
#if PY_MAJOR_VERSION >= 3
static struct PyModuleDef __pyx_moduledef = {
+ #if PY_VERSION_HEX < 0x03020000
+ { PyObject_HEAD_INIT(NULL) NULL, 0, NULL },
+ #else
PyModuleDef_HEAD_INIT,
+ #endif
__Pyx_NAMESTR("cvcf"),
0, /* m_doc */
-1, /* m_size */
@@ -24041,15 +24457,57 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_171, __pyx_k_171, sizeof(__pyx_k_171), 0, 0, 1, 0},
{&__pyx_kp_s_172, __pyx_k_172, sizeof(__pyx_k_172), 0, 0, 1, 0},
{&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0},
+ {&__pyx_n_s_176, __pyx_k_176, sizeof(__pyx_k_176), 0, 0, 1, 1},
{&__pyx_n_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 1},
+ {&__pyx_n_s_180, __pyx_k_180, sizeof(__pyx_k_180), 0, 0, 1, 1},
+ {&__pyx_n_s_183, __pyx_k_183, sizeof(__pyx_k_183), 0, 0, 1, 1},
+ {&__pyx_n_s_186, __pyx_k_186, sizeof(__pyx_k_186), 0, 0, 1, 1},
+ {&__pyx_n_s_189, __pyx_k_189, sizeof(__pyx_k_189), 0, 0, 1, 1},
{&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
+ {&__pyx_n_s_192, __pyx_k_192, sizeof(__pyx_k_192), 0, 0, 1, 1},
+ {&__pyx_n_s_195, __pyx_k_195, sizeof(__pyx_k_195), 0, 0, 1, 1},
+ {&__pyx_n_s_198, __pyx_k_198, sizeof(__pyx_k_198), 0, 0, 1, 1},
{&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
{&__pyx_n_s_20, __pyx_k_20, sizeof(__pyx_k_20), 0, 0, 1, 1},
+ {&__pyx_n_s_201, __pyx_k_201, sizeof(__pyx_k_201), 0, 0, 1, 1},
+ {&__pyx_n_s_204, __pyx_k_204, sizeof(__pyx_k_204), 0, 0, 1, 1},
+ {&__pyx_n_s_207, __pyx_k_207, sizeof(__pyx_k_207), 0, 0, 1, 1},
{&__pyx_kp_s_21, __pyx_k_21, sizeof(__pyx_k_21), 0, 0, 1, 0},
+ {&__pyx_n_s_210, __pyx_k_210, sizeof(__pyx_k_210), 0, 0, 1, 1},
+ {&__pyx_n_s_213, __pyx_k_213, sizeof(__pyx_k_213), 0, 0, 1, 1},
+ {&__pyx_n_s_216, __pyx_k_216, sizeof(__pyx_k_216), 0, 0, 1, 1},
+ {&__pyx_n_s_219, __pyx_k_219, sizeof(__pyx_k_219), 0, 0, 1, 1},
+ {&__pyx_n_s_222, __pyx_k_222, sizeof(__pyx_k_222), 0, 0, 1, 1},
+ {&__pyx_n_s_225, __pyx_k_225, sizeof(__pyx_k_225), 0, 0, 1, 1},
+ {&__pyx_n_s_228, __pyx_k_228, sizeof(__pyx_k_228), 0, 0, 1, 1},
+ {&__pyx_n_s_231, __pyx_k_231, sizeof(__pyx_k_231), 0, 0, 1, 1},
+ {&__pyx_n_s_234, __pyx_k_234, sizeof(__pyx_k_234), 0, 0, 1, 1},
+ {&__pyx_n_s_237, __pyx_k_237, sizeof(__pyx_k_237), 0, 0, 1, 1},
{&__pyx_kp_s_24, __pyx_k_24, sizeof(__pyx_k_24), 0, 0, 1, 0},
+ {&__pyx_n_s_240, __pyx_k_240, sizeof(__pyx_k_240), 0, 0, 1, 1},
+ {&__pyx_n_s_243, __pyx_k_243, sizeof(__pyx_k_243), 0, 0, 1, 1},
+ {&__pyx_n_s_246, __pyx_k_246, sizeof(__pyx_k_246), 0, 0, 1, 1},
+ {&__pyx_n_s_249, __pyx_k_249, sizeof(__pyx_k_249), 0, 0, 1, 1},
{&__pyx_kp_s_25, __pyx_k_25, sizeof(__pyx_k_25), 0, 0, 1, 0},
+ {&__pyx_n_s_252, __pyx_k_252, sizeof(__pyx_k_252), 0, 0, 1, 1},
+ {&__pyx_n_s_255, __pyx_k_255, sizeof(__pyx_k_255), 0, 0, 1, 1},
+ {&__pyx_n_s_258, __pyx_k_258, sizeof(__pyx_k_258), 0, 0, 1, 1},
+ {&__pyx_n_s_261, __pyx_k_261, sizeof(__pyx_k_261), 0, 0, 1, 1},
+ {&__pyx_n_s_264, __pyx_k_264, sizeof(__pyx_k_264), 0, 0, 1, 1},
+ {&__pyx_n_s_267, __pyx_k_267, sizeof(__pyx_k_267), 0, 0, 1, 1},
{&__pyx_n_s_27, __pyx_k_27, sizeof(__pyx_k_27), 0, 0, 1, 1},
+ {&__pyx_n_s_270, __pyx_k_270, sizeof(__pyx_k_270), 0, 0, 1, 1},
+ {&__pyx_n_s_273, __pyx_k_273, sizeof(__pyx_k_273), 0, 0, 1, 1},
+ {&__pyx_n_s_276, __pyx_k_276, sizeof(__pyx_k_276), 0, 0, 1, 1},
+ {&__pyx_n_s_279, __pyx_k_279, sizeof(__pyx_k_279), 0, 0, 1, 1},
{&__pyx_kp_s_28, __pyx_k_28, sizeof(__pyx_k_28), 0, 0, 1, 0},
+ {&__pyx_n_s_282, __pyx_k_282, sizeof(__pyx_k_282), 0, 0, 1, 1},
+ {&__pyx_n_s_285, __pyx_k_285, sizeof(__pyx_k_285), 0, 0, 1, 1},
+ {&__pyx_n_s_288, __pyx_k_288, sizeof(__pyx_k_288), 0, 0, 1, 1},
+ {&__pyx_n_s_291, __pyx_k_291, sizeof(__pyx_k_291), 0, 0, 1, 1},
+ {&__pyx_n_s_294, __pyx_k_294, sizeof(__pyx_k_294), 0, 0, 1, 1},
+ {&__pyx_n_s_298, __pyx_k_298, sizeof(__pyx_k_298), 0, 0, 1, 1},
+ {&__pyx_n_s_301, __pyx_k_301, sizeof(__pyx_k_301), 0, 0, 1, 1},
{&__pyx_kp_s_32, __pyx_k_32, sizeof(__pyx_k_32), 0, 0, 1, 0},
{&__pyx_n_s_36, __pyx_k_36, sizeof(__pyx_k_36), 0, 0, 1, 1},
{&__pyx_n_s_37, __pyx_k_37, sizeof(__pyx_k_37), 0, 0, 1, 1},
@@ -24384,16 +24842,16 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{0, 0, 0, 0, 0, 0, 0}
};
static int __Pyx_InitCachedBuiltins(void) {
- __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 209; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 473; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 480; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_min = __Pyx_GetName(__pyx_b, __pyx_n_s__min); if (!__pyx_builtin_min) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 851; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_object = __Pyx_GetName(__pyx_b, __pyx_n_s__object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_ValueError = __Pyx_GetName(__pyx_b, __pyx_n_s__ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 78; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_range = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 212; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __pyx_n_s__enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 476; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 483; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_min = __Pyx_GetName(__pyx_b, __pyx_n_s__min); if (!__pyx_builtin_min) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_zip = __Pyx_GetName(__pyx_b, __pyx_n_s__zip); if (!__pyx_builtin_zip) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 854; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_StopIteration = __Pyx_GetName(__pyx_b, __pyx_n_s__StopIteration); if (!__pyx_builtin_StopIteration) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 910; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_KeyError = __Pyx_GetName(__pyx_b, __pyx_n_s__KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_builtin_NotImplementedError = __Pyx_GetName(__pyx_b, __pyx_n_s__NotImplementedError); if (!__pyx_builtin_NotImplementedError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1039; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
__pyx_L1_error:;
return -1;
@@ -24403,1949 +24861,1088 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "pysam/cvcf.pyx":70
+ /* "pysam/cvcf.pyx":71
* def parse_regions( string ):
* result = []
* for r in string.split(','): # <<<<<<<<<<<<<<
* elts = r.split(':')
* chrom, start, end = elts[0], 0, 3000000000
*/
- __pyx_k_tuple_3 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_3 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_k_tuple_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_3);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_3, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_3));
- /* "pysam/cvcf.pyx":71
+ /* "pysam/cvcf.pyx":72
* result = []
* for r in string.split(','):
* elts = r.split(':') # <<<<<<<<<<<<<<
* chrom, start, end = elts[0], 0, 3000000000
* if len(elts)==1: pass
*/
- __pyx_k_tuple_5 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_5 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_5);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_5, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5));
- /* "pysam/cvcf.pyx":76
+ /* "pysam/cvcf.pyx":77
* elif len(elts)==2:
* if len(elts[1])>0:
* ielts = elts[1].split('-') # <<<<<<<<<<<<<<
* if len(ielts) != 2: ValueError("Don't understand region string '%s'" % r)
* try: start, end = int(ielts[0])-1, int(ielts[1])
*/
- __pyx_k_tuple_7 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 76; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_7 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_6)); if (unlikely(!__pyx_k_tuple_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 77; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_7);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_6));
- PyTuple_SET_ITEM(__pyx_k_tuple_7, 0, ((PyObject *)__pyx_kp_s_6));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_7));
- /* "pysam/cvcf.pyx":157
+ /* "pysam/cvcf.pyx":159
* alt = self.fields[4]
* if alt == ".": alt = []
* else: alt = alt.upper().split(',') # <<<<<<<<<<<<<<
* return alt
*
*/
- __pyx_k_tuple_10 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_10 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_k_tuple_10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 159; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_10);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_10, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
- /* "pysam/cvcf.pyx":173
+ /* "pysam/cvcf.pyx":176
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if f == b"." or f == b"PASS" or f == b"0": return []
* else: return f.split(';') # <<<<<<<<<<<<<<
*
* property info:
*/
- __pyx_k_tuple_12 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 173; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_12 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 176; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_12);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_11));
- PyTuple_SET_ITEM(__pyx_k_tuple_12, 0, ((PyObject *)__pyx_kp_s_11));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
- /* "pysam/cvcf.pyx":181
+ /* "pysam/cvcf.pyx":184
* info = {}
* if col != b".":
* for blurp in col.split(';'): # <<<<<<<<<<<<<<
* elts = blurp.split('=')
* if len(elts) == 1: v = None
*/
- __pyx_k_tuple_13 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_13 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_13)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 184; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_13);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_11));
- PyTuple_SET_ITEM(__pyx_k_tuple_13, 0, ((PyObject *)__pyx_kp_s_11));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
- /* "pysam/cvcf.pyx":182
+ /* "pysam/cvcf.pyx":185
* if col != b".":
* for blurp in col.split(';'):
* elts = blurp.split('=') # <<<<<<<<<<<<<<
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
*/
- __pyx_k_tuple_15 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_15 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 185; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_15);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_15, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
- /* "pysam/cvcf.pyx":191
+ /* "pysam/cvcf.pyx":194
* property format:
* def __get__(self):
* return self.fields[8].split(':') # <<<<<<<<<<<<<<
*
* property samples:
*/
- __pyx_k_tuple_16 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 191; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_16 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_16)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 194; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_16);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_16, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_16));
- /* "pysam/cvcf.pyx":200
+ /* "pysam/cvcf.pyx":203
*
* # parse sample columns
* values = self.fields[self.vcf._sample2column[key]].split(':') # <<<<<<<<<<<<<<
* alt = self.alt
* format = self.format
*/
- __pyx_k_tuple_17 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 200; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_17 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_17)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 203; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_17);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_17, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17));
- /* "pysam/cvcf.pyx":316
+ /* "pysam/cvcf.pyx":319
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
* # make error identifiers accessible by name
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id # <<<<<<<<<<<<<<
* if _copy != None:
* self._leftalign = _copy._leftalign
*/
- __pyx_k_tuple_22 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 316; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_22 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_22);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_22, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_22));
- /* "pysam/cvcf.pyx":337
+ /* "pysam/cvcf.pyx":340
* def error(self,line,error,opt=None):
* if error in self._ignored_errors: return
* errorlabel, errorstring = self._errors[error].split(':') # <<<<<<<<<<<<<<
* if opt: errorstring = errorstring % opt
* errwarn = ["Error","Warning"][error in self._warn_errors]
*/
- __pyx_k_tuple_23 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 337; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_23 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_23)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 340; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_23);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_23, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
- /* "pysam/cvcf.pyx":346
+ /* "pysam/cvcf.pyx":349
* def parse_format(self,line,format,filter=False):
* if self._version == 40:
* if not format.startswith('<'): # <<<<<<<<<<<<<<
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format = "<"+format
*/
- __pyx_k_tuple_26 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 346; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_26 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_25)); if (unlikely(!__pyx_k_tuple_26)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_26);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_25));
- PyTuple_SET_ITEM(__pyx_k_tuple_26, 0, ((PyObject *)__pyx_kp_s_25));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
- /* "pysam/cvcf.pyx":349
+ /* "pysam/cvcf.pyx":352
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format = "<"+format
* if not format.endswith('>'): # <<<<<<<<<<<<<<
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format += ">"
*/
- __pyx_k_tuple_29 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 349; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_29 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_28)); if (unlikely(!__pyx_k_tuple_29)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_29);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_28));
- PyTuple_SET_ITEM(__pyx_k_tuple_29, 0, ((PyObject *)__pyx_kp_s_28));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_28));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29));
- /* "pysam/cvcf.pyx":356
+ /* "pysam/cvcf.pyx":359
* idx = 0
* while len(format.strip())>0:
* elts = format.strip().split(',') # <<<<<<<<<<<<<<
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
*/
- __pyx_k_tuple_30 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 356; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_30 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_k_tuple_30)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_30);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_30, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_30));
- /* "pysam/cvcf.pyx":358
+ /* "pysam/cvcf.pyx":361
* elts = format.strip().split(',')
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<<
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_k_tuple_31 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_31 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_31)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_31);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_31, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_31));
- __pyx_k_tuple_33 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_33 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_k_tuple_33)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_33);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_k_tuple_33, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_33));
- __pyx_k_tuple_34 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_34 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_34)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_34);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_34, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_34));
- __pyx_k_tuple_35 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_35 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_k_tuple_35)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 361; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_35);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_k_tuple_35, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35));
- /* "pysam/cvcf.pyx":362
+ /* "pysam/cvcf.pyx":365
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<<
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
*/
- __pyx_k_tuple_42 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_42 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_38)); if (unlikely(!__pyx_k_tuple_42)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_42);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_38));
- PyTuple_SET_ITEM(__pyx_k_tuple_42, 0, ((PyObject *)__pyx_kp_s_38));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_38));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_42));
- __pyx_k_tuple_43 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 362; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_43 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_43)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_43);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_43, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43));
- /* "pysam/cvcf.pyx":363
+ /* "pysam/cvcf.pyx":366
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<<
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='):
*/
- __pyx_k_tuple_44 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_44 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_39)); if (unlikely(!__pyx_k_tuple_44)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_44);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_39));
- PyTuple_SET_ITEM(__pyx_k_tuple_44, 0, ((PyObject *)__pyx_kp_s_39));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_39));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_44));
- __pyx_k_tuple_45 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_45 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_45)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_45);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_45, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_45));
- /* "pysam/cvcf.pyx":364
+ /* "pysam/cvcf.pyx":367
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<<
* elif first.startswith('Description='):
* elts = format.split('"')
*/
- __pyx_k_tuple_46 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_46 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_40)); if (unlikely(!__pyx_k_tuple_46)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_46);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_40));
- PyTuple_SET_ITEM(__pyx_k_tuple_46, 0, ((PyObject *)__pyx_kp_s_40));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_40));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_46));
- __pyx_k_tuple_47 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 364; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_47 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_47)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 367; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_47);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_47, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
- /* "pysam/cvcf.pyx":365
+ /* "pysam/cvcf.pyx":368
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='): # <<<<<<<<<<<<<<
* elts = format.split('"')
* if len(elts)<3:
*/
- __pyx_k_tuple_48 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 365; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_48 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_41)); if (unlikely(!__pyx_k_tuple_48)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 368; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_48);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_41));
- PyTuple_SET_ITEM(__pyx_k_tuple_48, 0, ((PyObject *)__pyx_kp_s_41));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_41));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48));
- /* "pysam/cvcf.pyx":366
+ /* "pysam/cvcf.pyx":369
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='):
* elts = format.split('"') # <<<<<<<<<<<<<<
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES)
*/
- __pyx_k_tuple_49 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 366; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_49 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_32)); if (unlikely(!__pyx_k_tuple_49)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_49);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_32));
- PyTuple_SET_ITEM(__pyx_k_tuple_49, 0, ((PyObject *)__pyx_kp_s_32));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
- /* "pysam/cvcf.pyx":369
+ /* "pysam/cvcf.pyx":372
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES)
* elts = first.split('=') + [rest] # <<<<<<<<<<<<<<
* data['descr'] = elts[1]
* rest = '"'.join(elts[2:])
*/
- __pyx_k_tuple_51 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_51 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_51)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_51);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_51, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
- /* "pysam/cvcf.pyx":372
+ /* "pysam/cvcf.pyx":375
* data['descr'] = elts[1]
* rest = '"'.join(elts[2:])
* if rest.startswith(','): rest = rest[1:] # <<<<<<<<<<<<<<
* else:
* self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
*/
- __pyx_k_tuple_52 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 372; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_52 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_k_tuple_52)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 375; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_52);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_52, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
- /* "pysam/cvcf.pyx":492
+ /* "pysam/cvcf.pyx":495
* # snip off trailing missing data
* while len(output) > 1:
* last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<<
* if len(last)>0: break
* output = output[:-1]
*/
- __pyx_k_tuple_62 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_62 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_2), ((PyObject *)__pyx_kp_s_1)); if (unlikely(!__pyx_k_tuple_62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_62);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_62, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_1));
- PyTuple_SET_ITEM(__pyx_k_tuple_62, 1, ((PyObject *)__pyx_kp_s_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_1));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_62));
- __pyx_k_tuple_63 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 492; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_63 = PyTuple_Pack(2, ((PyObject *)__pyx_kp_s_9), ((PyObject *)__pyx_kp_s_1)); if (unlikely(!__pyx_k_tuple_63)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 495; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_63);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_9));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 0, ((PyObject *)__pyx_kp_s_9));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_1));
- PyTuple_SET_ITEM(__pyx_k_tuple_63, 1, ((PyObject *)__pyx_kp_s_1));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_1));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
- /* "pysam/cvcf.pyx":518
+ /* "pysam/cvcf.pyx":521
*
* def parse_header( self, line ):
* assert line.startswith('##') # <<<<<<<<<<<<<<
* elts = line[2:].split('=')
* key = elts[0].strip()
*/
- __pyx_k_tuple_77 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 518; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_77 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_76)); if (unlikely(!__pyx_k_tuple_77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 521; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_77);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
- PyTuple_SET_ITEM(__pyx_k_tuple_77, 0, ((PyObject *)__pyx_kp_s_76));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
- /* "pysam/cvcf.pyx":519
+ /* "pysam/cvcf.pyx":522
* def parse_header( self, line ):
* assert line.startswith('##')
* elts = line[2:].split('=') # <<<<<<<<<<<<<<
* key = elts[0].strip()
* value = '='.join(elts[1:]).strip()
*/
- __pyx_k_tuple_78 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 519; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_78 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_78)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 522; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_78);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_78, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
- /* "pysam/cvcf.pyx":554
+ /* "pysam/cvcf.pyx":557
*
* def parse_heading( self, line ):
* assert line.startswith('#') # <<<<<<<<<<<<<<
* assert not line.startswith('##')
* headings = line[1:].split('\t')
*/
- __pyx_k_tuple_86 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 554; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_86 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_85)); if (unlikely(!__pyx_k_tuple_86)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 557; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_86);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_85));
- PyTuple_SET_ITEM(__pyx_k_tuple_86, 0, ((PyObject *)__pyx_kp_s_85));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
- /* "pysam/cvcf.pyx":555
+ /* "pysam/cvcf.pyx":558
* def parse_heading( self, line ):
* assert line.startswith('#')
* assert not line.startswith('##') # <<<<<<<<<<<<<<
* headings = line[1:].split('\t')
* # test for 8, as FORMAT field might be missing
*/
- __pyx_k_tuple_87 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 555; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_87 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_76)); if (unlikely(!__pyx_k_tuple_87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 558; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_87);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
- PyTuple_SET_ITEM(__pyx_k_tuple_87, 0, ((PyObject *)__pyx_kp_s_76));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
- /* "pysam/cvcf.pyx":556
+ /* "pysam/cvcf.pyx":559
* assert line.startswith('#')
* assert not line.startswith('##')
* headings = line[1:].split('\t') # <<<<<<<<<<<<<<
* # test for 8, as FORMAT field might be missing
* if len(headings)==1 and len(line[1:].split()) >= 8:
*/
- __pyx_k_tuple_89 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_89 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_88)); if (unlikely(!__pyx_k_tuple_89)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 559; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_89);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_88));
- PyTuple_SET_ITEM(__pyx_k_tuple_89, 0, ((PyObject *)__pyx_kp_s_88));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_88));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89));
- /* "pysam/cvcf.pyx":608
+ /* "pysam/cvcf.pyx":611
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
* return []
* values = value.split(',') # <<<<<<<<<<<<<<
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
*/
- __pyx_k_tuple_97 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 608; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_97 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_k_tuple_97)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_97);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_97, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
- /* "pysam/cvcf.pyx":610
+ /* "pysam/cvcf.pyx":613
* values = value.split(',')
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<<
* self.error(line,self.ERROR_TRAILING_DATA,values[-1])
* values[-1] = values[-1].split(';')[0]
*/
- __pyx_k_tuple_98 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 610; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_98 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_98)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 613; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_98);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_11));
- PyTuple_SET_ITEM(__pyx_k_tuple_98, 0, ((PyObject *)__pyx_kp_s_11));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
- /* "pysam/cvcf.pyx":612
+ /* "pysam/cvcf.pyx":615
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
* self.error(line,self.ERROR_TRAILING_DATA,values[-1])
* values[-1] = values[-1].split(';')[0] # <<<<<<<<<<<<<<
* if f.type == "Integer":
* for idx,v in enumerate(values):
*/
- __pyx_k_tuple_99 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 612; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_99 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_99)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 615; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_99);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_11));
- PyTuple_SET_ITEM(__pyx_k_tuple_99, 0, ((PyObject *)__pyx_kp_s_11));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
- /* "pysam/cvcf.pyx":648
+ /* "pysam/cvcf.pyx":651
*
* def parse_data( self, line, lineparse=False ):
* cols = line.split('\t') # <<<<<<<<<<<<<<
* if len(cols) != len(self._samples)+9:
* # gracefully deal with absent FORMAT column
*/
- __pyx_k_tuple_103 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 648; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_103 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_88)); if (unlikely(!__pyx_k_tuple_103)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 651; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_103);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_88));
- PyTuple_SET_ITEM(__pyx_k_tuple_103, 0, ((PyObject *)__pyx_kp_s_88));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_88));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
- /* "pysam/cvcf.pyx":694
+ /* "pysam/cvcf.pyx":697
* # convert v3.3 to v4.0 alleles below
* if cols[4] == ".": alt = []
* else: alt = cols[4].upper().split(',') # <<<<<<<<<<<<<<
*
* if cols[5] == ".": qual = -1
*/
- __pyx_k_tuple_107 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_107)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_107 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_2)); if (unlikely(!__pyx_k_tuple_107)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 697; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_107);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_2));
- PyTuple_SET_ITEM(__pyx_k_tuple_107, 0, ((PyObject *)__pyx_kp_s_2));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_107));
- /* "pysam/cvcf.pyx":703
+ /* "pysam/cvcf.pyx":706
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if cols[6] == "." or cols[6] == "PASS" or cols[6] == "0": filter = []
* else: filter = cols[6].split(';') # <<<<<<<<<<<<<<
*
* # dictionary of keys, and list of values
*/
- __pyx_k_tuple_108 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_108)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_108 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_108)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_108);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_11));
- PyTuple_SET_ITEM(__pyx_k_tuple_108, 0, ((PyObject *)__pyx_kp_s_11));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_108));
- /* "pysam/cvcf.pyx":708
+ /* "pysam/cvcf.pyx":711
* info = {}
* if cols[7] != ".":
* for blurp in cols[7].split(';'): # <<<<<<<<<<<<<<
* elts = blurp.split('=')
* if len(elts) == 1: v = None
*/
- __pyx_k_tuple_109 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_109)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_109 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_11)); if (unlikely(!__pyx_k_tuple_109)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_109);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_11));
- PyTuple_SET_ITEM(__pyx_k_tuple_109, 0, ((PyObject *)__pyx_kp_s_11));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109));
- /* "pysam/cvcf.pyx":709
+ /* "pysam/cvcf.pyx":712
* if cols[7] != ".":
* for blurp in cols[7].split(';'):
* elts = blurp.split('=') # <<<<<<<<<<<<<<
* if len(elts) == 1: v = None
* elif len(elts) == 2: v = elts[1]
*/
- __pyx_k_tuple_110 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_110)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_110 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_14)); if (unlikely(!__pyx_k_tuple_110)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 712; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_110);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_14));
- PyTuple_SET_ITEM(__pyx_k_tuple_110, 0, ((PyObject *)__pyx_kp_s_14));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110));
- /* "pysam/cvcf.pyx":720
+ /* "pysam/cvcf.pyx":723
* # Gracefully deal with absent FORMAT column
* if cols[8] == "": format = []
* else: format = cols[8].split(':') # <<<<<<<<<<<<<<
*
* # check: all filters are defined
*/
- __pyx_k_tuple_111 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_111)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_111 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_111)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_111);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_111, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_111));
- /* "pysam/cvcf.pyx":738
+ /* "pysam/cvcf.pyx":741
* for a in alt:
* if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference # <<<<<<<<<<<<<<
* elif a.startswith('D'): # allow D<seq> and D<num>
* have_deletions = True
*/
- __pyx_k_tuple_112 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 738; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_112 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__I)); if (unlikely(!__pyx_k_tuple_112)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_112);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__I));
- PyTuple_SET_ITEM(__pyx_k_tuple_112, 0, ((PyObject *)__pyx_n_s__I));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__I));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112));
- /* "pysam/cvcf.pyx":739
+ /* "pysam/cvcf.pyx":742
* if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
* elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
* elif a.startswith('D'): # allow D<seq> and D<num> # <<<<<<<<<<<<<<
* have_deletions = True
* try:
*/
- __pyx_k_tuple_113 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_113)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_113 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__D)); if (unlikely(!__pyx_k_tuple_113)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 742; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_113);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__D));
- PyTuple_SET_ITEM(__pyx_k_tuple_113, 0, ((PyObject *)__pyx_n_s__D));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__D));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_113));
- /* "pysam/cvcf.pyx":820
+ /* "pysam/cvcf.pyx":823
* for sample in cols[9:]:
* dict = {}
* values = sample.split(':') # <<<<<<<<<<<<<<
* if len(values) > len(format):
* self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
*/
- __pyx_k_tuple_117 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_117 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_4)); if (unlikely(!__pyx_k_tuple_117)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_117);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_4));
- PyTuple_SET_ITEM(__pyx_k_tuple_117, 0, ((PyObject *)__pyx_kp_s_4));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117));
- /* "pysam/cvcf.pyx":890
+ /* "pysam/cvcf.pyx":893
* for line in stream:
* self._lineno += 1
* if line.startswith('##'): # <<<<<<<<<<<<<<
* self.parse_header( line.strip() )
* elif line.startswith('#'):
*/
- __pyx_k_tuple_119 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_119)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 890; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_119 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_76)); if (unlikely(!__pyx_k_tuple_119)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 893; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_119);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
- PyTuple_SET_ITEM(__pyx_k_tuple_119, 0, ((PyObject *)__pyx_kp_s_76));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_119));
- /* "pysam/cvcf.pyx":892
+ /* "pysam/cvcf.pyx":895
* if line.startswith('##'):
* self.parse_header( line.strip() )
* elif line.startswith('#'): # <<<<<<<<<<<<<<
* self.parse_heading( line.strip() )
* self.enter_default_format()
*/
- __pyx_k_tuple_120 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 892; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_120 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_85)); if (unlikely(!__pyx_k_tuple_120)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_120);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_85));
- PyTuple_SET_ITEM(__pyx_k_tuple_120, 0, ((PyObject *)__pyx_kp_s_85));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_120));
- /* "pysam/cvcf.pyx":901
+ /* "pysam/cvcf.pyx":904
* def _parse(self, line, stream):
* # deal with files with header only
* if line.startswith("##"): return # <<<<<<<<<<<<<<
* if len(line.strip()) > 0:
* d = self.parse_data( line.strip() )
*/
- __pyx_k_tuple_122 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 901; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_122 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_76)); if (unlikely(!__pyx_k_tuple_122)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 904; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_122);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_76));
- PyTuple_SET_ITEM(__pyx_k_tuple_122, 0, ((PyObject *)__pyx_kp_s_76));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
- /* "pysam/cvcf.pyx":958
+ /* "pysam/cvcf.pyx":961
*
* def setversion(self, version):
* if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files") # <<<<<<<<<<<<<<
* self._version = version
*
*/
- __pyx_k_tuple_124 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_124 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_123)); if (unlikely(!__pyx_k_tuple_124)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_124);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_123));
- PyTuple_SET_ITEM(__pyx_k_tuple_124, 0, ((PyObject *)__pyx_kp_s_123));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_123));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
- /* "pysam/cvcf.pyx":1036
+ /* "pysam/cvcf.pyx":1039
* '''
*
* raise NotImplementedError( "needs to be checked" ) # <<<<<<<<<<<<<<
*
* chrom, pos = record.chrom, record.pos
*/
- __pyx_k_tuple_127 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_127)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1036; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_127 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_126)); if (unlikely(!__pyx_k_tuple_127)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1039; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_127);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_126));
- PyTuple_SET_ITEM(__pyx_k_tuple_127, 0, ((PyObject *)__pyx_kp_s_126));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_126));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_127));
- /* "pysam/cvcf.pyx":54
+ /* "pysam/cvcf.pyx":55
* import pysam
*
* gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<<
* alleleRegEx = re.compile('^[ACGTN]+$')
*
*/
- __pyx_k_tuple_129 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_129)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_129 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_128)); if (unlikely(!__pyx_k_tuple_129)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_129);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_128));
- PyTuple_SET_ITEM(__pyx_k_tuple_129, 0, ((PyObject *)__pyx_kp_s_128));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_128));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_129));
- /* "pysam/cvcf.pyx":55
+ /* "pysam/cvcf.pyx":56
*
* gtsRegEx = re.compile("[|/\\\\]")
* alleleRegEx = re.compile('^[ACGTN]+$') # <<<<<<<<<<<<<<
*
* # Utility function. Uses 0-based coordinates
*/
- __pyx_k_tuple_131 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_131 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_130)); if (unlikely(!__pyx_k_tuple_131)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_131);
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_130));
- PyTuple_SET_ITEM(__pyx_k_tuple_131, 0, ((PyObject *)__pyx_kp_s_130));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_130));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131));
- /* "pysam/cvcf.pyx":58
+ /* "pysam/cvcf.pyx":59
*
* # Utility function. Uses 0-based coordinates
* def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
* # obtain sequence from .fa file, without truncation
* if end<=start: return ""
*/
- __pyx_k_tuple_132 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_132)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_132 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__chrom), ((PyObject *)__pyx_n_s__start), ((PyObject *)__pyx_n_s__end), ((PyObject *)__pyx_n_s__fa), ((PyObject *)__pyx_n_s__sequence)); if (unlikely(!__pyx_k_tuple_132)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_132);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom));
- PyTuple_SET_ITEM(__pyx_k_tuple_132, 0, ((PyObject *)__pyx_n_s__chrom));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__start));
- PyTuple_SET_ITEM(__pyx_k_tuple_132, 1, ((PyObject *)__pyx_n_s__start));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__end));
- PyTuple_SET_ITEM(__pyx_k_tuple_132, 2, ((PyObject *)__pyx_n_s__end));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fa));
- PyTuple_SET_ITEM(__pyx_k_tuple_132, 3, ((PyObject *)__pyx_n_s__fa));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fa));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__sequence));
- PyTuple_SET_ITEM(__pyx_k_tuple_132, 4, ((PyObject *)__pyx_n_s__sequence));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__sequence));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_132));
- __pyx_k_codeobj_133 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_132, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_sequence, 58, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_133 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_132, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_sequence, 59, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_133)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":68
+ /* "pysam/cvcf.pyx":69
*
* # Utility function. Parses a region string
* def parse_regions( string ): # <<<<<<<<<<<<<<
* result = []
* for r in string.split(','):
*/
- __pyx_k_tuple_136 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_136)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_136 = PyTuple_Pack(8, ((PyObject *)__pyx_n_s__string), ((PyObject *)__pyx_n_s__result), ((PyObject *)__pyx_n_s__r), ((PyObject *)__pyx_n_s__elts), ((PyObject *)__pyx_n_s__chrom), ((PyObject *)__pyx_n_s__start), ((PyObject *)__pyx_n_s__end), ((PyObject *)__pyx_n_s__ielts)); if (unlikely(!__pyx_k_tuple_136)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_136);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__string));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 0, ((PyObject *)__pyx_n_s__string));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__string));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__result));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 1, ((PyObject *)__pyx_n_s__result));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__result));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 2, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__elts));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 3, ((PyObject *)__pyx_n_s__elts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 4, ((PyObject *)__pyx_n_s__chrom));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__start));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 5, ((PyObject *)__pyx_n_s__start));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__end));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 6, ((PyObject *)__pyx_n_s__end));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ielts));
- PyTuple_SET_ITEM(__pyx_k_tuple_136, 7, ((PyObject *)__pyx_n_s__ielts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ielts));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_136));
- __pyx_k_codeobj_137 = (PyObject*)__Pyx_PyCode_New(1, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_136, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_regions, 68, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_137)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_137 = (PyObject*)__Pyx_PyCode_New(1, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_136, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_regions, 69, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_137)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":86
+ /* "pysam/cvcf.pyx":87
*
*
* FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<<
*
* ###########################################################################################################
*/
- __pyx_k_tuple_139 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_139 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__FORMAT), ((PyObject *)__pyx_kp_s_138)); if (unlikely(!__pyx_k_tuple_139)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_139);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__FORMAT));
- PyTuple_SET_ITEM(__pyx_k_tuple_139, 0, ((PyObject *)__pyx_n_s__FORMAT));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__FORMAT));
- __Pyx_INCREF(((PyObject *)__pyx_kp_s_138));
- PyTuple_SET_ITEM(__pyx_k_tuple_139, 1, ((PyObject *)__pyx_kp_s_138));
- __Pyx_GIVEREF(((PyObject *)__pyx_kp_s_138));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_139));
- /* "pysam/cvcf.pyx":314
+ /* "pysam/cvcf.pyx":317
* _lines = None
*
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # <<<<<<<<<<<<<<
* # make error identifiers accessible by name
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
*/
- __pyx_k_tuple_174 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_174 = PyTuple_Pack(7, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s___copy), ((PyObject *)__pyx_n_s__reference), ((PyObject *)__pyx_n_s__regions), ((PyObject *)__pyx_n_s__lines), ((PyObject *)__pyx_n_s__leftalign), ((PyObject *)__pyx_n_s__id)); if (unlikely(!__pyx_k_tuple_174)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_174);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s___copy));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 1, ((PyObject *)__pyx_n_s___copy));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s___copy));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__reference));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 2, ((PyObject *)__pyx_n_s__reference));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__reference));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__regions));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 3, ((PyObject *)__pyx_n_s__regions));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__regions));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__lines));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 4, ((PyObject *)__pyx_n_s__lines));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__lines));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__leftalign));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 5, ((PyObject *)__pyx_n_s__leftalign));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__leftalign));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__id));
- PyTuple_SET_ITEM(__pyx_k_tuple_174, 6, ((PyObject *)__pyx_n_s__id));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_174));
- __pyx_k_codeobj_175 = (PyObject*)__Pyx_PyCode_New(6, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_174, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s____init__, 314, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_codeobj_175 = (PyObject*)__Pyx_PyCode_New(6, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_174, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s____init__, 317, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_175)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":335
+ /* "pysam/cvcf.pyx":338
* self._lines = lines
*
* def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
* if error in self._ignored_errors: return
* errorlabel, errorstring = self._errors[error].split(':')
*/
- __pyx_k_tuple_176 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_176)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_176);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 1, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__error));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 2, ((PyObject *)__pyx_n_s__error));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__error));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__opt));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 3, ((PyObject *)__pyx_n_s__opt));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__opt));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__errorlabel));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 4, ((PyObject *)__pyx_n_s__errorlabel));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorlabel));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__errorstring));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 5, ((PyObject *)__pyx_n_s__errorstring));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorstring));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__errwarn));
- PyTuple_SET_ITEM(__pyx_k_tuple_176, 6, ((PyObject *)__pyx_n_s__errwarn));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errwarn));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_176));
- __pyx_k_codeobj_177 = (PyObject*)__Pyx_PyCode_New(4, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_176, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__error, 335, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_177)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_k_tuple_178 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_178)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_178);
- __Pyx_INCREF(((PyObject *)Py_None));
- PyTuple_SET_ITEM(__pyx_k_tuple_178, 0, ((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_178));
+ __pyx_k_tuple_177 = PyTuple_Pack(7, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__error), ((PyObject *)__pyx_n_s__opt), ((PyObject *)__pyx_n_s__errorlabel), ((PyObject *)__pyx_n_s__errorstring), ((PyObject *)__pyx_n_s__errwarn)); if (unlikely(!__pyx_k_tuple_177)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_177);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_177));
+ __pyx_k_codeobj_178 = (PyObject*)__Pyx_PyCode_New(4, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_177, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__error, 338, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_178)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_179 = PyTuple_Pack(1, ((PyObject *)Py_None)); if (unlikely(!__pyx_k_tuple_179)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_179);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_179));
- /* "pysam/cvcf.pyx":344
+ /* "pysam/cvcf.pyx":347
* raise ValueError(errorstring)
*
* def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
* if self._version == 40:
* if not format.startswith('<'):
*/
- __pyx_k_tuple_179 = PyTuple_New(11); if (unlikely(!__pyx_k_tuple_179)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_179);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 1, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__format));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 2, ((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filter));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 3, ((PyObject *)__pyx_n_s__filter));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__data));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 4, ((PyObject *)__pyx_n_s__data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__idx));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 5, ((PyObject *)__pyx_n_s__idx));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__elts));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 6, ((PyObject *)__pyx_n_s__elts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__first));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 7, ((PyObject *)__pyx_n_s__first));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__first));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__rest));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 8, ((PyObject *)__pyx_n_s__rest));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__rest));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__n));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 9, ((PyObject *)__pyx_n_s__n));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__n));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__t));
- PyTuple_SET_ITEM(__pyx_k_tuple_179, 10, ((PyObject *)__pyx_n_s__t));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__t));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_179));
- __pyx_k_codeobj_180 = (PyObject*)__Pyx_PyCode_New(4, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_179, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_format, 344, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_180)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_181 = PyTuple_Pack(11, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__format), ((PyObject *)__pyx_n_s__filter), ((PyObject *)__pyx_n_s__data), ((PyObject *)__pyx_n_s__idx), ((PyObject *)__pyx_n_s__elts), ((PyObject *)__pyx_n_s__first), ((PyObject *)__pyx_n_s__rest), ((PyObject *)__pyx_n_s__n), ((PyObject *)__pyx_n_s__t)); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; got [...]
+ __Pyx_GOTREF(__pyx_k_tuple_181);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181));
+ __pyx_k_codeobj_182 = (PyObject*)__Pyx_PyCode_New(4, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_181, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_format, 347, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":416
+ /* "pysam/cvcf.pyx":419
* return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
*
* def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
* values = [('ID',fmt.id)]
* if fmt.number != None and not filter:
*/
- __pyx_k_tuple_181 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_181)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_181);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fmt));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 1, ((PyObject *)__pyx_n_s__fmt));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fmt));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filter));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 2, ((PyObject *)__pyx_n_s__filter));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__values));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 3, ((PyObject *)__pyx_n_s__values));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__values));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__nmb));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 4, ((PyObject *)__pyx_n_s__nmb));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__nmb));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__format));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 5, ((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__k));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 6, ((PyObject *)__pyx_n_s__k));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__k));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__v));
- PyTuple_SET_ITEM(__pyx_k_tuple_181, 7, ((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_181));
- __pyx_k_codeobj_182 = (PyObject*)__Pyx_PyCode_New(3, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_181, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_format, 416, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_182)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_184 = PyTuple_Pack(8, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__fmt), ((PyObject *)__pyx_n_s__filter), ((PyObject *)__pyx_n_s__values), ((PyObject *)__pyx_n_s__nmb), ((PyObject *)__pyx_n_s__format), ((PyObject *)__pyx_n_s__k), ((PyObject *)__pyx_n_s__v)); if (unlikely(!__pyx_k_tuple_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_184);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_184));
+ __pyx_k_codeobj_185 = (PyObject*)__Pyx_PyCode_New(3, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_184, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_format, 419, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_185)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":436
+ /* "pysam/cvcf.pyx":439
* return format
*
* def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
* fmt = formatdict[format]
* if fmt.numbertype == self.NT_UNKNOWN: return -1
*/
- __pyx_k_tuple_183 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_183)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_183);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__format));
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 1, ((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__formatdict));
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 2, ((PyObject *)__pyx_n_s__formatdict));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formatdict));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__alt));
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 3, ((PyObject *)__pyx_n_s__alt));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__fmt));
- PyTuple_SET_ITEM(__pyx_k_tuple_183, 4, ((PyObject *)__pyx_n_s__fmt));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__fmt));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_183));
- __pyx_k_codeobj_184 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_183, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_expected, 436, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_184)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_187 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__format), ((PyObject *)__pyx_n_s__formatdict), ((PyObject *)__pyx_n_s__alt), ((PyObject *)__pyx_n_s__fmt)); if (unlikely(!__pyx_k_tuple_187)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_187);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_187));
+ __pyx_k_codeobj_188 = (PyObject*)__Pyx_PyCode_New(4, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_187, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__get_expected, 439, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_188)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":447
+ /* "pysam/cvcf.pyx":450
*
*
* def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
* if key in formatdict: return
* self.error(line,self.ERROR_UNKNOWN_KEY,key)
*/
- __pyx_k_tuple_185 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_185)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_185);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_185, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__formatdict));
- PyTuple_SET_ITEM(__pyx_k_tuple_185, 1, ((PyObject *)__pyx_n_s__formatdict));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formatdict));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__key));
- PyTuple_SET_ITEM(__pyx_k_tuple_185, 2, ((PyObject *)__pyx_n_s__key));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__data));
- PyTuple_SET_ITEM(__pyx_k_tuple_185, 3, ((PyObject *)__pyx_n_s__data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_185, 4, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_185));
- __pyx_k_codeobj_186 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_185, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___add_definition, 447, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_186)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":464
+ __pyx_k_tuple_190 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__formatdict), ((PyObject *)__pyx_n_s__key), ((PyObject *)__pyx_n_s__data), ((PyObject *)__pyx_n_s__line)); if (unlikely(!__pyx_k_tuple_190)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_190);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_190));
+ __pyx_k_codeobj_191 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_190, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___add_definition, 450, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_191)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":467
*
* # todo: trim trailing missing values
* def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
* output, sdata = [], []
* if type(data) == type([]): # for FORMAT field, make data with dummy values
*/
- __pyx_k_tuple_187 = PyTuple_New(13); if (unlikely(!__pyx_k_tuple_187)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_187);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__data));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 1, ((PyObject *)__pyx_n_s__data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__format));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 2, ((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__key));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 3, ((PyObject *)__pyx_n_s__key));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__value));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 4, ((PyObject *)__pyx_n_s__value));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__separator));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 5, ((PyObject *)__pyx_n_s__separator));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__separator));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__output));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 6, ((PyObject *)__pyx_n_s__output));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__output));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__sdata));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 7, ((PyObject *)__pyx_n_s__sdata));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__sdata));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__d));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 8, ((PyObject *)__pyx_n_s__d));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__d));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__k));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 9, ((PyObject *)__pyx_n_s__k));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__k));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__idx));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 10, ((PyObject *)__pyx_n_s__idx));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__v));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 11, ((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__last));
- PyTuple_SET_ITEM(__pyx_k_tuple_187, 12, ((PyObject *)__pyx_n_s__last));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__last));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_187));
- __pyx_k_codeobj_188 = (PyObject*)__Pyx_PyCode_New(6, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_187, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_formatdata, 464, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_188)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_193 = PyTuple_Pack(13, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__data), ((PyObject *)__pyx_n_s__format), ((PyObject *)__pyx_n_s__key), ((PyObject *)__pyx_n_s__value), ((PyObject *)__pyx_n_s__separator), ((PyObject *)__pyx_n_s__output), ((PyObject *)__pyx_n_s__sdata), ((PyObject *)__pyx_n_s__d), ((PyObject *)__pyx_n_s__k), ((PyObject *)__pyx_n_s__idx), ((PyObject *)__pyx_n_s__v), ((PyObject *)__pyx_n_s__last)); if (unlikely(!__pyx_k_tuple_193)) {__pyx_filename [...]
+ __Pyx_GOTREF(__pyx_k_tuple_193);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_193));
+ __pyx_k_codeobj_194 = (PyObject*)__Pyx_PyCode_New(6, 0, 13, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_193, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__format_formatdata, 467, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_194)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":498
+ /* "pysam/cvcf.pyx":501
*
*
* def enter_default_format(self): # <<<<<<<<<<<<<<
* for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
*/
- __pyx_k_tuple_189 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_189)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_189);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_189, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__f));
- PyTuple_SET_ITEM(__pyx_k_tuple_189, 1, ((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_189));
- __pyx_k_codeobj_190 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_189, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s_121, 498, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_190)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":517
+ __pyx_k_tuple_196 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__f)); if (unlikely(!__pyx_k_tuple_196)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_196);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_196));
+ __pyx_k_codeobj_197 = (PyObject*)__Pyx_PyCode_New(1, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_196, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s_121, 501, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_197)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":520
* self._format[f.id] = f
*
* def parse_header( self, line ): # <<<<<<<<<<<<<<
* assert line.startswith('##')
* elts = line[2:].split('=')
*/
- __pyx_k_tuple_191 = PyTuple_New(6); if (unlikely(!__pyx_k_tuple_191)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_191);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_191, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_191, 1, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__elts));
- PyTuple_SET_ITEM(__pyx_k_tuple_191, 2, ((PyObject *)__pyx_n_s__elts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__key));
- PyTuple_SET_ITEM(__pyx_k_tuple_191, 3, ((PyObject *)__pyx_n_s__key));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__value));
- PyTuple_SET_ITEM(__pyx_k_tuple_191, 4, ((PyObject *)__pyx_n_s__value));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__f));
- PyTuple_SET_ITEM(__pyx_k_tuple_191, 5, ((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_191));
- __pyx_k_codeobj_192 = (PyObject*)__Pyx_PyCode_New(2, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_191, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_header, 517, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_192)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":546
+ __pyx_k_tuple_199 = PyTuple_Pack(6, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__elts), ((PyObject *)__pyx_n_s__key), ((PyObject *)__pyx_n_s__value), ((PyObject *)__pyx_n_s__f)); if (unlikely(!__pyx_k_tuple_199)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_199);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_199));
+ __pyx_k_codeobj_200 = (PyObject*)__Pyx_PyCode_New(2, 0, 6, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_199, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_header, 520, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_200)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":549
*
*
* def write_header( self, stream ): # <<<<<<<<<<<<<<
* stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
* for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
*/
- __pyx_k_tuple_193 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_193)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_193);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__key));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 2, ((PyObject *)__pyx_n_s__key));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__value));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 3, ((PyObject *)__pyx_n_s__value));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__var));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 4, ((PyObject *)__pyx_n_s__var));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__var));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__label));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 5, ((PyObject *)__pyx_n_s__label));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__label));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__f));
- PyTuple_SET_ITEM(__pyx_k_tuple_193, 6, ((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_193));
- __pyx_k_codeobj_194 = (PyObject*)__Pyx_PyCode_New(2, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_193, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_header, 546, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_194)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_202 = PyTuple_Pack(7, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream), ((PyObject *)__pyx_n_s__key), ((PyObject *)__pyx_n_s__value), ((PyObject *)__pyx_n_s__var), ((PyObject *)__pyx_n_s__label), ((PyObject *)__pyx_n_s__f)); if (unlikely(!__pyx_k_tuple_202)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_202);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_202));
+ __pyx_k_codeobj_203 = (PyObject*)__Pyx_PyCode_New(2, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_202, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_header, 549, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_203)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":553
+ /* "pysam/cvcf.pyx":556
*
*
* def parse_heading( self, line ): # <<<<<<<<<<<<<<
* assert line.startswith('#')
* assert not line.startswith('##')
*/
- __pyx_k_tuple_195 = PyTuple_New(8); if (unlikely(!__pyx_k_tuple_195)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_195);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 1, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__headings));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 2, ((PyObject *)__pyx_n_s__headings));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__headings));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 3, ((PyObject *)__pyx_n_s__i));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__s));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 4, ((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__err));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 5, ((PyObject *)__pyx_n_s__err));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__err));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__x));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 6, ((PyObject *)__pyx_n_s__x));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__x));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__y));
- PyTuple_SET_ITEM(__pyx_k_tuple_195, 7, ((PyObject *)__pyx_n_s__y));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__y));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_195));
- __pyx_k_codeobj_196 = (PyObject*)__Pyx_PyCode_New(2, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_195, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_heading, 553, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_196)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_205 = PyTuple_Pack(8, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__headings), ((PyObject *)__pyx_n_s__i), ((PyObject *)__pyx_n_s__s), ((PyObject *)__pyx_n_s__err), ((PyObject *)__pyx_n_s__x), ((PyObject *)__pyx_n_s__y)); if (unlikely(!__pyx_k_tuple_205)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_205);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_205));
+ __pyx_k_codeobj_206 = (PyObject*)__Pyx_PyCode_New(2, 0, 8, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_205, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_heading, 556, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_206)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":581
+ /* "pysam/cvcf.pyx":584
* self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
*
* def write_heading( self, stream ): # <<<<<<<<<<<<<<
* stream.write("#" + "\t".join(self._required + self._samples) + "\n")
*
*/
- __pyx_k_tuple_197 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_197)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_197);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_197, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_197, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_197));
- __pyx_k_codeobj_198 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_197, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_heading, 581, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_198)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_208 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream)); if (unlikely(!__pyx_k_tuple_208)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_208);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_208));
+ __pyx_k_codeobj_209 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_208, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_heading, 584, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_209)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":584
+ /* "pysam/cvcf.pyx":587
* stream.write("#" + "\t".join(self._required + self._samples) + "\n")
*
* def convertGT(self, GTstring): # <<<<<<<<<<<<<<
* if GTstring == ".": return ["."]
* try:
*/
- __pyx_k_tuple_199 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_199)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_199);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_199, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__GTstring));
- PyTuple_SET_ITEM(__pyx_k_tuple_199, 1, ((PyObject *)__pyx_n_s__GTstring));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__GTstring));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__gts));
- PyTuple_SET_ITEM(__pyx_k_tuple_199, 2, ((PyObject *)__pyx_n_s__gts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__gts));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_199));
- __pyx_k_codeobj_200 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_199, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGT, 584, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_200)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_211 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__GTstring), ((PyObject *)__pyx_n_s__gts)); if (unlikely(!__pyx_k_tuple_211)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_211);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_211));
+ __pyx_k_codeobj_212 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_211, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGT, 587, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_212)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":596
+ /* "pysam/cvcf.pyx":599
* return [".","|","."]
*
* def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
* return ''.join(map(str,GTdata))
*
*/
- __pyx_k_tuple_201 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_201)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_201);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_201, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__GTdata));
- PyTuple_SET_ITEM(__pyx_k_tuple_201, 1, ((PyObject *)__pyx_n_s__GTdata));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__GTdata));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_201));
- __pyx_k_codeobj_202 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_201, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGTback, 596, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_202)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_214 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__GTdata)); if (unlikely(!__pyx_k_tuple_214)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_214);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_214));
+ __pyx_k_codeobj_215 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_214, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__convertGTback, 599, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_215)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":599
+ /* "pysam/cvcf.pyx":602
* return ''.join(map(str,GTdata))
*
* def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
* # To do: check that the right number of values is present
* f = formatdict.get(key,None)
*/
- __pyx_k_tuple_203 = PyTuple_New(9); if (unlikely(!__pyx_k_tuple_203)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_203);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__key));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 1, ((PyObject *)__pyx_n_s__key));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__value));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 2, ((PyObject *)__pyx_n_s__value));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__formatdict));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 3, ((PyObject *)__pyx_n_s__formatdict));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__formatdict));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 4, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__f));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 5, ((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__values));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 6, ((PyObject *)__pyx_n_s__values));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__values));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__idx));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 7, ((PyObject *)__pyx_n_s__idx));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__v));
- PyTuple_SET_ITEM(__pyx_k_tuple_203, 8, ((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_203));
- __pyx_k_codeobj_204 = (PyObject*)__Pyx_PyCode_New(5, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_203, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_formatdata, 599, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_204)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":641
+ __pyx_k_tuple_217 = PyTuple_Pack(9, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__key), ((PyObject *)__pyx_n_s__value), ((PyObject *)__pyx_n_s__formatdict), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__f), ((PyObject *)__pyx_n_s__values), ((PyObject *)__pyx_n_s__idx), ((PyObject *)__pyx_n_s__v)); if (unlikely(!__pyx_k_tuple_217)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_217);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_217));
+ __pyx_k_codeobj_218 = (PyObject*)__Pyx_PyCode_New(5, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_217, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_formatdata, 602, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_218)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":644
* self.error(line,self.ERROR_INFO_STRING)
*
* def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
* if not self._regions: return True
* for r in self._regions:
*/
- __pyx_k_tuple_205 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_205)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_205);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_205, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom));
- PyTuple_SET_ITEM(__pyx_k_tuple_205, 1, ((PyObject *)__pyx_n_s__chrom));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__pos));
- PyTuple_SET_ITEM(__pyx_k_tuple_205, 2, ((PyObject *)__pyx_n_s__pos));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__r));
- PyTuple_SET_ITEM(__pyx_k_tuple_205, 3, ((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_205));
- __pyx_k_codeobj_206 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_205, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__inregion, 641, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_206)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_220 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__chrom), ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_n_s__r)); if (unlikely(!__pyx_k_tuple_220)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_220);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_220));
+ __pyx_k_codeobj_221 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_220, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__inregion, 644, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_221)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":647
+ /* "pysam/cvcf.pyx":650
* return False
*
* def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
* cols = line.split('\t')
* if len(cols) != len(self._samples)+9:
*/
- __pyx_k_tuple_207 = PyTuple_New(45); if (unlikely(!__pyx_k_tuple_207)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_207);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 1, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__lineparse));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 2, ((PyObject *)__pyx_n_s__lineparse));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__lineparse));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__cols));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 3, ((PyObject *)__pyx_n_s__cols));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__cols));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__chrom));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 4, ((PyObject *)__pyx_n_s__chrom));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__chrom));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__pos));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 5, ((PyObject *)__pyx_n_s__pos));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__id));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 6, ((PyObject *)__pyx_n_s__id));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__id));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ref));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 7, ((PyObject *)__pyx_n_s__ref));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__c));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 8, ((PyObject *)__pyx_n_s__c));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__c));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__left));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 9, ((PyObject *)__pyx_n_s__left));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__left));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__faref_leftflank));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 10, ((PyObject *)__pyx_n_s__faref_leftflank));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__faref_leftflank));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__faref));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 11, ((PyObject *)__pyx_n_s__faref));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__faref));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__alt));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 12, ((PyObject *)__pyx_n_s__alt));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__qual));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 13, ((PyObject *)__pyx_n_s__qual));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qual));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filter));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 14, ((PyObject *)__pyx_n_s__filter));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__info));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 15, ((PyObject *)__pyx_n_s__info));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__info));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__blurp));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 16, ((PyObject *)__pyx_n_s__blurp));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__blurp));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__elts));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 17, ((PyObject *)__pyx_n_s__elts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__elts));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__v));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 18, ((PyObject *)__pyx_n_s__v));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__v));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__format));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 19, ((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__f));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 20, ((PyObject *)__pyx_n_s__f));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__f));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__newalts));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 21, ((PyObject *)__pyx_n_s__newalts));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__newalts));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__have_deletions));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 22, ((PyObject *)__pyx_n_s__have_deletions));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__have_deletions));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__a));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 23, ((PyObject *)__pyx_n_s__a));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__a));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__l));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 24, ((PyObject *)__pyx_n_s__l));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__l));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__addns));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 25, ((PyObject *)__pyx_n_s__addns));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__addns));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__i));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 26, ((PyObject *)__pyx_n_s__i));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__i));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__na));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 27, ((PyObject *)__pyx_n_s__na));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__na));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__s));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 28, ((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__addn));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 29, ((PyObject *)__pyx_n_s__addn));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__addn));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__allele));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 30, ((PyObject *)__pyx_n_s__allele));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__allele));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__movable));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 31, ((PyObject *)__pyx_n_s__movable));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__movable));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__longest));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 32, ((PyObject *)__pyx_n_s__longest));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__longest));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__shortest));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 33, ((PyObject *)__pyx_n_s__shortest));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__shortest));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__samples));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 34, ((PyObject *)__pyx_n_s__samples));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__samples));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__sample));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 35, ((PyObject *)__pyx_n_s__sample));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__sample));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__dict));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 36, ((PyObject *)__pyx_n_s__dict));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__dict));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__values));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 37, ((PyObject *)__pyx_n_s__values));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__values));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__idx));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 38, ((PyObject *)__pyx_n_s__idx));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__idx));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__expected));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 39, ((PyObject *)__pyx_n_s__expected));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__expected));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__value));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 40, ((PyObject *)__pyx_n_s__value));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__value));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__d));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 41, ((PyObject *)__pyx_n_s__d));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__d));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__key));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 42, ((PyObject *)__pyx_n_s__key));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__key));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__genexpr));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 43, ((PyObject *)__pyx_n_s__genexpr));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__genexpr));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__genexpr));
- PyTuple_SET_ITEM(__pyx_k_tuple_207, 44, ((PyObject *)__pyx_n_s__genexpr));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__genexpr));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_207));
- __pyx_k_codeobj_208 = (PyObject*)__Pyx_PyCode_New(3, 0, 45, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_207, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_data, 647, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_208)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_223 = PyTuple_Pack(45, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__lineparse), ((PyObject *)__pyx_n_s__cols), ((PyObject *)__pyx_n_s__chrom), ((PyObject *)__pyx_n_s__pos), ((PyObject *)__pyx_n_s__id), ((PyObject *)__pyx_n_s__ref), ((PyObject *)__pyx_n_s__c), ((PyObject *)__pyx_n_s__left), ((PyObject *)__pyx_n_s__faref_leftflank), ((PyObject *)__pyx_n_s__faref), ((PyObject *)__pyx_n_s__alt), ((PyObject *)__pyx_n_s__qual), ((PyObjec [...]
+ __Pyx_GOTREF(__pyx_k_tuple_223);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_223));
+ __pyx_k_codeobj_224 = (PyObject*)__Pyx_PyCode_New(3, 0, 45, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_223, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse_data, 650, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_224)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":857
+ /* "pysam/cvcf.pyx":860
*
*
* def write_data(self, stream, data): # <<<<<<<<<<<<<<
* required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
* for k in required:
*/
- __pyx_k_tuple_209 = PyTuple_New(10); if (unlikely(!__pyx_k_tuple_209)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_209);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__data));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 2, ((PyObject *)__pyx_n_s__data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__required));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 3, ((PyObject *)__pyx_n_s__required));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__required));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__k));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 4, ((PyObject *)__pyx_n_s__k));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__k));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__alt));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 5, ((PyObject *)__pyx_n_s__alt));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filter));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 6, ((PyObject *)__pyx_n_s__filter));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__qual));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 7, ((PyObject *)__pyx_n_s__qual));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__qual));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__output));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 8, ((PyObject *)__pyx_n_s__output));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__output));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__s));
- PyTuple_SET_ITEM(__pyx_k_tuple_209, 9, ((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__s));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_209));
- __pyx_k_codeobj_210 = (PyObject*)__Pyx_PyCode_New(3, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_209, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_data, 857, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_210)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":886
+ __pyx_k_tuple_226 = PyTuple_Pack(10, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream), ((PyObject *)__pyx_n_s__data), ((PyObject *)__pyx_n_s__required), ((PyObject *)__pyx_n_s__k), ((PyObject *)__pyx_n_s__alt), ((PyObject *)__pyx_n_s__filter), ((PyObject *)__pyx_n_s__qual), ((PyObject *)__pyx_n_s__output), ((PyObject *)__pyx_n_s__s)); if (unlikely(!__pyx_k_tuple_226)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_226);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_226));
+ __pyx_k_codeobj_227 = (PyObject*)__Pyx_PyCode_New(3, 0, 10, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_226, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write_data, 860, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_227)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":889
* stream.write( "\t".join(output) + "\n" )
*
* def _parse_header(self, stream): # <<<<<<<<<<<<<<
* self._lineno = 0
* for line in stream:
*/
- __pyx_k_tuple_211 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_211)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_211);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_211, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_211, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_211, 2, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_211));
- __pyx_k_codeobj_212 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_211, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse_header, 886, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_212)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_229 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream), ((PyObject *)__pyx_n_s__line)); if (unlikely(!__pyx_k_tuple_229)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_229);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_229));
+ __pyx_k_codeobj_230 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_229, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse_header, 889, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_230)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":899
+ /* "pysam/cvcf.pyx":902
* return line
*
* def _parse(self, line, stream): # <<<<<<<<<<<<<<
* # deal with files with header only
* if line.startswith("##"): return
*/
- __pyx_k_tuple_213 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_213)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_213);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_213, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__line));
- PyTuple_SET_ITEM(__pyx_k_tuple_213, 1, ((PyObject *)__pyx_n_s__line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__line));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_213, 2, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__d));
- PyTuple_SET_ITEM(__pyx_k_tuple_213, 3, ((PyObject *)__pyx_n_s__d));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__d));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_213));
- __pyx_k_codeobj_214 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_213, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse, 899, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_214)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":917
+ __pyx_k_tuple_232 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__line), ((PyObject *)__pyx_n_s__stream), ((PyObject *)__pyx_n_s__d)); if (unlikely(!__pyx_k_tuple_232)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_232);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_232));
+ __pyx_k_codeobj_233 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_232, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s___parse, 902, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_233)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":920
* ######################################################################################################
*
* def getsamples(self): # <<<<<<<<<<<<<<
* """ List of samples in VCF file """
* return self._samples
*/
- __pyx_k_tuple_215 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_215)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_215);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_215, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_215));
- __pyx_k_codeobj_216 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_215, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getsamples, 917, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_216)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_235 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_235)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_235);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_235));
+ __pyx_k_codeobj_236 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_235, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getsamples, 920, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_236)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":921
+ /* "pysam/cvcf.pyx":924
* return self._samples
*
* def setsamples(self,samples): # <<<<<<<<<<<<<<
* """ List of samples in VCF file """
* self._samples = samples
*/
- __pyx_k_tuple_217 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_217)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_217);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_217, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__samples));
- PyTuple_SET_ITEM(__pyx_k_tuple_217, 1, ((PyObject *)__pyx_n_s__samples));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__samples));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_217));
- __pyx_k_codeobj_218 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_217, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setsamples, 921, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_218)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_238 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__samples)); if (unlikely(!__pyx_k_tuple_238)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_238);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_238));
+ __pyx_k_codeobj_239 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_238, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setsamples, 924, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_239)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":925
+ /* "pysam/cvcf.pyx":928
* self._samples = samples
*
* def getheader(self): # <<<<<<<<<<<<<<
* """ List of header key-value pairs (strings) """
* return self._header
*/
- __pyx_k_tuple_219 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_219)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_219);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_219, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_219));
- __pyx_k_codeobj_220 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_219, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getheader, 925, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_220)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_241 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_241)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_241);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_241));
+ __pyx_k_codeobj_242 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_241, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getheader, 928, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_242)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":929
+ /* "pysam/cvcf.pyx":932
* return self._header
*
* def setheader(self,header): # <<<<<<<<<<<<<<
* """ List of header key-value pairs (strings) """
* self._header = header
*/
- __pyx_k_tuple_221 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_221)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_221);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_221, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__header));
- PyTuple_SET_ITEM(__pyx_k_tuple_221, 1, ((PyObject *)__pyx_n_s__header));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__header));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_221));
- __pyx_k_codeobj_222 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_221, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setheader, 929, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_222)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":933
+ __pyx_k_tuple_244 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__header)); if (unlikely(!__pyx_k_tuple_244)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_244);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_244));
+ __pyx_k_codeobj_245 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_244, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setheader, 932, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_245)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":936
* self._header = header
*
* def getinfo(self): # <<<<<<<<<<<<<<
* """ Dictionary of ##INFO tags, as VCF.FORMAT values """
* return self._info
*/
- __pyx_k_tuple_223 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_223)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_223);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_223, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_223));
- __pyx_k_codeobj_224 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_223, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getinfo, 933, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_224)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_247 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_247)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_247);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_247));
+ __pyx_k_codeobj_248 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_247, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getinfo, 936, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_248)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":937
+ /* "pysam/cvcf.pyx":940
* return self._info
*
* def setinfo(self,info): # <<<<<<<<<<<<<<
* """ Dictionary of ##INFO tags, as VCF.FORMAT values """
* self._info = info
*/
- __pyx_k_tuple_225 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_225)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_225);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_225, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__info));
- PyTuple_SET_ITEM(__pyx_k_tuple_225, 1, ((PyObject *)__pyx_n_s__info));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__info));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_225));
- __pyx_k_codeobj_226 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_225, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setinfo, 937, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_226)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_250 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__info)); if (unlikely(!__pyx_k_tuple_250)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_250);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_250));
+ __pyx_k_codeobj_251 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_250, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setinfo, 940, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_251)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":941
+ /* "pysam/cvcf.pyx":944
* self._info = info
*
* def getformat(self): # <<<<<<<<<<<<<<
* """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
* return self._format
*/
- __pyx_k_tuple_227 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_227)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_227);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_227, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_227));
- __pyx_k_codeobj_228 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_227, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getformat, 941, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_228)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_253 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_253)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_253);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_253));
+ __pyx_k_codeobj_254 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_253, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getformat, 944, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":945
+ /* "pysam/cvcf.pyx":948
* return self._format
*
* def setformat(self,format): # <<<<<<<<<<<<<<
* """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
* self._format = format
*/
- __pyx_k_tuple_229 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_229)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_229);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_229, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__format));
- PyTuple_SET_ITEM(__pyx_k_tuple_229, 1, ((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__format));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_229));
- __pyx_k_codeobj_230 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_229, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setformat, 945, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_230)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_256 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__format)); if (unlikely(!__pyx_k_tuple_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_256);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_256));
+ __pyx_k_codeobj_257 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_256, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setformat, 948, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":949
+ /* "pysam/cvcf.pyx":952
* self._format = format
*
* def getfilter(self): # <<<<<<<<<<<<<<
* """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
* return self._filter
*/
- __pyx_k_tuple_231 = PyTuple_New(1); if (unlikely(!__pyx_k_tuple_231)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_231);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_231, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_231));
- __pyx_k_codeobj_232 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_231, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getfilter, 949, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_232)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_259 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_259);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_259));
+ __pyx_k_codeobj_260 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_259, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__getfilter, 952, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_260)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":953
+ /* "pysam/cvcf.pyx":956
* return self._filter
*
* def setfilter(self,filter): # <<<<<<<<<<<<<<
* """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
* self._filter = filter
*/
- __pyx_k_tuple_233 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_233)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_233);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_233, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filter));
- PyTuple_SET_ITEM(__pyx_k_tuple_233, 1, ((PyObject *)__pyx_n_s__filter));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filter));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_233));
- __pyx_k_codeobj_234 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_233, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setfilter, 953, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_234)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_262 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filter)); if (unlikely(!__pyx_k_tuple_262)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_262);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_262));
+ __pyx_k_codeobj_263 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_262, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setfilter, 956, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_263)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":957
+ /* "pysam/cvcf.pyx":960
* self._filter = filter
*
* def setversion(self, version): # <<<<<<<<<<<<<<
* if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
* self._version = version
*/
- __pyx_k_tuple_235 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_235)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_235);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_235, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__version));
- PyTuple_SET_ITEM(__pyx_k_tuple_235, 1, ((PyObject *)__pyx_n_s__version));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__version));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_235));
- __pyx_k_codeobj_236 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_235, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setversion, 957, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_236)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_265 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__version)); if (unlikely(!__pyx_k_tuple_265)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_265);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_265));
+ __pyx_k_codeobj_266 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_265, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setversion, 960, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_266)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":961
+ /* "pysam/cvcf.pyx":964
* self._version = version
*
* def setregions(self, regions): # <<<<<<<<<<<<<<
* self._regions = regions
*
*/
- __pyx_k_tuple_237 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_237)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_237);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_237, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__regions));
- PyTuple_SET_ITEM(__pyx_k_tuple_237, 1, ((PyObject *)__pyx_n_s__regions));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__regions));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_237));
- __pyx_k_codeobj_238 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_237, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setregions, 961, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_238)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_268 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__regions)); if (unlikely(!__pyx_k_tuple_268)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_268);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_268));
+ __pyx_k_codeobj_269 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_268, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setregions, 964, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_269)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":964
+ /* "pysam/cvcf.pyx":967
* self._regions = regions
*
* def setreference(self, ref): # <<<<<<<<<<<<<<
* """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
* self._reference = ref
*/
- __pyx_k_tuple_239 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_239)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_239);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_239, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ref));
- PyTuple_SET_ITEM(__pyx_k_tuple_239, 1, ((PyObject *)__pyx_n_s__ref));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_239));
- __pyx_k_codeobj_240 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_239, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setreference, 964, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_240)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_271 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__ref)); if (unlikely(!__pyx_k_tuple_271)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_271);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_271));
+ __pyx_k_codeobj_272 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_271, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__setreference, 967, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_272)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":968
+ /* "pysam/cvcf.pyx":971
* self._reference = ref
*
* def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
* try: self._ignored_errors.add(self.__dict__[errorstring])
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*/
- __pyx_k_tuple_241 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_241)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_241);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_241, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__errorstring));
- PyTuple_SET_ITEM(__pyx_k_tuple_241, 1, ((PyObject *)__pyx_n_s__errorstring));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorstring));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_241));
- __pyx_k_codeobj_242 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_241, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__ignoreerror, 968, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_242)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_274 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__errorstring)); if (unlikely(!__pyx_k_tuple_274)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_274);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_274));
+ __pyx_k_codeobj_275 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_274, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__ignoreerror, 971, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_275)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":972
+ /* "pysam/cvcf.pyx":975
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def warnerror(self, errorstring): # <<<<<<<<<<<<<<
* try: self._warn_errors.add(self.__dict__[errorstring])
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*/
- __pyx_k_tuple_243 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_243)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_243);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_243, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__errorstring));
- PyTuple_SET_ITEM(__pyx_k_tuple_243, 1, ((PyObject *)__pyx_n_s__errorstring));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__errorstring));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_243));
- __pyx_k_codeobj_244 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_243, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__warnerror, 972, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_244)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_277 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__errorstring)); if (unlikely(!__pyx_k_tuple_277)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_277);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_277));
+ __pyx_k_codeobj_278 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_277, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__warnerror, 975, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_278)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":976
+ /* "pysam/cvcf.pyx":979
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def parse(self, stream): # <<<<<<<<<<<<<<
* """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
* last_line = self._parse_header(stream)
*/
- __pyx_k_tuple_245 = PyTuple_New(3); if (unlikely(!__pyx_k_tuple_245)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_245);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_245, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_245, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__last_line));
- PyTuple_SET_ITEM(__pyx_k_tuple_245, 2, ((PyObject *)__pyx_n_s__last_line));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__last_line));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_245));
- __pyx_k_codeobj_246 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_245, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse, 976, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_246)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":983
+ __pyx_k_tuple_280 = PyTuple_Pack(3, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream), ((PyObject *)__pyx_n_s__last_line)); if (unlikely(!__pyx_k_tuple_280)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_280);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_280));
+ __pyx_k_codeobj_281 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_280, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__parse, 979, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_281)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":986
* return self._parse(last_line, stream)
*
* def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
* """ Writes a VCF file to a stream, using a data generator (or list) """
* self.write_header(stream)
*/
- __pyx_k_tuple_247 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_247)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_247);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_247, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_247, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__datagenerator));
- PyTuple_SET_ITEM(__pyx_k_tuple_247, 2, ((PyObject *)__pyx_n_s__datagenerator));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__datagenerator));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__data));
- PyTuple_SET_ITEM(__pyx_k_tuple_247, 3, ((PyObject *)__pyx_n_s__data));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__data));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_247));
- __pyx_k_codeobj_248 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_247, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write, 983, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_248)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_283 = PyTuple_Pack(4, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream), ((PyObject *)__pyx_n_s__datagenerator), ((PyObject *)__pyx_n_s__data)); if (unlikely(!__pyx_k_tuple_283)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_283);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_283));
+ __pyx_k_codeobj_284 = (PyObject*)__Pyx_PyCode_New(3, 0, 4, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_283, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__write, 986, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_284)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":989
+ /* "pysam/cvcf.pyx":992
* for data in datagenerator: self.write_data(stream,data)
*
* def writeheader(self, stream): # <<<<<<<<<<<<<<
* """ Writes a VCF header """
* self.write_header(stream)
*/
- __pyx_k_tuple_249 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_249)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_249);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_249, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__stream));
- PyTuple_SET_ITEM(__pyx_k_tuple_249, 1, ((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__stream));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_249));
- __pyx_k_codeobj_250 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_249, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__writeheader, 989, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_250)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_286 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__stream)); if (unlikely(!__pyx_k_tuple_286)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_286);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_286));
+ __pyx_k_codeobj_287 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_286, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__writeheader, 992, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_287)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":994
+ /* "pysam/cvcf.pyx":997
* self.write_heading(stream)
*
* def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
* """ Utility function: compares two calls for equality """
* # a variant should always be assigned to a unique position, one base before
*/
- __pyx_k_tuple_251 = PyTuple_New(7); if (unlikely(!__pyx_k_tuple_251)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_251);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__pos1));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 1, ((PyObject *)__pyx_n_s__pos1));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos1));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ref1));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 2, ((PyObject *)__pyx_n_s__ref1));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref1));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__alt1));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 3, ((PyObject *)__pyx_n_s__alt1));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt1));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__pos2));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 4, ((PyObject *)__pyx_n_s__pos2));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__pos2));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__ref2));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 5, ((PyObject *)__pyx_n_s__ref2));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__ref2));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__alt2));
- PyTuple_SET_ITEM(__pyx_k_tuple_251, 6, ((PyObject *)__pyx_n_s__alt2));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__alt2));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_251));
- __pyx_k_codeobj_252 = (PyObject*)__Pyx_PyCode_New(7, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_251, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__compare_calls, 994, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_252)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
-
- /* "pysam/cvcf.pyx":1016
+ __pyx_k_tuple_289 = PyTuple_Pack(7, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__pos1), ((PyObject *)__pyx_n_s__ref1), ((PyObject *)__pyx_n_s__alt1), ((PyObject *)__pyx_n_s__pos2), ((PyObject *)__pyx_n_s__ref2), ((PyObject *)__pyx_n_s__alt2)); if (unlikely(!__pyx_k_tuple_289)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_289);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_289));
+ __pyx_k_codeobj_290 = (PyObject*)__Pyx_PyCode_New(7, 0, 7, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_289, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__compare_calls, 997, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_290)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "pysam/cvcf.pyx":1019
* ###########################################################################################################
*
* def connect( self, filename ): # <<<<<<<<<<<<<<
* '''connect to tabix file.'''
* self.tabixfile = pysam.Tabixfile( filename )
*/
- __pyx_k_tuple_253 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_253)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_253);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_253, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__filename));
- PyTuple_SET_ITEM(__pyx_k_tuple_253, 1, ((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__filename));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_253));
- __pyx_k_codeobj_254 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_253, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__connect, 1016, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_254)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_292 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__filename)); if (unlikely(!__pyx_k_tuple_292)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_292);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_292));
+ __pyx_k_codeobj_293 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_292, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__connect, 1019, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_293)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":1021
+ /* "pysam/cvcf.pyx":1024
* self._parse_header(self.tabixfile.header)
*
* def fetch(self, # <<<<<<<<<<<<<<
* reference = None,
* start = None,
*/
- __pyx_k_tuple_255 = PyTuple_New(5); if (unlikely(!__pyx_k_tuple_255)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_255);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_255, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__reference));
- PyTuple_SET_ITEM(__pyx_k_tuple_255, 1, ((PyObject *)__pyx_n_s__reference));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__reference));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__start));
- PyTuple_SET_ITEM(__pyx_k_tuple_255, 2, ((PyObject *)__pyx_n_s__start));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__start));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__end));
- PyTuple_SET_ITEM(__pyx_k_tuple_255, 3, ((PyObject *)__pyx_n_s__end));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__end));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__region));
- PyTuple_SET_ITEM(__pyx_k_tuple_255, 4, ((PyObject *)__pyx_n_s__region));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__region));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_255));
- __pyx_k_codeobj_256 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_255, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__fetch, 1021, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_256)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_k_tuple_257 = PyTuple_New(4); if (unlikely(!__pyx_k_tuple_257)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_257);
- __Pyx_INCREF(((PyObject *)Py_None));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 0, ((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)Py_None));
- __Pyx_INCREF(((PyObject *)Py_None));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 1, ((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)Py_None));
- __Pyx_INCREF(((PyObject *)Py_None));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 2, ((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)Py_None));
- __Pyx_INCREF(((PyObject *)Py_None));
- PyTuple_SET_ITEM(__pyx_k_tuple_257, 3, ((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)Py_None));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_257));
+ __pyx_k_tuple_295 = PyTuple_Pack(5, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__reference), ((PyObject *)__pyx_n_s__start), ((PyObject *)__pyx_n_s__end), ((PyObject *)__pyx_n_s__region)); if (unlikely(!__pyx_k_tuple_295)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_295);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_295));
+ __pyx_k_codeobj_296 = (PyObject*)__Pyx_PyCode_New(5, 0, 5, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_295, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__fetch, 1024, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_296)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_297 = PyTuple_Pack(4, ((PyObject *)Py_None), ((PyObject *)Py_None), ((PyObject *)Py_None), ((PyObject *)Py_None)); if (unlikely(!__pyx_k_tuple_297)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_297);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_297));
- /* "pysam/cvcf.pyx":1030
+ /* "pysam/cvcf.pyx":1033
* return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) )
*
* def validate( self, record ): # <<<<<<<<<<<<<<
* '''validate vcf record.
*
*/
- __pyx_k_tuple_258 = PyTuple_New(2); if (unlikely(!__pyx_k_tuple_258)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_k_tuple_258);
- __Pyx_INCREF(((PyObject *)__pyx_n_s__self));
- PyTuple_SET_ITEM(__pyx_k_tuple_258, 0, ((PyObject *)__pyx_n_s__self));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__self));
- __Pyx_INCREF(((PyObject *)__pyx_n_s__record));
- PyTuple_SET_ITEM(__pyx_k_tuple_258, 1, ((PyObject *)__pyx_n_s__record));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s__record));
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_258));
- __pyx_k_codeobj_259 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_258, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__validate, 1030, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_259)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_k_tuple_299 = PyTuple_Pack(2, ((PyObject *)__pyx_n_s__self), ((PyObject *)__pyx_n_s__record)); if (unlikely(!__pyx_k_tuple_299)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_299);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_299));
+ __pyx_k_codeobj_300 = (PyObject*)__Pyx_PyCode_New(2, 0, 2, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_299, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_134, __pyx_n_s__validate, 1033, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_300)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -26441,16 +26038,23 @@ PyMODINIT_FUNC PyInit_cvcf(void)
#endif
/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("cvcf"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
#else
__pyx_m = PyModule_Create(&__pyx_moduledef);
#endif
- if (!__pyx_m) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
+ if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if PY_MAJOR_VERSION >= 3
+ {
+ PyObject *modules = PyImport_GetModuleDict(); if (unlikely(!modules)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!PyDict_GetItemString(modules, "pysam.cvcf")) {
+ if (unlikely(PyDict_SetItemString(modules, "pysam.cvcf", __pyx_m) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ }
+ #endif
+ __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -26471,20 +26075,20 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__pyx_vtable_5pysam_4cvcf_VCFRecord.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
__pyx_vtable_5pysam_4cvcf_VCFRecord.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_4cvcf_9VCFRecord_update;
__pyx_type_5pysam_4cvcf_VCFRecord.tp_base = __pyx_ptype_5pysam_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_5pysam_4cvcf_VCFRecord.tp_dict, __pyx_vtabptr_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_4cvcf_VCFRecord.tp_dict, __pyx_vtabptr_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 95; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf_VCFRecord = &__pyx_type_5pysam_4cvcf_VCFRecord;
__pyx_ptype_5pysam_6ctabix_Parser = __Pyx_ImportType("pysam.ctabix", "Parser", sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_type_5pysam_4cvcf_asVCFRecord.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 229; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf_asVCFRecord = &__pyx_type_5pysam_4cvcf_asVCFRecord;
- if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = &__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data;
- if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 793; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
- if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse;
/*--- Type import code ---*/
__pyx_ptype_5pysam_6ctabix_Tabixfile = __Pyx_ImportType("pysam.ctabix", "Tabixfile", sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -26577,7 +26181,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
* from operator import itemgetter
* import sys, re, copy, bisect # <<<<<<<<<<<<<<
*
- * from pysam cimport ctabix
+ * cimport ctabix
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -26596,268 +26200,268 @@ PyMODINIT_FUNC PyInit_cvcf(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__bisect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":52
- * from pysam cimport ctabix
- * from pysam cimport TabProxies
+ /* "pysam/cvcf.pyx":53
+ * cimport TabProxies
+ *
* import pysam # <<<<<<<<<<<<<<
*
* gtsRegEx = re.compile("[|/\\\\]")
*/
- __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__pysam), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__pysam), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__pysam, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__pysam, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":54
+ /* "pysam/cvcf.pyx":55
* import pysam
*
* gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<<
* alleleRegEx = re.compile('^[ACGTN]+$')
*
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_129), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_129), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gtsRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gtsRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":55
+ /* "pysam/cvcf.pyx":56
*
* gtsRegEx = re.compile("[|/\\\\]")
* alleleRegEx = re.compile('^[ACGTN]+$') # <<<<<<<<<<<<<<
*
* # Utility function. Uses 0-based coordinates
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__re); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__compile); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_131), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_k_tuple_131), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__alleleRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__alleleRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 56; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":58
+ /* "pysam/cvcf.pyx":59
*
* # Utility function. Uses 0-based coordinates
* def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
* # obtain sequence from .fa file, without truncation
* if end<=start: return ""
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_1get_sequence, NULL, __pyx_n_s_135); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_1get_sequence, NULL, __pyx_n_s_135); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__get_sequence, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__get_sequence, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":68
+ /* "pysam/cvcf.pyx":69
*
* # Utility function. Parses a region string
* def parse_regions( string ): # <<<<<<<<<<<<<<
* result = []
* for r in string.split(','):
*/
- __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3parse_regions, NULL, __pyx_n_s_135); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3parse_regions, NULL, __pyx_n_s_135); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__parse_regions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__parse_regions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":86
+ /* "pysam/cvcf.pyx":87
*
*
* FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<<
*
* ###########################################################################################################
*/
- __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__namedtuple); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__namedtuple); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyObject_Call(__pyx_t_1, ((PyObject *)__pyx_k_tuple_139), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__FORMAT, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__FORMAT, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":237
+ /* "pysam/cvcf.pyx":240
* return r
*
* class VCF(object): # <<<<<<<<<<<<<<
*
* # types
*/
- __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyDict_New(); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- /* "pysam/cvcf.pyx":240
+ /* "pysam/cvcf.pyx":243
*
* # types
* NT_UNKNOWN = 0 # <<<<<<<<<<<<<<
* NT_NUMBER = 1
* NT_ALLELES = 2
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_UNKNOWN, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_UNKNOWN, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":241
+ /* "pysam/cvcf.pyx":244
* # types
* NT_UNKNOWN = 0
* NT_NUMBER = 1 # <<<<<<<<<<<<<<
* NT_ALLELES = 2
* NT_NR_ALLELES = 3
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NUMBER, __pyx_int_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NUMBER, __pyx_int_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":242
+ /* "pysam/cvcf.pyx":245
* NT_UNKNOWN = 0
* NT_NUMBER = 1
* NT_ALLELES = 2 # <<<<<<<<<<<<<<
* NT_NR_ALLELES = 3
* NT_GENOTYPES = 4
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_ALLELES, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_ALLELES, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":243
+ /* "pysam/cvcf.pyx":246
* NT_NUMBER = 1
* NT_ALLELES = 2
* NT_NR_ALLELES = 3 # <<<<<<<<<<<<<<
* NT_GENOTYPES = 4
* NT_PHASED_GENOTYPES = 5
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NR_ALLELES, __pyx_int_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NR_ALLELES, __pyx_int_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":244
+ /* "pysam/cvcf.pyx":247
* NT_ALLELES = 2
* NT_NR_ALLELES = 3
* NT_GENOTYPES = 4 # <<<<<<<<<<<<<<
* NT_PHASED_GENOTYPES = 5
*
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_GENOTYPES, __pyx_int_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_GENOTYPES, __pyx_int_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":245
+ /* "pysam/cvcf.pyx":248
* NT_NR_ALLELES = 3
* NT_GENOTYPES = 4
* NT_PHASED_GENOTYPES = 5 # <<<<<<<<<<<<<<
*
* _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier",
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_PHASED_GENOTYPES, __pyx_int_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_PHASED_GENOTYPES, __pyx_int_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 248; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":247
+ /* "pysam/cvcf.pyx":250
* NT_PHASED_GENOTYPES = 5
*
* _errors = { 0:"UNKNOWN_FORMAT_STRING:Unknown file format identifier", # <<<<<<<<<<<<<<
* 1:"BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string",
* 2:"BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s",
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_0, ((PyObject *)__pyx_kp_s_140)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_1, ((PyObject *)__pyx_kp_s_141)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_2, ((PyObject *)__pyx_kp_s_142)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_3, ((PyObject *)__pyx_kp_s_143)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_4, ((PyObject *)__pyx_kp_s_144)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_5, ((PyObject *)__pyx_kp_s_145)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_6, ((PyObject *)__pyx_kp_s_146)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_7, ((PyObject *)__pyx_kp_s_147)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_8, ((PyObject *)__pyx_kp_s_148)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_9, ((PyObject *)__pyx_kp_s_149)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_10, ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_11, ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_12, ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_13, ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_14, ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_15, ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_16, ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_17, ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_18, ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_19, ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_20, ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_21, ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_22, ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_23, ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_24, ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_25, ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_26, ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_27, ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_28, ((PyObject *)__pyx_kp_s_168)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_29, ((PyObject *)__pyx_kp_s_169)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_30, ((PyObject *)__pyx_kp_s_170)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_31, ((PyObject *)__pyx_kp_s_171)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_32, ((PyObject *)__pyx_kp_s_172)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyDict_SetItem(__pyx_t_1, __pyx_int_33, ((PyObject *)__pyx_kp_s_173)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_0, ((PyObject *)__pyx_kp_s_140)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_1, ((PyObject *)__pyx_kp_s_141)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_2, ((PyObject *)__pyx_kp_s_142)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_3, ((PyObject *)__pyx_kp_s_143)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_4, ((PyObject *)__pyx_kp_s_144)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_5, ((PyObject *)__pyx_kp_s_145)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_6, ((PyObject *)__pyx_kp_s_146)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_7, ((PyObject *)__pyx_kp_s_147)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_8, ((PyObject *)__pyx_kp_s_148)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_9, ((PyObject *)__pyx_kp_s_149)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_10, ((PyObject *)__pyx_kp_s_150)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_11, ((PyObject *)__pyx_kp_s_151)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_12, ((PyObject *)__pyx_kp_s_152)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_13, ((PyObject *)__pyx_kp_s_153)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_14, ((PyObject *)__pyx_kp_s_154)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_15, ((PyObject *)__pyx_kp_s_155)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_16, ((PyObject *)__pyx_kp_s_156)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_17, ((PyObject *)__pyx_kp_s_157)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_18, ((PyObject *)__pyx_kp_s_158)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_19, ((PyObject *)__pyx_kp_s_159)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_20, ((PyObject *)__pyx_kp_s_160)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_21, ((PyObject *)__pyx_kp_s_161)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_22, ((PyObject *)__pyx_kp_s_162)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_23, ((PyObject *)__pyx_kp_s_163)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_24, ((PyObject *)__pyx_kp_s_164)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_25, ((PyObject *)__pyx_kp_s_165)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_26, ((PyObject *)__pyx_kp_s_166)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_27, ((PyObject *)__pyx_kp_s_167)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_28, ((PyObject *)__pyx_kp_s_168)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_29, ((PyObject *)__pyx_kp_s_169)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_30, ((PyObject *)__pyx_kp_s_170)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_31, ((PyObject *)__pyx_kp_s_171)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_32, ((PyObject *)__pyx_kp_s_172)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyDict_SetItem(__pyx_t_1, __pyx_int_33, ((PyObject *)__pyx_kp_s_173)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 250; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":284
+ /* "pysam/cvcf.pyx":287
*
* # tag-value pairs; tags are not unique; does not include fileformat, INFO, FILTER or FORMAT fields
* _header = [] # <<<<<<<<<<<<<<
*
* # version number; 33=v3.3; 40=v4.0
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___header, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___header, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":287
+ /* "pysam/cvcf.pyx":290
*
* # version number; 33=v3.3; 40=v4.0
* _version = 40 # <<<<<<<<<<<<<<
*
* # info, filter and format data
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___version, __pyx_int_40) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":290
+ /* "pysam/cvcf.pyx":293
*
* # info, filter and format data
* _info = {} # <<<<<<<<<<<<<<
* _filter = {}
* _format = {}
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___info, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 290; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___info, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 293; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":291
+ /* "pysam/cvcf.pyx":294
* # info, filter and format data
* _info = {}
* _filter = {} # <<<<<<<<<<<<<<
* _format = {}
*
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___filter, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 291; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___filter, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 294; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":292
+ /* "pysam/cvcf.pyx":295
* _info = {}
* _filter = {}
* _format = {} # <<<<<<<<<<<<<<
*
* # header; and required columns
*/
- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___format, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 292; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___format, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":295
+ /* "pysam/cvcf.pyx":298
*
* # header; and required columns
* _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"] # <<<<<<<<<<<<<<
* _samples = []
*
*/
- __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(9); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(((PyObject *)__pyx_n_s__CHROM));
PyList_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_n_s__CHROM));
@@ -26886,677 +26490,677 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__Pyx_INCREF(((PyObject *)__pyx_n_s__FORMAT));
PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s__FORMAT));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__FORMAT));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___required, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 295; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___required, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 298; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":296
+ /* "pysam/cvcf.pyx":299
* # header; and required columns
* _required = ["CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO","FORMAT"]
* _samples = [] # <<<<<<<<<<<<<<
*
* # control behaviour
*/
- __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyList_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___samples, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___samples, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":299
+ /* "pysam/cvcf.pyx":302
*
* # control behaviour
* _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD # <<<<<<<<<<<<<<
* _warn_errors = set([])
* _leftalign = False
*/
- __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (unlikely(PySet_Add(__pyx_t_1, __pyx_int_11) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (unlikely(PySet_Add(__pyx_t_1, __pyx_int_31) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___ignored_errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 299; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PySet_Add(__pyx_t_1, __pyx_int_11) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (unlikely(PySet_Add(__pyx_t_1, __pyx_int_31) < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___ignored_errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":300
+ /* "pysam/cvcf.pyx":303
* # control behaviour
* _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD
* _warn_errors = set([]) # <<<<<<<<<<<<<<
* _leftalign = False
*
*/
- __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PySet_New(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_1));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___warn_errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 300; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___warn_errors, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 303; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":301
+ /* "pysam/cvcf.pyx":304
* _ignored_errors = set([11,31]) # ERROR_UNKNOWN_KEY, ERROR_ZERO_FOR_NON_FLAG_FIELD
* _warn_errors = set([])
* _leftalign = False # <<<<<<<<<<<<<<
*
* # reference sequence
*/
- __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___leftalign, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 301; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___leftalign, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":304
+ /* "pysam/cvcf.pyx":307
*
* # reference sequence
* _reference = None # <<<<<<<<<<<<<<
*
* # regions to include; None includes everything
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___reference, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___reference, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":307
+ /* "pysam/cvcf.pyx":310
*
* # regions to include; None includes everything
* _regions = None # <<<<<<<<<<<<<<
*
* # statefull stuff
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___regions, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 307; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___regions, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":310
+ /* "pysam/cvcf.pyx":313
*
* # statefull stuff
* _lineno = -1 # <<<<<<<<<<<<<<
* _line = None
* _lines = None
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___lineno, __pyx_int_neg_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 310; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___lineno, __pyx_int_neg_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 313; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":311
+ /* "pysam/cvcf.pyx":314
* # statefull stuff
* _lineno = -1
* _line = None # <<<<<<<<<<<<<<
* _lines = None
*
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___line, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 311; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___line, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":312
+ /* "pysam/cvcf.pyx":315
* _lineno = -1
* _line = None
* _lines = None # <<<<<<<<<<<<<<
*
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
*/
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___lines, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 312; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___lines, Py_None) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 315; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/cvcf.pyx":314
+ /* "pysam/cvcf.pyx":317
* _lines = None
*
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False): # <<<<<<<<<<<<<<
* # make error identifiers accessible by name
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_1__init__, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_175)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_1__init__, 0, __pyx_n_s_176, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_175)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_CyFunction_Defaults(__pyx_defaults, __pyx_t_1)->__pyx_arg_leftalign = __pyx_t_3;
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_85__defaults__);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s____init__, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s____init__, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":335
+ /* "pysam/cvcf.pyx":338
* self._lines = lines
*
* def error(self,line,error,opt=None): # <<<<<<<<<<<<<<
* if error in self._ignored_errors: return
* errorlabel, errorstring = self._errors[error].split(':')
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_3error, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_177)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_3error, 0, __pyx_n_s_180, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_178)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_178));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__error, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 335; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_179));
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__error, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 338; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":344
+ /* "pysam/cvcf.pyx":347
* raise ValueError(errorstring)
*
* def parse_format(self,line,format,filter=False): # <<<<<<<<<<<<<<
* if self._version == 40:
* if not format.startswith('<'):
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_5parse_format, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_180)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_5parse_format, 0, __pyx_n_s_183, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_182)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults1), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults1), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_CyFunction_Defaults(__pyx_defaults1, __pyx_t_1)->__pyx_arg_filter = __pyx_t_3;
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_87__defaults__);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_format, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 344; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_format, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 347; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":416
+ /* "pysam/cvcf.pyx":419
* return FORMAT(data['id'],t,n,data['type'],data['descr'],data['missing'])
*
* def format_format( self, fmt, filter=False ): # <<<<<<<<<<<<<<
* values = [('ID',fmt.id)]
* if fmt.number != None and not filter:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_7format_format, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_182)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_7format_format, 0, __pyx_n_s_186, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_185)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults2), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults2), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_CyFunction_Defaults(__pyx_defaults2, __pyx_t_1)->__pyx_arg_filter = __pyx_t_3;
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_89__defaults__);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__format_format, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 416; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__format_format, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 419; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":436
+ /* "pysam/cvcf.pyx":439
* return format
*
* def get_expected(self, format, formatdict, alt): # <<<<<<<<<<<<<<
* fmt = formatdict[format]
* if fmt.numbertype == self.NT_UNKNOWN: return -1
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_9get_expected, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_184)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_9get_expected, 0, __pyx_n_s_189, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_188)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__get_expected, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__get_expected, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":447
+ /* "pysam/cvcf.pyx":450
*
*
* def _add_definition(self, formatdict, key, data, line ): # <<<<<<<<<<<<<<
* if key in formatdict: return
* self.error(line,self.ERROR_UNKNOWN_KEY,key)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_11_add_definition, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_186)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_11_add_definition, 0, __pyx_n_s_192, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_191)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___add_definition, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 447; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___add_definition, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 450; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":464
+ /* "pysam/cvcf.pyx":467
*
* # todo: trim trailing missing values
* def format_formatdata( self, data, format, key=True, value=True, separator=":" ): # <<<<<<<<<<<<<<
* output, sdata = [], []
* if type(data) == type([]): # for FORMAT field, make data with dummy values
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_13format_formatdata, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_188)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_13format_formatdata, 0, __pyx_n_s_195, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_194)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults3), 2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults3), 2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_t_1)->__pyx_arg_key = __pyx_t_3;
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
- __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyBool_FromLong(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_CyFunction_Defaults(__pyx_defaults3, __pyx_t_1)->__pyx_arg_value = __pyx_t_3;
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_91__defaults__);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__format_formatdata, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 464; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__format_formatdata, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 467; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":498
+ /* "pysam/cvcf.pyx":501
*
*
* def enter_default_format(self): # <<<<<<<<<<<<<<
* for f in [FORMAT('GT',self.NT_NUMBER,1,'String','Genotype','.'),
* FORMAT('DP',self.NT_NUMBER,1,'Integer','Read depth at this position for this sample',-1),
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_15enter_default_format, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_190)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_15enter_default_format, 0, __pyx_n_s_198, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_197)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s_121, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 498; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s_121, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 501; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":517
+ /* "pysam/cvcf.pyx":520
* self._format[f.id] = f
*
* def parse_header( self, line ): # <<<<<<<<<<<<<<
* assert line.startswith('##')
* elts = line[2:].split('=')
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_17parse_header, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_192)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_17parse_header, 0, __pyx_n_s_201, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_200)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 517; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 520; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":546
+ /* "pysam/cvcf.pyx":549
*
*
* def write_header( self, stream ): # <<<<<<<<<<<<<<
* stream.write("##fileformat=VCFv%s.%s\n" % (self._version // 10, self._version % 10))
* for key,value in self._header: stream.write("##%s=%s\n" % (key,value))
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_19write_header, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_194)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_19write_header, 0, __pyx_n_s_204, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_203)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 549; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":553
+ /* "pysam/cvcf.pyx":556
*
*
* def parse_heading( self, line ): # <<<<<<<<<<<<<<
* assert line.startswith('#')
* assert not line.startswith('##')
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_21parse_heading, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_196)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_21parse_heading, 0, __pyx_n_s_207, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_206)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_heading, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 553; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_heading, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 556; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":581
+ /* "pysam/cvcf.pyx":584
* self._sample2column = dict( [(y,x+9) for x,y in enumerate( self._samples ) ] )
*
* def write_heading( self, stream ): # <<<<<<<<<<<<<<
* stream.write("#" + "\t".join(self._required + self._samples) + "\n")
*
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_23write_heading, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_198)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_23write_heading, 0, __pyx_n_s_210, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_209)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_heading, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 581; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_heading, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":584
+ /* "pysam/cvcf.pyx":587
* stream.write("#" + "\t".join(self._required + self._samples) + "\n")
*
* def convertGT(self, GTstring): # <<<<<<<<<<<<<<
* if GTstring == ".": return ["."]
* try:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_25convertGT, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_200)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_25convertGT, 0, __pyx_n_s_213, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_212)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__convertGT, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__convertGT, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 587; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":596
+ /* "pysam/cvcf.pyx":599
* return [".","|","."]
*
* def convertGTback(self, GTdata): # <<<<<<<<<<<<<<
* return ''.join(map(str,GTdata))
*
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_27convertGTback, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_202)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_27convertGTback, 0, __pyx_n_s_216, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_215)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__convertGTback, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 596; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__convertGTback, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":599
+ /* "pysam/cvcf.pyx":602
* return ''.join(map(str,GTdata))
*
* def parse_formatdata( self, key, value, formatdict, line ): # <<<<<<<<<<<<<<
* # To do: check that the right number of values is present
* f = formatdict.get(key,None)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_29parse_formatdata, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_204)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_29parse_formatdata, 0, __pyx_n_s_219, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_218)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_formatdata, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 599; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_formatdata, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 602; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":641
+ /* "pysam/cvcf.pyx":644
* self.error(line,self.ERROR_INFO_STRING)
*
* def inregion(self, chrom, pos): # <<<<<<<<<<<<<<
* if not self._regions: return True
* for r in self._regions:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_31inregion, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_206)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_31inregion, 0, __pyx_n_s_222, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_221)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__inregion, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 641; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__inregion, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":647
+ /* "pysam/cvcf.pyx":650
* return False
*
* def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
* cols = line.split('\t')
* if len(cols) != len(self._samples)+9:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_33parse_data, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_208)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_33parse_data, 0, __pyx_n_s_225, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_224)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults4), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (!__Pyx_CyFunction_InitDefaults(__pyx_t_1, sizeof(__pyx_defaults4), 1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_PyBool_FromLong(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_CyFunction_Defaults(__pyx_defaults4, __pyx_t_1)->__pyx_arg_lineparse = __pyx_t_3;
__Pyx_GIVEREF(__pyx_t_3);
__pyx_t_3 = 0;
__Pyx_CyFunction_SetDefaultsGetter(__pyx_t_1, __pyx_pf_5pysam_4cvcf_3VCF_93__defaults__);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 650; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":857
+ /* "pysam/cvcf.pyx":860
*
*
* def write_data(self, stream, data): # <<<<<<<<<<<<<<
* required = ['chrom','pos','id','ref','alt','qual','filter','info','format'] + self._samples
* for k in required:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_35write_data, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_210)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_35write_data, 0, __pyx_n_s_228, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_227)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write_data, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 860; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":886
+ /* "pysam/cvcf.pyx":889
* stream.write( "\t".join(output) + "\n" )
*
* def _parse_header(self, stream): # <<<<<<<<<<<<<<
* self._lineno = 0
* for line in stream:
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_37_parse_header, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_212)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_37_parse_header, 0, __pyx_n_s_231, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_230)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___parse_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___parse_header, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":899
+ /* "pysam/cvcf.pyx":902
* return line
*
* def _parse(self, line, stream): # <<<<<<<<<<<<<<
* # deal with files with header only
* if line.startswith("##"): return
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_39_parse, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_214)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_39_parse, 0, __pyx_n_s_234, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_233)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s___parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 902; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":917
+ /* "pysam/cvcf.pyx":920
* ######################################################################################################
*
* def getsamples(self): # <<<<<<<<<<<<<<
* """ List of samples in VCF file """
* return self._samples
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_42getsamples, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_216)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_42getsamples, 0, __pyx_n_s_237, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_236)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getsamples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 917; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getsamples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 920; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":921
+ /* "pysam/cvcf.pyx":924
* return self._samples
*
* def setsamples(self,samples): # <<<<<<<<<<<<<<
* """ List of samples in VCF file """
* self._samples = samples
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_44setsamples, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_218)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_44setsamples, 0, __pyx_n_s_240, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_239)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setsamples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 921; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setsamples, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 924; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":925
+ /* "pysam/cvcf.pyx":928
* self._samples = samples
*
* def getheader(self): # <<<<<<<<<<<<<<
* """ List of header key-value pairs (strings) """
* return self._header
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_46getheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_220)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_46getheader, 0, __pyx_n_s_243, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_242)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 925; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":929
+ /* "pysam/cvcf.pyx":932
* return self._header
*
* def setheader(self,header): # <<<<<<<<<<<<<<
* """ List of header key-value pairs (strings) """
* self._header = header
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_48setheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_222)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_48setheader, 0, __pyx_n_s_246, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_245)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 929; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 932; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":933
+ /* "pysam/cvcf.pyx":936
* self._header = header
*
* def getinfo(self): # <<<<<<<<<<<<<<
* """ Dictionary of ##INFO tags, as VCF.FORMAT values """
* return self._info
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_50getinfo, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_224)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_50getinfo, 0, __pyx_n_s_249, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_248)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getinfo, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 933; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getinfo, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 936; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":937
+ /* "pysam/cvcf.pyx":940
* return self._info
*
* def setinfo(self,info): # <<<<<<<<<<<<<<
* """ Dictionary of ##INFO tags, as VCF.FORMAT values """
* self._info = info
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_52setinfo, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_226)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_52setinfo, 0, __pyx_n_s_252, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_251)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setinfo, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 937; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setinfo, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":941
+ /* "pysam/cvcf.pyx":944
* self._info = info
*
* def getformat(self): # <<<<<<<<<<<<<<
* """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
* return self._format
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_54getformat, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_228)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_54getformat, 0, __pyx_n_s_255, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_254)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getformat, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 941; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getformat, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 944; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":945
+ /* "pysam/cvcf.pyx":948
* return self._format
*
* def setformat(self,format): # <<<<<<<<<<<<<<
* """ Dictionary of ##FORMAT tags, as VCF.FORMAT values """
* self._format = format
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_56setformat, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_230)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_56setformat, 0, __pyx_n_s_258, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_257)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setformat, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 945; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setformat, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 948; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":949
+ /* "pysam/cvcf.pyx":952
* self._format = format
*
* def getfilter(self): # <<<<<<<<<<<<<<
* """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
* return self._filter
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_58getfilter, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_232)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_58getfilter, 0, __pyx_n_s_261, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_260)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getfilter, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 949; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__getfilter, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 952; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":953
+ /* "pysam/cvcf.pyx":956
* return self._filter
*
* def setfilter(self,filter): # <<<<<<<<<<<<<<
* """ Dictionary of ##FILTER tags, as VCF.FORMAT values """
* self._filter = filter
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_60setfilter, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_234)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_60setfilter, 0, __pyx_n_s_264, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_263)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setfilter, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 953; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setfilter, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 956; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":957
+ /* "pysam/cvcf.pyx":960
* self._filter = filter
*
* def setversion(self, version): # <<<<<<<<<<<<<<
* if version != 33 and version != 40: raise ValueError("Can only handle v3.3 and v4.0 VCF files")
* self._version = version
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_62setversion, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_236)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_62setversion, 0, __pyx_n_s_267, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_266)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setversion, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 957; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setversion, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 960; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":961
+ /* "pysam/cvcf.pyx":964
* self._version = version
*
* def setregions(self, regions): # <<<<<<<<<<<<<<
* self._regions = regions
*
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_64setregions, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_238)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_64setregions, 0, __pyx_n_s_270, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_269)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setregions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 961; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setregions, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":964
+ /* "pysam/cvcf.pyx":967
* self._regions = regions
*
* def setreference(self, ref): # <<<<<<<<<<<<<<
* """ Provide a reference sequence; a Python class supporting a fetch(chromosome, start, end) method, e.g. PySam.FastaFile """
* self._reference = ref
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_66setreference, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_240)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_66setreference, 0, __pyx_n_s_273, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_272)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setreference, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 964; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__setreference, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 967; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":968
+ /* "pysam/cvcf.pyx":971
* self._reference = ref
*
* def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
* try: self._ignored_errors.add(self.__dict__[errorstring])
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_68ignoreerror, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_242)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_68ignoreerror, 0, __pyx_n_s_276, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_275)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__ignoreerror, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__ignoreerror, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 971; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":972
+ /* "pysam/cvcf.pyx":975
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def warnerror(self, errorstring): # <<<<<<<<<<<<<<
* try: self._warn_errors.add(self.__dict__[errorstring])
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_70warnerror, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_244)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_70warnerror, 0, __pyx_n_s_279, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_278)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__warnerror, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 972; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__warnerror, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 975; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":976
+ /* "pysam/cvcf.pyx":979
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def parse(self, stream): # <<<<<<<<<<<<<<
* """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
* last_line = self._parse_header(stream)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_72parse, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_246)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_72parse, 0, __pyx_n_s_282, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_281)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 979; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":983
+ /* "pysam/cvcf.pyx":986
* return self._parse(last_line, stream)
*
* def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
* """ Writes a VCF file to a stream, using a data generator (or list) """
* self.write_header(stream)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_74write, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_248)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_74write, 0, __pyx_n_s_285, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_284)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 986; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":989
+ /* "pysam/cvcf.pyx":992
* for data in datagenerator: self.write_data(stream,data)
*
* def writeheader(self, stream): # <<<<<<<<<<<<<<
* """ Writes a VCF header """
* self.write_header(stream)
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_76writeheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_250)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_76writeheader, 0, __pyx_n_s_288, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_287)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__writeheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__writeheader, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 992; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":994
+ /* "pysam/cvcf.pyx":997
* self.write_heading(stream)
*
* def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
* """ Utility function: compares two calls for equality """
* # a variant should always be assigned to a unique position, one base before
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_78compare_calls, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_252)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_78compare_calls, 0, __pyx_n_s_291, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_290)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__compare_calls, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__compare_calls, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 997; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":1016
+ /* "pysam/cvcf.pyx":1019
* ###########################################################################################################
*
* def connect( self, filename ): # <<<<<<<<<<<<<<
* '''connect to tabix file.'''
* self.tabixfile = pysam.Tabixfile( filename )
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_80connect, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_254)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_80connect, 0, __pyx_n_s_294, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_293)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__connect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__connect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1019; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":1021
+ /* "pysam/cvcf.pyx":1024
* self._parse_header(self.tabixfile.header)
*
* def fetch(self, # <<<<<<<<<<<<<<
* reference = None,
* start = None,
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_82fetch, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_256)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_82fetch, 0, __pyx_n_s_298, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_296)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_257));
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__fetch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_297));
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__fetch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1024; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":1030
+ /* "pysam/cvcf.pyx":1033
* return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) )
*
* def validate( self, record ): # <<<<<<<<<<<<<<
* '''validate vcf record.
*
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_84validate, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_84validate, 0, __pyx_n_s_301, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_300)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__validate, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__validate, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1033; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/cvcf.pyx":237
+ /* "pysam/cvcf.pyx":240
* return r
*
* class VCF(object): # <<<<<<<<<<<<<<
*
* # types
*/
- __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_INCREF(__pyx_builtin_object);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_builtin_object);
__Pyx_GIVEREF(__pyx_builtin_object);
- __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s_135); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s__VCF, __pyx_n_s_135); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VCF, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VCF, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "pysam/cvcf.pyx":1155
+ /* "pysam/cvcf.pyx":1158
* pos -= 1
*
* __all__ = [ # <<<<<<<<<<<<<<
* "VCF", "VCFRecord", ]
*
*/
- __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyList_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_INCREF(((PyObject *)__pyx_n_s__VCF));
PyList_SET_ITEM(__pyx_t_2, 0, ((PyObject *)__pyx_n_s__VCF));
@@ -27564,7 +27168,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__Pyx_INCREF(((PyObject *)__pyx_n_s__VCFRecord));
PyList_SET_ITEM(__pyx_t_2, 1, ((PyObject *)__pyx_n_s__VCFRecord));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__VCFRecord));
- if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1158; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
/* "pysam/cvcf.pyx":1
@@ -27648,7 +27252,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -27662,7 +27266,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -27683,48 +27287,72 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
}
}
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -27743,10 +27371,9 @@ bad:
return -1;
}
-
-
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -27755,19 +27382,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -27775,10 +27410,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
@@ -27825,33 +27463,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -27884,6 +27527,7 @@ raise_error:
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -27901,12 +27545,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -27923,9 +27591,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -27939,12 +27604,16 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
+#if CYTHON_COMPILING_IN_PYPY
+ float_value = PyNumber_Float(obj);
+#else
if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
return PyFloat_AsDouble(obj);
} else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
@@ -27961,6 +27630,7 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyTuple_SET_ITEM(args, 0, 0);
Py_DECREF(args);
}
+#endif
if (likely(float_value)) {
double value = PyFloat_AS_DOUBLE(float_value);
Py_DECREF(float_value);
@@ -27974,19 +27644,49 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
@@ -27994,31 +27694,210 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else if (PyErr_Occurred()) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
+ } else {
+ return __Pyx_IterFinish();
+ }
+ return 0;
+}
+
+static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
+ Py_ssize_t q = a / b;
+ Py_ssize_t r = a - q*b;
+ q -= ((r != 0) & ((r ^ b) < 0));
+ return q;
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
+}
+
+static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
+ if (t == Py_None) {
+ __Pyx_RaiseNoneNotIterableError();
+ } else if (PyTuple_GET_SIZE(t) < index) {
+ __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
+ } else {
+ __Pyx_RaiseTooManyValuesError(index);
+ }
+}
+
+static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
+ int is_tuple, int has_known_size, int decref_tuple) {
+ Py_ssize_t index;
+ PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
+ if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
+ iternextfunc iternext;
+ iter = PyObject_GetIter(tuple);
+ if (unlikely(!iter)) goto bad;
+ if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
+ iternext = Py_TYPE(iter)->tp_iternext;
+ value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
+ value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
+ if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
+ Py_DECREF(iter);
+ } else {
+ if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
+ __Pyx_UnpackTupleError(tuple, 2);
+ goto bad;
+ }
+#if CYTHON_COMPILING_IN_PYPY
+ value1 = PySequence_ITEM(tuple, 0);
+ if (unlikely(!value1)) goto bad;
+ value2 = PySequence_ITEM(tuple, 1);
+ if (unlikely(!value2)) goto bad;
+#else
+ value1 = PyTuple_GET_ITEM(tuple, 0);
+ value2 = PyTuple_GET_ITEM(tuple, 1);
+ Py_INCREF(value1);
+ Py_INCREF(value2);
+#endif
+ if (decref_tuple) { Py_DECREF(tuple); }
+ }
+ *pvalue1 = value1;
+ *pvalue2 = value2;
+ return 0;
+unpacking_failed:
+ if (!has_known_size && __Pyx_IterFinish() == 0)
+ __Pyx_RaiseNeedMoreValuesError(index);
+bad:
+ Py_XDECREF(iter);
+ Py_XDECREF(value1);
+ Py_XDECREF(value2);
+ if (decref_tuple) { Py_XDECREF(tuple); }
+ return -1;
+}
+
+static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
+ Py_ssize_t* p_orig_length, int* p_source_is_dict) {
+ is_dict = is_dict || likely(PyDict_CheckExact(iterable));
+ *p_source_is_dict = is_dict;
+#if !CYTHON_COMPILING_IN_PYPY
+ if (is_dict) {
+ *p_orig_length = PyDict_Size(iterable);
+ Py_INCREF(iterable);
+ return iterable;
+ }
+#endif
+ *p_orig_length = 0;
+ if (method_name) {
+ PyObject* iter;
+ iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL);
+ if (!iterable)
+ return NULL;
+#if !CYTHON_COMPILING_IN_PYPY
+ if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
+ return iterable;
+#endif
+ iter = PyObject_GetIter(iterable);
+ Py_DECREF(iterable);
+ return iter;
+ }
+ return PyObject_GetIter(iterable);
+}
+static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
+ PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
+ PyObject* next_item;
+#if !CYTHON_COMPILING_IN_PYPY
+ if (source_is_dict) {
+ PyObject *key, *value;
+ if (unlikely(orig_length != PyDict_Size(iter_obj))) {
+ PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
+ return -1;
+ }
+ if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
return 0;
+ }
+ if (pitem) {
+ PyObject* tuple = PyTuple_New(2);
+ if (unlikely(!tuple)) {
+ return -1;
+ }
+ Py_INCREF(key);
+ Py_INCREF(value);
+ PyTuple_SET_ITEM(tuple, 0, key);
+ PyTuple_SET_ITEM(tuple, 1, value);
+ *pitem = tuple;
} else {
- return -1;
+ if (pkey) {
+ Py_INCREF(key);
+ *pkey = key;
+ }
+ if (pvalue) {
+ Py_INCREF(value);
+ *pvalue = value;
+ }
+ }
+ return 1;
+ } else if (PyTuple_CheckExact(iter_obj)) {
+ Py_ssize_t pos = *ppos;
+ if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
+ *ppos = pos + 1;
+ next_item = PyTuple_GET_ITEM(iter_obj, pos);
+ Py_INCREF(next_item);
+ } else if (PyList_CheckExact(iter_obj)) {
+ Py_ssize_t pos = *ppos;
+ if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
+ *ppos = pos + 1;
+ next_item = PyList_GET_ITEM(iter_obj, pos);
+ Py_INCREF(next_item);
+ } else
+#endif
+ {
+ next_item = PyIter_Next(iter_obj);
+ if (unlikely(!next_item)) {
+ return __Pyx_IterFinish();
}
}
- return 0;
+ if (pitem) {
+ *pitem = next_item;
+ } else if (pkey && pvalue) {
+ if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
+ return -1;
+ } else if (pkey) {
+ *pkey = next_item;
+ } else {
+ *pvalue = next_item;
+ }
+ return 1;
}
-static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
- Py_ssize_t q = a / b;
- Py_ssize_t r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
+static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
+ PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
}
+static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_dealloc != current_tp_dealloc)
+ type = type->tp_base;
+ while (type && type->tp_dealloc == current_tp_dealloc)
+ type = type->tp_base;
+ if (type)
+ type->tp_dealloc(obj);
+}
+
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_traverse != current_tp_traverse)
+ type = type->tp_base;
+ while (type && type->tp_traverse == current_tp_traverse)
+ type = type->tp_base;
+ if (type && type->tp_traverse)
+ return type->tp_traverse(obj, v, a);
+ return 0;
+}
-
-static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
- PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_clear != current_tp_clear)
+ type = type->tp_base;
+ while (type && type->tp_clear == current_tp_clear)
+ type = type->tp_base;
+ if (type && type->tp_clear)
+ type->tp_clear(obj);
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -28026,8 +27905,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -28039,18 +27922,23 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
- PyObject *py_import = 0;
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
PyObject *empty_list = 0;
PyObject *module = 0;
PyObject *global_dict = 0;
PyObject *empty_dict = 0;
PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import = 0;
py_import = __Pyx_GetAttrString(__pyx_b, "__import__");
if (!py_import)
goto bad;
+ #endif
if (from_list)
list = from_list;
else {
@@ -28070,13 +27958,17 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
#if PY_MAJOR_VERSION >= 3
if (level == -1) {
if (strchr(__Pyx_MODULE_NAME, '.')) {
- /* try package relative import first */
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(1);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
if (!module) {
if (!PyErr_ExceptionMatches(PyExc_ImportError))
goto bad;
@@ -28087,12 +27979,17 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
}
#endif
if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
PyObject *py_level = PyInt_FromLong(level);
if (!py_level)
goto bad;
module = PyObject_CallFunctionObjArgs(py_import,
name, global_dict, empty_dict, list, py_level, NULL);
Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
}
}
#else
@@ -28104,8 +28001,10 @@ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
name, global_dict, empty_dict, list, NULL);
#endif
bad:
- Py_XDECREF(empty_list);
+ #if PY_VERSION_HEX < 0x03030000
Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
Py_XDECREF(empty_dict);
return module;
}
@@ -28121,7 +28020,6 @@ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
- /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -28146,12 +28044,13 @@ static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
}
static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *name,
- PyObject *modname) {
+ PyObject *qualname, PyObject *modname) {
PyObject *result;
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
- /* Python2 __metaclass__ */
+ if (PyDict_SetItemString(dict, "__qualname__", qualname) < 0)
+ return NULL;
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -28166,16 +28065,19 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
static PyObject *
__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
{
- if (op->func_doc == NULL && op->func.m_ml->ml_doc) {
+ if (unlikely(op->func_doc == NULL)) {
+ if (op->func.m_ml->ml_doc) {
#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
+ op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
+ op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
#endif
- }
- if (op->func_doc == 0) {
- Py_INCREF(Py_None);
- return Py_None;
+ if (unlikely(op->func_doc == NULL))
+ return NULL;
+ } else {
+ Py_INCREF(Py_None);
+ return Py_None;
+ }
}
Py_INCREF(op->func_doc);
return op->func_doc;
@@ -28185,22 +28087,23 @@ __Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
{
PyObject *tmp = op->func_doc;
if (value == NULL)
- op->func_doc = Py_None; /* Mark as deleted */
- else
- op->func_doc = value;
- Py_INCREF(op->func_doc);
+ value = Py_None; /* Mark as deleted */
+ Py_INCREF(value);
+ op->func_doc = value;
Py_XDECREF(tmp);
return 0;
}
static PyObject *
__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
{
- if (op->func_name == NULL) {
+ if (unlikely(op->func_name == NULL)) {
#if PY_MAJOR_VERSION >= 3
op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
#else
op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
#endif
+ if (unlikely(op->func_name == NULL))
+ return NULL;
}
Py_INCREF(op->func_name);
return op->func_name;
@@ -28210,9 +28113,9 @@ __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
{
PyObject *tmp;
#if PY_MAJOR_VERSION >= 3
- if (value == NULL || !PyUnicode_Check(value)) {
+ if (unlikely(value == NULL || !PyUnicode_Check(value))) {
#else
- if (value == NULL || !PyString_Check(value)) {
+ if (unlikely(value == NULL || !PyString_Check(value))) {
#endif
PyErr_SetString(PyExc_TypeError,
"__name__ must be set to a string object");
@@ -28225,6 +28128,31 @@ __Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
return 0;
}
static PyObject *
+__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
+{
+ Py_INCREF(op->func_qualname);
+ return op->func_qualname;
+}
+static int
+__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
+{
+ PyObject *tmp;
+#if PY_MAJOR_VERSION >= 3
+ if (unlikely(value == NULL || !PyUnicode_Check(value))) {
+#else
+ if (unlikely(value == NULL || !PyString_Check(value))) {
+#endif
+ PyErr_SetString(PyExc_TypeError,
+ "__qualname__ must be set to a string object");
+ return -1;
+ }
+ tmp = op->func_qualname;
+ Py_INCREF(value);
+ op->func_qualname = value;
+ Py_XDECREF(tmp);
+ return 0;
+}
+static PyObject *
__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
{
PyObject *self;
@@ -28237,9 +28165,9 @@ __Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure
static PyObject *
__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
{
- if (op->func_dict == NULL) {
+ if (unlikely(op->func_dict == NULL)) {
op->func_dict = PyDict_New();
- if (op->func_dict == NULL)
+ if (unlikely(op->func_dict == NULL))
return NULL;
}
Py_INCREF(op->func_dict);
@@ -28249,12 +28177,12 @@ static int
__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
{
PyObject *tmp;
- if (value == NULL) {
+ if (unlikely(value == NULL)) {
PyErr_SetString(PyExc_TypeError,
"function's dictionary may not be deleted");
return -1;
}
- if (!PyDict_Check(value)) {
+ if (unlikely(!PyDict_Check(value))) {
PyErr_SetString(PyExc_TypeError,
"setting function's dictionary to a non-dict");
return -1;
@@ -28294,7 +28222,7 @@ __Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op)
}
if (op->defaults_getter) {
PyObject *res = op->defaults_getter((PyObject *) op);
- if (res) {
+ if (likely(res)) {
Py_INCREF(res);
op->defaults_tuple = res;
}
@@ -28308,6 +28236,7 @@ static PyGetSetDef __pyx_CyFunction_getsets[] = {
{(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
{(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
{(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
+ {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
{(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
{(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
{(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
@@ -28341,7 +28270,7 @@ static PyMethodDef __pyx_CyFunction_methods[] = {
{__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
{0, 0, 0, 0}
};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags,
+static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
PyObject *closure, PyObject *module, PyObject* code) {
__pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
if (op == NULL)
@@ -28356,6 +28285,8 @@ static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int f
op->func.m_module = module;
op->func_dict = NULL;
op->func_name = NULL;
+ Py_INCREF(qualname);
+ op->func_qualname = qualname;
op->func_doc = NULL;
op->func_classobj = NULL;
Py_XINCREF(code);
@@ -28374,6 +28305,7 @@ __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
Py_CLEAR(m->func.m_module);
Py_CLEAR(m->func_dict);
Py_CLEAR(m->func_name);
+ Py_CLEAR(m->func_qualname);
Py_CLEAR(m->func_doc);
Py_CLEAR(m->func_code);
Py_CLEAR(m->func_classobj);
@@ -28402,6 +28334,7 @@ static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit,
Py_VISIT(m->func.m_module);
Py_VISIT(m->func_dict);
Py_VISIT(m->func_name);
+ Py_VISIT(m->func_qualname);
Py_VISIT(m->func_doc);
Py_VISIT(m->func_code);
Py_VISIT(m->func_classobj);
@@ -28434,15 +28367,64 @@ static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObj
static PyObject*
__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
{
- PyObject *func_name = __Pyx_CyFunction_get_name(op);
#if PY_MAJOR_VERSION >= 3
return PyUnicode_FromFormat("<cyfunction %U at %p>",
- func_name, (void *)op);
+ op->func_qualname, (void *)op);
#else
return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(func_name), (void *)op);
+ PyString_AsString(op->func_qualname), (void *)op);
#endif
}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyCFunctionObject* f = (PyCFunctionObject*)func;
+ PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+ PyObject *self = PyCFunction_GET_SELF(func);
+ Py_ssize_t size;
+ switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ case METH_VARARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ return (*meth)(self, arg);
+ break;
+ case METH_VARARGS | METH_KEYWORDS:
+ return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+ case METH_NOARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 0)
+ return (*meth)(self, NULL);
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes no arguments (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ case METH_O:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 1)
+ return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes exactly one argument (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ default:
+ PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+ "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+ "longer supported!");
+ return NULL;
+ }
+ PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+ f->m_ml->ml_name);
+ return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ return PyCFunction_Call(func, arg, kw);
+}
+#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -28462,7 +28444,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_PyCFunction_Call, /*tp_call*/
+ __Pyx_CyFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -28498,15 +28480,16 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void)
-{
+static int __Pyx_CyFunction_init(void) {
+#if !CYTHON_COMPILING_IN_PYPY
+ __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
-{
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults = PyMem_Malloc(size);
if (!m->defaults)
@@ -28515,8 +28498,7 @@ void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
-{
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults_tuple = tuple;
Py_INCREF(tuple);
@@ -28547,78 +28529,6 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
}
}
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyBytes_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
- else
- return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
- } else {
- int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
@@ -29021,6 +28931,7 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
@@ -29028,6 +28939,10 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
+#else
+ PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
+ PyErr_SetExcInfo(*type, *value, *tb);
+#endif
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
@@ -29037,9 +28952,70 @@ static PyObject *__Pyx_Generator_Next(PyObject *self);
static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
static PyObject *__Pyx_Generator_Close(PyObject *self);
static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
+static PyTypeObject *__pyx_GeneratorType = 0;
+#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
+#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
+ PyObject *et, *ev, *tb;
+ PyObject *value = NULL;
+ __Pyx_ErrFetch(&et, &ev, &tb);
+ if (!et) {
+ Py_XDECREF(tb);
+ Py_XDECREF(ev);
+ Py_INCREF(Py_None);
+ *pvalue = Py_None;
+ return 0;
+ }
+ if (unlikely(et != PyExc_StopIteration) &&
+ unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ if (likely(et == PyExc_StopIteration)) {
+ if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
+ if (!ev) {
+ Py_INCREF(Py_None);
+ ev = Py_None;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+ *pvalue = ev;
+ return 0;
+ }
+ }
+ PyErr_NormalizeException(&et, &ev, &tb);
+ if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+#if PY_VERSION_HEX >= 0x030300A0
+ value = ((PyStopIterationObject *)ev)->value;
+ Py_INCREF(value);
+ Py_DECREF(ev);
+#else
+ {
+ PyObject* args = PyObject_GetAttrString(ev, "args");
+ Py_DECREF(ev);
+ if (likely(args)) {
+ value = PyObject_GetItem(args, 0);
+ Py_DECREF(args);
+ }
+ if (unlikely(!value)) {
+ __Pyx_ErrRestore(NULL, NULL, NULL);
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+ }
+#endif
+ *pvalue = value;
+ return 0;
+}
+#endif
static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
-{
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
PyObject *exc_type = self->exc_type;
PyObject *exc_value = self->exc_value;
PyObject *exc_traceback = self->exc_traceback;
@@ -29051,14 +29027,18 @@ void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
Py_XDECREF(exc_traceback);
}
static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
-{
- PyObject *retval;
- if (unlikely(self->is_running)) {
+int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
+ if (unlikely(gen->is_running)) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return NULL;
+ return 1;
}
+ return 0;
+}
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
+ PyObject *retval;
+ assert(!self->is_running);
if (unlikely(self->resume_label == 0)) {
if (unlikely(value && value != Py_None)) {
PyErr_SetString(PyExc_TypeError,
@@ -29071,81 +29051,240 @@ PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
- if (value)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (value) {
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Generators always return to their most recent caller, not
+ * necessarily their creator. */
+ if (self->exc_traceback) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_XINCREF(tstate->frame);
+ assert(f->f_back == NULL);
+ f->f_back = tstate->frame;
+ }
+#endif
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+ } else {
__Pyx_Generator_ExceptionClear(self);
+ }
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
- if (retval)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (retval) {
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Don't keep the reference to f_back any longer than necessary. It
+ * may keep a chain of frames alive or it could create a reference
+ * cycle. */
+ if (self->exc_traceback) {
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_CLEAR(f->f_back);
+ }
+#endif
+ } else {
__Pyx_Generator_ExceptionClear(self);
+ }
return retval;
}
-static PyObject *__Pyx_Generator_Next(PyObject *self)
-{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
+ PyObject *ret;
+ PyObject *val = NULL;
+ __Pyx_Generator_Undelegate(gen);
+ __Pyx_PyGen_FetchStopIterationValue(&val);
+ ret = __Pyx_Generator_SendEx(gen, val);
+ Py_XDECREF(val);
+ return ret;
+}
+static PyObject *__Pyx_Generator_Next(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ ret = Py_TYPE(yf)->tp_iternext(yf);
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, Py_None);
}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
-{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Send(yf, value);
+ } else {
+ if (value == Py_None)
+ ret = PyIter_Next(yf);
+ else
+ ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
+ }
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, value);
}
-static PyObject *__Pyx_Generator_Close(PyObject *self)
-{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
- PyObject *retval;
+static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
+ PyObject *retval = NULL;
+ int err = 0;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ retval = __Pyx_Generator_Close(yf);
+ if (!retval)
+ return -1;
+ } else {
+ PyObject *meth;
+ gen->is_running = 1;
+ meth = PyObject_GetAttrString(yf, "close");
+ if (unlikely(!meth)) {
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_WriteUnraisable(yf);
+ }
+ PyErr_Clear();
+ } else {
+ retval = PyObject_CallFunction(meth, NULL);
+ Py_DECREF(meth);
+ if (!retval)
+ err = -1;
+ }
+ gen->is_running = 0;
+ }
+ Py_XDECREF(retval);
+ return err;
+}
+static PyObject *__Pyx_Generator_Close(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject *retval, *raised_exception;
+ PyObject *yf = gen->yieldfrom;
+ int err = 0;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ Py_INCREF(yf);
+ err = __Pyx_Generator_CloseIter(gen, yf);
+ __Pyx_Generator_Undelegate(gen);
+ Py_DECREF(yf);
+ }
+ if (err == 0)
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(generator, NULL);
+ retval = __Pyx_Generator_SendEx(gen, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
-#if PY_VERSION_HEX < 0x02050000
- if (PyErr_ExceptionMatches(PyExc_StopIteration))
-#else
- if (PyErr_ExceptionMatches(PyExc_StopIteration)
- || PyErr_ExceptionMatches(PyExc_GeneratorExit))
+ raised_exception = PyErr_Occurred();
+ if (!raised_exception
+ || raised_exception == PyExc_StopIteration
+#if PY_VERSION_HEX >= 0x02050000
+ || raised_exception == PyExc_GeneratorExit
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
#endif
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- PyErr_Clear(); /* ignore these errors */
+ if (raised_exception) PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
-{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
+ PyObject *yf = gen->yieldfrom;
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ Py_INCREF(yf);
+#if PY_VERSION_HEX >= 0x02050000
+ if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
+ int err = __Pyx_Generator_CloseIter(gen, yf);
+ Py_DECREF(yf);
+ __Pyx_Generator_Undelegate(gen);
+ if (err < 0)
+ return __Pyx_Generator_SendEx(gen, NULL);
+ goto throw_here;
+ }
+#endif
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Throw(yf, args);
+ } else {
+ PyObject *meth = PyObject_GetAttrString(yf, "throw");
+ if (unlikely(!meth)) {
+ Py_DECREF(yf);
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ gen->is_running = 0;
+ return NULL;
+ }
+ PyErr_Clear();
+ __Pyx_Generator_Undelegate(gen);
+ gen->is_running = 0;
+ goto throw_here;
+ }
+ ret = PyObject_CallObject(meth, args);
+ Py_DECREF(meth);
+ }
+ gen->is_running = 0;
+ Py_DECREF(yf);
+ if (!ret) {
+ ret = __Pyx_Generator_FinishDelegation(gen);
+ }
+ return ret;
+ }
+throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(generator, NULL);
+ return __Pyx_Generator_SendEx(gen, NULL);
}
-static int
-__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
-{
+static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
Py_VISIT(gen->closure);
Py_VISIT(gen->classobj);
+ Py_VISIT(gen->yieldfrom);
Py_VISIT(gen->exc_type);
Py_VISIT(gen->exc_value);
Py_VISIT(gen->exc_traceback);
return 0;
}
-static void
-__Pyx_Generator_dealloc(PyObject *self)
-{
+static int __Pyx_Generator_clear(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_CLEAR(gen->closure);
+ Py_CLEAR(gen->classobj);
+ Py_CLEAR(gen->yieldfrom);
+ Py_CLEAR(gen->exc_type);
+ Py_CLEAR(gen->exc_value);
+ Py_CLEAR(gen->exc_traceback);
+ return 0;
+}
+static void __Pyx_Generator_dealloc(PyObject *self) {
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject_GC_UnTrack(gen);
if (gen->gi_weakreflist != NULL)
@@ -29157,16 +29296,10 @@ __Pyx_Generator_dealloc(PyObject *self)
return; /* resurrected. :( */
}
PyObject_GC_UnTrack(self);
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
+ __Pyx_Generator_clear(self);
PyObject_GC_Del(gen);
}
-static void
-__Pyx_Generator_del(PyObject *self)
-{
+static void __Pyx_Generator_del(PyObject *self) {
PyObject *res;
PyObject *error_type, *error_value, *error_traceback;
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
@@ -29195,11 +29328,13 @@ __Pyx_Generator_del(PyObject *self)
_Py_NewReference(self);
self->ob_refcnt = refcnt;
}
+#if CYTHON_COMPILING_FOR_CPYTHON
assert(PyType_IS_GC(self->ob_type) &&
_Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
/* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
* we need to undo that. */
_Py_DEC_REFTOTAL;
+#endif
/* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
* chain, so no more to do there.
* If COUNT_ALLOCS, the original decref bumped tp_frees, and
@@ -29207,13 +29342,17 @@ __Pyx_Generator_del(PyObject *self)
* undone.
*/
#ifdef COUNT_ALLOCS
- --self->ob_type->tp_frees;
- --self->ob_type->tp_allocs;
+ --Py_TYPE(self)->tp_frees;
+ --Py_TYPE(self)->tp_allocs;
#endif
}
static PyMemberDef __pyx_Generator_memberlist[] = {
{(char *) "gi_running",
- T_INT,
+#if PY_VERSION_HEX >= 0x02060000
+ T_BOOL,
+#else
+ T_BYTE,
+#endif
offsetof(__pyx_GeneratorObject, is_running),
READONLY,
NULL},
@@ -29225,7 +29364,7 @@ static PyMethodDef __pyx_Generator_methods[] = {
{__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_GeneratorType = {
+static PyTypeObject __pyx_GeneratorType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("generator"), /*tp_name*/
sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
@@ -29246,7 +29385,7 @@ static PyTypeObject __pyx_GeneratorType = {
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
- PyObject_GenericGetAttr, /*tp_getattro*/
+ 0, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
@@ -29255,7 +29394,7 @@ static PyTypeObject __pyx_GeneratorType = {
0, /*tp_clear*/
0, /*tp_richcompare*/
offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- PyObject_SelfIter, /*tp_iter*/
+ 0, /*tp_iter*/
(iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
__pyx_Generator_methods, /*tp_methods*/
__pyx_Generator_memberlist, /*tp_members*/
@@ -29280,12 +29419,10 @@ static PyTypeObject __pyx_GeneratorType = {
0, /*tp_version_tag*/
#endif
};
-static
-__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure)
-{
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure) {
__pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
if (gen == NULL)
return NULL;
gen->body = body;
@@ -29294,6 +29431,7 @@ __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
gen->is_running = 0;
gen->resume_label = 0;
gen->classobj = NULL;
+ gen->yieldfrom = NULL;
gen->exc_type = NULL;
gen->exc_value = NULL;
gen->exc_traceback = NULL;
@@ -29301,9 +29439,14 @@ __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject_GC_Track(gen);
return gen;
}
-static int __pyx_Generator_init(void)
-{
- return PyType_Ready(&__pyx_GeneratorType);
+static int __pyx_Generator_init(void) {
+ __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
+ __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
+ if (PyType_Ready(&__pyx_GeneratorType_type)) {
+ return -1;
+ }
+ __pyx_GeneratorType = &__pyx_GeneratorType_type;
+ return 0;
}
static int __Pyx_check_binary_version(void) {
@@ -29325,6 +29468,23 @@ static int __Pyx_check_binary_version(void) {
return 0;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -29334,6 +29494,10 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
PyObject *result = 0;
PyObject *py_name = 0;
char warning[200];
+ Py_ssize_t basicsize;
+#ifdef Py_LIMITED_API
+ PyObject *py_basicsize;
+#endif
py_module = __Pyx_ImportModule(module_name);
if (!py_module)
goto bad;
@@ -29353,7 +29517,19 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
module_name, class_name);
goto bad;
}
- if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) {
+#ifndef Py_LIMITED_API
+ basicsize = ((PyTypeObject *)result)->tp_basicsize;
+#else
+ py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
+ if (!py_basicsize)
+ goto bad;
+ basicsize = PyLong_AsSsize_t(py_basicsize);
+ Py_DECREF(py_basicsize);
+ py_basicsize = 0;
+ if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
+ goto bad;
+#endif
+ if (!strict && (size_t)basicsize > size) {
PyOS_snprintf(warning, sizeof(warning),
"%s.%s size changed, may indicate binary incompatibility",
module_name, class_name);
@@ -29363,7 +29539,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class
if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
#endif
}
- else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) {
+ else if ((size_t)basicsize != size) {
PyErr_Format(PyExc_ValueError,
"%s.%s has the wrong size, try recompiling",
module_name, class_name);
@@ -29377,23 +29553,6 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
@@ -29622,15 +29781,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
return 0;
}
-
-/* Type Conversion Functions */
-
static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
int is_true = x == Py_True;
if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
else return PyObject_IsTrue(x);
}
-
static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
PyNumberMethods *m;
const char *name = NULL;
@@ -29676,7 +29831,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
}
return res;
}
-
static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_ssize_t ival;
PyObject* x = PyNumber_Index(b);
@@ -29685,7 +29839,6 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
Py_DECREF(x);
return ival;
}
-
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
#if PY_VERSION_HEX < 0x02050000
if (ival <= LONG_MAX)
@@ -29699,7 +29852,6 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
return PyInt_FromSize_t(ival);
#endif
}
-
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) {
unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x);
if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {
diff --git a/pysam/cvcf.pyx b/pysam/cvcf.pyx
index edde706..09616d9 100644
--- a/pysam/cvcf.pyx
+++ b/pysam/cvcf.pyx
@@ -47,8 +47,9 @@ from collections import namedtuple, defaultdict
from operator import itemgetter
import sys, re, copy, bisect
-from pysam cimport ctabix
-from pysam cimport TabProxies
+cimport ctabix
+cimport TabProxies
+
import pysam
gtsRegEx = re.compile("[|/\\\\]")
@@ -104,7 +105,7 @@ cdef class VCFRecord( TabProxies.TupleProxy):
def __init__(self, vcf):
self.vcf = vcf
# if len(data) != len(self.vcf._samples):
- # self.error(str(data),
+ # self.vcf.error(str(data),
# self.BAD_NUMBER_OF_COLUMNS,
# "expected %s for %s samples (%s), got %s" % \
# (len(self.vcf._samples),
@@ -147,7 +148,8 @@ cdef class VCFRecord( TabProxies.TupleProxy):
def __get__(self): return self.fields[2]
property ref:
- def __get__(self): return self.fields[3]
+ def __get__(self):
+ return self.fields[3]
property alt:
def __get__(self):
@@ -164,6 +166,7 @@ cdef class VCFRecord( TabProxies.TupleProxy):
else:
try: qual = float(qual)
except: self.vcf.error(str(self),self.QUAL_NOT_NUMERICAL)
+ return qual
property filter:
def __get__(self):
@@ -202,7 +205,7 @@ cdef class VCFRecord( TabProxies.TupleProxy):
format = self.format
if len(values) > len(format):
- self.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
+ self.vcf.error(str(self.line),self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" %\
(len(values),key,len(format)))
result = {}
@@ -215,8 +218,8 @@ cdef class VCFRecord( TabProxies.TupleProxy):
result[format[idx]] = self.vcf.parse_formatdata(format[idx], value, self.vcf._format, str(self.data))
if expected != -1 and len(result[format[idx]]) != expected:
- self.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
- "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
+ self.vcf.error(str(self.data),self.BAD_NUMBER_OF_PARAMETERS,
+ "id=%s, expected %s parameters, got %s" % (format[idx],expected,result[format[idx]]))
if len(result[format[idx]] ) < expected: result[format[idx]] += [result[format[idx]][-1]]*(expected-len(result[format[idx]]))
result[format[idx]] = result[format[idx]][:expected]
@@ -680,7 +683,7 @@ class VCF(object):
for c in ref:
if c not in "ACGTN": self.error(line,self.UNKNOWN_CHAR_IN_REF)
if "N" in ref: ref = get_sequence(chrom,pos,pos+len(ref),self._reference)
-
+
# make sure reference is sane
if self._reference:
left = max(0,pos-100)
diff --git a/pysam/pysam_util.c b/pysam/pysam_util.c
index c1eae5d..4990e64 100644
--- a/pysam/pysam_util.c
+++ b/pysam/pysam_util.c
@@ -206,7 +206,9 @@ typedef struct __bmc_aux_t {
// If tid < 0, return mapped reads without a coordinate (0)
uint32_t pysam_get_mapped( const bam_index_t *idx, const int tid )
{
-
+ // return no values if index data not present
+ if (idx==NULL) return 0;
+
if (tid >= 0)
{
khint_t k;
@@ -310,8 +312,13 @@ int main_phase(int argc, char *argv[]);
int main_cat(int argc, char *argv[]);
int main_depth(int argc, char *argv[]);
int main_bam2fq(int argc, char *argv[]);
+int main_pad2unpad(int argc, char *argv[]);
+int main_bedcov(int argc, char *argv[]);
+int main_bamshuf(int argc, char *argv[]);
+
int faidx_main(int argc, char *argv[]);
+
int pysam_dispatch(int argc, char *argv[] )
{
extern int optind;
@@ -346,12 +353,12 @@ int pysam_dispatch(int argc, char *argv[] )
else if (strcmp(argv[1], "cat") == 0) retval = main_cat(argc-1, argv+1);
else if (strcmp(argv[1], "targetcut") == 0) retval = main_cut_target(argc-1, argv+1);
else if (strcmp(argv[1], "phase") == 0) retval = main_phase(argc-1, argv+1);
- else if (strcmp(argv[1], "depth") == 0)
- {
- retval = main_depth(argc-1, argv+1);
- }
-
+ else if (strcmp(argv[1], "depth") == 0) retval = main_depth(argc-1, argv+1);
else if (strcmp(argv[1], "bam2fq") == 0) retval = main_bam2fq(argc-1, argv+1);
+ else if (strcmp(argv[1], "pad2unpad") == 0) retval = main_pad2unpad(argc-1, argv+1);
+ else if (strcmp(argv[1], "depad") == 0) retval = main_pad2unpad(argc-1, argv+1);
+ else if (strcmp(argv[1], "bedcov") == 0) retval = main_bedcov(argc-1, argv+1);
+ else if (strcmp(argv[1], "bamshuf") == 0) retval = main_bamshuf(argc-1, argv+1);
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) retval = bam_tview_main(argc-1, argv+1);
diff --git a/pysam/tabix_util.h b/pysam/tabix_util.h
new file mode 100644
index 0000000..6a7db92
--- /dev/null
+++ b/pysam/tabix_util.h
@@ -0,0 +1,6 @@
+/* See issue 122
+ On some MACOSX systems getline is not defined.
+ */
+#if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700)
+ssize_t getline(char **line, size_t *linelen, FILE *fp);
+#endif
diff --git a/pysam/version.py b/pysam/version.py
index 22b95fa..52609de 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,7 +1,7 @@
# pysam versioning information
-__version__ = "0.7.4"
+__version__ = "0.7.5"
-__samtools_version__ = "0.1.18"
+__samtools_version__ = "0.1.19"
__tabix_version__ = "0.2.6"
diff --git a/samtools/bam.c.pysam.c b/samtools/bam.c.pysam.c
index ad26339..cf15e9e 100644
--- a/samtools/bam.c.pysam.c
+++ b/samtools/bam.c.pysam.c
@@ -9,7 +9,7 @@
#include "kstring.h"
#include "sam_header.h"
-int bam_is_be = 0, bam_verbose = 2;
+int bam_is_be = 0, bam_verbose = 2, bam_no_B = 0;
char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
/**************************
@@ -18,12 +18,26 @@ char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
uint32_t bam_calend(const bam1_core_t *c, const uint32_t *cigar)
{
- uint32_t k, end;
- end = c->pos;
+ int k, end = c->pos;
for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP)
- end += cigar[k] >> BAM_CIGAR_SHIFT;
+ int op = bam_cigar_op(cigar[k]);
+ int len = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CBACK) { // move backward
+ int l, u, v;
+ if (k == c->n_cigar - 1) break; // skip trailing 'B'
+ for (l = k - 1, u = v = 0; l >= 0; --l) {
+ int op1 = bam_cigar_op(cigar[l]);
+ int len1 = bam_cigar_oplen(cigar[l]);
+ if (bam_cigar_type(op1)&1) { // consume query
+ if (u + len1 >= len) { // stop
+ if (bam_cigar_type(op1)&2) v += len - u;
+ break;
+ } else u += len1;
+ }
+ if (bam_cigar_type(op1)&2) v += len1;
+ }
+ end = l < 0? c->pos : end - v;
+ } else if (bam_cigar_type(op)&2) end += bam_cigar_oplen(cigar[k]);
}
return end;
}
@@ -32,11 +46,9 @@ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
{
uint32_t k;
int32_t l = 0;
- for (k = 0; k < c->n_cigar; ++k) {
- int op = cigar[k] & BAM_CIGAR_MASK;
- if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
- l += cigar[k] >> BAM_CIGAR_SHIFT;
- }
+ for (k = 0; k < c->n_cigar; ++k)
+ if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
+ l += bam_cigar_oplen(cigar[k]);
return l;
}
@@ -208,6 +220,7 @@ int bam_read1(bamFile fp, bam1_t *b)
if (bam_read(fp, b->data, b->data_len) != b->data_len) return -4;
b->l_aux = b->data_len - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
if (bam_is_be) swap_endian_data(c, b->data_len, b->data);
+ if (bam_no_B) bam_remove_B(b);
return 4 + block_len;
}
@@ -268,9 +281,10 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
if (c->n_cigar == 0) kputc('*', &str);
else {
+ uint32_t *cigar = bam1_cigar(b);
for (i = 0; i < c->n_cigar; ++i) {
kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
- kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+ kputc(bam_cigar_opchr(cigar[i]), &str);
}
}
kputc('\t', &str);
@@ -362,3 +376,101 @@ const char *bam_get_library(bam_header_t *h, const bam1_t *b)
rg = bam_aux_get(b, "RG");
return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1));
}
+
+/************
+ * Remove B *
+ ************/
+
+int bam_remove_B(bam1_t *b)
+{
+ int i, j, end_j, k, l, no_qual;
+ uint32_t *cigar, *new_cigar;
+ uint8_t *seq, *qual, *p;
+ // test if removal is necessary
+ if (b->core.flag & BAM_FUNMAP) return 0; // unmapped; do nothing
+ cigar = bam1_cigar(b);
+ for (k = 0; k < b->core.n_cigar; ++k)
+ if (bam_cigar_op(cigar[k]) == BAM_CBACK) break;
+ if (k == b->core.n_cigar) return 0; // no 'B'
+ if (bam_cigar_op(cigar[0]) == BAM_CBACK) goto rmB_err; // cannot be removed
+ // allocate memory for the new CIGAR
+ if (b->data_len + (b->core.n_cigar + 1) * 4 > b->m_data) { // not enough memory
+ b->m_data = b->data_len + b->core.n_cigar * 4;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ cigar = bam1_cigar(b); // after realloc, cigar may be changed
+ }
+ new_cigar = (uint32_t*)(b->data + (b->m_data - b->core.n_cigar * 4)); // from the end of b->data
+ // the core loop
+ seq = bam1_seq(b); qual = bam1_qual(b);
+ no_qual = (qual[0] == 0xff); // test whether base quality is available
+ i = j = 0; end_j = -1;
+ for (k = l = 0; k < b->core.n_cigar; ++k) {
+ int op = bam_cigar_op(cigar[k]);
+ int len = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CBACK) { // the backward operation
+ int t, u;
+ if (k == b->core.n_cigar - 1) break; // ignore 'B' at the end of CIGAR
+ if (len > j) goto rmB_err; // an excessively long backward
+ for (t = l - 1, u = 0; t >= 0; --t) { // look back
+ int op1 = bam_cigar_op(new_cigar[t]);
+ int len1 = bam_cigar_oplen(new_cigar[t]);
+ if (bam_cigar_type(op1)&1) { // consume the query
+ if (u + len1 >= len) { // stop
+ new_cigar[t] -= (len - u) << BAM_CIGAR_SHIFT;
+ break;
+ } else u += len1;
+ }
+ }
+ if (bam_cigar_oplen(new_cigar[t]) == 0) --t; // squeeze out the zero-length operation
+ l = t + 1;
+ end_j = j; j -= len;
+ } else { // other CIGAR operations
+ new_cigar[l++] = cigar[k];
+ if (bam_cigar_type(op)&1) { // consume the query
+ if (i != j) { // no need to copy if i == j
+ int u, c, c0;
+ for (u = 0; u < len; ++u) { // construct the consensus
+ c = bam1_seqi(seq, i+u);
+ if (j + u < end_j) { // in an overlap
+ c0 = bam1_seqi(seq, j+u);
+ if (c != c0) { // a mismatch; choose the better base
+ if (qual[j+u] < qual[i+u]) { // the base in the 2nd segment is better
+ bam1_seq_seti(seq, j+u, c);
+ qual[j+u] = qual[i+u] - qual[j+u];
+ } else qual[j+u] -= qual[i+u]; // the 1st is better; reduce base quality
+ } else qual[j+u] = qual[j+u] > qual[i+u]? qual[j+u] : qual[i+u];
+ } else { // not in an overlap; copy over
+ bam1_seq_seti(seq, j+u, c);
+ qual[j+u] = qual[i+u];
+ }
+ }
+ }
+ i += len, j += len;
+ }
+ }
+ }
+ if (no_qual) qual[0] = 0xff; // in very rare cases, this may be modified
+ // merge adjacent operations if possible
+ for (k = 1; k < l; ++k)
+ if (bam_cigar_op(new_cigar[k]) == bam_cigar_op(new_cigar[k-1]))
+ new_cigar[k] += new_cigar[k-1] >> BAM_CIGAR_SHIFT << BAM_CIGAR_SHIFT, new_cigar[k-1] &= 0xf;
+ // kill zero length operations
+ for (k = i = 0; k < l; ++k)
+ if (new_cigar[k] >> BAM_CIGAR_SHIFT)
+ new_cigar[i++] = new_cigar[k];
+ l = i;
+ // update b
+ memcpy(cigar, new_cigar, l * 4); // set CIGAR
+ p = b->data + b->core.l_qname + l * 4;
+ memmove(p, seq, (j+1)>>1); p += (j+1)>>1; // set SEQ
+ memmove(p, qual, j); p += j; // set QUAL
+ memmove(p, bam1_aux(b), b->l_aux); p += b->l_aux; // set optional fields
+ b->core.n_cigar = l, b->core.l_qseq = j; // update CIGAR length and query length
+ b->data_len = p - b->data; // update record length
+ return 0;
+
+rmB_err:
+ b->core.flag |= BAM_FUNMAP;
+ return -1;
+}
diff --git a/samtools/bam.h b/samtools/bam.h
index 346c750..80e8703 100644
--- a/samtools/bam.h
+++ b/samtools/bam.h
@@ -40,7 +40,7 @@
@copyright Genome Research Ltd.
*/
-#define BAM_VERSION "0.1.18 (r982:295)"
+#define BAM_VERSION "0.1.19-44428cd"
#include <stdint.h>
#include <stdlib.h>
@@ -89,7 +89,7 @@ typedef struct {
char **target_name;
uint32_t *target_len;
void *dict, *hash, *rg2lib;
- size_t l_text, n_text;
+ uint32_t l_text, n_text;
char *text;
} bam_header_t;
@@ -150,15 +150,24 @@ typedef struct {
/*! @abstract CIGAR: P = padding */
#define BAM_CPAD 6
/*! @abstract CIGAR: equals = match */
-#define BAM_CEQUAL 7
+#define BAM_CEQUAL 7
/*! @abstract CIGAR: X = mismatch */
-#define BAM_CDIFF 8
+#define BAM_CDIFF 8
+#define BAM_CBACK 9
+
+#define BAM_CIGAR_STR "MIDNSHP=XB"
+#define BAM_CIGAR_TYPE 0x3C1A7
+
+#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
+#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
+#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
+#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
+#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference
/*! @typedef
@abstract Structure for core alignment information.
@field tid chromosome ID, defined by bam_header_t
@field pos 0-based leftmost coordinate
- @field strand strand; 0 for forward and 1 otherwise
@field bin bin calculated by bam_reg2bin()
@field qual mapping quality
@field l_qname length of the query name
@@ -183,13 +192,15 @@ typedef struct {
@field l_aux length of auxiliary data
@field data_len current length of bam1_t::data
@field m_data maximum length of bam1_t::data
- @field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
+ @field data all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
@discussion Notes:
1. qname is zero tailing and core.l_qname includes the tailing '\0'.
2. l_qseq is calculated from the total length of an alignment block
on reading or from CIGAR.
+ 3. cigar data is encoded 4 bytes per CIGAR operation.
+ 4. seq is nybble-encoded according to bam_nt16_table.
*/
typedef struct {
bam1_core_t core;
@@ -245,7 +256,10 @@ typedef struct __bam_iter_t *bam_iter_t;
@param i The i-th position, 0-based
@return 4-bit integer representing the base.
*/
-#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+//#define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
+#define bam1_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)
+
+#define bam1_seq_seti(s, i, c) ( (s)[(i)>>1] = ((s)[(i)>>1] & 0xf<<(((i)&1)<<2)) | (c)<<((~(i)&1)<<2) )
/*! @function
@abstract Get query sequence and quality
@@ -275,6 +289,8 @@ extern int bam_is_be;
*/
extern int bam_verbose;
+extern int bam_no_B;
+
/*! @abstract Table for converting a nucleotide character to the 4-bit encoding. */
extern unsigned char bam_nt16_table[256];
@@ -420,6 +436,8 @@ extern "C" {
*/
int bam_read1(bamFile fp, bam1_t *b);
+ int bam_remove_B(bam1_t *b);
+
/*!
@abstract Write an alignment to BAM.
@param fp BAM file handler
@@ -755,9 +773,21 @@ static inline int bam_aux_type2size(int x)
{
if (x == 'C' || x == 'c' || x == 'A') return 1;
else if (x == 'S' || x == 's') return 2;
- else if (x == 'I' || x == 'i' || x == 'f') return 4;
+ else if (x == 'I' || x == 'i' || x == 'f' || x == 'F') return 4;
else return 0;
}
+/*********************************
+ *** Compatibility with htslib ***
+ *********************************/
+
+typedef bam_header_t bam_hdr_t;
+
+#define bam_get_qname(b) bam1_qname(b)
+#define bam_get_cigar(b) bam1_cigar(b)
+
+#define bam_hdr_read(fp) bam_header_read(fp)
+#define bam_hdr_write(fp, h) bam_header_write(fp, h)
+#define bam_hdr_destroy(fp) bam_header_destroy(fp)
#endif
diff --git a/samtools/bam2bcf.c.pysam.c b/samtools/bam2bcf.c.pysam.c
index ece837a..9faed79 100644
--- a/samtools/bam2bcf.c.pysam.c
+++ b/samtools/bam2bcf.c.pysam.c
@@ -2,6 +2,7 @@
#include <math.h>
#include <stdint.h>
+#include <assert.h>
#include "bam.h"
#include "kstring.h"
#include "bam2bcf.h"
@@ -28,20 +29,55 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
bca->e = errmod_init(1. - theta);
bca->min_frac = 0.002;
bca->min_support = 1;
- return bca;
+ bca->per_sample_flt = 0;
+ bca->npos = 100;
+ bca->ref_pos = calloc(bca->npos, sizeof(int));
+ bca->alt_pos = calloc(bca->npos, sizeof(int));
+ return bca;
+}
+
+
+static int get_position(const bam_pileup1_t *p, int *len)
+{
+ int icig, n_tot_bases = 0, iread = 0, edist = p->qpos + 1;
+ for (icig=0; icig<p->b->core.n_cigar; icig++)
+ {
+ // Conversion from uint32_t to MIDNSHP
+ // 0123456
+ // MIDNSHP
+ int cig = bam1_cigar(p->b)[icig] & BAM_CIGAR_MASK;
+ int ncig = bam1_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT;
+ if ( cig==0 )
+ {
+ n_tot_bases += ncig;
+ iread += ncig;
+ }
+ else if ( cig==1 )
+ {
+ n_tot_bases += ncig;
+ iread += ncig;
+ }
+ else if ( cig==4 )
+ {
+ iread += ncig;
+ if ( iread<=p->qpos ) edist -= ncig;
+ }
+ }
+ *len = n_tot_bases;
+ return edist;
}
void bcf_call_destroy(bcf_callaux_t *bca)
{
if (bca == 0) return;
errmod_destroy(bca->e);
+ if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; }
free(bca->bases); free(bca->inscns); free(bca);
}
/* ref_base is the 4-bit representation of the reference base. It is
* negative if we are looking at an indel. */
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
{
- static int *var_pos = NULL, nvar_pos = 0;
int i, n, ref4, is_indel, ori_depth = 0;
memset(r, 0, sizeof(bcf_callret1_t));
if (ref_base >= 0) {
@@ -56,8 +92,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
}
// fill the bases array
- memset(r, 0, sizeof(bcf_callret1_t));
- for (i = n = 0; i < _n; ++i) {
+ for (i = n = r->n_supp = 0; i < _n; ++i) {
const bam_pileup1_t *p = pl + i;
int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
// set base
@@ -80,6 +115,7 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
b = p->aux>>16&0x3f;
is_diff = (b != 0);
}
+ if (is_diff) ++r->n_supp;
bca->bases[n++] = q<<5 | (int)bam1_strand(p->b)<<4 | b;
// collect annotations
if (b < 4) r->qsum[b] += q;
@@ -93,97 +129,163 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t
r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
r->anno[3<<2|is_diff<<1|0] += min_dist;
r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
+
+ // collect read positions for ReadPosBias
+ int len, pos = get_position(p, &len);
+ int epos = (double)pos/(len+1) * bca->npos;
+ if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base )
+ bca->ref_pos[epos]++;
+ else
+ bca->alt_pos[epos]++;
}
r->depth = n; r->ori_depth = ori_depth;
// glfgen
errmod_cal(bca->e, n, 5, bca->bases, r->p);
+ return r->depth;
+}
- // Calculate the Variant Distance Bias (make it optional?)
- if ( nvar_pos < _n ) {
- nvar_pos = _n;
- var_pos = realloc(var_pos,sizeof(int)*nvar_pos);
- }
- int alt_dp=0, read_len=0;
- for (i=0; i<_n; i++) {
- const bam_pileup1_t *p = pl + i;
- if ( bam1_seqi(bam1_seq(p->b),p->qpos) == ref_base )
- continue;
+double mann_whitney_1947(int n, int m, int U)
+{
+ if (U<0) return 0;
+ if (n==0||m==0) return U==0 ? 1 : 0;
+ return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U);
+}
- var_pos[alt_dp] = p->qpos;
- if ( (bam1_cigar(p->b)[0]&BAM_CIGAR_MASK)==4 )
- var_pos[alt_dp] -= bam1_cigar(p->b)[0]>>BAM_CIGAR_SHIFT;
+void calc_ReadPosBias(bcf_callaux_t *bca, bcf_call_t *call)
+{
+ int i, nref = 0, nalt = 0;
+ unsigned long int U = 0;
+ for (i=0; i<bca->npos; i++)
+ {
+ nref += bca->ref_pos[i];
+ nalt += bca->alt_pos[i];
+ U += nref*bca->alt_pos[i];
+ bca->ref_pos[i] = 0;
+ bca->alt_pos[i] = 0;
+ }
+#if 0
+//todo
+ double var = 0, avg = (double)(nref+nalt)/bca->npos;
+ for (i=0; i<bca->npos; i++)
+ {
+ double ediff = bca->ref_pos[i] + bca->alt_pos[i] - avg;
+ var += ediff*ediff;
+ bca->ref_pos[i] = 0;
+ bca->alt_pos[i] = 0;
+ }
+ call->read_pos.avg = avg;
+ call->read_pos.var = sqrt(var/bca->npos);
+ call->read_pos.dp = nref+nalt;
+#endif
+ if ( !nref || !nalt )
+ {
+ call->read_pos_bias = -1;
+ return;
+ }
- alt_dp++;
- read_len += p->b->core.l_qseq;
+ if ( nref>=8 || nalt>=8 )
+ {
+ // normal approximation
+ double mean = ((double)nref*nalt+1.0)/2.0;
+ double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0;
+ double z = (U-mean)/sqrt(var2);
+ call->read_pos_bias = z;
+ //fprintf(pysamerr,"nref=%d nalt=%d U=%ld mean=%e var=%e zval=%e\n", nref,nalt,U,mean,sqrt(var2),call->read_pos_bias);
}
- float mvd=0;
- int j;
- n=0;
- for (i=0; i<alt_dp; i++) {
- for (j=0; j<i; j++) {
- mvd += abs(var_pos[i] - var_pos[j]);
- n++;
+ else
+ {
+ double p = mann_whitney_1947(nalt,nref,U);
+ // biased form claimed by GATK to behave better empirically
+ // double var2 = (1.0+1.0/(nref+nalt+1.0))*(double)nref*nalt*(nref+nalt+1.0)/12.0;
+ double var2 = (double)nref*nalt*(nref+nalt+1.0)/12.0;
+ double z;
+ if ( p >= 1./sqrt(var2*2*M_PI) ) z = 0; // equal to mean
+ else
+ {
+ if ( U >= nref*nalt/2. ) z = sqrt(-2*log(sqrt(var2*2*M_PI)*p));
+ else z = -sqrt(-2*log(sqrt(var2*2*M_PI)*p));
}
+ call->read_pos_bias = z;
+ //fprintf(pysamerr,"nref=%d nalt=%d U=%ld p=%e var2=%e zval=%e\n", nref,nalt,U, p,var2,call->read_pos_bias);
}
- r->mvd[0] = n ? mvd/n : 0;
- r->mvd[1] = alt_dp;
- r->mvd[2] = alt_dp ? read_len/alt_dp : 0;
-
- return r->depth;
}
-
-void calc_vdb(int n, const bcf_callret1_t *calls, bcf_call_t *call)
+float mean_diff_to_prob(float mdiff, int dp, int readlen)
{
- // Variant distance bias. Samples merged by means of DP-weighted average.
-
- float weight=0, tot_prob=0;
-
- int i;
- for (i=0; i<n; i++)
+ if ( dp==2 )
{
- int mvd = calls[i].mvd[0];
- int dp = calls[i].mvd[1];
- int read_len = calls[i].mvd[2];
+ if ( mdiff==0 )
+ return (2.0*readlen + 4.0*(readlen-1.0))/((float)readlen*readlen);
+ else
+ return 8.0*(readlen - 4.0*mdiff)/((float)readlen*readlen);
+ }
- if ( dp<2 ) continue;
+ // This is crude empirical approximation and is not very accurate for
+ // shorter read lengths (<100bp). There certainly is a room for
+ // improvement.
+ const float mv[24][2] = { {0,0}, {0,0}, {0,0},
+ { 9.108, 4.934}, { 9.999, 3.991}, {10.273, 3.485}, {10.579, 3.160},
+ {10.828, 2.889}, {11.014, 2.703}, {11.028, 2.546}, {11.244, 2.391},
+ {11.231, 2.320}, {11.323, 2.138}, {11.403, 2.123}, {11.394, 1.994},
+ {11.451, 1.928}, {11.445, 1.862}, {11.516, 1.815}, {11.560, 1.761},
+ {11.544, 1.728}, {11.605, 1.674}, {11.592, 1.652}, {11.674, 1.613},
+ {11.641, 1.570} };
- float prob = 0;
- if ( dp==2 )
- {
- // Exact formula
- prob = (mvd==0) ? 1.0/read_len : (read_len-mvd)*2.0/read_len/read_len;
- }
- else if ( dp==3 )
- {
- // Sin, quite accurate approximation
- float mu = read_len/2.9;
- prob = mvd>2*mu ? 0 : sin(mvd*3.14/2/mu) / (4*mu/3.14);
- }
- else
- {
- // Scaled gaussian curve, crude approximation, but behaves well. Using fixed depth for bigger depths.
- if ( dp>5 )
- dp = 5;
- float sigma2 = (read_len/1.9/(dp+1)) * (read_len/1.9/(dp+1));
- float norm = 1.125*sqrt(2*3.14*sigma2);
- float mu = read_len/2.9;
- if ( mvd < mu )
- prob = exp(-(mvd-mu)*(mvd-mu)/2/sigma2)/norm;
- else
- prob = exp(-(mvd-mu)*(mvd-mu)/3.125/sigma2)/norm;
- }
+ float m, v;
+ if ( dp>=24 )
+ {
+ m = readlen/8.;
+ if (dp>100) dp = 100;
+ v = 1.476/(0.182*pow(dp,0.514));
+ v = v*(readlen/100.);
+ }
+ else
+ {
+ m = mv[dp][0];
+ v = mv[dp][1];
+ m = m*readlen/100.;
+ v = v*readlen/100.;
+ v *= 1.2; // allow more variability
+ }
+ return 1.0/(v*sqrt(2*M_PI)) * exp(-0.5*((mdiff-m)/v)*((mdiff-m)/v));
+}
- //fprintf(pysamerr,"dp=%d mvd=%d read_len=%d -> prob=%f\n", dp,mvd,read_len,prob);
- tot_prob += prob*dp;
- weight += dp;
+void calc_vdb(bcf_callaux_t *bca, bcf_call_t *call)
+{
+ int i, dp = 0;
+ float mean_pos = 0, mean_diff = 0;
+ for (i=0; i<bca->npos; i++)
+ {
+ if ( !bca->alt_pos[i] ) continue;
+ dp += bca->alt_pos[i];
+ int j = i<bca->npos/2 ? i : bca->npos - i;
+ mean_pos += bca->alt_pos[i]*j;
+ }
+ if ( dp<2 )
+ {
+ call->vdb = -1;
+ return;
}
- tot_prob = weight ? tot_prob/weight : 1;
- //fprintf(pysamerr,"prob=%f\n", tot_prob);
- call->vdb = tot_prob;
+ mean_pos /= dp;
+ for (i=0; i<bca->npos; i++)
+ {
+ if ( !bca->alt_pos[i] ) continue;
+ int j = i<bca->npos/2 ? i : bca->npos - i;
+ mean_diff += bca->alt_pos[i] * fabs(j - mean_pos);
+ }
+ mean_diff /= dp;
+ call->vdb = mean_diff_to_prob(mean_diff, dp, bca->npos);
}
-int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call)
+/**
+ * bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles
+ * @n: number of samples
+ * @calls: each sample's calls
+ * @bca: auxiliary data structure for holding temporary values
+ * @ref_base: the reference base
+ * @call: filled with the annotations
+ */
+int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call)
{
int ref4, i, j, qsum[4];
int64_t tmp;
@@ -196,6 +298,8 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
for (i = 0; i < n; ++i)
for (j = 0; j < 4; ++j)
qsum[j] += calls[i].qsum[j];
+ int qsum_tot=0;
+ for (j=0; j<4; j++) { qsum_tot += qsum[j]; call->qsum[j] = 0; }
for (j = 0; j < 4; ++j) qsum[j] = qsum[j] << 2 | j;
// find the top 2 alleles
for (i = 1; i < 4; ++i) // insertion sort
@@ -207,9 +311,15 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
call->a[0] = ref4;
for (i = 3, j = 1; i >= 0; --i) {
if ((qsum[i]&3) != ref4) {
- if (qsum[i]>>2 != 0) call->a[j++] = qsum[i]&3;
+ if (qsum[i]>>2 != 0)
+ {
+ if ( j<4 ) call->qsum[j] = (float)(qsum[i]>>2)/qsum_tot; // ref N can make j>=4
+ call->a[j++] = qsum[i]&3;
+ }
else break;
}
+ else
+ call->qsum[0] = (float)(qsum[i]>>2)/qsum_tot;
}
if (ref_base >= 0) { // for SNPs, find the "unseen" base
if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
@@ -257,12 +367,13 @@ int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/,
for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
}
- calc_vdb(n, calls, call);
+ calc_vdb(bca, call);
+ calc_ReadPosBias(bca, call);
return 0;
}
-int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
const bcf_callaux_t *bca, const char *ref)
{
extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
@@ -306,34 +417,39 @@ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bc
}
kputc('\0', &s);
// INFO
- if (bc->ori_ref < 0) kputs("INDEL;", &s);
+ if (bc->ori_ref < 0) ksprintf(&s,"INDEL;IS=%d,%f;", bca->max_support, bca->max_frac);
kputs("DP=", &s); kputw(bc->ori_depth, &s); kputs(";I16=", &s);
for (i = 0; i < 16; ++i) {
if (i) kputc(',', &s);
kputw(bc->anno[i], &s);
}
- if ( bc->vdb!=1 )
- {
- ksprintf(&s, ";VDB=%.4f", bc->vdb);
- }
+ //ksprintf(&s,";RPS=%d,%f,%f", bc->read_pos.dp,bc->read_pos.avg,bc->read_pos.var);
+ ksprintf(&s,";QS=%f,%f,%f,%f", bc->qsum[0],bc->qsum[1],bc->qsum[2],bc->qsum[3]);
+ if (bc->vdb != -1)
+ ksprintf(&s, ";VDB=%e", bc->vdb);
+ if (bc->read_pos_bias != -1 )
+ ksprintf(&s, ";RPB=%e", bc->read_pos_bias);
kputc('\0', &s);
// FMT
kputs("PL", &s);
- if (bcr) {
- kputs(":DP", &s);
- if (is_SP) kputs(":SP", &s);
+ if (bcr && fmt_flag) {
+ if (fmt_flag & B2B_FMT_DP) kputs(":DP", &s);
+ if (fmt_flag & B2B_FMT_DV) kputs(":DV", &s);
+ if (fmt_flag & B2B_FMT_SP) kputs(":SP", &s);
}
kputc('\0', &s);
b->m_str = s.m; b->str = s.s; b->l_str = s.l;
bcf_sync(b);
memcpy(b->gi[0].data, bc->PL, b->gi[0].len * bc->n);
- if (bcr) {
- uint16_t *dp = (uint16_t*)b->gi[1].data;
- int32_t *sp = is_SP? b->gi[2].data : 0;
+ if (bcr && fmt_flag) {
+ uint16_t *dp = (fmt_flag & B2B_FMT_DP)? b->gi[1].data : 0;
+ uint16_t *dv = (fmt_flag & B2B_FMT_DV)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0)].data : 0;
+ int32_t *sp = (fmt_flag & B2B_FMT_SP)? b->gi[1 + ((fmt_flag & B2B_FMT_DP) != 0) + ((fmt_flag & B2B_FMT_DV) != 0)].data : 0;
for (i = 0; i < bc->n; ++i) {
bcf_callret1_t *p = bcr + i;
- dp[i] = p->depth < 0xffff? p->depth : 0xffff;
- if (is_SP) {
+ if (dp) dp[i] = p->depth < 0xffff? p->depth : 0xffff;
+ if (dv) dv[i] = p->n_supp < 0xffff? p->n_supp : 0xffff;
+ if (sp) {
if (p->anno[0] + p->anno[1] < 2 || p->anno[2] + p->anno[3] < 2
|| p->anno[0] + p->anno[2] < 2 || p->anno[1] + p->anno[3] < 2)
{
diff --git a/samtools/bam2bcf.h b/samtools/bam2bcf.h
index 4af080c..b2b1825 100644
--- a/samtools/bam2bcf.h
+++ b/samtools/bam2bcf.h
@@ -7,15 +7,22 @@
#define B2B_INDEL_NULL 10000
+#define B2B_FMT_DP 0x1
+#define B2B_FMT_SP 0x2
+#define B2B_FMT_DV 0x4
+
typedef struct __bcf_callaux_t {
int capQ, min_baseQ;
int openQ, extQ, tandemQ; // for indels
- int min_support; // for collecting indel candidates
- double min_frac; // for collecting indel candidates
+ int min_support, max_support; // for collecting indel candidates
+ double min_frac, max_frac; // for collecting indel candidates
+ int per_sample_flt; // indel filtering strategy
+ int *ref_pos, *alt_pos, npos; // for ReadPosBias
// for internal uses
int max_bases;
int indel_types[4];
int maxins, indelreg;
+ int read_len;
char *inscns;
uint16_t *bases;
errmod_t *e;
@@ -23,18 +30,21 @@ typedef struct __bcf_callaux_t {
} bcf_callaux_t;
typedef struct {
- int depth, ori_depth, qsum[4];
- int anno[16];
+ int depth, n_supp, ori_depth, qsum[4];
+ unsigned int anno[16];
float p[25];
- int mvd[3]; // mean variant distance, number of variant reads, average read length
} bcf_callret1_t;
typedef struct {
int a[5]; // alleles: ref, alt, alt2, alt3
+ float qsum[4];
int n, n_alleles, shift, ori_ref, unseen;
- int anno[16], depth, ori_depth;
+ int n_supp; // number of supporting non-reference reads
+ unsigned int anno[16], depth, ori_depth;
uint8_t *PL;
float vdb; // variant distance bias
+ float read_pos_bias;
+ struct { float avg, var; int dp; } read_pos;
} bcf_call_t;
#ifdef __cplusplus
@@ -44,8 +54,8 @@ extern "C" {
bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
void bcf_call_destroy(bcf_callaux_t *bca);
int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
- int bcf_call_combine(int n, const bcf_callret1_t *calls, int ref_base /*4-bit*/, bcf_call_t *call);
- int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int is_SP,
+ int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
+ int bcf_call2bcf(int tid, int pos, bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
const bcf_callaux_t *bca, const char *ref);
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash);
diff --git a/samtools/bam2bcf_indel.c.pysam.c b/samtools/bam2bcf_indel.c.pysam.c
index cf86ca3..cdf16d0 100644
--- a/samtools/bam2bcf_indel.c.pysam.c
+++ b/samtools/bam2bcf_indel.c.pysam.c
@@ -111,6 +111,9 @@ static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
return max_i - pos;
}
+/*
+ * @n: number of samples
+ */
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
const void *rghash)
{
@@ -144,32 +147,48 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
if (s == n) return -1; // there is no indel at this position.
for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
{ // find out how many types of indels are present
- int m, n_alt = 0, n_tot = 0;
+ bca->max_support = bca->max_frac = 0;
+ int m, n_alt = 0, n_tot = 0, indel_support_ok = 0;
uint32_t *aux;
aux = calloc(N + 1, 4);
m = max_rd_len = 0;
aux[m++] = MINUS_CONST; // zero indel is always a type
for (s = 0; s < n; ++s) {
+ int na = 0, nt = 0;
for (i = 0; i < n_plp[s]; ++i) {
const bam_pileup1_t *p = plp[s] + i;
if (rghash == 0 || p->aux == 0) {
- ++n_tot;
+ ++nt;
if (p->indel != 0) {
- ++n_alt;
+ ++na;
aux[m++] = MINUS_CONST + p->indel;
}
}
j = bam_cigar2qlen(&p->b->core, bam1_cigar(p->b));
if (j > max_rd_len) max_rd_len = j;
}
+ float frac = (float)na/nt;
+ if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac )
+ indel_support_ok = 1;
+ if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac;
+ n_alt += na;
+ n_tot += nt;
}
+ // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
+ // check the number of N's in the sequence and skip places where half or more reference bases are Ns.
+ int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
+ if ( nN*2>i ) { free(aux); return -1; }
+
ks_introsort(uint32_t, m, aux);
// squeeze out identical types
for (i = 1, n_types = 1; i < m; ++i)
if (aux[i] != aux[i-1]) ++n_types;
- if (n_types == 1 || (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support) { // then skip
- free(aux); return -1;
- }
+ // Taking totals makes it hard to call rare indels
+ if ( !bca->per_sample_flt )
+ indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
+ if ( n_types == 1 || !indel_support_ok ) { // then skip
+ free(aux); return -1;
+ }
if (n_types >= 64) {
free(aux);
if (bam_verbose >= 2)
@@ -201,6 +220,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
* reduces the power because sometimes, substitutions caused by
* indels are not distinguishable from true mutations. Multiple
* sequence realignment helps to increase the power.
+ *
+ * Masks mismatches present in at least 70% of the reads with 'N'.
*/
{ // construct per-sample consensus
int L = right - left + 1, max_i, max2_i;
@@ -244,7 +265,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
if (max_i >= 0) r[max_i] = 15;
if (max2_i >= 0) r[max2_i] = 15;
-// for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], pysamerr); fputc('\n', pysamerr);
+ //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], pysamerr); fputc('\n', pysamerr);
}
free(ref0); free(cns);
}
@@ -261,9 +282,9 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
}
}
// construct the consensus sequence
- max_ins = types[n_types - 1]; // max_ins is at least 0
+ max_ins = types[n_types - 1]; // max_ins is at least 0
if (max_ins > 0) {
- int *inscns_aux = calloc(4 * n_types * max_ins, sizeof(int));
+ int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
// count the number of occurrences of each base at each position for each type of insertion
for (t = 0; t < n_types; ++t) {
if (types[t] > 0) {
@@ -274,7 +295,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
uint8_t *seq = bam1_seq(p->b);
for (k = 1; k <= p->indel; ++k) {
int c = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos + k)];
- if (c < 4) ++inscns_aux[(t*max_ins+(k-1))*4 + c];
+ assert(c<5);
+ ++inscns_aux[(t*max_ins+(k-1))*5 + c];
}
}
}
@@ -285,11 +307,12 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
inscns = calloc(n_types * max_ins, 1);
for (t = 0; t < n_types; ++t) {
for (j = 0; j < types[t]; ++j) {
- int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*4];
- for (k = 0; k < 4; ++k)
+ int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+ for (k = 0; k < 5; ++k)
if (ia[k] > max)
max = ia[k], max_k = k;
inscns[t*max_ins + j] = max? max_k : 4;
+ if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's
}
}
free(inscns_aux);
diff --git a/samtools/bam2depth.c.pysam.c b/samtools/bam2depth.c.pysam.c
index d22837e..a27e8ba 100644
--- a/samtools/bam2depth.c.pysam.c
+++ b/samtools/bam2depth.c.pysam.c
@@ -15,7 +15,7 @@
typedef struct { // auxiliary data structure
bamFile fp; // the file handler
bam_iter_t iter; // NULL if a region not specified
- int min_mapQ; // mapQ filter
+ int min_mapQ, min_len; // mapQ filter; length filter
} aux_t;
void *bed_read(const char *fn); // read a BED or position list file
@@ -27,40 +27,65 @@ static int read_bam(void *data, bam1_t *b) // read level filters better go here
{
aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
- if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+ if (!(b->core.flag&BAM_FUNMAP)) {
+ if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+ else if (aux->min_len && bam_cigar2qlen(&b->core, bam1_cigar(b)) < aux->min_len) b->core.flag |= BAM_FUNMAP;
+ }
return ret;
}
+int read_file_list(const char *file_list,int *n,char **argv[]);
+
#ifdef _MAIN_BAM2DEPTH
int main(int argc, char *argv[])
#else
int main_depth(int argc, char *argv[])
#endif
{
- int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0;
+ int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, nfiles;
const bam_pileup1_t **plp;
char *reg = 0; // specified region
void *bed = 0; // BED data structure
+ char *file_list = NULL, **fn = NULL;
bam_header_t *h = 0; // BAM header of the 1st input
aux_t **data;
bam_mplp_t mplp;
// parse the command line
- while ((n = getopt(argc, argv, "r:b:q:Q:")) >= 0) {
+ while ((n = getopt(argc, argv, "r:b:q:Q:l:f:")) >= 0) {
switch (n) {
+ case 'l': min_len = atoi(optarg); break; // minimum query length
case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
case 'q': baseQ = atoi(optarg); break; // base quality threshold
case 'Q': mapQ = atoi(optarg); break; // mapping quality threshold
+ case 'f': file_list = optarg; break;
}
}
- if (optind == argc) {
- fprintf(pysamerr, "Usage: bam2depth [-r reg] [-q baseQthres] [-Q mapQthres] [-b in.bed] <in1.bam> [...]\n");
+ if (optind == argc && !file_list) {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n");
+ fprintf(pysamerr, "Options:\n");
+ fprintf(pysamerr, " -b <bed> list of positions or regions\n");
+ fprintf(pysamerr, " -f <list> list of input BAM filenames, one per line [null]\n");
+ fprintf(pysamerr, " -l <int> minQLen\n");
+ fprintf(pysamerr, " -q <int> base quality threshold\n");
+ fprintf(pysamerr, " -Q <int> mapping quality threshold\n");
+ fprintf(pysamerr, " -r <chr:from-to> region\n");
+ fprintf(pysamerr, "\n");
return 1;
}
// initialize the auxiliary data structures
- n = argc - optind; // the number of BAMs on the command line
+ if (file_list)
+ {
+ if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+ n = nfiles;
+ argv = fn;
+ optind = 0;
+ }
+ else
+ n = argc - optind; // the number of BAMs on the command line
data = calloc(n, sizeof(void*)); // data[i] for the i-th input
beg = 0; end = 1<<30; tid = -1; // set the default region
for (i = 0; i < n; ++i) {
@@ -68,6 +93,7 @@ int main_depth(int argc, char *argv[])
data[i] = calloc(1, sizeof(aux_t));
data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
data[i]->min_mapQ = mapQ; // set the mapQ filter
+ data[i]->min_len = min_len; // set the qlen filter
htmp = bam_header_read(data[i]->fp); // read the BAM header
if (i == 0) {
h = htmp; // keep the header of the 1st BAM
@@ -110,5 +136,10 @@ int main_depth(int argc, char *argv[])
}
free(data); free(reg);
if (bed) bed_destroy(bed);
+ if ( file_list )
+ {
+ for (i=0; i<n; i++) free(fn[i]);
+ free(fn);
+ }
return 0;
}
diff --git a/samtools/bam_aux.c.pysam.c b/samtools/bam_aux.c.pysam.c
index 14209cd..258a705 100644
--- a/samtools/bam_aux.c.pysam.c
+++ b/samtools/bam_aux.c.pysam.c
@@ -143,6 +143,10 @@ int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *be
} else s[name_end] = ':', name_end = l;
}
} else iter = kh_get(s, h, str);
+ if (iter == kh_end(h)) {
+ free(s);
+ return -1;
+ }
*ref_id = kh_val(h, iter);
// parse the interval
if (name_end < l) {
diff --git a/samtools/bam_cat.c.pysam.c b/samtools/bam_cat.c.pysam.c
index 0cc1167..5faefc0 100644
--- a/samtools/bam_cat.c.pysam.c
+++ b/samtools/bam_cat.c.pysam.c
@@ -61,6 +61,7 @@ all:bam_cat
#include <stdlib.h>
#include <unistd.h>
+#include "knetfile.h"
#include "bgzf.h"
#include "bam.h"
@@ -99,7 +100,7 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
fprintf(pysamerr, "[%s] ERROR: fail to open file '%s'.\n", __func__, fn[i]);
return -1;
}
- if (in->open_mode != 'r') return -1;
+ if (in->is_write) return -1;
old = bam_header_read(in);
if (h == 0 && i == 0) bam_header_write(fp, old);
@@ -111,10 +112,10 @@ int bam_cat(int nfn, char * const *fn, const bam_header_t *h, const char* outbam
j=0;
#ifdef _USE_KNETFILE
- fp_file=fp->x.fpw;
- while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0) {
+ fp_file = fp->fp;
+ while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0) {
#else
- fp_file=fp->file;
+ fp_file = fp->fp;
while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0) {
#endif
if(len<es){
diff --git a/samtools/bam_color.c.pysam.c b/samtools/bam_color.c.pysam.c
index f71c65f..2e8ac13 100644
--- a/samtools/bam_color.c.pysam.c
+++ b/samtools/bam_color.c.pysam.c
@@ -21,8 +21,14 @@ char bam_aux_getCSi(bam1_t *b, int i)
cs = bam_aux2Z(c);
// adjust for strandedness and leading adaptor
- if(bam1_strand(b)) i = strlen(cs) - 1 - i;
- else i++;
+ if(bam1_strand(b)) {
+ i = strlen(cs) - 1 - i;
+ // adjust for leading hard clip
+ uint32_t cigar = bam1_cigar(b)[0];
+ if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+ i -= cigar >> BAM_CIGAR_SHIFT;
+ }
+ } else { i++; }
return cs[i];
}
@@ -44,7 +50,14 @@ char bam_aux_getCQi(bam1_t *b, int i)
cq = bam_aux2Z(c);
// adjust for strandedness
- if(bam1_strand(b)) i = strlen(cq) - 1 - i;
+ if(bam1_strand(b)) {
+ i = strlen(cq) - 1 - i;
+ // adjust for leading hard clip
+ uint32_t cigar = bam1_cigar(b)[0];
+ if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+ i -= (cigar >> BAM_CIGAR_SHIFT);
+ }
+ }
return cq[i];
}
@@ -100,6 +113,11 @@ char bam_aux_getCEi(bam1_t *b, int i)
// adjust for strandedness and leading adaptor
if(bam1_strand(b)) { //reverse strand
cs_i = strlen(cs) - 1 - i;
+ // adjust for leading hard clip
+ uint32_t cigar = bam1_cigar(b)[0];
+ if((cigar & BAM_CIGAR_MASK) == BAM_CHARD_CLIP) {
+ cs_i -= cigar >> BAM_CIGAR_SHIFT;
+ }
// get current color
cur_color = cs[cs_i];
// get previous base. Note: must rc adaptor
diff --git a/samtools/bam_import.c.pysam.c b/samtools/bam_import.c.pysam.c
index 36a8024..afdfb2f 100644
--- a/samtools/bam_import.c.pysam.c
+++ b/samtools/bam_import.c.pysam.c
@@ -185,7 +185,7 @@ static inline void append_text(bam_header_t *header, kstring_t *str)
// Sanity check
if ( header->l_text+str->l+1 >= header->n_text )
{
- fprintf(pysamerr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,header->n_text,x,y);
+ fprintf(pysamerr,"append_text FIXME: %ld>=%ld, x=%ld,y=%ld\n", header->l_text+str->l+1,(long)header->n_text,x,y);
abort();
}
strncpy(header->text + header->l_text, str->s, str->l+1); // we cannot use strcpy() here.
@@ -293,11 +293,13 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -3;
z += str->l + 1;
if (str->s[0] != '*') {
+ uint32_t *cigar;
for (s = str->s; *s; ++s) {
if ((isalpha(*s)) || (*s=='=')) ++c->n_cigar;
else if (!isdigit(*s)) parse_error(fp->n_lines, "invalid CIGAR character");
}
b->data = alloc_data(b, doff + c->n_cigar * 4);
+ cigar = bam1_cigar(b);
for (i = 0, s = str->s; i != c->n_cigar; ++i) {
x = strtol(s, &t, 10);
op = toupper(*t);
@@ -310,12 +312,13 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
else if (op == 'P') op = BAM_CPAD;
else if (op == '=') op = BAM_CEQUAL;
else if (op == 'X') op = BAM_CDIFF;
+ else if (op == 'B') op = BAM_CBACK;
else parse_error(fp->n_lines, "invalid CIGAR operation");
s = t + 1;
- bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
+ cigar[i] = bam_cigar_gen(x, op);
}
if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
- c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
+ c->bin = bam_reg2bin(c->pos, bam_calend(c, cigar));
doff += c->n_cigar * 4;
} else {
if (!(c->flag&BAM_FUNMAP)) {
@@ -342,9 +345,9 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
if (strcmp(str->s, "*")) {
c->l_qseq = strlen(str->s);
if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b))) {
- fprintf(pysamerr, "Line %ld, sequence length %i vs %i from CIGAR\n",
- (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
- parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+ fprintf(pysamerr, "Line %ld, sequence length %i vs %i from CIGAR\n",
+ (long)fp->n_lines, c->l_qseq, (int32_t)bam_cigar2qlen(c, bam1_cigar(b)));
+ parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
}
p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
memset(p, 0, (c->l_qseq+1)/2);
@@ -461,6 +464,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
}
b->l_aux = doff - doff0;
b->data_len = doff;
+ if (bam_no_B) bam_remove_B(b);
return z;
}
diff --git a/samtools/bam_index.c.pysam.c b/samtools/bam_index.c.pysam.c
index 6ae2ac3..284f191 100644
--- a/samtools/bam_index.c.pysam.c
+++ b/samtools/bam_index.c.pysam.c
@@ -161,9 +161,14 @@ bam_index_t *bam_index_core(bamFile fp)
bam1_core_t *c;
uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
+ h = bam_header_read(fp);
+ if(h == 0) {
+ fprintf(pysamerr, "[bam_index_core] Invalid BAM header.");
+ return NULL;
+ }
+
idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
b = (bam1_t*)calloc(1, sizeof(bam1_t));
- h = bam_header_read(fp);
c = &b->core;
idx->n = h->n_targets;
@@ -461,6 +466,7 @@ bam_index_t *bam_index_load(const char *fn)
strcat(strcpy(fnidx, fn), ".bai");
fprintf(pysamerr, "[bam_index_load] attempting to download the remote index file.\n");
download_from_remote(fnidx);
+ free(fnidx);
idx = bam_index_load_local(fn);
}
if (idx == 0) fprintf(pysamerr, "[bam_index_load] fail to load BAM index.\n");
@@ -491,6 +497,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
if (fpidx == 0) {
fprintf(pysamerr, "[bam_index_build2] fail to create the index file.\n");
free(fnidx);
+ bam_index_destroy(idx);
return -1;
}
bam_index_save(idx, fpidx);
diff --git a/samtools/bam_mate.c.pysam.c b/samtools/bam_mate.c.pysam.c
index ebb797b..a09157b 100644
--- a/samtools/bam_mate.c.pysam.c
+++ b/samtools/bam_mate.c.pysam.c
@@ -2,15 +2,45 @@
#include <stdlib.h>
#include <string.h>
+#include <unistd.h>
+#include "kstring.h"
#include "bam.h"
+void bam_template_cigar(bam1_t *b1, bam1_t *b2, kstring_t *str)
+{
+ bam1_t *swap;
+ int i, end;
+ uint32_t *cigar;
+ str->l = 0;
+ if (b1->core.tid != b2->core.tid || b1->core.tid < 0) return; // coordinateless or not on the same chr; skip
+ if (b1->core.pos > b2->core.pos) swap = b1, b1 = b2, b2 = swap; // make sure b1 has a smaller coordinate
+ kputc((b1->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+ kputc((b1->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+ for (i = 0, cigar = bam1_cigar(b1); i < b1->core.n_cigar; ++i) {
+ kputw(bam_cigar_oplen(cigar[i]), str);
+ kputc(bam_cigar_opchr(cigar[i]), str);
+ }
+ end = bam_calend(&b1->core, cigar);
+ kputw(b2->core.pos - end, str);
+ kputc('T', str);
+ kputc((b2->core.flag & BAM_FREAD1)? '1' : '2', str); // segment index
+ kputc((b2->core.flag & BAM_FREVERSE)? 'R' : 'F', str); // strand
+ for (i = 0, cigar = bam1_cigar(b2); i < b2->core.n_cigar; ++i) {
+ kputw(bam_cigar_oplen(cigar[i]), str);
+ kputc(bam_cigar_opchr(cigar[i]), str);
+ }
+ bam_aux_append(b1, "CT", 'Z', str->l+1, (uint8_t*)str->s);
+}
+
// currently, this function ONLY works if each read has one hit
-void bam_mating_core(bamFile in, bamFile out)
+void bam_mating_core(bamFile in, bamFile out, int remove_reads)
{
bam_header_t *header;
bam1_t *b[2];
- int curr, has_prev;
+ int curr, has_prev, pre_end = 0, cur_end;
+ kstring_t str;
+ str.l = str.m = 0; str.s = 0;
header = bam_header_read(in);
bam_header_write(out, header);
@@ -19,16 +49,28 @@ void bam_mating_core(bamFile in, bamFile out)
curr = 0; has_prev = 0;
while (bam_read1(in, b[curr]) >= 0) {
bam1_t *cur = b[curr], *pre = b[1-curr];
+ if (cur->core.tid < 0)
+ {
+ if ( !remove_reads ) bam_write1(out, cur);
+ continue;
+ }
+ cur_end = bam_calend(&cur->core, bam1_cigar(cur));
+ if (cur_end > (int)header->target_len[cur->core.tid]) cur->core.flag |= BAM_FUNMAP;
+ if (cur->core.flag & BAM_FSECONDARY)
+ {
+ if ( !remove_reads ) bam_write1(out, cur);
+ continue; // skip secondary alignments
+ }
if (has_prev) {
if (strcmp(bam1_qname(cur), bam1_qname(pre)) == 0) { // identical pair name
cur->core.mtid = pre->core.tid; cur->core.mpos = pre->core.pos;
pre->core.mtid = cur->core.tid; pre->core.mpos = cur->core.pos;
if (pre->core.tid == cur->core.tid && !(cur->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))
- && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP)))
+ && !(pre->core.flag&(BAM_FUNMAP|BAM_FMUNMAP))) // set TLEN/ISIZE
{
uint32_t cur5, pre5;
- cur5 = (cur->core.flag&BAM_FREVERSE)? bam_calend(&cur->core, bam1_cigar(cur)) : cur->core.pos;
- pre5 = (pre->core.flag&BAM_FREVERSE)? bam_calend(&pre->core, bam1_cigar(pre)) : pre->core.pos;
+ cur5 = (cur->core.flag&BAM_FREVERSE)? cur_end : cur->core.pos;
+ pre5 = (pre->core.flag&BAM_FREVERSE)? pre_end : pre->core.pos;
cur->core.isize = pre5 - cur5; pre->core.isize = cur5 - pre5;
} else cur->core.isize = pre->core.isize = 0;
if (pre->core.flag&BAM_FREVERSE) cur->core.flag |= BAM_FMREVERSE;
@@ -37,6 +79,7 @@ void bam_mating_core(bamFile in, bamFile out)
else pre->core.flag &= ~BAM_FMREVERSE;
if (cur->core.flag & BAM_FUNMAP) { pre->core.flag |= BAM_FMUNMAP; pre->core.flag &= ~BAM_FPROPER_PAIR; }
if (pre->core.flag & BAM_FUNMAP) { cur->core.flag |= BAM_FMUNMAP; cur->core.flag &= ~BAM_FPROPER_PAIR; }
+ bam_template_cigar(pre, cur, &str);
bam_write1(out, pre);
bam_write1(out, cur);
has_prev = 0;
@@ -50,23 +93,38 @@ void bam_mating_core(bamFile in, bamFile out)
}
} else has_prev = 1;
curr = 1 - curr;
+ pre_end = cur_end;
}
if (has_prev) bam_write1(out, b[1-curr]);
bam_header_destroy(header);
bam_destroy1(b[0]);
bam_destroy1(b[1]);
+ free(str.s);
+}
+
+void usage()
+{
+ fprintf(pysamerr,"Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
+ fprintf(pysamerr,"Options:\n");
+ fprintf(pysamerr," -r remove unmapped reads and secondary alignments\n");
+ exit(1);
}
int bam_mating(int argc, char *argv[])
{
bamFile in, out;
- if (argc < 3) {
- fprintf(pysamerr, "samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>\n");
- return 1;
- }
- in = (strcmp(argv[1], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[1], "r");
- out = (strcmp(argv[2], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[2], "w");
- bam_mating_core(in, out);
+ int c, remove_reads=0;
+ while ((c = getopt(argc, argv, "r")) >= 0) {
+ switch (c) {
+ case 'r': remove_reads=1; break;
+ }
+ }
+ if (optind+1 >= argc) usage();
+ in = (strcmp(argv[optind], "-") == 0)? bam_dopen(fileno(stdin), "r") : bam_open(argv[optind], "r");
+ out = (strcmp(argv[optind+1], "-") == 0)? bam_dopen(fileno(stdout), "w") : bam_open(argv[optind+1], "w");
+ bam_mating_core(in, out, remove_reads);
bam_close(in); bam_close(out);
return 0;
}
+
+
diff --git a/samtools/bam_md.c.pysam.c b/samtools/bam_md.c.pysam.c
index 50ecaf1..e0cf67b 100644
--- a/samtools/bam_md.c.pysam.c
+++ b/samtools/bam_md.c.pysam.c
@@ -190,7 +190,7 @@ int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
{
- int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1;
+ int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1, redo_baq = flag&4;
uint32_t *cigar = bam1_cigar(b);
bam1_core_t *c = &b->core;
kpa_par_t conf = kpa_par_def;
@@ -199,6 +199,11 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
// test if BQ or ZQ is present
if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
+ if (bq && redo_baq)
+ {
+ bam_aux_del(b, bq-1);
+ bq = 0;
+ }
if (bq && zq) { // remove the ZQ tag
bam_aux_del(b, zq-1);
zq = 0;
diff --git a/samtools/bam_plcmd.c.pysam.c b/samtools/bam_plcmd.c.pysam.c
index 473d409..79917c9 100644
--- a/samtools/bam_plcmd.c.pysam.c
+++ b/samtools/bam_plcmd.c.pysam.c
@@ -6,9 +6,12 @@
#include <ctype.h>
#include <string.h>
#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
#include "sam.h"
#include "faidx.h"
#include "kstring.h"
+#include "sam_header.h"
static inline int printw(int c, FILE *fp)
{
@@ -68,24 +71,24 @@ static inline void pileup_seq(const bam_pileup1_t *p, int pos, int ref_len, cons
#define MPLP_NO_COMP 0x20
#define MPLP_NO_ORPHAN 0x40
#define MPLP_REALN 0x80
-#define MPLP_FMT_DP 0x100
-#define MPLP_FMT_SP 0x200
#define MPLP_NO_INDEL 0x400
-#define MPLP_EXT_BAQ 0x800
+#define MPLP_REDO_BAQ 0x800
#define MPLP_ILLUMINA13 0x1000
#define MPLP_IGNORE_RG 0x2000
#define MPLP_PRINT_POS 0x4000
#define MPLP_PRINT_MAPQ 0x8000
+#define MPLP_PER_SAMPLE 0x10000
void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
typedef struct {
- int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth;
+ int max_mq, min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
+ int rflag_require, rflag_filter;
int openQ, extQ, tandemQ, min_support; // for indels
double min_frac; // for indels
- char *reg, *pl_list;
+ char *reg, *pl_list, *fai_fname;
faidx_t *fai;
void *bed, *rghash;
} mplp_conf_t;
@@ -120,6 +123,8 @@ static int mplp_func(void *data, bam1_t *b)
skip = 1;
continue;
}
+ if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+ if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
if (ma->conf->bed) { // test overlap
skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
if (skip) continue;
@@ -137,7 +142,7 @@ static int mplp_func(void *data, bam1_t *b)
}
has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
skip = 0;
- if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_EXT_BAQ)? 3 : 1);
+ if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
if (has_ref && ma->conf->capQ_thres > 10) {
int q = bam_cap_mapQ(b, ma->ref, ma->conf->capQ_thres);
if (q < 0) skip = 1;
@@ -211,8 +216,17 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
bam_header_t *h_tmp;
data[i] = calloc(1, sizeof(mplp_aux_t));
data[i]->fp = strcmp(fn[i], "-") == 0? bam_dopen(fileno(stdin), "r") : bam_open(fn[i], "r");
+ if ( !data[i]->fp )
+ {
+ fprintf(pysamerr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
+ exit(1);
+ }
data[i]->conf = conf;
h_tmp = bam_header_read(data[i]->fp);
+ if ( !h_tmp ) {
+ fprintf(pysamerr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+ exit(1);
+ }
data[i]->h = i? h : h_tmp; // for i==0, "h" has not been set yet
bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
@@ -221,11 +235,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
bam_index_t *idx;
idx = bam_index_load(fn[i]);
if (idx == 0) {
- fprintf(pysamerr, "[%s] fail to load index for %d-th input.\n", __func__, i+1);
+ fprintf(pysamerr, "[%s] fail to load index for %s\n", __func__, fn[i]);
exit(1);
}
if (bam_parse_region(h_tmp, conf->reg, &tid, &beg, &end) < 0) {
- fprintf(pysamerr, "[%s] malformatted region or wrong seqname for %d-th input.\n", __func__, i+1);
+ fprintf(pysamerr, "[%s] malformatted region or wrong seqname for %s\n", __func__, fn[i]);
exit(1);
}
if (i == 0) tid0 = tid, beg0 = beg, end0 = end;
@@ -264,9 +278,24 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
bh->l_smpl = s.l;
bh->sname = malloc(s.l);
memcpy(bh->sname, s.s, s.l);
- bh->txt = malloc(strlen(BAM_VERSION) + 64);
- bh->l_txt = 1 + sprintf(bh->txt, "##samtoolsVersion=%s\n", BAM_VERSION);
- free(s.s);
+ s.l = 0;
+ ksprintf(&s, "##samtoolsVersion=%s\n", BAM_VERSION);
+ if (conf->fai_fname) ksprintf(&s, "##reference=file://%s\n", conf->fai_fname);
+ h->dict = sam_header_parse2(h->text);
+ int nseq;
+ const char *tags[] = {"SN","LN","UR","M5",NULL};
+ char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &nseq);
+ for (i=0; i<nseq; i++)
+ {
+ ksprintf(&s, "##contig=<ID=%s", tbl[4*i]);
+ if ( tbl[4*i+1] ) ksprintf(&s, ",length=%s", tbl[4*i+1]);
+ if ( tbl[4*i+2] ) ksprintf(&s, ",URL=%s", tbl[4*i+2]);
+ if ( tbl[4*i+3] ) ksprintf(&s, ",md5=%s", tbl[4*i+3]);
+ kputs(">\n", &s);
+ }
+ if (tbl) free(tbl);
+ bh->txt = s.s;
+ bh->l_txt = 1 + s.l;
bcf_hdr_sync(bh);
bcf_hdr_write(bp, bh);
bca = bcf_call_init(-1., conf->min_baseQ);
@@ -275,6 +304,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
bca->min_frac = conf->min_frac;
bca->min_support = conf->min_support;
+ bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
}
if (tid0 >= 0 && conf->fai) { // region is set
ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
@@ -309,19 +339,17 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
ref16 = bam_nt16_table[_ref0];
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
- bcf_call_combine(gplp.n, bcr, ref16, &bc);
- bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
- (conf->flag&MPLP_FMT_SP), 0, 0);
+ bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
+ bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, 0, 0);
bcf_write(bp, bh, b);
bcf_destroy(b);
// call indels
if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0) {
for (i = 0; i < gplp.n; ++i)
bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
- if (bcf_call_combine(gplp.n, bcr, -1, &bc) >= 0) {
+ if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
b = calloc(1, sizeof(bcf1_t));
- bcf_call2bcf(tid, pos, &bc, b, (conf->flag&(MPLP_FMT_DP|MPLP_FMT_SP))? bcr : 0,
- (conf->flag&MPLP_FMT_SP), bca, ref);
+ bcf_call2bcf(tid, pos, &bc, b, bcr, conf->fmt_flag, bca, ref);
bcf_write(bp, bh, b);
bcf_destroy(b);
}
@@ -329,20 +357,29 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
} else {
printf("%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
for (i = 0; i < n; ++i) {
- int j;
- printf("\t%d\t", n_plp[i]);
+ int j, cnt;
+ for (j = cnt = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ) ++cnt;
+ }
+ printf("\t%d\t", cnt);
if (n_plp[i] == 0) {
printf("*\t*"); // FIXME: printf() is very slow...
if (conf->flag & MPLP_PRINT_POS) printf("\t*");
} else {
- for (j = 0; j < n_plp[i]; ++j)
- pileup_seq(plp[i] + j, pos, ref_len, ref);
+ for (j = 0; j < n_plp[i]; ++j) {
+ const bam_pileup1_t *p = plp[i] + j;
+ if (bam1_qual(p->b)[p->qpos] >= conf->min_baseQ)
+ pileup_seq(plp[i] + j, pos, ref_len, ref);
+ }
putchar('\t');
for (j = 0; j < n_plp[i]; ++j) {
const bam_pileup1_t *p = plp[i] + j;
- int c = bam1_qual(p->b)[p->qpos] + 33;
- if (c > 126) c = 126;
- putchar(c);
+ int c = bam1_qual(p->b)[p->qpos];
+ if (c >= conf->min_baseQ) {
+ c = c + 33 < 126? c + 33 : 126;
+ putchar(c);
+ }
}
if (conf->flag & MPLP_PRINT_MAPQ) {
putchar('\t');
@@ -383,11 +420,15 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
}
#define MAX_PATH_LEN 1024
-static int read_file_list(const char *file_list,int *n,char **argv[])
+int read_file_list(const char *file_list,int *n,char **argv[])
{
char buf[MAX_PATH_LEN];
- int len, nfiles;
- char **files;
+ int len, nfiles = 0;
+ char **files = NULL;
+ struct stat sb;
+
+ *n = 0;
+ *argv = NULL;
FILE *fh = fopen(file_list,"r");
if ( !fh )
@@ -396,28 +437,33 @@ static int read_file_list(const char *file_list,int *n,char **argv[])
return 1;
}
- // Speed is not an issue here, determine the number of files by reading the file twice
- nfiles = 0;
- while ( fgets(buf,MAX_PATH_LEN,fh) ) nfiles++;
-
- if ( fseek(fh, 0L, SEEK_SET) )
- {
- fprintf(pysamerr,"%s: %s\n", file_list,strerror(errno));
- return 1;
- }
-
files = calloc(nfiles,sizeof(char*));
nfiles = 0;
while ( fgets(buf,MAX_PATH_LEN,fh) )
{
+ // allow empty lines and trailing spaces
len = strlen(buf);
while ( len>0 && isspace(buf[len-1]) ) len--;
if ( !len ) continue;
- files[nfiles] = malloc(sizeof(char)*(len+1));
- strncpy(files[nfiles],buf,len);
- files[nfiles][len] = 0;
+ // check sanity of the file list
+ buf[len] = 0;
+ if (stat(buf, &sb) != 0)
+ {
+ // no such file, check if it is safe to print its name
+ int i, safe_to_print = 1;
+ for (i=0; i<len; i++)
+ if (!isprint(buf[i])) { safe_to_print = 0; break; }
+ if ( safe_to_print )
+ fprintf(pysamerr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+ else
+ fprintf(pysamerr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+ return 1;
+ }
+
nfiles++;
+ files = realloc(files,nfiles*sizeof(char*));
+ files[nfiles-1] = strdup(buf);
}
fclose(fh);
if ( !nfiles )
@@ -439,7 +485,6 @@ int bam_mpileup(int argc, char *argv[])
int nfiles = 0, use_orphan = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
- #define MPLP_PRINT_POS 0x4000
mplp.max_mq = 60;
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
@@ -447,24 +492,35 @@ int bam_mpileup(int argc, char *argv[])
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN;
- while ((c = getopt(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:o:e:h:Im:F:EG:6Os")) >= 0) {
+ static struct option lopts[] =
+ {
+ {"rf",1,0,1}, // require flag
+ {"ff",1,0,2}, // filter flag
+ {0,0,0,0}
+ };
+ while ((c = getopt_long(argc, argv, "Agf:r:l:M:q:Q:uaRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsV1:2:",lopts,NULL)) >= 0) {
switch (c) {
+ case 1 : mplp.rflag_require = strtol(optarg,0,0); break;
+ case 2 : mplp.rflag_filter = strtol(optarg,0,0); break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == 0) return 1;
+ mplp.fai_fname = optarg;
break;
case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg = strdup(optarg); break;
case 'l': mplp.bed = bed_read(optarg); break;
case 'P': mplp.pl_list = strdup(optarg); break;
+ case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
case 'g': mplp.flag |= MPLP_GLF; break;
case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_GLF; break;
case 'a': mplp.flag |= MPLP_NO_ORPHAN | MPLP_REALN; break;
case 'B': mplp.flag &= ~MPLP_REALN; break;
- case 'D': mplp.flag |= MPLP_FMT_DP; break;
- case 'S': mplp.flag |= MPLP_FMT_SP; break;
+ case 'D': mplp.fmt_flag |= B2B_FMT_DP; break;
+ case 'S': mplp.fmt_flag |= B2B_FMT_SP; break;
+ case 'V': mplp.fmt_flag |= B2B_FMT_DV; break;
case 'I': mplp.flag |= MPLP_NO_INDEL; break;
- case 'E': mplp.flag |= MPLP_EXT_BAQ; break;
+ case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
case '6': mplp.flag |= MPLP_ILLUMINA13; break;
case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
@@ -502,10 +558,10 @@ int bam_mpileup(int argc, char *argv[])
fprintf(pysamerr, " -6 assume the quality is in the Illumina-1.3+ encoding\n");
fprintf(pysamerr, " -A count anomalous read pairs\n");
fprintf(pysamerr, " -B disable BAQ computation\n");
- fprintf(pysamerr, " -b FILE list of input BAM files [null]\n");
+ fprintf(pysamerr, " -b FILE list of input BAM filenames, one per line [null]\n");
fprintf(pysamerr, " -C INT parameter for adjusting mapQ; 0 to disable [0]\n");
fprintf(pysamerr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
- fprintf(pysamerr, " -E extended BAQ for higher sensitivity but lower specificity\n");
+ fprintf(pysamerr, " -E recalculate extended BAQ on the fly thus ignoring existing BQs\n");
fprintf(pysamerr, " -f FILE faidx indexed reference sequence file [null]\n");
fprintf(pysamerr, " -G FILE exclude read groups listed in FILE [null]\n");
fprintf(pysamerr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
@@ -514,6 +570,8 @@ int bam_mpileup(int argc, char *argv[])
fprintf(pysamerr, " -R ignore RG tags\n");
fprintf(pysamerr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
fprintf(pysamerr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+ fprintf(pysamerr, " --rf INT required flags: skip reads with mask bits unset []\n");
+ fprintf(pysamerr, " --ff INT filter flags: skip reads with mask bits set []\n");
fprintf(pysamerr, "\nOutput options:\n\n");
fprintf(pysamerr, " -D output per-sample DP in BCF (require -g/-u)\n");
fprintf(pysamerr, " -g generate BCF output (genotype likelihoods)\n");
@@ -529,11 +587,13 @@ int bam_mpileup(int argc, char *argv[])
fprintf(pysamerr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
fprintf(pysamerr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
fprintf(pysamerr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+ fprintf(pysamerr, " -p apply -m and -F per-sample to increase sensitivity\n");
fprintf(pysamerr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(pysamerr, "\n");
fprintf(pysamerr, "Notes: Assuming diploid individuals.\n\n");
return 1;
}
+ bam_no_B = 1;
if (file_list) {
if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
mpileup(&mplp,nfiles,fn);
diff --git a/samtools/bam_reheader.c.pysam.c b/samtools/bam_reheader.c.pysam.c
index 35154d7..dca0c42 100644
--- a/samtools/bam_reheader.c.pysam.c
+++ b/samtools/bam_reheader.c.pysam.c
@@ -2,6 +2,7 @@
#include <stdio.h>
#include <stdlib.h>
+#include "knetfile.h"
#include "bgzf.h"
#include "bam.h"
@@ -13,7 +14,7 @@ int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
bam_header_t *old;
int len;
uint8_t *buf;
- if (in->open_mode != 'r') return -1;
+ if (in->is_write) return -1;
buf = malloc(BUF_SIZE);
old = bam_header_read(in);
fp = bgzf_fdopen(fd, "w");
@@ -23,8 +24,8 @@ int bam_reheader(BGZF *in, const bam_header_t *h, int fd)
bgzf_flush(fp);
}
#ifdef _USE_KNETFILE
- while ((len = knet_read(in->x.fpr, buf, BUF_SIZE)) > 0)
- fwrite(buf, 1, len, fp->x.fpw);
+ while ((len = knet_read(in->fp, buf, BUF_SIZE)) > 0)
+ fwrite(buf, 1, len, fp->fp);
#else
while (!feof(in->file) && (len = fread(buf, 1, BUF_SIZE, in->file)) > 0)
fwrite(buf, 1, len, fp->file);
diff --git a/samtools/bam_sort.c.pysam.c b/samtools/bam_sort.c.pysam.c
index 8737edc..9d86d48 100644
--- a/samtools/bam_sort.c.pysam.c
+++ b/samtools/bam_sort.c.pysam.c
@@ -12,24 +12,28 @@
static int g_is_by_qname = 0;
-static inline int strnum_cmp(const char *a, const char *b)
+static int strnum_cmp(const char *_a, const char *_b)
{
- char *pa, *pb;
- pa = (char*)a; pb = (char*)b;
+ const unsigned char *a = (const unsigned char*)_a, *b = (const unsigned char*)_b;
+ const unsigned char *pa = a, *pb = b;
while (*pa && *pb) {
if (isdigit(*pa) && isdigit(*pb)) {
- long ai, bi;
- ai = strtol(pa, &pa, 10);
- bi = strtol(pb, &pb, 10);
- if (ai != bi) return ai<bi? -1 : ai>bi? 1 : 0;
+ while (*pa == '0') ++pa;
+ while (*pb == '0') ++pb;
+ while (isdigit(*pa) && isdigit(*pb) && *pa == *pb) ++pa, ++pb;
+ if (isdigit(*pa) && isdigit(*pb)) {
+ int i = 0;
+ while (isdigit(pa[i]) && isdigit(pb[i])) ++i;
+ return isdigit(pa[i])? 1 : isdigit(pb[i])? -1 : (int)*pa - (int)*pb;
+ } else if (isdigit(*pa)) return 1;
+ else if (isdigit(*pb)) return -1;
+ else if (pa - a != pb - b) return pa - a < pb - b? 1 : -1;
} else {
- if (*pa != *pb) break;
+ if (*pa != *pb) return (int)*pa - (int)*pb;
++pa; ++pb;
}
}
- if (*pa == *pb)
- return (pa-a) < (pb-b)? -1 : (pa-a) > (pb-b)? 1 : 0;
- return *pa<*pb? -1 : *pa>*pb? 1 : 0;
+ return *pa? 1 : *pb? -1 : 0;
}
#define HEAP_EMPTY 0xffffffffffffffffull
@@ -48,7 +52,7 @@ static inline int heap_lt(const heap1_t a, const heap1_t b)
int t;
if (a.b == 0 || b.b == 0) return a.b == 0? 1 : 0;
t = strnum_cmp(bam1_qname(a.b), bam1_qname(b.b));
- return (t > 0 || (t == 0 && __pos_cmp(a, b)));
+ return (t > 0 || (t == 0 && (a.b->core.flag&0xc0) > (b.b->core.flag&0xc0)));
} else return __pos_cmp(a, b);
}
@@ -87,8 +91,7 @@ static void swap_header_text(bam_header_t *h1, bam_header_t *h2)
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
-int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn,
- int flag, const char *reg)
+int bam_merge_core2(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads, int level)
{
bamFile fpout, *fp;
heap1_t *heap;
@@ -96,7 +99,7 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
bam_header_t *hheaders = NULL;
int i, j, *RG_len = 0;
uint64_t idx = 0;
- char **RG = 0;
+ char **RG = 0, mode[8];
bam_iter_t *iter = 0;
if (headers) {
@@ -211,15 +214,17 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
}
else h->pos = HEAP_EMPTY;
}
- if (flag & MERGE_UNCOMP) fpout = strcmp(out, "-")? bam_open(out, "wu") : bam_dopen(fileno(stdout), "wu");
- else if (flag & MERGE_LEVEL1) fpout = strcmp(out, "-")? bam_open(out, "w1") : bam_dopen(fileno(stdout), "w1");
- else fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w");
- if (fpout == 0) {
+ if (flag & MERGE_UNCOMP) level = 0;
+ else if (flag & MERGE_LEVEL1) level = 1;
+ strcpy(mode, "w");
+ if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
+ if ((fpout = strcmp(out, "-")? bam_open(out, "w") : bam_dopen(fileno(stdout), "w")) == 0) {
fprintf(pysamerr, "[%s] fail to create the output file.\n", __func__);
return -1;
}
bam_header_write(fpout, hout);
bam_header_destroy(hout);
+ if (!(flag & MERGE_UNCOMP)) bgzf_mt(fpout, n_threads, 256);
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
@@ -254,12 +259,17 @@ int bam_merge_core(int by_qname, const char *out, const char *headers, int n, ch
return 0;
}
+int bam_merge_core(int by_qname, const char *out, const char *headers, int n, char * const *fn, int flag, const char *reg)
+{
+ return bam_merge_core2(by_qname, out, headers, n, fn, flag, reg, 0, -1);
+}
+
int bam_merge(int argc, char *argv[])
{
- int c, is_by_qname = 0, flag = 0, ret = 0;
+ int c, is_by_qname = 0, flag = 0, ret = 0, n_threads = 0, level = -1;
char *fn_headers = NULL, *reg = 0;
- while ((c = getopt(argc, argv, "h:nru1R:f")) >= 0) {
+ while ((c = getopt(argc, argv, "h:nru1R:f@:l:")) >= 0) {
switch (c) {
case 'r': flag |= MERGE_RG; break;
case 'f': flag |= MERGE_FORCE; break;
@@ -268,6 +278,8 @@ int bam_merge(int argc, char *argv[])
case '1': flag |= MERGE_LEVEL1; break;
case 'u': flag |= MERGE_UNCOMP; break;
case 'R': reg = strdup(optarg); break;
+ case 'l': level = atoi(optarg); break;
+ case '@': n_threads = atoi(optarg); break;
}
}
if (optind + 2 >= argc) {
@@ -278,6 +290,8 @@ int bam_merge(int argc, char *argv[])
fprintf(pysamerr, " -u uncompressed BAM output\n");
fprintf(pysamerr, " -f overwrite the output BAM if exist\n");
fprintf(pysamerr, " -1 compress level 1\n");
+ fprintf(pysamerr, " -l INT compression level, from 0 to 9 [-1]\n");
+ fprintf(pysamerr, " -@ INT number of BAM compression threads [0]\n");
fprintf(pysamerr, " -R STR merge file in the specified region STR [all]\n");
fprintf(pysamerr, " -h FILE copy the header in FILE to <out.bam> [in1.bam]\n\n");
fprintf(pysamerr, "Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users\n");
@@ -293,51 +307,126 @@ int bam_merge(int argc, char *argv[])
return 1;
}
}
- if (bam_merge_core(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg) < 0) ret = 1;
+ if (bam_merge_core2(is_by_qname, argv[optind], fn_headers, argc - optind - 1, argv + optind + 1, flag, reg, n_threads, level) < 0) ret = 1;
free(reg);
free(fn_headers);
return ret;
}
+/***************
+ * BAM sorting *
+ ***************/
+
+#include <pthread.h>
+
typedef bam1_t *bam1_p;
+static int change_SO(bam_header_t *h, const char *so)
+{
+ char *p, *q, *beg = 0, *end = 0, *newtext;
+ if (h->l_text > 3) {
+ if (strncmp(h->text, "@HD", 3) == 0) {
+ if ((p = strchr(h->text, '\n')) == 0) return -1;
+ *p = '\0';
+ if ((q = strstr(h->text, "\tSO:")) != 0) {
+ *p = '\n'; // change back
+ if (strncmp(q + 4, so, p - q - 4) != 0) {
+ beg = q;
+ for (q += 4; *q != '\n' && *q != '\t'; ++q);
+ end = q;
+ } else return 0; // no need to change
+ } else beg = end = p, *p = '\n';
+ }
+ }
+ if (beg == 0) { // no @HD
+ h->l_text += strlen(so) + 15;
+ newtext = malloc(h->l_text + 1);
+ sprintf(newtext, "@HD\tVN:1.3\tSO:%s\n", so);
+ strcat(newtext, h->text);
+ } else { // has @HD but different or no SO
+ h->l_text = (beg - h->text) + (4 + strlen(so)) + (h->text + h->l_text - end);
+ newtext = malloc(h->l_text + 1);
+ strncpy(newtext, h->text, beg - h->text);
+ sprintf(newtext + (beg - h->text), "\tSO:%s", so);
+ strcat(newtext, end);
+ }
+ free(h->text);
+ h->text = newtext;
+ return 0;
+}
+
static inline int bam1_lt(const bam1_p a, const bam1_p b)
{
if (g_is_by_qname) {
int t = strnum_cmp(bam1_qname(a), bam1_qname(b));
- return (t < 0 || (t == 0 && (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)))));
- } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)));
+ return (t < 0 || (t == 0 && (a->core.flag&0xc0) < (b->core.flag&0xc0)));
+ } else return (((uint64_t)a->core.tid<<32|(a->core.pos+1)<<1|bam1_strand(a)) < ((uint64_t)b->core.tid<<32|(b->core.pos+1)<<1|bam1_strand(b)));
}
KSORT_INIT(sort, bam1_p, bam1_lt)
-static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam_header_t *h, int is_stdout)
+typedef struct {
+ size_t buf_len;
+ const char *prefix;
+ bam1_p *buf;
+ const bam_header_t *h;
+ int index;
+} worker_t;
+
+static void write_buffer(const char *fn, const char *mode, size_t l, bam1_p *buf, const bam_header_t *h, int n_threads)
{
- char *name, mode[3];
- int i;
+ size_t i;
bamFile fp;
- ks_mergesort(sort, k, buf, 0);
- name = (char*)calloc(strlen(prefix) + 20, 1);
- if (n >= 0) {
- sprintf(name, "%s.%.4d.bam", prefix, n);
- strcpy(mode, "w1");
- } else {
- sprintf(name, "%s.bam", prefix);
- strcpy(mode, "w");
- }
- fp = is_stdout? bam_dopen(fileno(stdout), mode) : bam_open(name, mode);
- if (fp == 0) {
- fprintf(pysamerr, "[sort_blocks] fail to create file %s.\n", name);
- free(name);
- // FIXME: possible memory leak
- return;
- }
- free(name);
+ fp = strcmp(fn, "-")? bam_open(fn, mode) : bam_dopen(fileno(stdout), mode);
+ if (fp == 0) return;
bam_header_write(fp, h);
- for (i = 0; i < k; ++i)
+ if (n_threads > 1) bgzf_mt(fp, n_threads, 256);
+ for (i = 0; i < l; ++i)
bam_write1_core(fp, &buf[i]->core, buf[i]->data_len, buf[i]->data);
bam_close(fp);
}
+static void *worker(void *data)
+{
+ worker_t *w = (worker_t*)data;
+ char *name;
+ ks_mergesort(sort, w->buf_len, w->buf, 0);
+ name = (char*)calloc(strlen(w->prefix) + 20, 1);
+ sprintf(name, "%s.%.4d.bam", w->prefix, w->index);
+ write_buffer(name, "w1", w->buf_len, w->buf, w->h, 0);
+ free(name);
+ return 0;
+}
+
+static int sort_blocks(int n_files, size_t k, bam1_p *buf, const char *prefix, const bam_header_t *h, int n_threads)
+{
+ int i;
+ size_t rest;
+ bam1_p *b;
+ pthread_t *tid;
+ pthread_attr_t attr;
+ worker_t *w;
+
+ if (n_threads < 1) n_threads = 1;
+ if (k < n_threads * 64) n_threads = 1; // use a single thread if we only sort a small batch of records
+ pthread_attr_init(&attr);
+ pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+ w = calloc(n_threads, sizeof(worker_t));
+ tid = calloc(n_threads, sizeof(pthread_t));
+ b = buf; rest = k;
+ for (i = 0; i < n_threads; ++i) {
+ w[i].buf_len = rest / (n_threads - i);
+ w[i].buf = b;
+ w[i].prefix = prefix;
+ w[i].h = h;
+ w[i].index = n_files + i;
+ b += w[i].buf_len; rest -= w[i].buf_len;
+ pthread_create(&tid[i], &attr, worker, &w[i]);
+ }
+ for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
+ free(tid); free(w);
+ return n_files + n_threads;
+}
+
/*!
@abstract Sort an unsorted BAM file based on the chromosome order
and the leftmost position of an alignment
@@ -347,68 +436,94 @@ static void sort_blocks(int n, int k, bam1_p *buf, const char *prefix, const bam
@param prefix prefix of the output and the temporary files; upon
sucessess, prefix.bam will be written.
@param max_mem approxiate maximum memory (very inaccurate)
+ @param full_path the given output path is the full path and not just the prefix
@discussion It may create multiple temporary subalignment files
and then merge them by calling bam_merge_core(). This function is
NOT thread safe.
*/
-void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t max_mem, int is_stdout)
+void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size_t _max_mem, int is_stdout, int n_threads, int level, int full_path)
{
- int n, ret, k, i;
- size_t mem;
+ int ret, i, n_files = 0;
+ size_t mem, max_k, k, max_mem;
bam_header_t *header;
bamFile fp;
bam1_t *b, **buf;
+ char *fnout = 0;
+ char const *suffix = ".bam";
+ if (full_path) suffix += 4;
+ if (n_threads < 2) n_threads = 1;
g_is_by_qname = is_by_qname;
- n = k = 0; mem = 0;
+ max_k = k = 0; mem = 0;
+ max_mem = _max_mem * n_threads;
+ buf = 0;
fp = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
if (fp == 0) {
fprintf(pysamerr, "[bam_sort_core] fail to open file %s\n", fn);
return;
}
header = bam_header_read(fp);
- buf = (bam1_t**)calloc(max_mem / BAM_CORE_SIZE, sizeof(bam1_t*));
+ if (is_by_qname) change_SO(header, "queryname");
+ else change_SO(header, "coordinate");
// write sub files
for (;;) {
+ if (k == max_k) {
+ size_t old_max = max_k;
+ max_k = max_k? max_k<<1 : 0x10000;
+ buf = realloc(buf, max_k * sizeof(void*));
+ memset(buf + old_max, 0, sizeof(void*) * (max_k - old_max));
+ }
if (buf[k] == 0) buf[k] = (bam1_t*)calloc(1, sizeof(bam1_t));
b = buf[k];
if ((ret = bam_read1(fp, b)) < 0) break;
- mem += ret;
+ if (b->data_len < b->m_data>>2) { // shrink
+ b->m_data = b->data_len;
+ kroundup32(b->m_data);
+ b->data = realloc(b->data, b->m_data);
+ }
+ mem += sizeof(bam1_t) + b->m_data + sizeof(void*) + sizeof(void*); // two sizeof(void*) for the data allocated to pointer arrays
++k;
if (mem >= max_mem) {
- sort_blocks(n++, k, buf, prefix, header, 0);
- mem = 0; k = 0;
+ n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
+ mem = k = 0;
}
}
if (ret != -1)
fprintf(pysamerr, "[bam_sort_core] truncated file. Continue anyway.\n");
- if (n == 0) sort_blocks(-1, k, buf, prefix, header, is_stdout);
- else { // then merge
- char **fns, *fnout;
- fprintf(pysamerr, "[bam_sort_core] merging from %d files...\n", n+1);
- sort_blocks(n++, k, buf, prefix, header, 0);
- fnout = (char*)calloc(strlen(prefix) + 20, 1);
- if (is_stdout) sprintf(fnout, "-");
- else sprintf(fnout, "%s.bam", prefix);
- fns = (char**)calloc(n, sizeof(char*));
- for (i = 0; i < n; ++i) {
+ // output file name
+ fnout = calloc(strlen(prefix) + 20, 1);
+ if (is_stdout) sprintf(fnout, "-");
+ else sprintf(fnout, "%s%s", prefix, suffix);
+ // write the final output
+ if (n_files == 0) { // a single block
+ char mode[8];
+ strcpy(mode, "w");
+ if (level >= 0) sprintf(mode + 1, "%d", level < 9? level : 9);
+ ks_mergesort(sort, k, buf, 0);
+ write_buffer(fnout, mode, k, buf, header, n_threads);
+ } else { // then merge
+ char **fns;
+ n_files = sort_blocks(n_files, k, buf, prefix, header, n_threads);
+ fprintf(pysamerr, "[bam_sort_core] merging from %d files...\n", n_files);
+ fns = (char**)calloc(n_files, sizeof(char*));
+ for (i = 0; i < n_files; ++i) {
fns[i] = (char*)calloc(strlen(prefix) + 20, 1);
- sprintf(fns[i], "%s.%.4d.bam", prefix, i);
+ sprintf(fns[i], "%s.%.4d%s", prefix, i, suffix);
}
- bam_merge_core(is_by_qname, fnout, 0, n, fns, 0, 0);
- free(fnout);
- for (i = 0; i < n; ++i) {
+ bam_merge_core2(is_by_qname, fnout, 0, n_files, fns, 0, 0, n_threads, level);
+ for (i = 0; i < n_files; ++i) {
unlink(fns[i]);
free(fns[i]);
}
free(fns);
}
- for (k = 0; k < max_mem / BAM_CORE_SIZE; ++k) {
- if (buf[k]) {
- free(buf[k]->data);
- free(buf[k]);
- }
+ free(fnout);
+ // free
+ for (k = 0; k < max_k; ++k) {
+ if (!buf[k]) continue;
+ free(buf[k]->data);
+ free(buf[k]);
}
free(buf);
bam_header_destroy(header);
@@ -417,24 +532,42 @@ void bam_sort_core_ext(int is_by_qname, const char *fn, const char *prefix, size
void bam_sort_core(int is_by_qname, const char *fn, const char *prefix, size_t max_mem)
{
- bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0);
+ bam_sort_core_ext(is_by_qname, fn, prefix, max_mem, 0, 0, -1, 0);
}
int bam_sort(int argc, char *argv[])
{
- size_t max_mem = 500000000;
- int c, is_by_qname = 0, is_stdout = 0;
- while ((c = getopt(argc, argv, "nom:")) >= 0) {
+ size_t max_mem = 768<<20; // 512MB
+ int c, is_by_qname = 0, is_stdout = 0, n_threads = 0, level = -1, full_path = 0;
+ while ((c = getopt(argc, argv, "fnom:@:l:")) >= 0) {
switch (c) {
+ case 'f': full_path = 1; break;
case 'o': is_stdout = 1; break;
case 'n': is_by_qname = 1; break;
- case 'm': max_mem = atol(optarg); break;
+ case 'm': {
+ char *q;
+ max_mem = strtol(optarg, &q, 0);
+ if (*q == 'k' || *q == 'K') max_mem <<= 10;
+ else if (*q == 'm' || *q == 'M') max_mem <<= 20;
+ else if (*q == 'g' || *q == 'G') max_mem <<= 30;
+ break;
+ }
+ case '@': n_threads = atoi(optarg); break;
+ case 'l': level = atoi(optarg); break;
}
}
if (optind + 2 > argc) {
- fprintf(pysamerr, "Usage: samtools sort [-on] [-m <maxMem>] <in.bam> <out.prefix>\n");
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: samtools sort [options] <in.bam> <out.prefix>\n\n");
+ fprintf(pysamerr, "Options: -n sort by read name\n");
+ fprintf(pysamerr, " -f use <out.prefix> as full file name instead of prefix\n");
+ fprintf(pysamerr, " -o final output to stdout\n");
+ fprintf(pysamerr, " -l INT compression level, from 0 to 9 [-1]\n");
+ fprintf(pysamerr, " -@ INT number of sorting and compression threads [1]\n");
+ fprintf(pysamerr, " -m INT max memory per thread; suffix K/M/G recognized [768M]\n");
+ fprintf(pysamerr, "\n");
return 1;
}
- bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout);
+ bam_sort_core_ext(is_by_qname, argv[optind], argv[optind+1], max_mem, is_stdout, n_threads, level, full_path);
return 0;
}
diff --git a/samtools/bam_tview.c.pysam.c b/samtools/bam_tview.c.pysam.c
index 3709702..26679eb 100644
--- a/samtools/bam_tview.c.pysam.c
+++ b/samtools/bam_tview.c.pysam.c
@@ -1,63 +1,83 @@
#include "pysam.h"
-#undef _HAVE_CURSES
-
-#if _CURSES_LIB == 0
-#elif _CURSES_LIB == 1
-#include <curses.h>
-#ifndef NCURSES_VERSION
-#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
-#else
-#define _HAVE_CURSES
-#endif
-#elif _CURSES_LIB == 2
-#include <xcurses.h>
-#define _HAVE_CURSES
-#else
-#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
-#endif
-
-#ifdef _HAVE_CURSES
-#include <ctype.h>
#include <assert.h>
-#include <string.h>
-#include <math.h>
-#include "bam.h"
-#include "faidx.h"
-#include "bam2bcf.h"
-
-char bam_aux_getCEi(bam1_t *b, int i);
-char bam_aux_getCSi(bam1_t *b, int i);
-char bam_aux_getCQi(bam1_t *b, int i);
+#include "bam_tview.h"
-#define TV_MIN_ALNROW 2
-#define TV_MAX_GOTO 40
-#define TV_LOW_MAPQ 10
+int base_tv_init(tview_t* tv,const char *fn, const char *fn_fa, const char *samples)
+ {
+ assert(tv!=NULL);
+ assert(fn!=NULL);
+ tv->mrow = 24; tv->mcol = 80;
+ tv->color_for = TV_COLOR_MAPQ;
+ tv->is_dot = 1;
+
+ tv->fp = bam_open(fn, "r");
+ if(tv->fp==0)
+ {
+ fprintf(pysamerr,"bam_open %s. %s\n", fn,fn_fa);
+ exit(EXIT_FAILURE);
+ }
+ bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
+ assert(tv->fp);
+
+ tv->header = bam_header_read(tv->fp);
+ if(tv->header==0)
+ {
+ fprintf(pysamerr,"Cannot read '%s'.\n", fn);
+ exit(EXIT_FAILURE);
+ }
+ tv->idx = bam_index_load(fn);
+ if (tv->idx == 0)
+ {
+ fprintf(pysamerr,"Cannot read index for '%s'.\n", fn);
+ exit(EXIT_FAILURE);
+ }
+ tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
+ if (fn_fa) tv->fai = fai_load(fn_fa);
+ tv->bca = bcf_call_init(0.83, 13);
+ tv->ins = 1;
-#define TV_COLOR_MAPQ 0
-#define TV_COLOR_BASEQ 1
-#define TV_COLOR_NUCL 2
-#define TV_COLOR_COL 3
-#define TV_COLOR_COLQ 4
+ if ( samples )
+ {
+ if ( !tv->header->dict ) tv->header->dict = sam_header_parse2(tv->header->text);
+ void *iter = tv->header->dict;
+ const char *key, *val;
+ int n = 0;
+ tv->rg_hash = kh_init(kh_rg);
+ while ( (iter = sam_header2key_val(iter, "RG","ID","SM", &key, &val)) )
+ {
+ if ( !strcmp(samples,key) || (val && !strcmp(samples,val)) )
+ {
+ khiter_t k = kh_get(kh_rg, tv->rg_hash, key);
+ if ( k != kh_end(tv->rg_hash) ) continue;
+ int ret;
+ k = kh_put(kh_rg, tv->rg_hash, key, &ret);
+ kh_value(tv->rg_hash, k) = val;
+ n++;
+ }
+ }
+ if ( !n )
+ {
+ fprintf(pysamerr,"The sample or read group \"%s\" not present.\n", samples);
+ exit(EXIT_FAILURE);
+ }
+ }
-#define TV_BASE_NUCL 0
-#define TV_BASE_COLOR_SPACE 1
+ return 0;
+ }
-typedef struct {
- int mrow, mcol;
- WINDOW *wgoto, *whelp;
- bam_index_t *idx;
- bam_lplbuf_t *lplbuf;
- bam_header_t *header;
- bamFile fp;
- int curr_tid, left_pos;
- faidx_t *fai;
- bcf_callaux_t *bca;
+void base_tv_destroy(tview_t* tv)
+ {
+ bam_lplbuf_destroy(tv->lplbuf);
+ bcf_call_destroy(tv->bca);
+ bam_index_destroy(tv->idx);
+ if (tv->fai) fai_destroy(tv->fai);
+ free(tv->ref);
+ bam_header_destroy(tv->header);
+ bam_close(tv->fp);
+ }
- int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
- char *ref;
-} tview_t;
int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
{
@@ -69,11 +89,11 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
// print referece
rb = (tv->ref && pos - tv->left_pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N';
for (i = tv->last_pos + 1; i < pos; ++i) {
- if (i%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", i+1);
+ if (i%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", i+1);
c = tv->ref? tv->ref[i - tv->left_pos] : 'N';
- mvaddch(1, tv->ccol++, c);
+ tv->my_mvaddch(tv,1, tv->ccol++, c);
}
- if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
{ // call consensus
bcf_callret1_t bcr;
int qsum[4], a1, a2, tmp;
@@ -91,15 +111,15 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
else if (p[2] < p[1] && p[2] < p[0]) call = (1<<a2)<<16 | (int)((p[0]<p[1]?p[0]:p[1]) - p[2] + .499);
else call = (1<<a1|1<<a2)<<16 | (int)((p[0]<p[2]?p[0]:p[2]) - p[1] + .499);
}
- attr = A_UNDERLINE;
+ attr = tv->my_underline(tv);
c = ",ACMGRSVTWYHKDBN"[call>>16&0xf];
i = (call&0xffff)/10+1;
if (i > 4) i = 4;
- attr |= COLOR_PAIR(i);
+ attr |= tv->my_colorpair(tv,i);
if (c == toupper(rb)) c = '.';
- attron(attr);
- mvaddch(2, tv->ccol, c);
- attroff(attr);
+ tv->my_attron(tv,attr);
+ tv->my_mvaddch(tv,2, tv->ccol, c);
+ tv->my_attroff(tv,attr);
if(tv->ins) {
// calculate maximum insert
for (i = 0; i < n; ++i) {
@@ -116,7 +136,6 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
if (!p->is_del) {
if (tv->base_for == TV_BASE_COLOR_SPACE &&
(c = bam_aux_getCSi(p->b, p->qpos))) {
- c = bam_aux_getCSi(p->b, p->qpos);
// assume that if we found one color, we will be able to get the color error
if (tv->is_dot && '-' == bam_aux_getCEi(p->b, p->qpos)) c = bam1_strand(p->b)? ',' : '.';
} else {
@@ -150,18 +169,18 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
int x;
attr = 0;
if (((p->b->core.flag&BAM_FPAIRED) && !(p->b->core.flag&BAM_FPROPER_PAIR))
- || (p->b->core.flag & BAM_FSECONDARY)) attr |= A_UNDERLINE;
+ || (p->b->core.flag & BAM_FSECONDARY)) attr |= tv->my_underline(tv);
if (tv->color_for == TV_COLOR_BASEQ) {
x = bam1_qual(p->b)[p->qpos]/10 + 1;
if (x > 4) x = 4;
- attr |= COLOR_PAIR(x);
+ attr |= tv->my_colorpair(tv,x);
} else if (tv->color_for == TV_COLOR_MAPQ) {
x = p->b->core.qual/10 + 1;
if (x > 4) x = 4;
- attr |= COLOR_PAIR(x);
+ attr |= tv->my_colorpair(tv,x);
} else if (tv->color_for == TV_COLOR_NUCL) {
x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)] + 5;
- attr |= COLOR_PAIR(x);
+ attr |= tv->my_colorpair(tv,x);
} else if(tv->color_for == TV_COLOR_COL) {
x = 0;
switch(bam_aux_getCSi(p->b, p->qpos)) {
@@ -173,87 +192,44 @@ int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void
default: x = bam_nt16_nt4_table[bam1_seqi(bam1_seq(p->b), p->qpos)]; break;
}
x+=5;
- attr |= COLOR_PAIR(x);
+ attr |= tv->my_colorpair(tv,x);
} else if(tv->color_for == TV_COLOR_COLQ) {
x = bam_aux_getCQi(p->b, p->qpos);
if(0 == x) x = bam1_qual(p->b)[p->qpos];
x = x/10 + 1;
if (x > 4) x = 4;
- attr |= COLOR_PAIR(x);
+ attr |= tv->my_colorpair(tv,x);
}
- attron(attr);
- mvaddch(row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
- attroff(attr);
+ tv->my_attron(tv,attr);
+ tv->my_mvaddch(tv,row, tv->ccol, bam1_strand(p->b)? tolower(c) : toupper(c));
+ tv->my_attroff(tv,attr);
}
}
c = j? '*' : rb;
if (c == '*') {
- attr = COLOR_PAIR(8);
- attron(attr);
- mvaddch(1, tv->ccol++, c);
- attroff(attr);
- } else mvaddch(1, tv->ccol++, c);
+ attr = tv->my_colorpair(tv,8);
+ tv->my_attron(tv,attr);
+ tv->my_mvaddch(tv,1, tv->ccol++, c);
+ tv->my_attroff(tv,attr);
+ } else tv->my_mvaddch(tv,1, tv->ccol++, c);
}
tv->last_pos = pos;
return 0;
}
-tview_t *tv_init(const char *fn, const char *fn_fa)
-{
- tview_t *tv = (tview_t*)calloc(1, sizeof(tview_t));
- tv->is_dot = 1;
- tv->fp = bam_open(fn, "r");
- bgzf_set_cache_size(tv->fp, 8 * 1024 *1024);
- assert(tv->fp);
- tv->header = bam_header_read(tv->fp);
- tv->idx = bam_index_load(fn);
- if (tv->idx == 0) exit(1);
- tv->lplbuf = bam_lplbuf_init(tv_pl_func, tv);
- if (fn_fa) tv->fai = fai_load(fn_fa);
- tv->bca = bcf_call_init(0.83, 13);
- tv->ins = 1;
-
- initscr();
- keypad(stdscr, TRUE);
- clear();
- noecho();
- cbreak();
- tv->mrow = 24; tv->mcol = 80;
- getmaxyx(stdscr, tv->mrow, tv->mcol);
- tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
- tv->whelp = newwin(29, 40, 5, 5);
- tv->color_for = TV_COLOR_MAPQ;
- start_color();
- init_pair(1, COLOR_BLUE, COLOR_BLACK);
- init_pair(2, COLOR_GREEN, COLOR_BLACK);
- init_pair(3, COLOR_YELLOW, COLOR_BLACK);
- init_pair(4, COLOR_WHITE, COLOR_BLACK);
- init_pair(5, COLOR_GREEN, COLOR_BLACK);
- init_pair(6, COLOR_CYAN, COLOR_BLACK);
- init_pair(7, COLOR_YELLOW, COLOR_BLACK);
- init_pair(8, COLOR_RED, COLOR_BLACK);
- init_pair(9, COLOR_BLUE, COLOR_BLACK);
- return tv;
-}
-void tv_destroy(tview_t *tv)
-{
- delwin(tv->wgoto); delwin(tv->whelp);
- endwin();
- bam_lplbuf_destroy(tv->lplbuf);
- bcf_call_destroy(tv->bca);
- bam_index_destroy(tv->idx);
- if (tv->fai) fai_destroy(tv->fai);
- free(tv->ref);
- bam_header_destroy(tv->header);
- bam_close(tv->fp);
- free(tv);
-}
int tv_fetch_func(const bam1_t *b, void *data)
{
tview_t *tv = (tview_t*)data;
+ if ( tv->rg_hash )
+ {
+ const uint8_t *rg = bam_aux_get(b, "RG");
+ if ( !rg ) return 0;
+ khiter_t k = kh_get(kh_rg, tv->rg_hash, (const char*)(rg + 1));
+ if ( k == kh_end(tv->rg_hash) ) return 0;
+ }
if (tv->no_skip) {
uint32_t *cigar = bam1_cigar(b); // this is cheating...
int i;
@@ -266,10 +242,11 @@ int tv_fetch_func(const bam1_t *b, void *data)
return 0;
}
-int tv_draw_aln(tview_t *tv, int tid, int pos)
-{
+int base_draw_aln(tview_t *tv, int tid, int pos)
+ {
+ assert(tv!=NULL);
// reset
- clear();
+ tv->my_clear(tv);
tv->curr_tid = tid; tv->left_pos = pos;
tv->last_pos = tv->left_pos - 1;
tv->ccol = 0;
@@ -277,7 +254,10 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
if (tv->fai) {
char *str;
if (tv->ref) free(tv->ref);
+ assert(tv->curr_tid>=0);
+
str = (char*)calloc(strlen(tv->header->target_name[tv->curr_tid]) + 30, 1);
+ assert(str!=NULL);
sprintf(str, "%s:%d-%d", tv->header->target_name[tv->curr_tid], tv->left_pos + 1, tv->left_pos + tv->mcol);
tv->ref = fai_fetch(tv->fai, str, &tv->l_ref);
free(str);
@@ -289,154 +269,102 @@ int tv_draw_aln(tview_t *tv, int tid, int pos)
while (tv->ccol < tv->mcol) {
int pos = tv->last_pos + 1;
- if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) mvprintw(0, tv->ccol, "%-d", pos+1);
- mvaddch(1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
+ if (pos%10 == 0 && tv->mcol - tv->ccol >= 10) tv->my_mvprintw(tv,0, tv->ccol, "%-d", pos+1);
+ tv->my_mvaddch(tv,1, tv->ccol++, (tv->ref && pos < tv->l_ref)? tv->ref[pos - tv->left_pos] : 'N');
++tv->last_pos;
}
return 0;
}
-static void tv_win_goto(tview_t *tv, int *tid, int *pos)
-{
- char str[256], *p;
- int i, l = 0;
- wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
- mvwprintw(tv->wgoto, 1, 2, "Goto: ");
- for (;;) {
- int c = wgetch(tv->wgoto);
- wrefresh(tv->wgoto);
- if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
- --l;
- } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
- int _tid = -1, _beg, _end;
- if (str[0] == '=') {
- _beg = strtol(str+1, &p, 10) - 1;
- if (_beg > 0) {
- *pos = _beg;
- return;
- }
- } else {
- bam_parse_region(tv->header, str, &_tid, &_beg, &_end);
- if (_tid >= 0) {
- *tid = _tid; *pos = _beg;
- return;
- }
- }
- } else if (isgraph(c)) {
- if (l < TV_MAX_GOTO) str[l++] = c;
- } else if (c == '\027') l = 0;
- else if (c == '\033') return;
- str[l] = '\0';
- for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
- mvwprintw(tv->wgoto, 1, 8, "%s", str);
- }
-}
-static void tv_win_help(tview_t *tv) {
- int r = 1;
- WINDOW *win = tv->whelp;
- wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
- mvwprintw(win, r++, 2, " -=- Help -=- ");
- r++;
- mvwprintw(win, r++, 2, "? This window");
- mvwprintw(win, r++, 2, "Arrows Small scroll movement");
- mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
- mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
- mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
- mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
- mvwprintw(win, r++, 2, "space Scroll one screen");
- mvwprintw(win, r++, 2, "backspace Scroll back one screen");
- mvwprintw(win, r++, 2, "g Go to specific location");
- mvwprintw(win, r++, 2, "m Color for mapping qual");
- mvwprintw(win, r++, 2, "n Color for nucleotide");
- mvwprintw(win, r++, 2, "b Color for base quality");
- mvwprintw(win, r++, 2, "c Color for cs color");
- mvwprintw(win, r++, 2, "z Color for cs qual");
- mvwprintw(win, r++, 2, ". Toggle on/off dot view");
- mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
- mvwprintw(win, r++, 2, "r Toggle on/off rd name");
- mvwprintw(win, r++, 2, "N Turn on nt view");
- mvwprintw(win, r++, 2, "C Turn on cs view");
- mvwprintw(win, r++, 2, "i Toggle on/off ins");
- mvwprintw(win, r++, 2, "q Exit");
- r++;
- mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
- mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
- mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
- wrefresh(win);
- wgetch(win);
-}
-void tv_loop(tview_t *tv)
+
+static void error(const char *format, ...)
{
- int tid, pos;
- tid = tv->curr_tid; pos = tv->left_pos;
- while (1) {
- int c = getch();
- switch (c) {
- case '?': tv_win_help(tv); break;
- case '\033':
- case 'q': goto end_loop;
- case '/':
- case 'g': tv_win_goto(tv, &tid, &pos); break;
- case 'm': tv->color_for = TV_COLOR_MAPQ; break;
- case 'b': tv->color_for = TV_COLOR_BASEQ; break;
- case 'n': tv->color_for = TV_COLOR_NUCL; break;
- case 'c': tv->color_for = TV_COLOR_COL; break;
- case 'z': tv->color_for = TV_COLOR_COLQ; break;
- case 's': tv->no_skip = !tv->no_skip; break;
- case 'r': tv->show_name = !tv->show_name; break;
- case KEY_LEFT:
- case 'h': --pos; break;
- case KEY_RIGHT:
- case 'l': ++pos; break;
- case KEY_SLEFT:
- case 'H': pos -= 20; break;
- case KEY_SRIGHT:
- case 'L': pos += 20; break;
- case '.': tv->is_dot = !tv->is_dot; break;
- case 'N': tv->base_for = TV_BASE_NUCL; break;
- case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
- case 'i': tv->ins = !tv->ins; break;
- case '\010': pos -= 1000; break;
- case '\014': pos += 1000; break;
- case ' ': pos += tv->mcol; break;
- case KEY_UP:
- case 'j': --tv->row_shift; break;
- case KEY_DOWN:
- case 'k': ++tv->row_shift; break;
- case KEY_BACKSPACE:
- case '\177': pos -= tv->mcol; break;
- case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
- default: continue;
- }
- if (pos < 0) pos = 0;
- if (tv->row_shift < 0) tv->row_shift = 0;
- tv_draw_aln(tv, tid, pos);
- }
-end_loop:
- return;
+ if ( !format )
+ {
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: bamtk tview [options] <aln.bam> [ref.fasta]\n");
+ fprintf(pysamerr, "Options:\n");
+ fprintf(pysamerr, " -d display output as (H)tml or (C)urses or (T)ext \n");
+ fprintf(pysamerr, " -p chr:pos go directly to this position\n");
+ fprintf(pysamerr, " -s STR display only reads from this sample or group\n");
+ fprintf(pysamerr, "\n\n");
+ }
+ else
+ {
+ va_list ap;
+ va_start(ap, format);
+ vfprintf(pysamerr, format, ap);
+ va_end(ap);
+ }
+ exit(-1);
}
+enum dipsay_mode {display_ncurses,display_html,display_text};
+extern tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples);
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
+
int bam_tview_main(int argc, char *argv[])
-{
- tview_t *tv;
- if (argc == 1) {
- fprintf(pysamerr, "Usage: bamtk tview <aln.bam> [ref.fasta]\n");
- return 1;
+ {
+ int view_mode=display_ncurses;
+ tview_t* tv=NULL;
+ char *samples=NULL, *position=NULL;
+ int c;
+ while ((c = getopt(argc, argv, "s:p:d:")) >= 0) {
+ switch (c) {
+ case 's': samples=optarg; break;
+ case 'p': position=optarg; break;
+ case 'd':
+ {
+ switch(optarg[0])
+ {
+ case 'H': case 'h': view_mode=display_html;break;
+ case 'T': case 't': view_mode=display_text;break;
+ case 'C': case 'c': view_mode=display_ncurses;break;
+ default: view_mode=display_ncurses;break;
+ }
+ break;
+ }
+ default: error(NULL);
+ }
+ }
+ if (argc==optind) error(NULL);
+
+ switch(view_mode)
+ {
+ case display_ncurses:
+ {
+ tv = curses_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+ break;
+ }
+ case display_text:
+ {
+ tv = text_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+ break;
+ }
+ case display_html:
+ {
+ tv = html_tv_init(argv[optind], (optind+1>=argc)? 0 : argv[optind+1], samples);
+ break;
+ }
+ }
+ if(tv==NULL)
+ {
+ error("cannot create view");
+ return EXIT_FAILURE;
+ }
+
+ if ( position )
+ {
+ int _tid = -1, _beg, _end;
+ bam_parse_region(tv->header, position, &_tid, &_beg, &_end);
+ if (_tid >= 0) { tv->curr_tid = _tid; tv->left_pos = _beg; }
+ }
+ tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+ tv->my_loop(tv);
+ tv->my_destroy(tv);
+
+ return EXIT_SUCCESS;
}
- tv = tv_init(argv[1], (argc == 2)? 0 : argv[2]);
- tv_draw_aln(tv, 0, 0);
- tv_loop(tv);
- tv_destroy(tv);
- return 0;
-}
-#else // #ifdef _HAVE_CURSES
-#include <stdio.h>
-#warning "No curses library is available; tview is disabled."
-int bam_tview_main(int argc, char *argv[])
-{
- fprintf(pysamerr, "[bam_tview_main] The ncurses library is unavailable; tview is not compiled.\n");
- return 1;
-}
-#endif // #ifdef _HAVE_CURSES
diff --git a/samtools/bam_tview.h b/samtools/bam_tview.h
new file mode 100644
index 0000000..80f0464
--- /dev/null
+++ b/samtools/bam_tview.h
@@ -0,0 +1,75 @@
+#ifndef BAM_TVIEW_H
+#define BAM_TVIEW_H
+
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include <math.h>
+#include <unistd.h>
+#include <stdarg.h>
+#include "bam.h"
+#include "faidx.h"
+#include "bam2bcf.h"
+#include "sam_header.h"
+#include "khash.h"
+
+KHASH_MAP_INIT_STR(kh_rg, const char *)
+
+typedef struct AbstractTview {
+ int mrow, mcol;
+
+ bam_index_t *idx;
+ bam_lplbuf_t *lplbuf;
+ bam_header_t *header;
+ bamFile fp;
+ int curr_tid, left_pos;
+ faidx_t *fai;
+ bcf_callaux_t *bca;
+
+ int ccol, last_pos, row_shift, base_for, color_for, is_dot, l_ref, ins, no_skip, show_name;
+ char *ref;
+ khash_t(kh_rg) *rg_hash;
+ /* callbacks */
+ void (*my_destroy)(struct AbstractTview* );
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+ void (*my_mvaddch)(struct AbstractTview*,int,int,int);
+ void (*my_attron)(struct AbstractTview*,int);
+ void (*my_attroff)(struct AbstractTview*,int);
+ void (*my_clear)(struct AbstractTview*);
+ int (*my_colorpair)(struct AbstractTview*,int);
+ int (*my_drawaln)(struct AbstractTview*,int,int);
+ int (*my_loop)(struct AbstractTview*);
+ int (*my_underline)(struct AbstractTview*);
+} tview_t;
+
+
+char bam_aux_getCEi(bam1_t *b, int i);
+char bam_aux_getCSi(bam1_t *b, int i);
+char bam_aux_getCQi(bam1_t *b, int i);
+
+#define TV_MIN_ALNROW 2
+#define TV_MAX_GOTO 40
+#define TV_LOW_MAPQ 10
+
+#define TV_COLOR_MAPQ 0
+#define TV_COLOR_BASEQ 1
+#define TV_COLOR_NUCL 2
+#define TV_COLOR_COL 3
+#define TV_COLOR_COLQ 4
+
+#define TV_BASE_NUCL 0
+#define TV_BASE_COLOR_SPACE 1
+
+int tv_pl_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data);
+int base_tv_init(tview_t*,const char *fn, const char *fn_fa, const char *samples);
+void base_tv_destroy(tview_t*);
+int base_draw_aln(tview_t *tv, int tid, int pos);
+
+typedef struct Tixel
+ {
+ int ch;
+ int attributes;
+ }tixel_t;
+
+#endif
+
diff --git a/samtools/bam_tview_curses.c.pysam.c b/samtools/bam_tview_curses.c.pysam.c
new file mode 100644
index 0000000..fb14594
--- /dev/null
+++ b/samtools/bam_tview_curses.c.pysam.c
@@ -0,0 +1,299 @@
+#include "pysam.h"
+
+#undef _HAVE_CURSES
+
+#if _CURSES_LIB == 0
+#elif _CURSES_LIB == 1
+#include <curses.h>
+#ifndef NCURSES_VERSION
+#warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled"
+#else
+#define _HAVE_CURSES
+#endif
+#elif _CURSES_LIB == 2
+#include <xcurses.h>
+#define _HAVE_CURSES
+#else
+#warning "_CURSES_LIB is not 0, 1 or 2; tview is NOT compiled"
+#endif
+
+
+#include "bam_tview.h"
+
+#ifdef _HAVE_CURSES
+
+
+
+typedef struct CursesTview {
+ tview_t view;
+ WINDOW *wgoto, *whelp;
+ } curses_tview_t;
+
+
+
+
+#define FROM_TV(ptr) ((curses_tview_t*)ptr)
+
+static void curses_destroy(tview_t* base)
+ {
+ curses_tview_t* tv=(curses_tview_t*)base;
+
+
+ delwin(tv->wgoto); delwin(tv->whelp);
+ endwin();
+
+ base_tv_destroy(base);
+
+ free(tv);
+ }
+
+/*
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+ void (*my_)(struct AbstractTview*,int,int,int);
+ void (*my_attron)(struct AbstractTview*,int);
+ void (*my_attroff)(struct AbstractTview*,int);
+ void (*my_clear)(struct AbstractTview*);
+ int (*my_colorpair)(struct AbstractTview*,int);
+*/
+
+static void curses_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
+ {
+ unsigned int size=tv->mcol+2;
+ char* str=malloc(size);
+ if(str==0) exit(EXIT_FAILURE);
+ va_list argptr;
+ va_start(argptr, fmt);
+ vsnprintf(str,size, fmt, argptr);
+ va_end(argptr);
+ mvprintw(y,x,str);
+ free(str);
+ }
+
+static void curses_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
+ {
+ mvaddch(y,x,ch);
+ }
+
+static void curses_attron(struct AbstractTview* tv,int flag)
+ {
+ attron(flag);
+ }
+static void curses_attroff(struct AbstractTview* tv,int flag)
+ {
+ attroff(flag);
+ }
+static void curses_clear(struct AbstractTview* tv)
+ {
+ clear();
+ }
+
+static int curses_colorpair(struct AbstractTview* tv,int flag)
+ {
+ return COLOR_PAIR(flag);
+ }
+
+static int curses_drawaln(struct AbstractTview* tv, int tid, int pos)
+ {
+ return base_draw_aln(tv, tid, pos);
+ }
+
+
+
+static void tv_win_goto(curses_tview_t *tv, int *tid, int *pos)
+ {
+ char str[256], *p;
+ int i, l = 0;
+ tview_t *base=(tview_t*)tv;
+ wborder(tv->wgoto, '|', '|', '-', '-', '+', '+', '+', '+');
+ mvwprintw(tv->wgoto, 1, 2, "Goto: ");
+ for (;;) {
+ int c = wgetch(tv->wgoto);
+ wrefresh(tv->wgoto);
+ if (c == KEY_BACKSPACE || c == '\010' || c == '\177') {
+ if(l > 0) --l;
+ } else if (c == KEY_ENTER || c == '\012' || c == '\015') {
+ int _tid = -1, _beg, _end;
+ if (str[0] == '=') {
+ _beg = strtol(str+1, &p, 10) - 1;
+ if (_beg > 0) {
+ *pos = _beg;
+ return;
+ }
+ } else {
+ bam_parse_region(base->header, str, &_tid, &_beg, &_end);
+ if (_tid >= 0) {
+ *tid = _tid; *pos = _beg;
+ return;
+ }
+ }
+ } else if (isgraph(c)) {
+ if (l < TV_MAX_GOTO) str[l++] = c;
+ } else if (c == '\027') l = 0;
+ else if (c == '\033') return;
+ str[l] = '\0';
+ for (i = 0; i < TV_MAX_GOTO; ++i) mvwaddch(tv->wgoto, 1, 8 + i, ' ');
+ mvwprintw(tv->wgoto, 1, 8, "%s", str);
+ }
+}
+
+
+
+
+static void tv_win_help(curses_tview_t *tv) {
+ int r = 1;
+ tview_t* base=(tview_t*)base;
+ WINDOW *win = tv->whelp;
+ wborder(win, '|', '|', '-', '-', '+', '+', '+', '+');
+ mvwprintw(win, r++, 2, " -=- Help -=- ");
+ r++;
+ mvwprintw(win, r++, 2, "? This window");
+ mvwprintw(win, r++, 2, "Arrows Small scroll movement");
+ mvwprintw(win, r++, 2, "h,j,k,l Small scroll movement");
+ mvwprintw(win, r++, 2, "H,J,K,L Large scroll movement");
+ mvwprintw(win, r++, 2, "ctrl-H Scroll 1k left");
+ mvwprintw(win, r++, 2, "ctrl-L Scroll 1k right");
+ mvwprintw(win, r++, 2, "space Scroll one screen");
+ mvwprintw(win, r++, 2, "backspace Scroll back one screen");
+ mvwprintw(win, r++, 2, "g Go to specific location");
+ mvwprintw(win, r++, 2, "m Color for mapping qual");
+ mvwprintw(win, r++, 2, "n Color for nucleotide");
+ mvwprintw(win, r++, 2, "b Color for base quality");
+ mvwprintw(win, r++, 2, "c Color for cs color");
+ mvwprintw(win, r++, 2, "z Color for cs qual");
+ mvwprintw(win, r++, 2, ". Toggle on/off dot view");
+ mvwprintw(win, r++, 2, "s Toggle on/off ref skip");
+ mvwprintw(win, r++, 2, "r Toggle on/off rd name");
+ mvwprintw(win, r++, 2, "N Turn on nt view");
+ mvwprintw(win, r++, 2, "C Turn on cs view");
+ mvwprintw(win, r++, 2, "i Toggle on/off ins");
+ mvwprintw(win, r++, 2, "q Exit");
+ r++;
+ mvwprintw(win, r++, 2, "Underline: Secondary or orphan");
+ mvwprintw(win, r++, 2, "Blue: 0-9 Green: 10-19");
+ mvwprintw(win, r++, 2, "Yellow: 20-29 White: >=30");
+ wrefresh(win);
+ wgetch(win);
+}
+
+static int curses_underline(tview_t* tv)
+ {
+ return A_UNDERLINE;
+ }
+
+static int curses_loop(tview_t* tv)
+ {
+ int tid, pos;
+ curses_tview_t *CTV=(curses_tview_t *)tv;
+ tid = tv->curr_tid; pos = tv->left_pos;
+ while (1) {
+ int c = getch();
+ switch (c) {
+ case '?': tv_win_help(CTV); break;
+ case '\033':
+ case 'q': goto end_loop;
+ case '/':
+ case 'g': tv_win_goto(CTV, &tid, &pos); break;
+ case 'm': tv->color_for = TV_COLOR_MAPQ; break;
+ case 'b': tv->color_for = TV_COLOR_BASEQ; break;
+ case 'n': tv->color_for = TV_COLOR_NUCL; break;
+ case 'c': tv->color_for = TV_COLOR_COL; break;
+ case 'z': tv->color_for = TV_COLOR_COLQ; break;
+ case 's': tv->no_skip = !tv->no_skip; break;
+ case 'r': tv->show_name = !tv->show_name; break;
+ case KEY_LEFT:
+ case 'h': --pos; break;
+ case KEY_RIGHT:
+ case 'l': ++pos; break;
+ case KEY_SLEFT:
+ case 'H': pos -= 20; break;
+ case KEY_SRIGHT:
+ case 'L': pos += 20; break;
+ case '.': tv->is_dot = !tv->is_dot; break;
+ case 'N': tv->base_for = TV_BASE_NUCL; break;
+ case 'C': tv->base_for = TV_BASE_COLOR_SPACE; break;
+ case 'i': tv->ins = !tv->ins; break;
+ case '\010': pos -= 1000; break;
+ case '\014': pos += 1000; break;
+ case ' ': pos += tv->mcol; break;
+ case KEY_UP:
+ case 'j': --tv->row_shift; break;
+ case KEY_DOWN:
+ case 'k': ++tv->row_shift; break;
+ case KEY_BACKSPACE:
+ case '\177': pos -= tv->mcol; break;
+ case KEY_RESIZE: getmaxyx(stdscr, tv->mrow, tv->mcol); break;
+ default: continue;
+ }
+ if (pos < 0) pos = 0;
+ if (tv->row_shift < 0) tv->row_shift = 0;
+ tv->my_drawaln(tv, tid, pos);
+ }
+end_loop:
+ return 0;
+}
+
+
+
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ curses_tview_t *tv = (curses_tview_t*)calloc(1, sizeof(curses_tview_t));
+ tview_t* base=(tview_t*)tv;
+ if(tv==0)
+ {
+ fprintf(pysamerr,"Calloc failed\n");
+ return 0;
+ }
+
+ base_tv_init(base,fn,fn_fa,samples);
+ /* initialize callbacks */
+#define SET_CALLBACK(fun) base->my_##fun=curses_##fun;
+ SET_CALLBACK(destroy);
+ SET_CALLBACK(mvprintw);
+ SET_CALLBACK(mvaddch);
+ SET_CALLBACK(attron);
+ SET_CALLBACK(attroff);
+ SET_CALLBACK(clear);
+ SET_CALLBACK(colorpair);
+ SET_CALLBACK(drawaln);
+ SET_CALLBACK(loop);
+ SET_CALLBACK(underline);
+#undef SET_CALLBACK
+
+ initscr();
+ keypad(stdscr, TRUE);
+ clear();
+ noecho();
+ cbreak();
+
+ getmaxyx(stdscr, base->mrow, base->mcol);
+ tv->wgoto = newwin(3, TV_MAX_GOTO + 10, 10, 5);
+ tv->whelp = newwin(29, 40, 5, 5);
+
+ start_color();
+ init_pair(1, COLOR_BLUE, COLOR_BLACK);
+ init_pair(2, COLOR_GREEN, COLOR_BLACK);
+ init_pair(3, COLOR_YELLOW, COLOR_BLACK);
+ init_pair(4, COLOR_WHITE, COLOR_BLACK);
+ init_pair(5, COLOR_GREEN, COLOR_BLACK);
+ init_pair(6, COLOR_CYAN, COLOR_BLACK);
+ init_pair(7, COLOR_YELLOW, COLOR_BLACK);
+ init_pair(8, COLOR_RED, COLOR_BLACK);
+ init_pair(9, COLOR_BLUE, COLOR_BLACK);
+ return base;
+ }
+
+
+#else // #ifdef _HAVE_CURSES
+#include <stdio.h>
+#warning "No curses library is available; tview with curses is disabled."
+
+extern tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples);
+
+tview_t* curses_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ return text_tv_init(fn,fn_fa,samples);
+ }
+#endif // #ifdef _HAVE_CURSES
+
+
diff --git a/samtools/bam_tview_html.c.pysam.c b/samtools/bam_tview_html.c.pysam.c
new file mode 100644
index 0000000..95dadd7
--- /dev/null
+++ b/samtools/bam_tview_html.c.pysam.c
@@ -0,0 +1,351 @@
+#include "pysam.h"
+
+#include <unistd.h>
+#include "bam_tview.h"
+
+#define UNDERLINE_FLAG 10
+
+typedef struct HtmlTview {
+ tview_t view;
+ int row_count;
+ tixel_t** screen;
+ FILE* out;
+ int attributes;/* color... */
+ } html_tview_t;
+
+#define FROM_TV(ptr) ((html_tview_t*)ptr)
+
+static void html_destroy(tview_t* base)
+ {
+ int i;
+ html_tview_t* tv=(html_tview_t*)base;
+ if(tv->screen!=NULL)
+ {
+ for(i=0;i< tv->row_count;++i) free(tv->screen[i]);
+ free(tv->screen);
+ }
+ base_tv_destroy(base);
+ free(tv);
+ }
+
+/*
+ void (*my_mvprintw)(struct AbstractTview* ,int,int,const char*,...);
+ void (*my_)(struct AbstractTview*,int,int,int);
+ void (*my_attron)(struct AbstractTview*,int);
+ void (*my_attroff)(struct AbstractTview*,int);
+ void (*my_clear)(struct AbstractTview*);
+ int (*my_colorpair)(struct AbstractTview*,int);
+*/
+
+static void html_mvprintw(struct AbstractTview* tv,int y ,int x,const char* fmt,...)
+ {
+ int i,nchars=0;
+ unsigned int size=tv->mcol+2;
+ char* str=malloc(size);
+ if(str==0) exit(EXIT_FAILURE);
+ va_list argptr;
+ va_start(argptr, fmt);
+ nchars=vsnprintf(str,size, fmt, argptr);
+ va_end(argptr);
+
+ for(i=0;i< nchars;++i)
+ {
+ tv->my_mvaddch(tv,y,x+i,str[i]);
+ }
+ free(str);
+ }
+
+static void html_mvaddch(struct AbstractTview* tv,int y,int x,int ch)
+ {
+ tixel_t* row=NULL;
+ html_tview_t* ptr=FROM_TV(tv);
+ if( x >= tv->mcol ) return; //out of screen
+ while(ptr->row_count<=y)
+ {
+ int x;
+ row=(tixel_t*)calloc(tv->mcol,sizeof(tixel_t));
+ if(row==0) exit(EXIT_FAILURE);
+ for(x=0;x<tv->mcol;++x) {row[x].ch=' ';row[x].attributes=0;}
+ ptr->screen=(tixel_t**)realloc(ptr->screen,sizeof(tixel_t*)*(ptr->row_count+1));
+ ptr->screen[ptr->row_count++]=row;
+ }
+ row=ptr->screen[y];
+ row[x].ch=ch;
+ row[x].attributes=ptr->attributes;
+ }
+
+static void html_attron(struct AbstractTview* tv,int flag)
+ {
+ html_tview_t* ptr=FROM_TV(tv);
+ ptr->attributes |= flag;
+
+
+ }
+
+static void html_attroff(struct AbstractTview* tv,int flag)
+ {
+ html_tview_t* ptr=FROM_TV(tv);
+ ptr->attributes &= ~(flag);
+ }
+
+static void html_clear(struct AbstractTview* tv)
+ {
+ html_tview_t* ptr=FROM_TV(tv);
+ if(ptr->screen!=NULL)
+ {
+ int i;
+ for(i=0;i< ptr->row_count;++i) free(ptr->screen[i]);
+ free(ptr->screen);
+ ptr->screen=NULL;
+ }
+ ptr->row_count=0;
+ ptr->attributes=0;
+ }
+
+static int html_colorpair(struct AbstractTview* tv,int flag)
+ {
+ return (1 << (flag));
+ }
+
+static int html_drawaln(struct AbstractTview* tv, int tid, int pos)
+ {
+ int y,x;
+ html_tview_t* ptr=FROM_TV(tv);
+ html_clear(tv);
+ base_draw_aln(tv, tid, pos);
+ fputs("<html><head>",ptr->out);
+ fprintf(ptr->out,"<title>%s:%d</title>",
+ tv->header->target_name[tid],
+ pos+1
+ );
+ //style
+
+ fputs("<style type='text/css'>\n",ptr->out);
+ fputs(".tviewbody { margin:5px; background-color:white;text-align:center;}\n",ptr->out);
+ fputs(".tviewtitle {text-align:center;}\n",ptr->out);
+ fputs(".tviewpre { margin:5px; background-color:white;}\n",ptr->out);
+ #define CSS(id,col) fprintf(ptr->out,".tviewc%d {color:%s;}\n.tviewcu%d {color:%s;text-decoration:underline;}\n",id,col,id,col);
+ CSS(0, "black");
+ CSS(1, "blue");
+ CSS(2, "green");
+ CSS(3, "yellow");
+ CSS(4, "black");
+ CSS(5, "green");
+ CSS(6, "cyan");
+ CSS(7, "yellow");
+ CSS(8, "red");
+ CSS(9, "blue");
+ #undef CSS
+ fputs("</style>",ptr->out);
+
+ fputs("</head><body>",ptr->out);
+
+ fprintf(ptr->out,"<div class='tviewbody'><div class='tviewtitle'>%s:%d</div>",
+ tv->header->target_name[tid],
+ pos+1
+ );
+
+ fputs("<pre class='tviewpre'>",ptr->out);
+ for(y=0;y< ptr->row_count;++y)
+ {
+
+ for(x=0;x< tv->mcol;++x)
+ {
+
+
+ if(x== 0 || ptr->screen[y][x].attributes != ptr->screen[y][x-1].attributes)
+ {
+ int css=0;
+ fprintf(ptr->out,"<span");
+ while(css<32)
+ {
+ //if(y>1) fprintf(pysamerr,"css=%d pow2=%d vs %d\n",css,(1 << (css)),ptr->screen[y][x].attributes);
+ if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
+ {
+
+ fprintf(ptr->out," class='tviewc%s%d'",
+ (( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)) )!=0?"u":""),
+ css);
+ break;
+ }
+ ++css;
+ }
+
+
+ fputs(">",ptr->out);
+ }
+
+ int ch=ptr->screen[y][x].ch;
+ switch(ch)
+ {
+ case '<': fputs("<",ptr->out);break;
+ case '>': fputs(">",ptr->out);break;
+ case '&': fputs("&",ptr->out);break;
+ default: fputc(ch,ptr->out); break;
+ }
+
+
+ if(x+1 == tv->mcol || ptr->screen[y][x].attributes!=ptr->screen[y][x+1].attributes)
+ {
+ fputs("</span>",ptr->out);
+ }
+ }
+ if(y+1 < ptr->row_count) fputs("<br/>",ptr->out);
+ }
+ fputs("</pre></div></body></html>",ptr->out);
+ return 0;
+ }
+
+
+#define ANSI_COLOR_RED "\x1b[31m"
+#define ANSI_COLOR_GREEN "\x1b[32m"
+#define ANSI_COLOR_YELLOW "\x1b[33m"
+#define ANSI_COLOR_BLUE "\x1b[34m"
+#define ANSI_COLOR_MAGENTA "\x1b[35m"
+#define ANSI_COLOR_CYAN "\x1b[36m"
+#define ANSI_COLOR_BLACK "\x1b[0m"
+#define ANSI_COLOR_RESET ANSI_COLOR_BLACK
+
+#define ANSI_UNDERLINE_SET "\033[4m"
+#define ANSI_UNDERLINE_UNSET "\033[0m"
+
+static int text_drawaln(struct AbstractTview* tv, int tid, int pos)
+ {
+ int y,x;
+ html_tview_t* ptr=FROM_TV(tv);
+ html_clear(tv);
+ base_draw_aln(tv, tid, pos);
+ int is_term= isatty(fileno(ptr->out));
+
+ for(y=0;y< ptr->row_count;++y)
+ {
+ for(x=0;x< tv->mcol;++x)
+ {
+ if(is_term)
+ {
+ int css=0;
+ while(css<32)
+ {
+ if(( (ptr->screen[y][x].attributes) & (1 << (css)))!=0)
+ {
+ break;
+ }
+ ++css;
+ }
+ switch(css)
+ {
+ //CSS(0, "black");
+ case 1: fputs(ANSI_COLOR_BLUE,ptr->out); break;
+ case 2: fputs(ANSI_COLOR_GREEN,ptr->out); break;
+ case 3: fputs(ANSI_COLOR_YELLOW,ptr->out); break;
+ //CSS(4, "black");
+ case 5: fputs(ANSI_COLOR_GREEN,ptr->out); break;
+ case 6: fputs(ANSI_COLOR_CYAN,ptr->out); break;
+ case 7: fputs(ANSI_COLOR_YELLOW,ptr->out); break;
+ case 8: fputs(ANSI_COLOR_RED,ptr->out); break;
+ case 9: fputs(ANSI_COLOR_BLUE,ptr->out); break;
+ default:break;
+ }
+ if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0)
+ {
+ fputs(ANSI_UNDERLINE_SET,ptr->out);
+ }
+
+ }
+
+
+ int ch=ptr->screen[y][x].ch;
+
+ fputc(ch,ptr->out);
+ if(is_term)
+ {
+ fputs(ANSI_COLOR_RESET,ptr->out);
+ if(( (ptr->screen[y][x].attributes) & (1 << (UNDERLINE_FLAG)))!=0)
+ {
+ fputs(ANSI_UNDERLINE_UNSET,ptr->out);
+ }
+ }
+ }
+ fputc('\n',ptr->out);
+ }
+ return 0;
+ }
+
+
+static int html_loop(tview_t* tv)
+ {
+ //tv->my_drawaln(tv, tv->curr_tid, tv->left_pos);
+ return 0;
+ }
+
+static int html_underline(tview_t* tv)
+ {
+ return (1 << UNDERLINE_FLAG);
+ }
+
+/*
+static void init_pair(html_tview_t *tv,int id_ge_1, const char* pen, const char* paper)
+ {
+
+ }
+*/
+
+tview_t* html_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ char* colstr=getenv("COLUMNS");
+ html_tview_t *tv = (html_tview_t*)calloc(1, sizeof(html_tview_t));
+ tview_t* base=(tview_t*)tv;
+ if(tv==0)
+ {
+ fprintf(pysamerr,"Calloc failed\n");
+ return 0;
+ }
+ tv->row_count=0;
+ tv->screen=NULL;
+ tv->out=stdout;
+ tv->attributes=0;
+ base_tv_init(base,fn,fn_fa,samples);
+ /* initialize callbacks */
+#define SET_CALLBACK(fun) base->my_##fun=html_##fun;
+ SET_CALLBACK(destroy);
+ SET_CALLBACK(mvprintw);
+ SET_CALLBACK(mvaddch);
+ SET_CALLBACK(attron);
+ SET_CALLBACK(attroff);
+ SET_CALLBACK(clear);
+ SET_CALLBACK(colorpair);
+ SET_CALLBACK(drawaln);
+ SET_CALLBACK(loop);
+ SET_CALLBACK(underline);
+#undef SET_CALLBACK
+
+
+ if(colstr!=0)
+ {
+ base->mcol=atoi(colstr);
+ if(base->mcol<10) base->mcol=80;
+ }
+ base->mrow=99999;
+
+/*
+ init_pair(tv,1, "blue", "white");
+ init_pair(tv,2, "green", "white");
+ init_pair(tv,3, "yellow", "white");
+ init_pair(tv,4, "white", "white");
+ init_pair(tv,5, "green", "white");
+ init_pair(tv,6, "cyan", "white");
+ init_pair(tv,7, "yellow", "white");
+ init_pair(tv,8, "red", "white");
+ init_pair(tv,9, "blue", "white");
+ */
+ return base;
+ }
+
+
+tview_t* text_tv_init(const char *fn, const char *fn_fa, const char *samples)
+ {
+ tview_t* tv=html_tv_init(fn,fn_fa,samples);
+ tv->my_drawaln=text_drawaln;
+ return tv;
+ }
+
diff --git a/samtools/bamshuf.c.pysam.c b/samtools/bamshuf.c.pysam.c
new file mode 100644
index 0000000..d64b094
--- /dev/null
+++ b/samtools/bamshuf.c.pysam.c
@@ -0,0 +1,148 @@
+#include "pysam.h"
+
+#include <unistd.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include "sam.h"
+#include "ksort.h"
+
+#define DEF_CLEVEL 1
+
+static inline unsigned hash_Wang(unsigned key)
+{
+ key += ~(key << 15);
+ key ^= (key >> 10);
+ key += (key << 3);
+ key ^= (key >> 6);
+ key += ~(key << 11);
+ key ^= (key >> 16);
+ return key;
+}
+
+static inline unsigned hash_X31_Wang(const char *s)
+{
+ unsigned h = *s;
+ if (h) {
+ for (++s ; *s; ++s) h = (h << 5) - h + *s;
+ return hash_Wang(h);
+ } else return 0;
+}
+
+typedef struct {
+ unsigned key;
+ bam1_t *b;
+} elem_t;
+
+static inline int elem_lt(elem_t x, elem_t y)
+{
+ if (x.key < y.key) return 1;
+ if (x.key == y.key) {
+ int t;
+ t = strcmp(bam_get_qname(x.b), bam_get_qname(y.b));
+ if (t < 0) return 1;
+ return (t == 0 && ((x.b->core.flag>>6&3) < (y.b->core.flag>>6&3)));
+ } else return 0;
+}
+
+KSORT_INIT(bamshuf, elem_t, elem_lt)
+
+static void bamshuf(const char *fn, int n_files, const char *pre, int clevel, int is_stdout)
+{
+ BGZF *fp, *fpw, **fpt;
+ char **fnt, modew[8];
+ bam1_t *b;
+ int i, l;
+ bam_hdr_t *h;
+ int64_t *cnt;
+
+ // split
+ fp = strcmp(fn, "-")? bgzf_open(fn, "r") : bgzf_dopen(fileno(stdin), "r");
+ assert(fp);
+ h = bam_hdr_read(fp);
+ fnt = (char**)calloc(n_files, sizeof(void*));
+ fpt = (BGZF**)calloc(n_files, sizeof(void*));
+ cnt = (int64_t*)calloc(n_files, 8);
+ l = strlen(pre);
+ for (i = 0; i < n_files; ++i) {
+ fnt[i] = (char*)calloc(l + 10, 1);
+ sprintf(fnt[i], "%s.%.4d.bam", pre, i);
+ fpt[i] = bgzf_open(fnt[i], "w1");
+ bam_hdr_write(fpt[i], h);
+ }
+ b = bam_init1();
+ while (bam_read1(fp, b) >= 0) {
+ uint32_t x;
+ x = hash_X31_Wang(bam_get_qname(b)) % n_files;
+ bam_write1(fpt[x], b);
+ ++cnt[x];
+ }
+ bam_destroy1(b);
+ for (i = 0; i < n_files; ++i) bgzf_close(fpt[i]);
+ free(fpt);
+ bgzf_close(fp);
+ // merge
+ sprintf(modew, "w%d", (clevel >= 0 && clevel <= 9)? clevel : DEF_CLEVEL);
+ if (!is_stdout) { // output to a file
+ char *fnw = (char*)calloc(l + 5, 1);
+ sprintf(fnw, "%s.bam", pre);
+ fpw = bgzf_open(fnw, modew);
+ free(fnw);
+ } else fpw = bgzf_dopen(fileno(stdout), modew); // output to stdout
+ bam_hdr_write(fpw, h);
+ bam_hdr_destroy(h);
+ for (i = 0; i < n_files; ++i) {
+ int64_t j, c = cnt[i];
+ elem_t *a;
+ fp = bgzf_open(fnt[i], "r");
+ bam_hdr_destroy(bam_hdr_read(fp));
+ a = (elem_t*)calloc(c, sizeof(elem_t));
+ for (j = 0; j < c; ++j) {
+ a[j].b = bam_init1();
+ // added by pysam to prevent seg-fault
+ // was: assert( bam_read1(fp, a[j].b );
+ // Assume that assertion was optimized out
+ // and a[j].b not set.
+ int _l = bam_read1(fp, a[j].b);
+ assert( _l >= 0 );
+ a[j].key = hash_X31_Wang(bam_get_qname(a[j].b));
+ }
+ bgzf_close(fp);
+ unlink(fnt[i]);
+ free(fnt[i]);
+ ks_introsort(bamshuf, c, a);
+ for (j = 0; j < c; ++j) {
+ bam_write1(fpw, a[j].b);
+ bam_destroy1(a[j].b);
+ }
+ free(a);
+ }
+ bgzf_close(fpw);
+ free(fnt); free(cnt);
+}
+
+int main_bamshuf(int argc, char *argv[])
+{
+ int c, n_files = 64, clevel = DEF_CLEVEL, is_stdout = 0, is_un = 0;
+ while ((c = getopt(argc, argv, "n:l:uO")) >= 0) {
+ switch (c) {
+ case 'n': n_files = atoi(optarg); break;
+ case 'l': clevel = atoi(optarg); break;
+ case 'u': is_un = 1; break;
+ case 'O': is_stdout = 1; break;
+ }
+ }
+ if (is_un) clevel = 0;
+ if (optind + 2 > argc) {
+ fprintf(pysamerr, "\nUsage: bamshuf [-Ou] [-n nFiles] [-c cLevel] <in.bam> <out.prefix>\n\n");
+ fprintf(pysamerr, "Options: -O output to stdout\n");
+ fprintf(pysamerr, " -u uncompressed BAM output\n");
+ fprintf(pysamerr, " -l INT compression level [%d]\n", DEF_CLEVEL);
+ fprintf(pysamerr, " -n INT number of temporary files [%d]\n", n_files);
+ fprintf(pysamerr, "\n");
+ return 1;
+ }
+ bamshuf(argv[optind], n_files, argv[optind+1], clevel, is_stdout);
+ return 0;
+}
diff --git a/samtools/bcftools/bcf.c.pysam.c b/samtools/bcftools/bcf.c.pysam.c
index e1c823d..dcde831 100644
--- a/samtools/bcftools/bcf.c.pysam.c
+++ b/samtools/bcftools/bcf.c.pysam.c
@@ -15,9 +15,6 @@ bcf_t *bcf_open(const char *fn, const char *mode)
} else {
b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
}
-#ifndef BCF_LITE
- b->fp->owned_file = 1;
-#endif
return b;
}
@@ -142,7 +139,7 @@ int bcf_sync(bcf1_t *b)
for (i = 0; i < b->n_gi; ++i) {
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
b->gi[i].len = b->n_alleles * (b->n_alleles + 1) / 2;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("HQ", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
b->gi[i].len = 2;
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2) || b->gi[i].fmt == bcf_str2int("GT", 2)) {
b->gi[i].len = 1;
@@ -235,32 +232,59 @@ void bcf_fmt_core(const bcf_hdr_t *h, bcf1_t *b, kstring_t *s)
}
x = b->n_alleles * (b->n_alleles + 1) / 2;
if (b->n_gi == 0) return;
+ int iPL = -1;
+ if ( b->n_alleles > 2 ) {
+ for (i=0; i<b->n_gi; i++) {
+ if ( b->gi[i].fmt == bcf_str2int("PL", 2) ) {
+ iPL = i;
+ break;
+ }
+ }
+ }
for (j = 0; j < h->n_smpl; ++j) {
+ int ploidy = b->ploidy ? b->ploidy[j] : 2;
kputc('\t', s);
for (i = 0; i < b->n_gi; ++i) {
if (i) kputc(':', s);
if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
uint8_t *d = (uint8_t*)b->gi[i].data + j * x;
int k;
- for (k = 0; k < x; ++k) {
- if (k > 0) kputc(',', s);
- kputw(d[k], s);
- }
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ if ( ploidy==1 )
+ for (k=0; k<b->n_alleles; k++)
+ {
+ if (k>0) kputc(',', s);
+ kputw(d[(k+1)*(k+2)/2-1], s);
+ }
+ else
+ for (k = 0; k < x; ++k) {
+ if (k > 0) kputc(',', s);
+ kputw(d[k], s);
+ }
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
kputw(((uint16_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GQ", 2)) {
kputw(((uint8_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
kputw(((int32_t*)b->gi[i].data)[j], s);
} else if (b->gi[i].fmt == bcf_str2int("GT", 2)) {
- int y = ((uint8_t*)b->gi[i].data)[j];
- if (y>>7&1) {
- kputsn("./.", 3, s);
- } else {
- kputc('0' + (y>>3&7), s);
- kputc("/|"[y>>6&1], s);
- kputc('0' + (y&7), s);
- }
+ int y = ((uint8_t*)b->gi[i].data)[j];
+ if ( ploidy==1 )
+ {
+ if ( y>>7&1 )
+ kputc('.', s);
+ else
+ kputc('0' + (y>>3&7), s);
+ }
+ else
+ {
+ if ( y>>7&1 )
+ kputsn("./.", 3, s);
+ else {
+ kputc('0' + (y>>3&7), s);
+ kputc("/|"[y>>6&1], s);
+ kputc('0' + (y&7), s);
+ }
+ }
} else if (b->gi[i].fmt == bcf_str2int("GL", 2)) {
float *d = (float*)b->gi[i].data + j * x;
int k;
@@ -301,6 +325,50 @@ int bcf_append_info(bcf1_t *b, const char *info, int l)
return 0;
}
+int remove_tag(char *str, const char *tag, char delim)
+{
+ char *tmp = str, *p;
+ int len_diff = 0, ori_len = strlen(str);
+ while ( *tmp && (p = strstr(tmp,tag)) )
+ {
+ if ( p>str )
+ {
+ if ( *(p-1)!=delim ) { tmp=p+1; continue; } // shared substring
+ p--;
+ }
+ char *q=p+1;
+ while ( *q && *q!=delim ) q++;
+ if ( p==str && *q ) q++; // the tag is first, don't move the delim char
+ len_diff += q-p;
+ if ( ! *q ) { *p = 0; break; } // the tag was last, no delim follows
+ else
+ memmove(p,q,ori_len-(int)(p-str)-(int)(q-p)); // *q==delim
+ }
+ if ( len_diff==ori_len )
+ str[0]='.', str[1]=0, len_diff--;
+
+ return len_diff;
+}
+
+
+void rm_info(kstring_t *s, const char *key)
+{
+ char *p = s->s;
+ int n = 0;
+ while ( n<4 )
+ {
+ if ( !*p ) n++;
+ p++;
+ }
+ char *q = p+1;
+ while ( *q && q-s->s<s->l ) q++;
+
+ int nrm = remove_tag(p, key, ';');
+ if ( nrm )
+ memmove(q-nrm, q, s->s+s->l-q+1);
+ s->l -= nrm;
+}
+
int bcf_cpy(bcf1_t *r, const bcf1_t *b)
{
char *t1 = r->str;
diff --git a/samtools/bcftools/bcf.h b/samtools/bcftools/bcf.h
index 822ae5c..f722525 100644
--- a/samtools/bcftools/bcf.h
+++ b/samtools/bcftools/bcf.h
@@ -28,7 +28,7 @@
#ifndef BCF_H
#define BCF_H
-#define BCF_VERSION "0.1.17-dev (r973:277)"
+#define BCF_VERSION "0.1.19-44428cd"
#include <stdint.h>
#include <zlib.h>
@@ -73,6 +73,7 @@ typedef struct {
bcf_ginfo_t *gi; // array of geno fields
int n_alleles, n_smpl; // number of alleles and samples
// derived info: ref, alt, flt, info, fmt (<-str), n_gi (<-fmt), n_alleles (<-alt), n_smpl (<-bcf_hdr_t::n_smpl)
+ uint8_t *ploidy; // ploidy of all samples; if NULL, ploidy of 2 is assumed.
} bcf1_t;
typedef struct {
@@ -122,6 +123,10 @@ extern "C" {
char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b);
// append more info
int bcf_append_info(bcf1_t *b, const char *info, int l);
+ // remove tag
+ int remove_tag(char *string, const char *tag, char delim);
+ // remove info tag, string is the kstring holder of bcf1_t.str
+ void rm_info(kstring_t *string, const char *key);
// copy
int bcf_cpy(bcf1_t *r, const bcf1_t *b);
@@ -142,6 +147,8 @@ extern "C" {
// keep the first n alleles and discard the rest
int bcf_shrink_alt(bcf1_t *b, int n);
+ // keep the masked alleles and discard the rest
+ void bcf_fit_alt(bcf1_t *b, int mask);
// convert GL to PL
int bcf_gl2pl(bcf1_t *b);
// if the site is an indel
diff --git a/samtools/bcftools/bcfutils.c.pysam.c b/samtools/bcftools/bcfutils.c.pysam.c
index 110d0bb..9bcea7d 100644
--- a/samtools/bcftools/bcfutils.c.pysam.c
+++ b/samtools/bcftools/bcfutils.c.pysam.c
@@ -2,6 +2,7 @@
#include <string.h>
#include <math.h>
+#include <assert.h>
#include "bcf.h"
#include "kstring.h"
#include "khash.h"
@@ -68,6 +69,112 @@ int bcf_str2id_add(void *_hash, const char *str)
return kh_val(hash, k);
}
+void bcf_fit_alt(bcf1_t *b, int mask)
+{
+ mask |= 1; // REF must be always present
+
+ int i,j,nals=0;
+ for (i=0; i<sizeof(int); i++)
+ if ( mask&1<<i) nals++;
+ if ( b->n_alleles <= nals ) return;
+
+ // update ALT, in principle any of the alleles can be removed
+ char *p;
+ if ( nals>1 )
+ {
+ char *dst, *src;
+ int n=0, nalts=nals-1;
+ for (src=dst=p=b->alt, i=1; *p; p++)
+ {
+ if ( *p!=',' ) continue;
+
+ if ( mask&1<<i )
+ {
+ n++;
+ if ( src!=dst )
+ {
+ memmove(dst,src,p-src);
+ dst += p-src;
+ }
+ else dst = p;
+ if ( n<nalts ) { *dst=','; dst++; }
+ }
+ i++;
+
+ if ( n>=nalts ) { *dst=0; break; }
+ src = p+1;
+ }
+ if ( n<nalts )
+ {
+ memmove(dst,src,p-src);
+ dst += p-src;
+ *dst = 0;
+ }
+ p = dst;
+ }
+ else p = b->alt, *p = '\0';
+ p++;
+ memmove(p, b->flt, b->str + b->l_str - b->flt);
+ b->l_str -= b->flt - p;
+
+ // update PL and GT
+ int ipl=-1, igt=-1;
+ for (i = 0; i < b->n_gi; ++i)
+ {
+ bcf_ginfo_t *g = b->gi + i;
+ if (g->fmt == bcf_str2int("PL", 2)) ipl = i;
+ if (g->fmt == bcf_str2int("GT", 2)) igt = i;
+ }
+
+ // .. create mapping between old and new indexes
+ int npl = nals * (nals+1) / 2;
+ int *map = malloc(sizeof(int)*(npl>b->n_alleles ? npl : b->n_alleles));
+ int kori=0,knew=0;
+ for (i=0; i<b->n_alleles; i++)
+ {
+ for (j=0; j<=i; j++)
+ {
+ int skip=0;
+ if ( i && !(mask&1<<i) ) skip=1;
+ if ( j && !(mask&1<<j) ) skip=1;
+ if ( !skip ) { map[knew++] = kori; }
+ kori++;
+ }
+ }
+ // .. apply to all samples
+ int n_smpl = b->n_smpl;
+ for (i = 0; i < b->n_gi; ++i)
+ {
+ bcf_ginfo_t *g = b->gi + i;
+ if (g->fmt == bcf_str2int("PL", 2))
+ {
+ g->len = npl;
+ uint8_t *d = (uint8_t*)g->data;
+ int ismpl, npl_ori = b->n_alleles * (b->n_alleles + 1) / 2;
+ for (knew=ismpl=0; ismpl<n_smpl; ismpl++)
+ {
+ uint8_t *dl = d + ismpl * npl_ori;
+ for (j=0; j<npl; j++) d[knew++] = dl[map[j]];
+ }
+ } // FIXME: to add GL
+ }
+ // update GTs
+ map[0] = 0;
+ for (i=1, knew=0; i<b->n_alleles; i++)
+ map[i] = mask&1<<i ? ++knew : -1;
+ for (i=0; i<n_smpl; i++)
+ {
+ uint8_t gt = ((uint8_t*)b->gi[igt].data)[i];
+ int a1 = (gt>>3)&7;
+ int a2 = gt&7;
+ assert( map[a1]>=0 && map[a2]>=0 );
+ ((uint8_t*)b->gi[igt].data)[i] = ((1<<7|1<<6)>) | map[a1]<<3 | map[a2];
+ }
+ free(map);
+ b->n_alleles = nals;
+ bcf_sync(b);
+}
+
int bcf_shrink_alt(bcf1_t *b, int n)
{
char *p;
@@ -135,7 +242,7 @@ int bcf_fix_gt(bcf1_t *b)
bcf_ginfo_t gt;
// check the presence of the GT FMT
if ((s = strstr(b->fmt, ":GT")) == 0) return 0; // no GT or GT is already the first
- if (s[3] != '\0' && s[3] != ':') return 0; // :GTX in fact
+ assert(s[3] == '\0' || s[3] == ':'); // :GTX in fact
tmp = bcf_str2int("GT", 2);
for (i = 0; i < b->n_gi; ++i)
if (b->gi[i].fmt == tmp) break;
@@ -144,7 +251,10 @@ int bcf_fix_gt(bcf1_t *b)
// move GT to the first
for (; i > 0; --i) b->gi[i] = b->gi[i-1];
b->gi[0] = gt;
- memmove(b->fmt + 3, b->fmt, s + 1 - b->fmt);
+ if ( s[3]==0 )
+ memmove(b->fmt + 3, b->fmt, s - b->fmt); // :GT
+ else
+ memmove(b->fmt + 3, b->fmt, s - b->fmt + 1); // :GT:
b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':';
return 0;
}
@@ -289,7 +399,11 @@ bcf_hdr_t *bcf_hdr_subsam(const bcf_hdr_t *h0, int n, char *const* samples, int
kputs(samples[i], &s); kputc('\0', &s);
}
}
- if (j < n) fprintf(pysamerr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+ if (j < n)
+ {
+ fprintf(pysamerr, "<%s> %d samples in the list but not in BCF.", __func__, n - j);
+ exit(1);
+ }
kh_destroy(str2id, hash);
h = calloc(1, sizeof(bcf_hdr_t));
*h = *h0;
diff --git a/samtools/bcftools/call1.c.pysam.c b/samtools/bcftools/call1.c.pysam.c
index fcd2456..2e5e5e0 100644
--- a/samtools/bcftools/call1.c.pysam.c
+++ b/samtools/bcftools/call1.c.pysam.c
@@ -35,13 +35,14 @@ KSTREAM_INIT(gzFile, gzread, 16384)
#define VC_EM 0x10000
#define VC_PAIRCALL 0x20000
#define VC_QCNT 0x40000
+#define VC_INDEL_ONLY 0x80000
typedef struct {
int flag, prior_type, n1, n_sub, *sublist, n_perm;
uint32_t *trio_aux;
char *prior_file, **subsam, *fn_dict;
uint8_t *ploidy;
- double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt;
+ double theta, pref, indel_frac, min_perm_p, min_smpl_frac, min_lrt, min_ma_lrt;
void *bed;
} viewconf_t;
@@ -49,11 +50,6 @@ void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
-typedef struct {
- double p[4];
- int mq, depth, is_tested, d[4];
-} anno16_t;
-
static double ttest(int n1, int n2, int a[4])
{
extern double kf_betai(double a, double b, double x);
@@ -84,7 +80,7 @@ static int test16_core(int anno[16], anno16_t *a)
return 0;
}
-static int test16(bcf1_t *b, anno16_t *a)
+int test16(bcf1_t *b, anno16_t *a)
{
char *p;
int i, anno[16];
@@ -101,17 +97,6 @@ static int test16(bcf1_t *b, anno16_t *a)
return test16_core(anno, a);
}
-static void rm_info(bcf1_t *b, const char *key)
-{
- char *p, *q;
- if ((p = strstr(b->info, key)) == 0) return;
- for (q = p; *q && *q != ';'; ++q);
- if (p > b->info && *(p-1) == ';') --p;
- memmove(p, q, b->l_str - (q - b->str));
- b->l_str -= q - p;
- bcf_sync(b);
-}
-
static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr, double pref, int flag, double em[10], int cons_llr, int64_t cons_gt)
{
kstring_t s;
@@ -120,7 +105,7 @@ static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr,
anno16_t a;
has_I16 = test16(b, &a) >= 0? 1 : 0;
- rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
+ //rm_info(b, "I16="); // FIXME: probably this function has a bug. If I move it below, I16 will not be removed!
memset(&s, 0, sizeof(kstring_t));
kputc('\0', &s); kputs(b->ref, &s); kputc('\0', &s);
@@ -171,6 +156,8 @@ static int update_bcf1(bcf1_t *b, const bcf_p1aux_t *pa, const bcf_p1rst_t *pr,
}
if (has_I16 && a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
kputc('\0', &s);
+ rm_info(&s, "QS=");
+ rm_info(&s, "I16=");
kputs(b->fmt, &s); kputc('\0', &s);
free(b->str);
b->m_str = s.m; b->l_str = s.l; b->str = s.s;
@@ -205,7 +192,27 @@ static char **read_samples(const char *fn, int *_n)
*_n = 0;
s.l = s.m = 0; s.s = 0;
fp = gzopen(fn, "r");
- if (fp == 0) return 0; // fail to open file
+ if (fp == 0)
+ {
+ // interpret as sample names, not as a file name
+ const char *t = fn, *p = t;
+ while (*t)
+ {
+ t++;
+ if ( *t==',' || !*t )
+ {
+ sam = realloc(sam, sizeof(void*)*(n+1));
+ sam[n] = (char*) malloc(sizeof(char)*(t-p+2));
+ memcpy(sam[n], p, t-p);
+ sam[n][t-p] = 0;
+ sam[n][t-p+1] = 2; // assume diploid
+ p = t+1;
+ n++;
+ }
+ }
+ *_n = n;
+ return sam; // fail to open file
+ }
ks = ks_init(fp);
while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
int l;
@@ -251,6 +258,12 @@ static void write_header(bcf_hdr_t *h)
kputs("##INFO=<ID=AF1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele frequency (assuming HWE)\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=AC1,"))
kputs("##INFO=<ID=AC1,Number=1,Type=Float,Description=\"Max-likelihood estimate of the first ALT allele count (no HWE assumption)\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AN,"))
+ kputs("##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=IS,"))
+ kputs("##INFO=<ID=IS,Number=2,Type=Float,Description=\"Maximum number of reads supporting an indel and fraction of indel reads\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=AC,"))
+ kputs("##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes for each ALT allele, in the same order as listed\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=G3,"))
kputs("##INFO=<ID=G3,Number=3,Type=Float,Description=\"ML estimate of genotype frequencies\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=HWE,"))
@@ -275,8 +288,16 @@ static void write_header(bcf_hdr_t *h)
kputs("##INFO=<ID=QCHI2,Number=1,Type=Integer,Description=\"Phred scaled PCHI2.\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=RP,"))
kputs("##INFO=<ID=PR,Number=1,Type=Integer,Description=\"# permutations yielding a smaller PCHI2.\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=QBD,"))
+ kputs("##INFO=<ID=QBD,Number=1,Type=Float,Description=\"Quality by Depth: QUAL/#reads\">\n", &str);
+ //if (!strstr(str.s, "##INFO=<ID=RPS,"))
+ // kputs("##INFO=<ID=RPS,Number=3,Type=Float,Description=\"Read Position Stats: depth, average, stddev\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=RPB,"))
+ kputs("##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Read Position Bias\">\n", &str);
+ if (!strstr(str.s, "##INFO=<ID=MDV,"))
+ kputs("##INFO=<ID=MDV,Number=1,Type=Integer,Description=\"Maximum number of high-quality nonRef reads in samples\">\n", &str);
if (!strstr(str.s, "##INFO=<ID=VDB,"))
- kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias\">\n", &str);
+ kputs("##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken.\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GT,"))
kputs("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=GQ,"))
@@ -285,6 +306,8 @@ static void write_header(bcf_hdr_t *h)
kputs("##FORMAT=<ID=GL,Number=3,Type=Float,Description=\"Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=DP,"))
kputs("##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"# high-quality bases\">\n", &str);
+ if (!strstr(str.s, "##FORMAT=<ID=DV,"))
+ kputs("##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"# high-quality non-reference bases\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=SP,"))
kputs("##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">\n", &str);
if (!strstr(str.s, "##FORMAT=<ID=PL,"))
@@ -305,6 +328,9 @@ int bcfview(int argc, char *argv[])
extern int bcf_trio_call(uint32_t *prep, const bcf1_t *b, int *llr, int64_t *gt);
extern int bcf_pair_call(const bcf1_t *b);
extern int bcf_min_diff(const bcf1_t *b);
+ extern int bcf_p1_get_M(bcf_p1aux_t *b);
+
+ extern gzFile bcf_p1_fp_lk;
bcf_t *bp, *bout = 0;
bcf1_t *b, *blast;
@@ -318,12 +344,12 @@ int bcfview(int argc, char *argv[])
tid = begin = end = -1;
memset(&vc, 0, sizeof(viewconf_t));
- vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1;
+ vc.prior_type = vc.n1 = -1; vc.theta = 1e-3; vc.pref = 0.5; vc.indel_frac = -1.; vc.n_perm = 0; vc.min_perm_p = 0.01; vc.min_smpl_frac = 0; vc.min_lrt = 1; vc.min_ma_lrt = -1;
memset(qcnt, 0, 8 * 256);
- while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Y")) >= 0) {
+ while ((c = getopt(argc, argv, "FN1:l:cC:eHAGvbSuP:t:p:QgLi:IMs:D:U:X:d:T:Ywm:K:")) >= 0) {
switch (c) {
case '1': vc.n1 = atoi(optarg); break;
- case 'l': vc.bed = bed_read(optarg); break;
+ case 'l': vc.bed = bed_read(optarg); if (!vc.bed) { fprintf(pysamerr,"Could not read \"%s\"\n", optarg); return 1; } break;
case 'D': vc.fn_dict = strdup(optarg); break;
case 'F': vc.flag |= VC_FIX_PL; break;
case 'N': vc.flag |= VC_ACGT_ONLY; break;
@@ -337,8 +363,10 @@ int bcfview(int argc, char *argv[])
case 'u': vc.flag |= VC_UNCOMP | VC_BCFOUT; break;
case 'g': vc.flag |= VC_CALL_GT | VC_CALL; break;
case 'I': vc.flag |= VC_NO_INDEL; break;
+ case 'w': vc.flag |= VC_INDEL_ONLY; break;
case 'M': vc.flag |= VC_ANNO_MAX; break;
case 'Y': vc.flag |= VC_QCNT; break;
+ case 'm': vc.min_ma_lrt = atof(optarg); break;
case 't': vc.theta = atof(optarg); break;
case 'p': vc.pref = atof(optarg); break;
case 'i': vc.indel_frac = atof(optarg); break;
@@ -348,6 +376,7 @@ int bcfview(int argc, char *argv[])
case 'C': vc.min_lrt = atof(optarg); break;
case 'X': vc.min_perm_p = atof(optarg); break;
case 'd': vc.min_smpl_frac = atof(optarg); break;
+ case 'K': bcf_p1_fp_lk = gzopen(optarg, "w"); break;
case 's': vc.subsam = read_samples(optarg, &vc.n_sub);
vc.ploidy = calloc(vc.n_sub + 1, 1);
for (tid = 0; tid < vc.n_sub; ++tid) vc.ploidy[tid] = vc.subsam[tid][strlen(vc.subsam[tid]) + 1];
@@ -394,6 +423,7 @@ int bcfview(int argc, char *argv[])
fprintf(pysamerr, " -g call genotypes at variant sites (force -c)\n");
fprintf(pysamerr, " -i FLOAT indel-to-substitution ratio [%.4g]\n", vc.indel_frac);
fprintf(pysamerr, " -I skip indels\n");
+ fprintf(pysamerr, " -m FLOAT alternative model for multiallelic and rare-variant calling, include if P(chi^2)>=FLOAT\n");
fprintf(pysamerr, " -p FLOAT variant if P(ref|D)<FLOAT [%.3g]\n", vc.pref);
fprintf(pysamerr, " -P STR type of prior: full, cond2, flat [full]\n");
fprintf(pysamerr, " -t FLOAT scaled substitution mutation rate [%.4g]\n", vc.theta);
@@ -436,7 +466,7 @@ int bcfview(int argc, char *argv[])
vc.sublist = calloc(vc.n_sub, sizeof(int));
hout = bcf_hdr_subsam(hin, vc.n_sub, vc.subsam, vc.sublist);
}
- if (vc.flag & VC_CALL) write_header(hout);
+ write_header(hout); // always print the header
vcf_hdr_write(bout, hout);
}
if (vc.flag & VC_CALL) {
@@ -470,6 +500,10 @@ int bcfview(int argc, char *argv[])
}
}
}
+ if (bcf_p1_fp_lk && p1) {
+ int32_t M = bcf_p1_get_M(p1);
+ gzwrite(bcf_p1_fp_lk, &M, 4);
+ }
while (vcf_read(bp, hin, b) > 0) {
int is_indel, cons_llr = -1;
int64_t cons_gt = -1;
@@ -484,6 +518,7 @@ int bcfview(int argc, char *argv[])
if (vc.flag & VC_FIX_PL) bcf_fix_pl(b);
is_indel = bcf_is_indel(b);
if ((vc.flag & VC_NO_INDEL) && is_indel) continue;
+ if ((vc.flag & VC_INDEL_ONLY) && !is_indel) continue;
if ((vc.flag & VC_ACGT_ONLY) && !is_indel) {
int x;
if (b->ref[0] == 0 || b->ref[1] != 0) continue;
@@ -517,9 +552,19 @@ int bcfview(int argc, char *argv[])
int i;
for (i = 0; i < 9; ++i) em[i] = -1.;
}
- if (vc.flag & VC_CALL) { // call variants
+ if ( !(vc.flag&VC_KEEPALT) && (vc.flag&VC_CALL) && vc.min_ma_lrt>=0 )
+ {
+ bcf_p1_set_ploidy(b, p1); // could be improved: do this per site to allow pseudo-autosomal regions
+ int gts = call_multiallelic_gt(b, p1, vc.min_ma_lrt, vc.flag&VC_VARONLY);
+ if ( gts<=1 && vc.flag & VC_VARONLY ) continue;
+ }
+ else if (vc.flag & VC_CALL) { // call variants
bcf_p1rst_t pr;
- int calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
+ int calret;
+ gzwrite(bcf_p1_fp_lk, &b->tid, 4);
+ gzwrite(bcf_p1_fp_lk, &b->pos, 4);
+ gzwrite(bcf_p1_fp_lk, &em[0], sizeof(double));
+ calret = bcf_p1_cal(b, (em[7] >= 0 && em[7] < vc.min_lrt), p1, &pr);
if (n_processed % 100000 == 0) {
fprintf(pysamerr, "[%s] %ld sites processed.\n", __func__, (long)n_processed);
bcf_p1_dump_afs(p1);
@@ -564,6 +609,8 @@ int bcfview(int argc, char *argv[])
} else bcf_fix_gt(b);
vcf_write(bout, hout, b);
}
+
+ if (bcf_p1_fp_lk) gzclose(bcf_p1_fp_lk);
if (vc.prior_file) free(vc.prior_file);
if (vc.flag & VC_CALL) bcf_p1_dump_afs(p1);
if (hin != hout) bcf_hdr_destroy(hout);
diff --git a/samtools/bcftools/index.c.pysam.c b/samtools/bcftools/index.c.pysam.c
index 8258854..a713aaa 100644
--- a/samtools/bcftools/index.c.pysam.c
+++ b/samtools/bcftools/index.c.pysam.c
@@ -261,6 +261,7 @@ int bcf_idx_build2(const char *fn, const char *_fnidx)
if (fpidx == 0) {
fprintf(pysamerr, "[bcf_idx_build2] fail to create the index file.\n");
free(fnidx);
+ bcf_idx_destroy(idx);
return -1;
}
bcf_idx_save(idx, fpidx);
diff --git a/samtools/bcftools/prob1.c.pysam.c b/samtools/bcftools/prob1.c.pysam.c
index 5bc52a5..235c83b 100644
--- a/samtools/bcftools/prob1.c.pysam.c
+++ b/samtools/bcftools/prob1.c.pysam.c
@@ -6,7 +6,10 @@
#include <stdio.h>
#include <errno.h>
#include <assert.h>
+#include <limits.h>
+#include <zlib.h>
#include "prob1.h"
+#include "kstring.h"
#include "kseq.h"
KSTREAM_INIT(gzFile, gzread, 16384)
@@ -15,6 +18,8 @@ KSTREAM_INIT(gzFile, gzread, 16384)
#define MC_EM_EPS 1e-5
#define MC_DEF_INDEL 0.15
+gzFile bcf_p1_fp_lk;
+
unsigned char seq_nt4_table[256] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
@@ -165,6 +170,8 @@ bcf_p1aux_t *bcf_p1_init(int n, uint8_t *ploidy)
return ma;
}
+int bcf_p1_get_M(bcf_p1aux_t *b) { return b->M; }
+
int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
{
if (n1 == 0 || n1 >= b->n) return -1;
@@ -176,6 +183,13 @@ int bcf_p1_set_n1(bcf_p1aux_t *b, int n1)
return 0;
}
+void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma)
+{
+ // bcf_p1aux_t fields are not visible outside of prob1.c, hence this wrapper.
+ // Ideally, this should set ploidy per site to allow pseudo-autosomal regions
+ b->ploidy = ma->ploidy;
+}
+
void bcf_p1_destroy(bcf_p1aux_t *ma)
{
if (ma) {
@@ -193,28 +207,446 @@ void bcf_p1_destroy(bcf_p1aux_t *ma)
}
}
+extern double kf_gammap(double s, double z);
+int test16(bcf1_t *b, anno16_t *a);
+
+// Wigginton 2005, PMID: 15789306
+// written by Jan Wigginton
+double calc_hwe(int obs_hom1, int obs_hom2, int obs_hets)
+{
+ if (obs_hom1 + obs_hom2 + obs_hets == 0 ) return 1;
+
+ assert(obs_hom1 >= 0 && obs_hom2 >= 0 && obs_hets >= 0);
+
+ int obs_homc = obs_hom1 < obs_hom2 ? obs_hom2 : obs_hom1;
+ int obs_homr = obs_hom1 < obs_hom2 ? obs_hom1 : obs_hom2;
+
+ int rare_copies = 2 * obs_homr + obs_hets;
+ int genotypes = obs_hets + obs_homc + obs_homr;
+
+ double *het_probs = (double*) calloc(rare_copies+1, sizeof(double));
+
+ /* start at midpoint */
+ int mid = rare_copies * (2 * genotypes - rare_copies) / (2 * genotypes);
+
+ /* check to ensure that midpoint and rare alleles have same parity */
+ if ((rare_copies & 1) ^ (mid & 1)) mid++;
+
+ int curr_hets = mid;
+ int curr_homr = (rare_copies - mid) / 2;
+ int curr_homc = genotypes - curr_hets - curr_homr;
+
+ het_probs[mid] = 1.0;
+ double sum = het_probs[mid];
+ for (curr_hets = mid; curr_hets > 1; curr_hets -= 2)
+ {
+ het_probs[curr_hets - 2] = het_probs[curr_hets] * curr_hets * (curr_hets - 1.0) / (4.0 * (curr_homr + 1.0) * (curr_homc + 1.0));
+ sum += het_probs[curr_hets - 2];
+
+ /* 2 fewer heterozygotes for next iteration -> add one rare, one common homozygote */
+ curr_homr++;
+ curr_homc++;
+ }
+
+ curr_hets = mid;
+ curr_homr = (rare_copies - mid) / 2;
+ curr_homc = genotypes - curr_hets - curr_homr;
+ for (curr_hets = mid; curr_hets <= rare_copies - 2; curr_hets += 2)
+ {
+ het_probs[curr_hets + 2] = het_probs[curr_hets] * 4.0 * curr_homr * curr_homc /((curr_hets + 2.0) * (curr_hets + 1.0));
+ sum += het_probs[curr_hets + 2];
+
+ /* add 2 heterozygotes for next iteration -> subtract one rare, one common homozygote */
+ curr_homr--;
+ curr_homc--;
+ }
+ int i;
+ for (i = 0; i <= rare_copies; i++) het_probs[i] /= sum;
+
+ /* p-value calculation for p_hwe */
+ double p_hwe = 0.0;
+ for (i = 0; i <= rare_copies; i++)
+ {
+ if (het_probs[i] > het_probs[obs_hets])
+ continue;
+ p_hwe += het_probs[i];
+ }
+
+ p_hwe = p_hwe > 1.0 ? 1.0 : p_hwe;
+ free(het_probs);
+ return p_hwe;
+
+}
+
+
+static void _bcf1_set_ref(bcf1_t *b, int idp)
+{
+ kstring_t s;
+ int old_n_gi = b->n_gi;
+ s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
+ kputs(":GT", &s); kputc('\0', &s);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+
+ // Call GTs
+ int isample, an = 0;
+ for (isample = 0; isample < b->n_smpl; isample++)
+ {
+ if ( idp>=0 && ((uint16_t*)b->gi[idp].data)[isample]==0 )
+ ((uint8_t*)b->gi[old_n_gi].data)[isample] = 1<<7;
+ else
+ {
+ ((uint8_t*)b->gi[old_n_gi].data)[isample] = 0;
+ an += b->ploidy ? b->ploidy[isample] : 2;
+ }
+ }
+ bcf_fit_alt(b,1);
+ b->qual = 999;
+
+ // Prepare BCF for output: ref, alt, filter, info, format
+ memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s);
+ kputs(b->ref, &s); kputc('\0', &s);
+ kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
+ {
+ ksprintf(&s, "AN=%d;", an);
+ kputs(b->info, &s);
+ anno16_t a;
+ int has_I16 = test16(b, &a) >= 0? 1 : 0;
+ if (has_I16 )
+ {
+ if ( a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
+ ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ }
+ kputc('\0', &s);
+ rm_info(&s, "I16=");
+ rm_info(&s, "QS=");
+ }
+ kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+}
+
+int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only)
+{
+ int nals = 1;
+ char *p;
+ for (p=b->alt; *p; p++)
+ {
+ if ( *p=='X' || p[0]=='.' ) break;
+ if ( p[0]==',' ) nals++;
+ }
+ if ( b->alt[0] && !*p ) nals++;
+
+ if ( nals>4 )
+ {
+ if ( *b->ref=='N' ) return 0;
+ fprintf(pysamerr,"Not ready for this, more than 4 alleles at %d: %s, %s\n", b->pos+1, b->ref,b->alt);
+ exit(1);
+ }
+
+ // find PL, DV and DP FORMAT indexes
+ uint8_t *pl = NULL;
+ int i, npl = 0, idp = -1, idv = -1;
+ for (i = 0; i < b->n_gi; ++i)
+ {
+ if (b->gi[i].fmt == bcf_str2int("PL", 2))
+ {
+ pl = (uint8_t*)b->gi[i].data;
+ npl = b->gi[i].len;
+ }
+ else if (b->gi[i].fmt == bcf_str2int("DP", 2)) idp=i;
+ else if (b->gi[i].fmt == bcf_str2int("DV", 2)) idv=i;
+ }
+ if ( nals==1 )
+ {
+ if ( !var_only ) _bcf1_set_ref(b, idp);
+ return 1;
+ }
+ if ( !pl ) return -1;
+
+ assert(ma->q2p[0] == 1);
+
+ // Init P(D|G)
+ int npdg = nals*(nals+1)/2;
+ double *pdg,*_pdg;
+ _pdg = pdg = malloc(sizeof(double)*ma->n*npdg);
+ for (i=0; i<ma->n; i++)
+ {
+ int j;
+ double sum = 0;
+ for (j=0; j<npdg; j++)
+ {
+ //_pdg[j] = pow(10,-0.1*pl[j]);
+ _pdg[j] = ma->q2p[pl[j]];
+ sum += _pdg[j];
+ }
+ if ( sum )
+ for (j=0; j<npdg; j++) _pdg[j] /= sum;
+ _pdg += npdg;
+ pl += npl;
+ }
+
+ if ((p = strstr(b->info, "QS=")) == 0) { fprintf(pysamerr,"INFO/QS is required with -m, exiting\n"); exit(1); }
+ double qsum[4];
+ if ( sscanf(p+3,"%lf,%lf,%lf,%lf",&qsum[0],&qsum[1],&qsum[2],&qsum[3])!=4 ) { fprintf(pysamerr,"Could not parse %s\n",p); exit(1); }
+
+
+ // Calculate the most likely combination of alleles, remembering the most and second most likely set
+ int ia,ib,ic, max_als=0, max_als2=0;
+ double ref_lk = 0, max_lk = INT_MIN, max_lk2 = INT_MIN, lk_sum = INT_MIN, lk_sums[3];
+ for (ia=0; ia<nals; ia++)
+ {
+ double lk_tot = 0;
+ int iaa = (ia+1)*(ia+2)/2-1;
+ int isample;
+ for (isample=0; isample<ma->n; isample++)
+ {
+ double *p = pdg + isample*npdg;
+ // assert( log(p[iaa]) <= 0 );
+ lk_tot += log(p[iaa]);
+ }
+ if ( ia==0 ) ref_lk = lk_tot;
+ if ( max_lk<lk_tot ) { max_lk2 = max_lk; max_als2 = max_als; max_lk = lk_tot; max_als = 1<<ia; }
+ else if ( max_lk2<lk_tot ) { max_lk2 = lk_tot; max_als2 = 1<<ia; }
+ lk_sum = lk_tot>lk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum));
+ }
+ lk_sums[0] = lk_sum;
+ if ( nals>1 )
+ {
+ for (ia=0; ia<nals; ia++)
+ {
+ if ( qsum[ia]==0 ) continue;
+ int iaa = (ia+1)*(ia+2)/2-1;
+ for (ib=0; ib<ia; ib++)
+ {
+ if ( qsum[ib]==0 ) continue;
+ double lk_tot = 0;
+ double fa = qsum[ia]/(qsum[ia]+qsum[ib]);
+ double fb = qsum[ib]/(qsum[ia]+qsum[ib]);
+ double fab = 2*fa*fb; fa *= fa; fb *= fb;
+ int isample, ibb = (ib+1)*(ib+2)/2-1, iab = iaa - ia + ib;
+ for (isample=0; isample<ma->n; isample++)
+ {
+ double *p = pdg + isample*npdg;
+ //assert( log(fa*p[iaa] + fb*p[ibb] + fab*p[iab]) <= 0 );
+ if ( b->ploidy && b->ploidy[isample]==1 )
+ lk_tot += log(fa*p[iaa] + fb*p[ibb]);
+ else
+ lk_tot += log(fa*p[iaa] + fb*p[ibb] + fab*p[iab]);
+ }
+ if ( max_lk<lk_tot ) { max_lk2 = max_lk; max_als2 = max_als; max_lk = lk_tot; max_als = 1<<ia|1<<ib; }
+ else if ( max_lk2<lk_tot ) { max_lk2 = lk_tot; max_als2 = 1<<ia|1<<ib; }
+ lk_sum = lk_tot>lk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum));
+ }
+ }
+ lk_sums[1] = lk_sum;
+ }
+ if ( nals>2 )
+ {
+ for (ia=0; ia<nals; ia++)
+ {
+ if ( qsum[ia]==0 ) continue;
+ int iaa = (ia+1)*(ia+2)/2-1;
+ for (ib=0; ib<ia; ib++)
+ {
+ if ( qsum[ib]==0 ) continue;
+ int ibb = (ib+1)*(ib+2)/2-1;
+ int iab = iaa - ia + ib;
+ for (ic=0; ic<ib; ic++)
+ {
+ if ( qsum[ic]==0 ) continue;
+ double lk_tot = 0;
+ double fa = qsum[ia]/(qsum[ia]+qsum[ib]+qsum[ic]);
+ double fb = qsum[ib]/(qsum[ia]+qsum[ib]+qsum[ic]);
+ double fc = qsum[ic]/(qsum[ia]+qsum[ib]+qsum[ic]);
+ double fab = 2*fa*fb, fac = 2*fa*fc, fbc = 2*fb*fc; fa *= fa; fb *= fb; fc *= fc;
+ int isample, icc = (ic+1)*(ic+2)/2-1;
+ int iac = iaa - ia + ic, ibc = ibb - ib + ic;
+ for (isample=0; isample<ma->n; isample++)
+ {
+ double *p = pdg + isample*npdg;
+ //assert( log(fa*p[iaa] + fb*p[ibb] + fc*p[icc] + fab*p[iab] + fac*p[iac] + fbc*p[ibc]) <= 0 );
+ if ( b->ploidy && b->ploidy[isample]==1 )
+ lk_tot += log(fa*p[iaa] + fb*p[ibb] + fc*p[icc]);
+ else
+ lk_tot += log(fa*p[iaa] + fb*p[ibb] + fc*p[icc] + fab*p[iab] + fac*p[iac] + fbc*p[ibc]);
+ }
+ if ( max_lk<lk_tot ) { max_lk2 = max_lk; max_als2 = max_als; max_lk = lk_tot; max_als = 1<<ia|1<<ib|1<<ic; }
+ else if ( max_lk2<lk_tot ) { max_lk2 = lk_tot; max_als2 = 1<<ia|1<<ib|1<<ic; }
+ lk_sum = lk_tot>lk_sum ? lk_tot + log(1+exp(lk_sum-lk_tot)) : lk_sum + log(1+exp(lk_tot-lk_sum));
+ }
+ }
+ }
+ lk_sums[2] = lk_sum;
+ }
+
+ // Should we add another allele, does it increase the likelihood significantly?
+ int n1=0, n2=0;
+ for (i=0; i<nals; i++) if ( max_als&1<<i) n1++;
+ for (i=0; i<nals; i++) if ( max_als2&1<<i) n2++;
+ if ( n2<n1 && kf_gammap(1,2.0*(max_lk-max_lk2))<threshold )
+ {
+ // the threshold not exceeded, use the second most likely set with fewer alleles
+ max_lk = max_lk2;
+ max_als = max_als2;
+ n1 = n2;
+ }
+ lk_sum = lk_sums[n1-1];
+
+ // Get the BCF record ready for GT and GQ
+ kstring_t s;
+ int old_n_gi = b->n_gi;
+ s.m = b->m_str; s.l = b->l_str - 1; s.s = b->str;
+ kputs(":GT:GQ", &s); kputc('\0', &s);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+
+ // Call GTs
+ int isample, gts=0, ac[4] = {0,0,0,0};
+ int nRR = 0, nAA = 0, nRA = 0, max_dv = 0;
+ for (isample = 0; isample < b->n_smpl; isample++)
+ {
+ int ploidy = b->ploidy ? b->ploidy[isample] : 2;
+ double *p = pdg + isample*npdg;
+ int ia, als = 0;
+ double lk = 0, lk_s = 0;
+ for (ia=0; ia<nals; ia++)
+ {
+ if ( !(max_als&1<<ia) ) continue;
+ int iaa = (ia+1)*(ia+2)/2-1;
+ double _lk = p[iaa]*qsum[ia]*qsum[ia];
+ if ( _lk > lk ) { lk = _lk; als = ia<<3 | ia; }
+ lk_s += _lk;
+ }
+ if ( ploidy==2 )
+ {
+ for (ia=0; ia<nals; ia++)
+ {
+ if ( !(max_als&1<<ia) ) continue;
+ int iaa = (ia+1)*(ia+2)/2-1;
+ for (ib=0; ib<ia; ib++)
+ {
+ if ( !(max_als&1<<ib) ) continue;
+ int iab = iaa - ia + ib;
+ double _lk = 2*qsum[ia]*qsum[ib]*p[iab];
+ if ( _lk > lk ) { lk = _lk; als = ib<<3 | ia; }
+ lk_s += _lk;
+ }
+ }
+ }
+ lk = -log(1-lk/lk_s)/0.2302585;
+ int dp = 0;
+ if ( idp>=0 && (dp=((uint16_t*)b->gi[idp].data)[isample])==0 )
+ {
+ // no coverage
+ ((uint8_t*)b->gi[old_n_gi].data)[isample] = 1<<7;
+ ((uint8_t*)b->gi[old_n_gi+1].data)[isample] = 0;
+ continue;
+ }
+ if ( lk>99 ) lk = 99;
+ ((uint8_t*)b->gi[old_n_gi].data)[isample] = als;
+ ((uint8_t*)b->gi[old_n_gi+1].data)[isample] = (int)lk;
+
+ // For MDV annotation
+ int dv;
+ if ( als && idv>=0 && (dv=((uint16_t*)b->gi[idv].data)[isample]) )
+ {
+ if ( max_dv < dv ) max_dv = dv;
+ }
+
+ // For HWE annotation; multiple ALT alleles treated as one
+ if ( !als ) nRR++;
+ else if ( !(als>>3&7) || !(als&7) ) nRA++;
+ else nAA++;
+
+ gts |= 1<<(als>>3&7) | 1<<(als&7);
+ ac[ als>>3&7 ]++;
+ ac[ als&7 ]++;
+ }
+ free(pdg);
+ bcf_fit_alt(b,max_als);
+
+ // The VCF spec is ambiguous about QUAL: is it the probability of anything else
+ // (that is QUAL(non-ref) = P(ref)+P(any non-ref other than ALT)) or is it
+ // QUAL(non-ref)=P(ref) and QUAL(ref)=1-P(ref)? Assuming the latter.
+ b->qual = gts>1 ? -4.343*(ref_lk - lk_sum) : -4.343*log(1-exp(ref_lk - lk_sum));
+ if ( b->qual>999 ) b->qual = 999;
+
+ // Prepare BCF for output: ref, alt, filter, info, format
+ memset(&s, 0, sizeof(kstring_t)); kputc('\0', &s);
+ kputs(b->ref, &s); kputc('\0', &s);
+ kputs(b->alt, &s); kputc('\0', &s); kputc('\0', &s);
+ {
+ int an=0, nalts=0;
+ for (i=0; i<nals; i++)
+ {
+ an += ac[i];
+ if ( i>0 && ac[i] ) nalts++;
+ }
+ ksprintf(&s, "AN=%d;", an);
+ if ( nalts )
+ {
+ kputs("AC=", &s);
+ for (i=1; i<nals; i++)
+ {
+ if ( !(gts&1<<i) ) continue;
+ nalts--;
+ ksprintf(&s,"%d", ac[i]);
+ if ( nalts>0 ) kputc(',', &s);
+ }
+ kputc(';', &s);
+ }
+ kputs(b->info, &s);
+ anno16_t a;
+ int has_I16 = test16(b, &a) >= 0? 1 : 0;
+ if (has_I16 )
+ {
+ if ( a.is_tested) ksprintf(&s, ";PV4=%.2g,%.2g,%.2g,%.2g", a.p[0], a.p[1], a.p[2], a.p[3]);
+ ksprintf(&s, ";DP4=%d,%d,%d,%d;MQ=%d", a.d[0], a.d[1], a.d[2], a.d[3], a.mq);
+ ksprintf(&s, ";QBD=%e", b->qual/(a.d[0] + a.d[1] + a.d[2] + a.d[3]));
+ if ( max_dv ) ksprintf(&s, ";MDV=%d", max_dv);
+ }
+ if ( nAA+nRA )
+ {
+ double hwe = calc_hwe(nAA, nRR, nRA);
+ ksprintf(&s, ";HWE=%e", hwe);
+ }
+ kputc('\0', &s);
+ rm_info(&s, "I16=");
+ rm_info(&s, "QS=");
+ }
+ kputs(b->fmt, &s); kputc('\0', &s);
+ free(b->str);
+ b->m_str = s.m; b->l_str = s.l; b->str = s.s;
+ bcf_sync(b);
+
+ return gts;
+}
+
static int cal_pdg(const bcf1_t *b, bcf_p1aux_t *ma)
{
- int i, j;
- long *p, tmp;
- p = alloca(b->n_alleles * sizeof(long));
- memset(p, 0, sizeof(long) * b->n_alleles);
- for (j = 0; j < ma->n; ++j) {
- const uint8_t *pi = ma->PL + j * ma->PL_len;
- double *pdg = ma->pdg + j * 3;
- pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
- for (i = 0; i < b->n_alleles; ++i)
- p[i] += (int)pi[(i+1)*(i+2)/2-1];
- }
- for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
- for (i = 1; i < b->n_alleles; ++i) // insertion sort
- for (j = i; j > 0 && p[j] < p[j-1]; --j)
- tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
- for (i = b->n_alleles - 1; i >= 0; --i)
- if ((p[i]&0xf) == 0) break;
- return i;
+ int i, j;
+ long *p, tmp;
+ p = alloca(b->n_alleles * sizeof(long));
+ memset(p, 0, sizeof(long) * b->n_alleles);
+ for (j = 0; j < ma->n; ++j) {
+ const uint8_t *pi = ma->PL + j * ma->PL_len;
+ double *pdg = ma->pdg + j * 3;
+ pdg[0] = ma->q2p[pi[2]]; pdg[1] = ma->q2p[pi[1]]; pdg[2] = ma->q2p[pi[0]];
+ for (i = 0; i < b->n_alleles; ++i)
+ p[i] += (int)pi[(i+1)*(i+2)/2-1];
+ }
+ for (i = 0; i < b->n_alleles; ++i) p[i] = p[i]<<4 | i;
+ for (i = 1; i < b->n_alleles; ++i) // insertion sort
+ for (j = i; j > 0 && p[j] < p[j-1]; --j)
+ tmp = p[j], p[j] = p[j-1], p[j-1] = tmp;
+ for (i = b->n_alleles - 1; i >= 0; --i)
+ if ((p[i]&0xf) == 0) break;
+ return i;
}
+
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k)
{
double sum, g[3];
@@ -324,6 +756,8 @@ static void mc_cal_y_core(bcf_p1aux_t *ma, int beg)
}
}
if (z[0] != ma->z) memcpy(ma->z, z[0], sizeof(double) * (ma->M + 1));
+ if (bcf_p1_fp_lk)
+ gzwrite(bcf_p1_fp_lk, ma->z, sizeof(double) * (ma->M + 1));
}
static void mc_cal_y(bcf_p1aux_t *ma)
diff --git a/samtools/bcftools/prob1.h b/samtools/bcftools/prob1.h
index 0a51a0a..6f93155 100644
--- a/samtools/bcftools/prob1.h
+++ b/samtools/bcftools/prob1.h
@@ -14,6 +14,11 @@ typedef struct {
double cmp[3], p_chi2, lrt; // used by contrast2()
} bcf_p1rst_t;
+typedef struct {
+ double p[4];
+ int mq, depth, is_tested, d[4];
+} anno16_t;
+
#define MC_PTYPE_FULL 1
#define MC_PTYPE_COND2 2
#define MC_PTYPE_FLAT 3
@@ -26,7 +31,9 @@ extern "C" {
void bcf_p1_init_prior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_init_subprior(bcf_p1aux_t *ma, int type, double theta);
void bcf_p1_destroy(bcf_p1aux_t *ma);
+ void bcf_p1_set_ploidy(bcf1_t *b, bcf_p1aux_t *ma);
int bcf_p1_cal(const bcf1_t *b, int do_contrast, bcf_p1aux_t *ma, bcf_p1rst_t *rst);
+ int call_multiallelic_gt(bcf1_t *b, bcf_p1aux_t *ma, double threshold, int var_only);
int bcf_p1_call_gt(const bcf_p1aux_t *ma, double f0, int k);
void bcf_p1_dump_afs(bcf_p1aux_t *ma);
int bcf_p1_read_prior(bcf_p1aux_t *ma, const char *fn);
diff --git a/samtools/bcftools/vcf.c.pysam.c b/samtools/bcftools/vcf.c.pysam.c
index a30de82..b67e915 100644
--- a/samtools/bcftools/vcf.c.pysam.c
+++ b/samtools/bcftools/vcf.c.pysam.c
@@ -32,7 +32,12 @@ bcf_hdr_t *vcf_hdr_read(bcf_t *bp)
memset(&smpl, 0, sizeof(kstring_t));
while (ks_getuntil(v->ks, '\n', &v->line, &dret) >= 0) {
if (v->line.l < 2) continue;
- if (v->line.s[0] != '#') return 0; // no sample line
+ if (v->line.s[0] != '#') {
+ free(meta.s);
+ free(smpl.s);
+ free(h);
+ return 0; // no sample line
+ }
if (v->line.s[0] == '#' && v->line.s[1] == '#') {
kputsn(v->line.s, v->line.l, &meta); kputc('\n', &meta);
} else if (v->line.s[0] == '#') {
@@ -188,7 +193,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
((uint8_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("SP", 2)) {
((int32_t*)b->gi[i].data)[k-9] = 0;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
((uint16_t*)b->gi[i].data)[k-9] = 0;
} else if (b->gi[i].fmt == bcf_str2int("PL", 2)) {
int y = b->n_alleles * (b->n_alleles + 1) / 2;
@@ -212,7 +217,7 @@ int vcf_read(bcf_t *bp, bcf_hdr_t *h, bcf1_t *b)
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint32_t*)b->gi[i].data)[k-9] = x;
- } else if (b->gi[i].fmt == bcf_str2int("DP", 2)) {
+ } else if (b->gi[i].fmt == bcf_str2int("DP", 2) || b->gi[i].fmt == bcf_str2int("DV", 2)) {
int x = strtol(q, &q, 10);
if (x > 0xffff) x = 0xffff;
((uint16_t*)b->gi[i].data)[k-9] = x;
diff --git a/samtools/bedcov.c.pysam.c b/samtools/bedcov.c.pysam.c
new file mode 100644
index 0000000..ea495a0
--- /dev/null
+++ b/samtools/bedcov.c.pysam.c
@@ -0,0 +1,129 @@
+#include "pysam.h"
+
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include "kstring.h"
+#include "bgzf.h"
+#include "bam.h"
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+typedef struct {
+ bamFile fp;
+ bam_iter_t iter;
+ int min_mapQ;
+} aux_t;
+
+static int read_bam(void *data, bam1_t *b)
+{
+ aux_t *aux = (aux_t*)data;
+ int ret = bam_iter_read(aux->fp, aux->iter, b);
+ if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+ return ret;
+}
+
+int main_bedcov(int argc, char *argv[])
+{
+ extern void bam_init_header_hash(bam_header_t*);
+ gzFile fp;
+ kstring_t str;
+ kstream_t *ks;
+ bam_index_t **idx;
+ bam_header_t *h = 0;
+ aux_t **aux;
+ int *n_plp, dret, i, n, c, min_mapQ = 0;
+ int64_t *cnt;
+ const bam_pileup1_t **plp;
+
+ while ((c = getopt(argc, argv, "Q:")) >= 0) {
+ switch (c) {
+ case 'Q': min_mapQ = atoi(optarg); break;
+ }
+ }
+ if (optind + 2 > argc) {
+ fprintf(pysamerr, "Usage: samtools bedcov <in.bed> <in1.bam> [...]\n");
+ return 1;
+ }
+ memset(&str, 0, sizeof(kstring_t));
+ n = argc - optind - 1;
+ aux = calloc(n, sizeof(void*));
+ idx = calloc(n, sizeof(void*));
+ for (i = 0; i < n; ++i) {
+ aux[i] = calloc(1, sizeof(aux_t));
+ aux[i]->min_mapQ = min_mapQ;
+ aux[i]->fp = bam_open(argv[i+optind+1], "r");
+ idx[i] = bam_index_load(argv[i+optind+1]);
+ if (aux[i]->fp == 0 || idx[i] == 0) {
+ fprintf(pysamerr, "ERROR: fail to open index BAM file '%s'\n", argv[i+optind+1]);
+ return 2;
+ }
+ bgzf_set_cache_size(aux[i]->fp, 20);
+ if (i == 0) h = bam_header_read(aux[0]->fp);
+ }
+ bam_init_header_hash(h);
+ cnt = calloc(n, 8);
+
+ fp = gzopen(argv[optind], "rb");
+ ks = ks_init(fp);
+ n_plp = calloc(n, sizeof(int));
+ plp = calloc(n, sizeof(void*));
+ while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+ char *p, *q;
+ int tid, beg, end, pos;
+ bam_mplp_t mplp;
+
+ for (p = q = str.s; *p && *p != '\t'; ++p);
+ if (*p != '\t') goto bed_error;
+ *p = 0; tid = bam_get_tid(h, q); *p = '\t';
+ if (tid < 0) goto bed_error;
+ for (q = p = p + 1; isdigit(*p); ++p);
+ if (*p != '\t') goto bed_error;
+ *p = 0; beg = atoi(q); *p = '\t';
+ for (q = p = p + 1; isdigit(*p); ++p);
+ if (*p == '\t' || *p == 0) {
+ int c = *p;
+ *p = 0; end = atoi(q); *p = c;
+ } else goto bed_error;
+
+ for (i = 0; i < n; ++i) {
+ if (aux[i]->iter) bam_iter_destroy(aux[i]->iter);
+ aux[i]->iter = bam_iter_query(idx[i], tid, beg, end);
+ }
+ mplp = bam_mplp_init(n, read_bam, (void**)aux);
+ bam_mplp_set_maxcnt(mplp, 64000);
+ memset(cnt, 0, 8 * n);
+ while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0)
+ if (pos >= beg && pos < end)
+ for (i = 0; i < n; ++i) cnt[i] += n_plp[i];
+ for (i = 0; i < n; ++i) {
+ kputc('\t', &str);
+ kputl(cnt[i], &str);
+ }
+ puts(str.s);
+ bam_mplp_destroy(mplp);
+ continue;
+
+bed_error:
+ fprintf(pysamerr, "Errors in BED line '%s'\n", str.s);
+ }
+ free(n_plp); free(plp);
+ ks_destroy(ks);
+ gzclose(fp);
+
+ free(cnt);
+ for (i = 0; i < n; ++i) {
+ if (aux[i]->iter) bam_iter_destroy(aux[i]->iter);
+ bam_index_destroy(idx[i]);
+ bam_close(aux[i]->fp);
+ free(aux[i]);
+ }
+ bam_header_destroy(h);
+ free(aux); free(idx);
+ free(str.s);
+ return 0;
+}
diff --git a/samtools/bgzf.c.pysam.c b/samtools/bgzf.c.pysam.c
index 067b89d..a3b857f 100644
--- a/samtools/bgzf.c.pysam.c
+++ b/samtools/bgzf.c.pysam.c
@@ -3,6 +3,7 @@
/* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+ 2011 Attractive Chaos <attractor at live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
@@ -23,400 +24,235 @@
THE SOFTWARE.
*/
-/*
- 2009-06-29 by lh3: cache recent uncompressed blocks.
- 2009-06-25 by lh3: optionally use my knetfile library to access file on a FTP.
- 2009-06-12 by lh3: support a mode string like "wu" where 'u' for uncompressed output */
-
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
-#include <fcntl.h>
+#include <assert.h>
+#include <pthread.h>
#include <sys/types.h>
-#include <sys/stat.h>
#include "bgzf.h"
-#include "khash.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+typedef knetFile *_bgzf_file_t;
+#define _bgzf_open(fn, mode) knet_open(fn, mode)
+#define _bgzf_dopen(fp, mode) knet_dopen(fp, mode)
+#define _bgzf_close(fp) knet_close(fp)
+#define _bgzf_fileno(fp) ((fp)->fd)
+#define _bgzf_tell(fp) knet_tell(fp)
+#define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence)
+#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len)
+#define _bgzf_write(fp, buf, len) knet_write(fp, buf, len)
+#else // ~defined(_USE_KNETFILE)
+#if defined(_WIN32) || defined(_MSC_VER)
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else // ~defined(_WIN32)
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif // ~defined(_WIN32)
+typedef FILE *_bgzf_file_t;
+#define _bgzf_open(fn, mode) fopen(fn, mode)
+#define _bgzf_dopen(fp, mode) fdopen(fp, mode)
+#define _bgzf_close(fp) fclose(fp)
+#define _bgzf_fileno(fp) fileno(fp)
+#define _bgzf_tell(fp) ftello(fp)
+#define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence)
+#define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp)
+#define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp)
+#endif // ~define(_USE_KNETFILE)
+
+#define BLOCK_HEADER_LENGTH 18
+#define BLOCK_FOOTER_LENGTH 8
+
+
+/* BGZF/GZIP header (speciallized from RFC 1952; little endian):
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN|
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+*/
+static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0";
+
+#ifdef BGZF_CACHE
typedef struct {
int size;
uint8_t *block;
int64_t end_offset;
} cache_t;
+#include "khash.h"
KHASH_MAP_INIT_INT64(cache, cache_t)
-
-#if defined(_WIN32) || defined(_MSC_VER)
-#define ftello(fp) ftell(fp)
-#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
-#else
-extern off_t ftello(FILE *stream);
-extern int fseeko(FILE *stream, off_t offset, int whence);
#endif
-typedef int8_t bgzf_byte_t;
-
-static const int DEFAULT_BLOCK_SIZE = 64 * 1024;
-static const int MAX_BLOCK_SIZE = 64 * 1024;
-
-static const int BLOCK_HEADER_LENGTH = 18;
-static const int BLOCK_FOOTER_LENGTH = 8;
-
-static const int GZIP_ID1 = 31;
-static const int GZIP_ID2 = 139;
-static const int CM_DEFLATE = 8;
-static const int FLG_FEXTRA = 4;
-static const int OS_UNKNOWN = 255;
-static const int BGZF_ID1 = 66; // 'B'
-static const int BGZF_ID2 = 67; // 'C'
-static const int BGZF_LEN = 2;
-static const int BGZF_XLEN = 6; // BGZF_LEN+4
-
-static const int GZIP_WINDOW_BITS = -15; // no zlib header
-static const int Z_DEFAULT_MEM_LEVEL = 8;
-
-
-inline
-void
-packInt16(uint8_t* buffer, uint16_t value)
+static inline void packInt16(uint8_t *buffer, uint16_t value)
{
- buffer[0] = value;
- buffer[1] = value >> 8;
+ buffer[0] = value;
+ buffer[1] = value >> 8;
}
-inline
-int
-unpackInt16(const uint8_t* buffer)
+static inline int unpackInt16(const uint8_t *buffer)
{
- return (buffer[0] | (buffer[1] << 8));
+ return buffer[0] | buffer[1] << 8;
}
-inline
-void
-packInt32(uint8_t* buffer, uint32_t value)
+static inline void packInt32(uint8_t *buffer, uint32_t value)
{
- buffer[0] = value;
- buffer[1] = value >> 8;
- buffer[2] = value >> 16;
- buffer[3] = value >> 24;
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+ buffer[2] = value >> 16;
+ buffer[3] = value >> 24;
}
-static inline
-int
-bgzf_min(int x, int y)
-{
- return (x < y) ? x : y;
-}
-
-static
-void
-report_error(BGZF* fp, const char* message) {
- fp->error = message;
-}
-
-int bgzf_check_bgzf(const char *fn)
+static BGZF *bgzf_read_init()
{
- BGZF *fp;
- uint8_t buf[10],magic[10]="\037\213\010\4\0\0\0\0\0\377";
- int n;
-
- if ((fp = bgzf_open(fn, "r")) == 0)
- {
- fprintf(pysamerr, "[bgzf_check_bgzf] failed to open the file: %s\n",fn);
- return -1;
- }
-
-#ifdef _USE_KNETFILE
- n = knet_read(fp->x.fpr, buf, 10);
-#else
- n = fread(buf, 1, 10, fp->file);
+ BGZF *fp;
+ fp = calloc(1, sizeof(BGZF));
+ fp->is_write = 0;
+ fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+ fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+#ifdef BGZF_CACHE
+ fp->cache = kh_init(cache);
#endif
- bgzf_close(fp);
-
- if ( n!=10 )
- return -1;
-
- if ( !memcmp(magic, buf, 10) ) return 1;
- return 0;
+ return fp;
}
-static BGZF *bgzf_read_init()
+static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level
{
BGZF *fp;
fp = calloc(1, sizeof(BGZF));
- fp->uncompressed_block_size = MAX_BLOCK_SIZE;
- fp->uncompressed_block = malloc(MAX_BLOCK_SIZE);
- fp->compressed_block_size = MAX_BLOCK_SIZE;
- fp->compressed_block = malloc(MAX_BLOCK_SIZE);
- fp->cache_size = 0;
- fp->cache = kh_init(cache);
+ fp->is_write = 1;
+ fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+ fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+ fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
+ if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
return fp;
}
-
-static
-BGZF*
-open_read(int fd)
+// get the compress level from the mode string
+static int mode2level(const char *__restrict mode)
{
-#ifdef _USE_KNETFILE
- knetFile *file = knet_dopen(fd, "r");
-#else
- FILE* file = fdopen(fd, "r");
-#endif
- BGZF* fp;
- if (file == 0) return 0;
- fp = bgzf_read_init();
- fp->file_descriptor = fd;
- fp->open_mode = 'r';
-#ifdef _USE_KNETFILE
- fp->x.fpr = file;
-#else
- fp->file = file;
-#endif
- return fp;
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i)
+ if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = (int)mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ return compress_level;
}
-static
-BGZF*
-open_write(int fd, int compress_level) // compress_level==-1 for the default level
+BGZF *bgzf_open(const char *path, const char *mode)
{
- FILE* file = fdopen(fd, "w");
- BGZF* fp;
- if (file == 0) return 0;
- fp = malloc(sizeof(BGZF));
- fp->file_descriptor = fd;
- fp->open_mode = 'w';
- fp->owned_file = 0;
- fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
- if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
-#ifdef _USE_KNETFILE
- fp->x.fpw = file;
-#else
- fp->file = file;
-#endif
- fp->uncompressed_block_size = DEFAULT_BLOCK_SIZE;
- fp->uncompressed_block = NULL;
- fp->compressed_block_size = MAX_BLOCK_SIZE;
- fp->compressed_block = malloc(MAX_BLOCK_SIZE);
- fp->block_address = 0;
- fp->block_offset = 0;
- fp->block_length = 0;
- fp->error = NULL;
- return fp;
-}
-
-BGZF*
-bgzf_open(const char* __restrict path, const char* __restrict mode)
-{
- BGZF* fp = NULL;
- if (strchr(mode, 'r') || strchr(mode, 'R')) { /* The reading mode is preferred. */
-#ifdef _USE_KNETFILE
- knetFile *file = knet_open(path, mode);
- if (file == 0) return 0;
+ BGZF *fp = 0;
+ assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+ if (strchr(mode, 'r') || strchr(mode, 'R')) {
+ _bgzf_file_t fpr;
+ if ((fpr = _bgzf_open(path, "r")) == 0) return 0;
fp = bgzf_read_init();
- fp->file_descriptor = -1;
- fp->open_mode = 'r';
- fp->x.fpr = file;
-#else
- int fd, oflag = O_RDONLY;
-#ifdef _WIN32
- oflag |= O_BINARY;
-#endif
- fd = open(path, oflag);
- if (fd == -1) return 0;
- fp = open_read(fd);
-#endif
- } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
- int fd, compress_level = -1, oflag = O_WRONLY | O_CREAT | O_TRUNC;
-#ifdef _WIN32
- oflag |= O_BINARY;
-#endif
- fd = open(path, oflag, 0666);
- if (fd == -1) return 0;
- { // set compress_level
- int i;
- for (i = 0; mode[i]; ++i)
- if (mode[i] >= '0' && mode[i] <= '9') break;
- if (mode[i]) compress_level = (int)mode[i] - '0';
- if (strchr(mode, 'u')) compress_level = 0;
- }
- fp = open_write(fd, compress_level);
- }
- if (fp != NULL) fp->owned_file = 1;
- return fp;
-}
-
-BGZF*
-bgzf_fdopen(int fd, const char * __restrict mode)
-{
- if (fd == -1) return 0;
- if (mode[0] == 'r' || mode[0] == 'R') {
- return open_read(fd);
- } else if (mode[0] == 'w' || mode[0] == 'W') {
- int i, compress_level = -1;
- for (i = 0; mode[i]; ++i)
- if (mode[i] >= '0' && mode[i] <= '9') break;
- if (mode[i]) compress_level = (int)mode[i] - '0';
- if (strchr(mode, 'u')) compress_level = 0;
- return open_write(fd, compress_level);
- } else {
- return NULL;
- }
+ fp->fp = fpr;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ FILE *fpw;
+ if ((fpw = fopen(path, "w")) == 0) return 0;
+ fp = bgzf_write_init(mode2level(mode));
+ fp->fp = fpw;
+ }
+ return fp;
}
-static
-int
-deflate_block(BGZF* fp, int block_length)
-{
- // Deflate the block in fp->uncompressed_block into fp->compressed_block.
- // Also adds an extra field that stores the compressed block length.
-
- bgzf_byte_t* buffer = fp->compressed_block;
- int buffer_size = fp->compressed_block_size;
-
- // Init gzip header
- buffer[0] = GZIP_ID1;
- buffer[1] = GZIP_ID2;
- buffer[2] = CM_DEFLATE;
- buffer[3] = FLG_FEXTRA;
- buffer[4] = 0; // mtime
- buffer[5] = 0;
- buffer[6] = 0;
- buffer[7] = 0;
- buffer[8] = 0;
- buffer[9] = OS_UNKNOWN;
- buffer[10] = BGZF_XLEN;
- buffer[11] = 0;
- buffer[12] = BGZF_ID1;
- buffer[13] = BGZF_ID2;
- buffer[14] = BGZF_LEN;
- buffer[15] = 0;
- buffer[16] = 0; // placeholder for block length
- buffer[17] = 0;
-
- // loop to retry for blocks that do not compress enough
- int input_length = block_length;
- int compressed_length = 0;
- while (1) {
- z_stream zs;
- zs.zalloc = NULL;
- zs.zfree = NULL;
- zs.next_in = fp->uncompressed_block;
- zs.avail_in = input_length;
- zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
- zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
-
- int status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED,
- GZIP_WINDOW_BITS, Z_DEFAULT_MEM_LEVEL, Z_DEFAULT_STRATEGY);
- if (status != Z_OK) {
- report_error(fp, "deflate init failed");
- return -1;
- }
- status = deflate(&zs, Z_FINISH);
- if (status != Z_STREAM_END) {
- deflateEnd(&zs);
- if (status == Z_OK) {
- // Not enough space in buffer.
- // Can happen in the rare case the input doesn't compress enough.
- // Reduce the amount of input until it fits.
- input_length -= 1024;
- if (input_length <= 0) {
- // should never happen
- report_error(fp, "input reduction failed");
- return -1;
- }
- continue;
- }
- report_error(fp, "deflate failed");
- return -1;
- }
- status = deflateEnd(&zs);
- if (status != Z_OK) {
- report_error(fp, "deflate end failed");
- return -1;
- }
- compressed_length = zs.total_out;
- compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
- if (compressed_length > MAX_BLOCK_SIZE) {
- // should never happen
- report_error(fp, "deflate overflow");
- return -1;
- }
- break;
- }
-
- packInt16((uint8_t*)&buffer[16], compressed_length-1);
- uint32_t crc = crc32(0L, NULL, 0L);
- crc = crc32(crc, fp->uncompressed_block, input_length);
- packInt32((uint8_t*)&buffer[compressed_length-8], crc);
- packInt32((uint8_t*)&buffer[compressed_length-4], input_length);
-
- int remaining = block_length - input_length;
- if (remaining > 0) {
- if (remaining > input_length) {
- // should never happen (check so we can use memcpy)
- report_error(fp, "remainder too large");
- return -1;
- }
- memcpy(fp->uncompressed_block,
- fp->uncompressed_block + input_length,
- remaining);
- }
- fp->block_offset = remaining;
- return compressed_length;
+BGZF *bgzf_dopen(int fd, const char *mode)
+{
+ BGZF *fp = 0;
+ assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+ if (strchr(mode, 'r') || strchr(mode, 'R')) {
+ _bgzf_file_t fpr;
+ if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0;
+ fp = bgzf_read_init();
+ fp->fp = fpr;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ FILE *fpw;
+ if ((fpw = fdopen(fd, "w")) == 0) return 0;
+ fp = bgzf_write_init(mode2level(mode));
+ fp->fp = fpw;
+ }
+ return fp;
}
-static
-int
-inflate_block(BGZF* fp, int block_length)
+static int bgzf_compress(void *_dst, int *dlen, void *src, int slen, int level)
{
- // Inflate the block in fp->compressed_block into fp->uncompressed_block
+ uint32_t crc;
+ z_stream zs;
+ uint8_t *dst = (uint8_t*)_dst;
+
+ // compress the body
+ zs.zalloc = NULL; zs.zfree = NULL;
+ zs.next_in = src;
+ zs.avail_in = slen;
+ zs.next_out = dst + BLOCK_HEADER_LENGTH;
+ zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+ if (deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY) != Z_OK) return -1; // -15 to disable zlib header/footer
+ if (deflate(&zs, Z_FINISH) != Z_STREAM_END) return -1;
+ if (deflateEnd(&zs) != Z_OK) return -1;
+ *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
+ // write the header
+ memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block
+ packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes
+ // write the footer
+ crc = crc32(crc32(0L, NULL, 0L), src, slen);
+ packInt32((uint8_t*)&dst[*dlen - 8], crc);
+ packInt32((uint8_t*)&dst[*dlen - 4], slen);
+ return 0;
+}
- z_stream zs;
- int status;
- zs.zalloc = NULL;
- zs.zfree = NULL;
- zs.next_in = fp->compressed_block + 18;
- zs.avail_in = block_length - 16;
- zs.next_out = fp->uncompressed_block;
- zs.avail_out = fp->uncompressed_block_size;
+// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.
+static int deflate_block(BGZF *fp, int block_length)
+{
+ int comp_size = BGZF_MAX_BLOCK_SIZE;
+ if (bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level) != 0) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ fp->block_offset = 0;
+ return comp_size;
+}
- status = inflateInit2(&zs, GZIP_WINDOW_BITS);
- if (status != Z_OK) {
- report_error(fp, "inflate init failed");
- return -1;
- }
- status = inflate(&zs, Z_FINISH);
- if (status != Z_STREAM_END) {
- inflateEnd(&zs);
- report_error(fp, "inflate failed");
- return -1;
- }
- status = inflateEnd(&zs);
- if (status != Z_OK) {
- report_error(fp, "inflate failed");
- return -1;
- }
- return zs.total_out;
+// Inflate the block in fp->compressed_block into fp->uncompressed_block
+static int inflate_block(BGZF* fp, int block_length)
+{
+ z_stream zs;
+ zs.zalloc = NULL;
+ zs.zfree = NULL;
+ zs.next_in = fp->compressed_block + 18;
+ zs.avail_in = block_length - 16;
+ zs.next_out = fp->uncompressed_block;
+ zs.avail_out = BGZF_MAX_BLOCK_SIZE;
+
+ if (inflateInit2(&zs, -15) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (inflate(&zs, Z_FINISH) != Z_STREAM_END) {
+ inflateEnd(&zs);
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (inflateEnd(&zs) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ return zs.total_out;
}
-static
-int
-check_header(const bgzf_byte_t* header)
+static int check_header(const uint8_t *header)
{
- return (header[0] == GZIP_ID1 &&
- header[1] == (bgzf_byte_t) GZIP_ID2 &&
- header[2] == Z_DEFLATED &&
- (header[3] & FLG_FEXTRA) != 0 &&
- unpackInt16((uint8_t*)&header[10]) == BGZF_XLEN &&
- header[12] == BGZF_ID1 &&
- header[13] == BGZF_ID2 &&
- unpackInt16((uint8_t*)&header[14]) == BGZF_LEN);
+ return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0
+ && unpackInt16((uint8_t*)&header[10]) == 6
+ && header[12] == 'B' && header[13] == 'C'
+ && unpackInt16((uint8_t*)&header[14]) == 2);
}
+#ifdef BGZF_CACHE
static void free_cache(BGZF *fp)
{
khint_t k;
khash_t(cache) *h = (khash_t(cache)*)fp->cache;
- if (fp->open_mode != 'r') return;
+ if (fp->is_write) return;
for (k = kh_begin(h); k < kh_end(h); ++k)
if (kh_exist(h, k)) free(kh_val(h, k).block);
kh_destroy(cache, h);
@@ -433,12 +269,8 @@ static int load_block_from_cache(BGZF *fp, int64_t block_address)
if (fp->block_length != 0) fp->block_offset = 0;
fp->block_address = block_address;
fp->block_length = p->size;
- memcpy(fp->uncompressed_block, p->block, MAX_BLOCK_SIZE);
-#ifdef _USE_KNETFILE
- knet_seek(fp->x.fpr, p->end_offset, SEEK_SET);
-#else
- fseeko(fp->file, p->end_offset, SEEK_SET);
-#endif
+ memcpy(fp->uncompressed_block, p->block, BGZF_MAX_BLOCK_SIZE);
+ _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET);
return p->size;
}
@@ -448,8 +280,8 @@ static void cache_block(BGZF *fp, int size)
khint_t k;
cache_t *p;
khash_t(cache) *h = (khash_t(cache)*)fp->cache;
- if (MAX_BLOCK_SIZE >= fp->cache_size) return;
- if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) {
+ if (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return;
+ if ((kh_size(h) + 1) * BGZF_MAX_BLOCK_SIZE > fp->cache_size) {
/* A better way would be to remove the oldest block in the
* cache, but here we remove a random one for simplicity. This
* should not have a big impact on performance. */
@@ -465,201 +297,300 @@ static void cache_block(BGZF *fp, int size)
p = &kh_val(h, k);
p->size = fp->block_length;
p->end_offset = fp->block_address + size;
- p->block = malloc(MAX_BLOCK_SIZE);
- memcpy(kh_val(h, k).block, fp->uncompressed_block, MAX_BLOCK_SIZE);
+ p->block = malloc(BGZF_MAX_BLOCK_SIZE);
+ memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE);
}
+#else
+static void free_cache(BGZF *fp) {}
+static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;}
+static void cache_block(BGZF *fp, int size) {}
+#endif
-int
-bgzf_read_block(BGZF* fp)
+int bgzf_read_block(BGZF *fp)
{
- bgzf_byte_t header[BLOCK_HEADER_LENGTH];
+ uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
int count, size = 0, block_length, remaining;
-#ifdef _USE_KNETFILE
- int64_t block_address = knet_tell(fp->x.fpr);
- if (load_block_from_cache(fp, block_address)) return 0;
- count = knet_read(fp->x.fpr, header, sizeof(header));
-#else
- int64_t block_address = ftello(fp->file);
- if (load_block_from_cache(fp, block_address)) return 0;
- count = fread(header, 1, sizeof(header), fp->file);
-#endif
- if (count == 0) {
- fp->block_length = 0;
- return 0;
- }
+ int64_t block_address;
+ block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0;
+ count = _bgzf_read(fp->fp, header, sizeof(header));
+ if (count == 0) { // no data read
+ fp->block_length = 0;
+ return 0;
+ }
+ if (count != sizeof(header) || !check_header(header)) {
+ fp->errcode |= BGZF_ERR_HEADER;
+ return -1;
+ }
size = count;
- if (count != sizeof(header)) {
- report_error(fp, "read failed");
- return -1;
- }
- if (!check_header(header)) {
- report_error(fp, "invalid block header");
- return -1;
- }
- block_length = unpackInt16((uint8_t*)&header[16]) + 1;
- bgzf_byte_t* compressed_block = (bgzf_byte_t*) fp->compressed_block;
- memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
- remaining = block_length - BLOCK_HEADER_LENGTH;
-#ifdef _USE_KNETFILE
- count = knet_read(fp->x.fpr, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
-#else
- count = fread(&compressed_block[BLOCK_HEADER_LENGTH], 1, remaining, fp->file);
-#endif
- if (count != remaining) {
- report_error(fp, "read failed");
- return -1;
- }
+ block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
+ compressed_block = (uint8_t*)fp->compressed_block;
+ memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
+ remaining = block_length - BLOCK_HEADER_LENGTH;
+ count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
+ if (count != remaining) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
size += count;
- count = inflate_block(fp, block_length);
- if (count < 0) return -1;
- if (fp->block_length != 0) {
- // Do not reset offset if this read follows a seek.
- fp->block_offset = 0;
- }
- fp->block_address = block_address;
- fp->block_length = count;
+ if ((count = inflate_block(fp, block_length)) < 0) return -1;
+ if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek.
+ fp->block_address = block_address;
+ fp->block_length = count;
cache_block(fp, size);
- return 0;
+ return 0;
}
-int
-bgzf_read(BGZF* fp, void* data, int length)
+ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length)
{
- if (length <= 0) {
- return 0;
- }
- if (fp->open_mode != 'r') {
- report_error(fp, "file not open for reading");
- return -1;
- }
+ ssize_t bytes_read = 0;
+ uint8_t *output = data;
+ if (length <= 0) return 0;
+ assert(fp->is_write == 0);
+ while (bytes_read < length) {
+ int copy_length, available = fp->block_length - fp->block_offset;
+ uint8_t *buffer;
+ if (available <= 0) {
+ if (bgzf_read_block(fp) != 0) return -1;
+ available = fp->block_length - fp->block_offset;
+ if (available <= 0) break;
+ }
+ copy_length = length - bytes_read < available? length - bytes_read : available;
+ buffer = fp->uncompressed_block;
+ memcpy(output, buffer + fp->block_offset, copy_length);
+ fp->block_offset += copy_length;
+ output += copy_length;
+ bytes_read += copy_length;
+ }
+ if (fp->block_offset == fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = fp->block_length = 0;
+ }
+ return bytes_read;
+}
- int bytes_read = 0;
- bgzf_byte_t* output = data;
- while (bytes_read < length) {
- int copy_length, available = fp->block_length - fp->block_offset;
- bgzf_byte_t *buffer;
- if (available <= 0) {
- if (bgzf_read_block(fp) != 0) {
- return -1;
- }
- available = fp->block_length - fp->block_offset;
- if (available <= 0) {
- break;
- }
- }
- copy_length = bgzf_min(length-bytes_read, available);
- buffer = fp->uncompressed_block;
- memcpy(output, buffer + fp->block_offset, copy_length);
- fp->block_offset += copy_length;
- output += copy_length;
- bytes_read += copy_length;
- }
- if (fp->block_offset == fp->block_length) {
-#ifdef _USE_KNETFILE
- fp->block_address = knet_tell(fp->x.fpr);
-#else
- fp->block_address = ftello(fp->file);
-#endif
- fp->block_offset = 0;
- fp->block_length = 0;
- }
- return bytes_read;
+/***** BEGIN: multi-threading *****/
+
+typedef struct {
+ BGZF *fp;
+ struct mtaux_t *mt;
+ void *buf;
+ int i, errcode, toproc;
+} worker_t;
+
+typedef struct mtaux_t {
+ int n_threads, n_blks, curr, done;
+ volatile int proc_cnt;
+ void **blk;
+ int *len;
+ worker_t *w;
+ pthread_t *tid;
+ pthread_mutex_t lock;
+ pthread_cond_t cv;
+} mtaux_t;
+
+static int worker_aux(worker_t *w)
+{
+ int i, tmp, stop = 0;
+ // wait for condition: to process or all done
+ pthread_mutex_lock(&w->mt->lock);
+ while (!w->toproc && !w->mt->done)
+ pthread_cond_wait(&w->mt->cv, &w->mt->lock);
+ if (w->mt->done) stop = 1;
+ w->toproc = 0;
+ pthread_mutex_unlock(&w->mt->lock);
+ if (stop) return 1; // to quit the thread
+ w->errcode = 0;
+ for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) {
+ int clen = BGZF_MAX_BLOCK_SIZE;
+ if (bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->fp->compress_level) != 0)
+ w->errcode |= BGZF_ERR_ZLIB;
+ memcpy(w->mt->blk[i], w->buf, clen);
+ w->mt->len[i] = clen;
+ }
+ tmp = __sync_fetch_and_add(&w->mt->proc_cnt, 1);
+ return 0;
}
-int bgzf_flush(BGZF* fp)
+static void *mt_worker(void *data)
{
- while (fp->block_offset > 0) {
- int count, block_length;
- block_length = deflate_block(fp, fp->block_offset);
- if (block_length < 0) return -1;
-#ifdef _USE_KNETFILE
- count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
-#else
- count = fwrite(fp->compressed_block, 1, block_length, fp->file);
-#endif
- if (count != block_length) {
- report_error(fp, "write failed");
- return -1;
- }
- fp->block_address += block_length;
- }
- return 0;
+ while (worker_aux(data) == 0);
+ return 0;
+}
+
+int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+{
+ int i;
+ mtaux_t *mt;
+ pthread_attr_t attr;
+ if (!fp->is_write || fp->mt || n_threads <= 1) return -1;
+ mt = calloc(1, sizeof(mtaux_t));
+ mt->n_threads = n_threads;
+ mt->n_blks = n_threads * n_sub_blks;
+ mt->len = calloc(mt->n_blks, sizeof(int));
+ mt->blk = calloc(mt->n_blks, sizeof(void*));
+ for (i = 0; i < mt->n_blks; ++i)
+ mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE);
+ mt->tid = calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master
+ mt->w = calloc(mt->n_threads, sizeof(worker_t));
+ for (i = 0; i < mt->n_threads; ++i) {
+ mt->w[i].i = i;
+ mt->w[i].mt = mt;
+ mt->w[i].fp = fp;
+ mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE);
+ }
+ pthread_attr_init(&attr);
+ pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+ pthread_mutex_init(&mt->lock, 0);
+ pthread_cond_init(&mt->cv, 0);
+ for (i = 1; i < mt->n_threads; ++i) // worker 0 is effectively launched by the master thread
+ pthread_create(&mt->tid[i], &attr, mt_worker, &mt->w[i]);
+ fp->mt = mt;
+ return 0;
+}
+
+static void mt_destroy(mtaux_t *mt)
+{
+ int i;
+ // signal all workers to quit
+ pthread_mutex_lock(&mt->lock);
+ mt->done = 1; mt->proc_cnt = 0;
+ pthread_cond_broadcast(&mt->cv);
+ pthread_mutex_unlock(&mt->lock);
+ for (i = 1; i < mt->n_threads; ++i) pthread_join(mt->tid[i], 0); // worker 0 is effectively launched by the master thread
+ // free other data allocated on heap
+ for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]);
+ for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf);
+ free(mt->blk); free(mt->len); free(mt->w); free(mt->tid);
+ pthread_cond_destroy(&mt->cv);
+ pthread_mutex_destroy(&mt->lock);
+ free(mt);
}
-int bgzf_flush_try(BGZF *fp, int size)
+static void mt_queue(BGZF *fp)
{
- if (fp->block_offset + size > fp->uncompressed_block_size)
- return bgzf_flush(fp);
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ assert(mt->curr < mt->n_blks); // guaranteed by the caller
+ memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset);
+ mt->len[mt->curr] = fp->block_offset;
+ fp->block_offset = 0;
+ ++mt->curr;
+}
+
+static int mt_flush(BGZF *fp)
+{
+ int i;
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ if (fp->block_offset) mt_queue(fp); // guaranteed that assertion does not fail
+ // signal all the workers to compress
+ pthread_mutex_lock(&mt->lock);
+ for (i = 0; i < mt->n_threads; ++i) mt->w[i].toproc = 1;
+ mt->proc_cnt = 0;
+ pthread_cond_broadcast(&mt->cv);
+ pthread_mutex_unlock(&mt->lock);
+ // worker 0 is doing things here
+ worker_aux(&mt->w[0]);
+ // wait for all the threads to complete
+ while (mt->proc_cnt < mt->n_threads);
+ // dump data to disk
+ for (i = 0; i < mt->n_threads; ++i) fp->errcode |= mt->w[i].errcode;
+ for (i = 0; i < mt->curr; ++i)
+ if (fwrite(mt->blk[i], 1, mt->len[i], fp->fp) != mt->len[i])
+ fp->errcode |= BGZF_ERR_IO;
+ mt->curr = 0;
+ return 0;
+}
+
+static int mt_lazy_flush(BGZF *fp)
+{
+ mtaux_t *mt = (mtaux_t*)fp->mt;
+ if (fp->block_offset) mt_queue(fp);
+ if (mt->curr == mt->n_blks)
+ return mt_flush(fp);
return -1;
}
-int bgzf_write(BGZF* fp, const void* data, int length)
+static ssize_t mt_write(BGZF *fp, const void *data, ssize_t length)
{
- const bgzf_byte_t *input = data;
- int block_length, bytes_written;
- if (fp->open_mode != 'w') {
- report_error(fp, "file not open for writing");
- return -1;
- }
+ const uint8_t *input = data;
+ ssize_t rest = length;
+ while (rest) {
+ int copy_length = BGZF_BLOCK_SIZE - fp->block_offset < rest? BGZF_BLOCK_SIZE - fp->block_offset : rest;
+ memcpy(fp->uncompressed_block + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length; input += copy_length; rest -= copy_length;
+ if (fp->block_offset == BGZF_BLOCK_SIZE) mt_lazy_flush(fp);
+ }
+ return length - rest;
+}
- if (fp->uncompressed_block == NULL)
- fp->uncompressed_block = malloc(fp->uncompressed_block_size);
-
- input = data;
- block_length = fp->uncompressed_block_size;
- bytes_written = 0;
- while (bytes_written < length) {
- int copy_length = bgzf_min(block_length - fp->block_offset, length - bytes_written);
- bgzf_byte_t* buffer = fp->uncompressed_block;
- memcpy(buffer + fp->block_offset, input, copy_length);
- fp->block_offset += copy_length;
- input += copy_length;
- bytes_written += copy_length;
- if (fp->block_offset == block_length) {
- if (bgzf_flush(fp) != 0) {
- break;
- }
- }
- }
- return bytes_written;
+/***** END: multi-threading *****/
+
+int bgzf_flush(BGZF *fp)
+{
+ if (!fp->is_write) return 0;
+ if (fp->mt) return mt_flush(fp);
+ while (fp->block_offset > 0) {
+ int block_length;
+ block_length = deflate_block(fp, fp->block_offset);
+ if (block_length < 0) return -1;
+ if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) {
+ fp->errcode |= BGZF_ERR_IO; // possibly truncated file
+ return -1;
+ }
+ fp->block_address += block_length;
+ }
+ return 0;
+}
+
+int bgzf_flush_try(BGZF *fp, ssize_t size)
+{
+ if (fp->block_offset + size > BGZF_BLOCK_SIZE) {
+ if (fp->mt) return mt_lazy_flush(fp);
+ else return bgzf_flush(fp);
+ }
+ return -1;
+}
+
+ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length)
+{
+ const uint8_t *input = data;
+ int block_length = BGZF_BLOCK_SIZE, bytes_written = 0;
+ assert(fp->is_write);
+ if (fp->mt) return mt_write(fp, data, length);
+ while (bytes_written < length) {
+ uint8_t* buffer = fp->uncompressed_block;
+ int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written;
+ memcpy(buffer + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length;
+ input += copy_length;
+ bytes_written += copy_length;
+ if (fp->block_offset == block_length && bgzf_flush(fp)) break;
+ }
+ return bytes_written;
}
int bgzf_close(BGZF* fp)
{
- if (fp->open_mode == 'w') {
- if (bgzf_flush(fp) != 0) return -1;
- { // add an empty block
- int count, block_length = deflate_block(fp, 0);
-#ifdef _USE_KNETFILE
- count = fwrite(fp->compressed_block, 1, block_length, fp->x.fpw);
-#else
- count = fwrite(fp->compressed_block, 1, block_length, fp->file);
-#endif
+ int ret, count, block_length;
+ if (fp == 0) return -1;
+ if (fp->is_write) {
+ if (bgzf_flush(fp) != 0) return -1;
+ fp->compress_level = -1;
+ block_length = deflate_block(fp, 0); // write an empty block
+ count = fwrite(fp->compressed_block, 1, block_length, fp->fp);
+ if (fflush(fp->fp) != 0) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
}
-#ifdef _USE_KNETFILE
- if (fflush(fp->x.fpw) != 0) {
-#else
- if (fflush(fp->file) != 0) {
-#endif
- report_error(fp, "flush failed");
- return -1;
- }
- }
- if (fp->owned_file) {
-#ifdef _USE_KNETFILE
- int ret;
- if (fp->open_mode == 'w') ret = fclose(fp->x.fpw);
- else ret = knet_close(fp->x.fpr);
- if (ret != 0) return -1;
-#else
- if (fclose(fp->file) != 0) return -1;
-#endif
- }
- free(fp->uncompressed_block);
- free(fp->compressed_block);
+ if (fp->mt) mt_destroy(fp->mt);
+ }
+ ret = fp->is_write? fclose(fp->fp) : _bgzf_close(fp->fp);
+ if (ret != 0) return -1;
+ free(fp->uncompressed_block);
+ free(fp->compressed_block);
free_cache(fp);
- free(fp);
- return 0;
+ free(fp);
+ return 0;
}
void bgzf_set_cache_size(BGZF *fp, int cache_size)
@@ -672,17 +603,10 @@ int bgzf_check_EOF(BGZF *fp)
static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
uint8_t buf[28];
off_t offset;
-#ifdef _USE_KNETFILE
- offset = knet_tell(fp->x.fpr);
- if (knet_seek(fp->x.fpr, -28, SEEK_END) != 0) return -1;
- knet_read(fp->x.fpr, buf, 28);
- knet_seek(fp->x.fpr, offset, SEEK_SET);
-#else
- offset = ftello(fp->file);
- if (fseeko(fp->file, -28, SEEK_END) != 0) return -1;
- fread(buf, 1, 28, fp->file);
- fseeko(fp->file, offset, SEEK_SET);
-#endif
+ offset = _bgzf_tell((_bgzf_file_t)fp->fp);
+ if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0;
+ _bgzf_read(fp->fp, buf, 28);
+ _bgzf_seek(fp->fp, offset, SEEK_SET);
return (memcmp(magic, buf, 28) == 0)? 1 : 0;
}
@@ -691,26 +615,82 @@ int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
int block_offset;
int64_t block_address;
- if (fp->open_mode != 'r') {
- report_error(fp, "file not open for read");
- return -1;
- }
- if (where != SEEK_SET) {
- report_error(fp, "unimplemented seek option");
- return -1;
+ if (fp->is_write || where != SEEK_SET) {
+ fp->errcode |= BGZF_ERR_MISUSE;
+ return -1;
+ }
+ block_offset = pos & 0xFFFF;
+ block_address = pos >> 16;
+ if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+ fp->block_length = 0; // indicates current block has not been loaded
+ fp->block_address = block_address;
+ fp->block_offset = block_offset;
+ return 0;
+}
+
+int bgzf_is_bgzf(const char *fn)
+{
+ uint8_t buf[16];
+ int n;
+ _bgzf_file_t fp;
+ if ((fp = _bgzf_open(fn, "r")) == 0) return 0;
+ n = _bgzf_read(fp, buf, 16);
+ _bgzf_close(fp);
+ if (n != 16) return 0;
+ return memcmp(g_magic, buf, 16) == 0? 1 : 0;
+}
+
+int bgzf_getc(BGZF *fp)
+{
+ int c;
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) return -2; /* error */
+ if (fp->block_length == 0) return -1; /* end-of-file */
+ }
+ c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+ if (fp->block_offset == fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = 0;
+ fp->block_length = 0;
}
- block_offset = pos & 0xFFFF;
- block_address = (pos >> 16) & 0xFFFFFFFFFFFFLL;
-#ifdef _USE_KNETFILE
- if (knet_seek(fp->x.fpr, block_address, SEEK_SET) != 0) {
-#else
- if (fseeko(fp->file, block_address, SEEK_SET) != 0) {
+ return c;
+}
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif
- report_error(fp, "seek failed");
- return -1;
- }
- fp->block_length = 0; // indicates current block is not loaded
- fp->block_address = block_address;
- fp->block_offset = block_offset;
- return 0;
+
+int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
+{
+ int l, state = 0;
+ unsigned char *buf = (unsigned char*)fp->uncompressed_block;
+ str->l = 0;
+ do {
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) { state = -2; break; }
+ if (fp->block_length == 0) { state = -1; break; }
+ }
+ for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l);
+ if (l < fp->block_length) state = 1;
+ l -= fp->block_offset;
+ if (str->l + l + 1 >= str->m) {
+ str->m = str->l + l + 2;
+ kroundup32(str->m);
+ str->s = (char*)realloc(str->s, str->m);
+ }
+ memcpy(str->s + str->l, buf + fp->block_offset, l);
+ str->l += l;
+ fp->block_offset += l + 1;
+ if (fp->block_offset >= fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ } while (state == 0);
+ if (str->l == 0 && state < 0) return state;
+ str->s[str->l] = 0;
+ return str->l;
}
diff --git a/samtools/bgzf.h b/samtools/bgzf.h
index 7295f37..cb67681 100644
--- a/samtools/bgzf.h
+++ b/samtools/bgzf.h
@@ -1,6 +1,7 @@
/* The MIT License
Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+ 2011, 2012 Attractive Chaos <attractor at live.co.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
@@ -21,137 +22,186 @@
THE SOFTWARE.
*/
+/* The BGZF library was originally written by Bob Handsaker from the Broad
+ * Institute. It was later improved by the SAMtools developers. */
+
#ifndef __BGZF_H
#define __BGZF_H
#include <stdint.h>
#include <stdio.h>
#include <zlib.h>
-#ifdef _USE_KNETFILE
-#include "knetfile.h"
-#endif
+#include <sys/types.h>
+
+#define BGZF_BLOCK_SIZE 0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
+#define BGZF_MAX_BLOCK_SIZE 0x10000
-//typedef int8_t bool;
+#define BGZF_ERR_ZLIB 1
+#define BGZF_ERR_HEADER 2
+#define BGZF_ERR_IO 4
+#define BGZF_ERR_MISUSE 8
typedef struct {
- int file_descriptor;
- char open_mode; // 'r' or 'w'
- int16_t owned_file, compress_level;
-#ifdef _USE_KNETFILE
- union {
- knetFile *fpr;
- FILE *fpw;
- } x;
-#else
- FILE* file;
-#endif
- int uncompressed_block_size;
- int compressed_block_size;
- void* uncompressed_block;
- void* compressed_block;
- int64_t block_address;
- int block_length;
- int block_offset;
+ int errcode:16, is_write:2, compress_level:14;
int cache_size;
- const char* error;
+ int block_length, block_offset;
+ int64_t block_address;
+ void *uncompressed_block, *compressed_block;
void *cache; // a pointer to a hash table
+ void *fp; // actual file handler; FILE* on writing; FILE* or knetFile* on reading
+ void *mt; // only used for multi-threading
} BGZF;
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+ size_t l, m;
+ char *s;
+} kstring_t;
+#endif
+
#ifdef __cplusplus
extern "C" {
#endif
-/*
- * Open an existing file descriptor for reading or writing.
- * Mode must be either "r" or "w".
- * A subsequent bgzf_close will not close the file descriptor.
- * Returns null on error.
- */
-BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
-
-/*
- * Open the specified file for reading or writing.
- * Mode must be either "r" or "w".
- * Returns null on error.
- */
-BGZF* bgzf_open(const char* path, const char* __restrict mode);
-
-/*
- * Close the BGZ file and free all associated resources.
- * Does not close the underlying file descriptor if created with bgzf_fdopen.
- * Returns zero on success, -1 on error.
- */
-int bgzf_close(BGZF* fp);
-
-/*
- * Read up to length bytes from the file storing into data.
- * Returns the number of bytes actually read.
- * Returns zero on end of file.
- * Returns -1 on error.
- */
-int bgzf_read(BGZF* fp, void* data, int length);
-
-/*
- * Write length bytes from data to the file.
- * Returns the number of bytes written.
- * Returns -1 on error.
- */
-int bgzf_write(BGZF* fp, const void* data, int length);
-
-/*
- * Return a virtual file pointer to the current location in the file.
- * No interpetation of the value should be made, other than a subsequent
- * call to bgzf_seek can be used to position the file at the same point.
- * Return value is non-negative on success.
- * Returns -1 on error.
- */
-#define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
-
-/*
- * Set the file to read from the location specified by pos, which must
- * be a value previously returned by bgzf_tell for this file (but not
- * necessarily one returned by this file handle).
- * The where argument must be SEEK_SET.
- * Seeking on a file opened for write is not supported.
- * Returns zero on success, -1 on error.
- */
-int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
-
-/*
- * Set the cache size. Zero to disable. By default, caching is
- * disabled. The recommended cache size for frequent random access is
- * about 8M bytes.
- */
-void bgzf_set_cache_size(BGZF *fp, int cache_size);
-
-int bgzf_check_EOF(BGZF *fp);
-int bgzf_read_block(BGZF* fp);
-int bgzf_flush(BGZF* fp);
-int bgzf_flush_try(BGZF *fp, int size);
-int bgzf_check_bgzf(const char *fn);
+ /******************
+ * Basic routines *
+ ******************/
+
+ /**
+ * Open an existing file descriptor for reading or writing.
+ *
+ * @param fd file descriptor
+ * @param mode mode matching /[rwu0-9]+/: 'r' for reading, 'w' for writing and a digit specifies
+ * the zlib compression level; if both 'r' and 'w' are present, 'w' is ignored.
+ * @return BGZF file handler; 0 on error
+ */
+ BGZF* bgzf_dopen(int fd, const char *mode);
+
+ #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
+
+ /**
+ * Open the specified file for reading or writing.
+ */
+ BGZF* bgzf_open(const char* path, const char *mode);
+
+ /**
+ * Close the BGZF and free all associated resources.
+ *
+ * @param fp BGZF file handler
+ * @return 0 on success and -1 on error
+ */
+ int bgzf_close(BGZF *fp);
+
+ /**
+ * Read up to _length_ bytes from the file storing into _data_.
+ *
+ * @param fp BGZF file handler
+ * @param data data array to read into
+ * @param length size of data to read
+ * @return number of bytes actually read; 0 on end-of-file and -1 on error
+ */
+ ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length);
+
+ /**
+ * Write _length_ bytes from _data_ to the file.
+ *
+ * @param fp BGZF file handler
+ * @param data data array to write
+ * @param length size of data to write
+ * @return number of bytes actually written; -1 on error
+ */
+ ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length);
+
+ /**
+ * Write the data in the buffer to the file.
+ */
+ int bgzf_flush(BGZF *fp);
+
+ /**
+ * Return a virtual file pointer to the current location in the file.
+ * No interpetation of the value should be made, other than a subsequent
+ * call to bgzf_seek can be used to position the file at the same point.
+ * Return value is non-negative on success.
+ */
+ #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
+
+ /**
+ * Set the file to read from the location specified by _pos_.
+ *
+ * @param fp BGZF file handler
+ * @param pos virtual file offset returned by bgzf_tell()
+ * @param whence must be SEEK_SET
+ * @return 0 on success and -1 on error
+ */
+ int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence);
+
+ /**
+ * Check if the BGZF end-of-file (EOF) marker is present
+ *
+ * @param fp BGZF file handler opened for reading
+ * @return 1 if EOF is present; 0 if not or on I/O error
+ */
+ int bgzf_check_EOF(BGZF *fp);
+
+ /**
+ * Check if a file is in the BGZF format
+ *
+ * @param fn file name
+ * @return 1 if _fn_ is BGZF; 0 if not or on I/O error
+ */
+ int bgzf_is_bgzf(const char *fn);
+
+ /*********************
+ * Advanced routines *
+ *********************/
+
+ /**
+ * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
+ *
+ * @param fp BGZF file handler
+ * @param size size of cache in bytes; 0 to disable caching (default)
+ */
+ void bgzf_set_cache_size(BGZF *fp, int size);
+
+ /**
+ * Flush the file if the remaining buffer size is smaller than _size_
+ */
+ int bgzf_flush_try(BGZF *fp, ssize_t size);
+
+ /**
+ * Read one byte from a BGZF file. It is faster than bgzf_read()
+ * @param fp BGZF file handler
+ * @return byte read; -1 on end-of-file or error
+ */
+ int bgzf_getc(BGZF *fp);
+
+ /**
+ * Read one line from a BGZF file. It is faster than bgzf_getc()
+ *
+ * @param fp BGZF file handler
+ * @param delim delimitor
+ * @param str string to write to; must be initialized
+ * @return length of the string; 0 on end-of-file; negative on error
+ */
+ int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
+
+ /**
+ * Read the next BGZF block.
+ */
+ int bgzf_read_block(BGZF *fp);
+
+ /**
+ * Enable multi-threading (only effective on writing)
+ *
+ * @param fp BGZF file handler; must be opened for writing
+ * @param n_threads #threads used for writing
+ * @param n_sub_blks #blocks processed by each thread; a value 64-256 is recommended
+ */
+ int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks);
#ifdef __cplusplus
}
#endif
-static inline int bgzf_getc(BGZF *fp)
-{
- int c;
- if (fp->block_offset >= fp->block_length) {
- if (bgzf_read_block(fp) != 0) return -2; /* error */
- if (fp->block_length == 0) return -1; /* end-of-file */
- }
- c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
- if (fp->block_offset == fp->block_length) {
-#ifdef _USE_KNETFILE
- fp->block_address = knet_tell(fp->x.fpr);
-#else
- fp->block_address = ftello(fp->file);
-#endif
- fp->block_offset = 0;
- fp->block_length = 0;
- }
- return c;
-}
-
#endif
diff --git a/samtools/faidx.c.pysam.c b/samtools/faidx.c.pysam.c
index 376629e..c011756 100644
--- a/samtools/faidx.c.pysam.c
+++ b/samtools/faidx.c.pysam.c
@@ -339,6 +339,11 @@ char *fai_fetch(const faidx_t *fai, const char *str, int *len)
} else s[name_end] = ':', name_end = l;
}
} else iter = kh_get(s, h, str);
+ if(iter == kh_end(h)) {
+ fprintf(pysamerr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
+ free(s);
+ return 0;
+ };
val = kh_value(h, iter);
// parse the interval
if (name_end < l) {
diff --git a/samtools/kprobaln.c.pysam.c b/samtools/kprobaln.c.pysam.c
index 3404936..045054a 100644
--- a/samtools/kprobaln.c.pysam.c
+++ b/samtools/kprobaln.c.pysam.c
@@ -79,6 +79,8 @@ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_quer
const uint8_t *ref, *query;
int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr;
+ if ( l_ref<=0 || l_query<=0 ) return 0; // FIXME: this may not be an ideal fix, just prevents sefgault
+
/*** initialization ***/
is_backward = state && q? 1 : 0;
ref = _ref - 1; query = _query - 1; // change to 1-based coordinate
@@ -89,7 +91,7 @@ int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_quer
// allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
f = calloc(l_query+1, sizeof(void*));
if (is_backward) b = calloc(l_query+1, sizeof(void*));
- for (i = 0; i <= l_query; ++i) {
+ for (i = 0; i <= l_query; ++i) { // FIXME: this will lead in segfault for l_query==0
f[i] = calloc(bw2 * 3 + 6, sizeof(double)); // FIXME: this is over-allocated for very short seqs
if (is_backward) b[i] = calloc(bw2 * 3 + 6, sizeof(double));
}
diff --git a/samtools/kseq.h b/samtools/kseq.h
index 0bbc7dc..a5cec7c 100644
--- a/samtools/kseq.h
+++ b/samtools/kseq.h
@@ -23,7 +23,7 @@
SOFTWARE.
*/
-/* Last Modified: 18AUG2011 */
+/* Last Modified: 05MAR2012 */
#ifndef AC_KSEQ_H
#define AC_KSEQ_H
@@ -34,7 +34,8 @@
#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
#define KS_SEP_TAB 1 // isspace() && !' '
-#define KS_SEP_MAX 1
+#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
+#define KS_SEP_MAX 2
#define __KS_TYPE(type_t) \
typedef struct __kstream_t { \
@@ -51,7 +52,7 @@
{ \
kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
ks->f = f; \
- ks->buf = malloc(__bufsize); \
+ ks->buf = (unsigned char*)malloc(__bufsize); \
return ks; \
} \
static inline void ks_destroy(kstream_t *ks) \
@@ -103,7 +104,10 @@ typedef struct __kstring_t {
if (ks->end == 0) break; \
} else break; \
} \
- if (delimiter > KS_SEP_MAX) { \
+ if (delimiter == KS_SEP_LINE) { \
+ for (i = ks->begin; i < ks->end; ++i) \
+ if (ks->buf[i] == '\n') break; \
+ } else if (delimiter > KS_SEP_MAX) { \
for (i = ks->begin; i < ks->end; ++i) \
if (ks->buf[i] == delimiter) break; \
} else if (delimiter == KS_SEP_SPACE) { \
@@ -113,7 +117,7 @@ typedef struct __kstring_t {
for (i = ks->begin; i < ks->end; ++i) \
if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
} else i = 0; /* never come to here! */ \
- if (str->m - str->l < i - ks->begin + 1) { \
+ if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \
str->m = str->l + (i - ks->begin) + 1; \
kroundup32(str->m); \
str->s = (char*)realloc(str->s, str->m); \
@@ -129,7 +133,7 @@ typedef struct __kstring_t {
if (str->s == 0) { \
str->m = 1; \
str->s = (char*)calloc(1, 1); \
- } \
+ } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
str->s[str->l] = '\0'; \
return str->l; \
} \
@@ -142,19 +146,16 @@ typedef struct __kstring_t {
__KS_GETC(__read, __bufsize) \
__KS_GETUNTIL(__read, __bufsize)
-#define __KSEQ_BASIC(type_t) \
- static inline kseq_t *kseq_init(type_t fd) \
+#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
+
+#define __KSEQ_BASIC(SCOPE, type_t) \
+ SCOPE kseq_t *kseq_init(type_t fd) \
{ \
kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
s->f = ks_init(fd); \
return s; \
} \
- static inline void kseq_rewind(kseq_t *ks) \
- { \
- ks->last_char = 0; \
- ks->f->is_eof = ks->f->begin = ks->f->end = 0; \
- } \
- static inline void kseq_destroy(kseq_t *ks) \
+ SCOPE void kseq_destroy(kseq_t *ks) \
{ \
if (!ks) return; \
free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
@@ -167,8 +168,8 @@ typedef struct __kstring_t {
-1 end-of-file
-2 truncated quality string
*/
-#define __KSEQ_READ \
- static int kseq_read(kseq_t *seq) \
+#define __KSEQ_READ(SCOPE) \
+ SCOPE int kseq_read(kseq_t *seq) \
{ \
int c; \
kstream_t *ks = seq->f; \
@@ -179,14 +180,15 @@ typedef struct __kstring_t {
} /* else: the first header char has been read in the previous call */ \
seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
- if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0); /* read FASTA/Q comment */ \
+ if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
seq->seq.m = 256; \
seq->seq.s = (char*)malloc(seq->seq.m); \
} \
while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+ if (c == '\n') continue; /* skip empty lines */ \
seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
- ks_getuntil2(ks, '\n', &seq->seq, 0, 1); /* read the rest of the line */ \
+ ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
} \
if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
@@ -202,7 +204,7 @@ typedef struct __kstring_t {
} \
while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
if (c == -1) return -2; /* error: no quality string */ \
- while (ks_getuntil2(ks, '\n', &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
+ while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
seq->last_char = 0; /* we have not come to the next header line */ \
if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
return seq->seq.l; \
@@ -215,10 +217,19 @@ typedef struct __kstring_t {
kstream_t *f; \
} kseq_t;
-#define KSEQ_INIT(type_t, __read) \
+#define KSEQ_INIT2(SCOPE, type_t, __read) \
KSTREAM_INIT(type_t, __read, 16384) \
__KSEQ_TYPE(type_t) \
- __KSEQ_BASIC(type_t) \
- __KSEQ_READ
+ __KSEQ_BASIC(SCOPE, type_t) \
+ __KSEQ_READ(SCOPE)
+
+#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
+
+#define KSEQ_DECLARE(type_t) \
+ __KS_TYPE(type_t) \
+ __KSEQ_TYPE(type_t) \
+ extern kseq_t *kseq_init(type_t fd); \
+ void kseq_destroy(kseq_t *ks); \
+ int kseq_read(kseq_t *seq);
#endif
diff --git a/samtools/ksort.h b/samtools/ksort.h
index f8d8c4c..aa0bb93 100644
--- a/samtools/ksort.h
+++ b/samtools/ksort.h
@@ -26,6 +26,10 @@
/* Contact: Heng Li <lh3 at sanger.ac.uk> */
/*
+ 2012-12-11 (0.1.4):
+
+ * Defined __ks_insertsort_##name as static to compile with C99.
+
2008-11-16 (0.1.4):
* Fixed a bug in introsort() that happens in rare cases.
@@ -141,7 +145,7 @@ typedef struct {
tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
} \
} \
- static inline void __ks_insertsort_##name(type_t *s, type_t *t) \
+ static inline void __ks_insertsort_##name(type_t *s, type_t *t) \
{ \
type_t *i, *j, swap_tmp; \
for (i = s + 1; i < t; ++i) \
diff --git a/samtools/kstring.c.pysam.c b/samtools/kstring.c.pysam.c
index c02bce0..ba37801 100644
--- a/samtools/kstring.c.pysam.c
+++ b/samtools/kstring.c.pysam.c
@@ -100,13 +100,13 @@ typedef unsigned char ubyte_t;
static int *ksBM_prep(const ubyte_t *pat, int m)
{
int i, *suff, *prep, *bmGs, *bmBc;
- prep = calloc(m + 256, sizeof(int));
+ prep = (int*)calloc(m + 256, sizeof(int));
bmGs = prep; bmBc = prep + m;
{ // preBmBc()
for (i = 0; i < 256; ++i) bmBc[i] = m;
for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
}
- suff = calloc(m, sizeof(int));
+ suff = (int*)calloc(m, sizeof(int));
{ // suffixes()
int f = 0, g;
suff[m - 1] = m;
diff --git a/samtools/kstring.h b/samtools/kstring.h
index ec5775b..abd8236 100644
--- a/samtools/kstring.h
+++ b/samtools/kstring.h
@@ -1,3 +1,28 @@
+/* The MIT License
+
+ Copyright (c) by Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
#ifndef KSTRING_H
#define KSTRING_H
@@ -42,7 +67,16 @@ extern "C" {
#ifdef __cplusplus
}
#endif
-
+
+static inline void ks_resize(kstring_t *s, size_t size)
+{
+ if (s->m < size) {
+ s->m = size;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+}
+
static inline int kputsn(const char *p, int l, kstring_t *s)
{
if (s->l + l + 1 >= s->m) {
@@ -78,7 +112,8 @@ static inline int kputw(int c, kstring_t *s)
char buf[16];
int l, x;
if (c == 0) return kputc('0', s);
- for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if(c < 0) for (l = 0, x = c; x < 0; x /= 10) buf[l++] = '0' - (x%10);
+ else for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
if (c < 0) buf[l++] = '-';
if (s->l + l + 1 >= s->m) {
s->m = s->l + l + 2;
@@ -107,6 +142,23 @@ static inline int kputuw(unsigned c, kstring_t *s)
return 0;
}
+static inline int kputl(long c, kstring_t *s)
+{
+ char buf[32];
+ long l, x;
+ if (c == 0) return kputc('0', s);
+ for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+ if (c < 0) buf[l++] = '-';
+ if (s->l + l + 1 >= s->m) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ }
+ for (x = l - 1; x >= 0; --x) s->s[s->l++] = buf[x];
+ s->s[s->l] = 0;
+ return 0;
+}
+
static inline int *ksplit(kstring_t *s, int delimiter, int *n)
{
int max = 0, *offsets = 0;
diff --git a/samtools/misc/ace2sam.c.pysam.c b/samtools/misc/ace2sam.c.pysam.c
new file mode 100644
index 0000000..a518c67
--- /dev/null
+++ b/samtools/misc/ace2sam.c.pysam.c
@@ -0,0 +1,251 @@
+#include "pysam.h"
+
+/* The MIT License
+
+ Copyright (c) 2011 Heng Li <lh3 at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <zlib.h>
+#include "kstring.h"
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 16384)
+
+#define N_TMPSTR 5
+#define LINE_LEN 60
+
+// append a CIGAR operation plus length
+#define write_cigar(_c, _n, _m, _v) do { \
+ if (_n == _m) { \
+ _m = _m? _m<<1 : 4; \
+ _c = realloc(_c, _m * sizeof(unsigned)); \
+ } \
+ _c[_n++] = (_v); \
+ } while (0)
+
+// a fatal error
+static void fatal(const char *msg)
+{
+ fprintf(pysamerr, "E %s\n", msg);
+ exit(1);
+}
+// remove pads
+static void remove_pads(const kstring_t *src, kstring_t *dst)
+{
+ int i, j;
+ dst->l = 0;
+ kputsn(src->s, src->l, dst);
+ for (i = j = 0; i < dst->l; ++i)
+ if (dst->s[i] != '*') dst->s[j++] = dst->s[i];
+ dst->s[j] = 0;
+ dst->l = j;
+}
+
+int main(int argc, char *argv[])
+{
+ gzFile fp;
+ kstream_t *ks;
+ kstring_t s, t[N_TMPSTR];
+ int dret, i, k, af_n, af_max, af_i, c, is_padded = 0, write_cns = 0, *p2u = 0;
+ long m_cigar = 0, n_cigar = 0;
+ unsigned *af, *cigar = 0;
+
+ while ((c = getopt(argc, argv, "pc")) >= 0) {
+ switch (c) {
+ case 'p': is_padded = 1; break;
+ case 'c': write_cns = 1; break;
+ }
+ }
+ if (argc == optind) {
+ fprintf(pysamerr, "\nUsage: ace2sam [-pc] <in.ace>\n\n");
+ fprintf(pysamerr, "Options: -p output padded SAM\n");
+ fprintf(pysamerr, " -c write the contig sequence in SAM\n\n");
+ fprintf(pysamerr, "Notes: 1. Fields must appear in the following order: (CO->[BQ]->(AF)->(RD->QA))\n");
+ fprintf(pysamerr, " 2. The order of reads in AF and in RD must be identical\n");
+ fprintf(pysamerr, " 3. Except in BQ, words and numbers must be separated by a single SPACE or TAB\n");
+ fprintf(pysamerr, " 4. This program writes the headerless SAM to stdout and header to pysamerr\n\n");
+ return 1;
+ }
+
+ s.l = s.m = 0; s.s = 0;
+ af_n = af_max = af_i = 0; af = 0;
+ for (i = 0; i < N_TMPSTR; ++i) t[i].l = t[i].m = 0, t[i].s = 0;
+ fp = strcmp(argv[1], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, &s, &dret) >= 0) {
+ if (strcmp(s.s, "CO") == 0) { // contig sequence
+ kstring_t *cns;
+ t[0].l = t[1].l = t[2].l = t[3].l = t[4].l = 0; // 0: name; 1: padded ctg; 2: unpadded ctg/padded read; 3: unpadded read; 4: SAM line
+ af_n = af_i = 0; // reset the af array
+ ks_getuntil(ks, 0, &s, &dret); kputs(s.s, &t[0]); // contig name
+ ks_getuntil(ks, '\n', &s, &dret); // read the whole line
+ while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputsn(s.s, s.l, &t[1]); // read the padded consensus sequence
+ remove_pads(&t[1], &t[2]); // construct the unpadded sequence
+ // compute the array for mapping padded positions to unpadded positions
+ p2u = realloc(p2u, t[1].m * sizeof(int));
+ for (i = k = 0; i < t[1].l; ++i) {
+ p2u[i] = k;
+ if (t[1].s[i] != '*') ++k;
+ }
+ // write out the SAM header and contig sequences
+ fprintf(pysamerr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
+ cns = &t[is_padded?1:2];
+ fprintf(pysamerr, "S >%s\n", t[0].s);
+ for (i = 0; i < cns->l; i += LINE_LEN) {
+ fputs("S ", pysamerr);
+ for (k = 0; k < LINE_LEN && i + k < cns->l; ++k)
+ fputc(cns->s[i + k], pysamerr);
+ fputc('\n', pysamerr);
+ }
+
+#define __padded2cigar(sp) do { \
+ int i, l_M = 0, l_D = 0; \
+ for (i = 0; i < sp.l; ++i) { \
+ if (sp.s[i] == '*') { \
+ if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \
+ ++l_D; l_M = 0; \
+ } else { \
+ if (l_D) write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \
+ ++l_M; l_D = 0; \
+ } \
+ } \
+ if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \
+ else write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \
+ } while (0)
+
+ if (write_cns) { // write the consensus SAM line (dummy read)
+ n_cigar = 0;
+ if (is_padded) __padded2cigar(t[1]);
+ else write_cigar(cigar, n_cigar, m_cigar, t[2].l<<4);
+ kputsn(t[0].s, t[0].l, &t[4]); kputs("\t516\t", &t[4]); kputsn(t[0].s, t[0].l, &t[4]); kputs("\t1\t60\t", &t[4]);
+ for (i = 0; i < n_cigar; ++i) {
+ kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]);
+ }
+ kputs("\t*\t0\t0\t", &t[4]); kputsn(t[2].s, t[2].l, &t[4]); kputs("\t*", &t[4]);
+ }
+ } else if (strcmp(s.s, "BQ") == 0) { // contig quality
+ if (t[0].l == 0) fatal("come to 'BQ' before reading 'CO'");
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire "BQ" line
+ if (write_cns) t[4].s[--t[4].l] = 0; // remove the trailing "*"
+ for (i = 0; i < t[2].l; ++i) { // read the consensus quality
+ int q;
+ if (ks_getuntil(ks, 0, &s, &dret) < 0) fprintf(pysamerr, "E truncated contig quality\n");
+ if (s.l) {
+ q = atoi(s.s) + 33;
+ if (q > 126) q = 126;
+ if (write_cns) kputc(q, &t[4]);
+ } else --i;
+ }
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ ks_getuntil(ks, '\n', &s, &dret); // skip the empty line
+ if (write_cns) puts(t[4].s); t[4].l = 0;
+ } else if (strcmp(s.s, "AF") == 0) { // padded read position
+ int reversed, neg, pos;
+ if (t[0].l == 0) fatal("come to 'AF' before reading 'CO'");
+ if (write_cns) {
+ if (t[4].l) puts(t[4].s);
+ t[4].l = 0;
+ }
+ ks_getuntil(ks, 0, &s, &dret); // read name
+ ks_getuntil(ks, 0, &s, &dret); reversed = s.s[0] == 'C'? 1 : 0; // strand
+ ks_getuntil(ks, 0, &s, &dret); pos = atoi(s.s); neg = pos < 0? 1 : 0; pos = pos < 0? -pos : pos; // position
+ if (af_n == af_max) { // double the af array
+ af_max = af_max? af_max<<1 : 4;
+ af = realloc(af, af_max * sizeof(unsigned));
+ }
+ af[af_n++] = pos << 2 | neg << 1 | reversed; // keep the placement information
+ } else if (strcmp(s.s, "RD") == 0) { // read sequence
+ if (af_i >= af_n) fatal("more 'RD' records than 'AF'");
+ t[2].l = t[3].l = t[4].l = 0;
+ ks_getuntil(ks, 0, &t[4], &dret); // QNAME
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret); // read the entire RD line
+ while (ks_getuntil(ks, '\n', &s, &dret) >= 0 && s.l > 0) kputs(s.s, &t[2]); // read the read sequence
+ } else if (strcmp(s.s, "QA") == 0) { // clipping
+ if (af_i >= af_n) fatal("more 'QA' records than 'AF'");
+ int beg, end, pos, op;
+ ks_getuntil(ks, 0, &s, &dret); ks_getuntil(ks, 0, &s, &dret); // skip quality clipping
+ ks_getuntil(ks, 0, &s, &dret); beg = atoi(s.s) - 1; // align clipping start
+ ks_getuntil(ks, 0, &s, &dret); end = atoi(s.s); // clipping end
+ if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ // compute 1-based POS
+ pos = af[af_i]>>2; // retrieve the position information
+ if (af[af_i]>>1&1) pos = -pos;
+ pos += beg; // now pos is the true padded position
+ // generate CIGAR
+ remove_pads(&t[2], &t[3]); // backup the unpadded read sequence
+ n_cigar = 0;
+ if (beg) write_cigar(cigar, n_cigar, m_cigar, beg<<4|4);
+ if (is_padded) {
+ __padded2cigar(t[2]);
+ if (beg && n_cigar > 1) cigar[1] -= beg<<4; // fix the left-hand CIGAR
+ if (end < t[2].l && n_cigar) cigar[n_cigar-1] -= (t[2].l - end)<<4; // fix the right-hand CIGAR
+ } else {
+ // generate flattened CIGAR string
+ for (i = beg, k = pos - 1; i < end; ++i, ++k)
+ t[2].s[i] = t[2].s[i] != '*'? (t[1].s[k] != '*'? 0 : 1) : (t[1].s[k] != '*'? 2 : 6);
+ // generate the proper CIGAR
+ for (i = beg + 1, k = 1, op = t[2].s[beg]; i < end; ++i) {
+ if (op != t[2].s[i]) {
+ write_cigar(cigar, n_cigar, m_cigar, k<<4|op);
+ op = t[2].s[i]; k = 1;
+ } else ++k;
+ }
+ write_cigar(cigar, n_cigar, m_cigar, k<<4|op);
+ // remove unnecessary "P" and possibly merge adjacent operations
+ for (i = 2; i < n_cigar; ++i) {
+ if ((cigar[i]&0xf) != 1 && (cigar[i-1]&0xf) == 6 && (cigar[i-2]&0xf) != 1) {
+ cigar[i-1] = 0;
+ if ((cigar[i]&0xf) == (cigar[i-2]&0xf)) // merge operations
+ cigar[i] += cigar[i-2], cigar[i-2] = 0;
+ }
+ }
+ for (i = k = 0; i < n_cigar; ++i) // squeeze out dumb operations
+ if (cigar[i]) cigar[k++] = cigar[i];
+ n_cigar = k;
+ }
+ if (end < t[2].l) write_cigar(cigar, n_cigar, m_cigar, (t[2].l - end)<<4|4);
+ // write the SAM line for the read
+ kputc('\t', &t[4]); // QNAME has already been written
+ kputw((af[af_i]&1)? 16 : 0, &t[4]); kputc('\t', &t[4]); // FLAG
+ kputsn(t[0].s, t[0].l, &t[4]); kputc('\t', &t[4]); // RNAME
+ kputw(is_padded? pos : p2u[pos-1]+1, &t[4]); // POS
+ kputs("\t60\t", &t[4]); // MAPQ
+ for (i = 0; i < n_cigar; ++i) { // CIGAR
+ kputw(cigar[i]>>4, &t[4]); kputc("MIDNSHP=X"[cigar[i]&0xf], &t[4]);
+ }
+ kputs("\t*\t0\t0\t", &t[4]); // empty MRNM, MPOS and TLEN
+ kputsn(t[3].s, t[3].l, &t[4]); // unpadded SEQ
+ kputs("\t*", &t[4]); // QUAL
+ puts(t[4].s); // print to stdout
+ ++af_i;
+ } else if (dret != '\n') ks_getuntil(ks, '\n', &s, &dret);
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(af); free(s.s); free(cigar); free(p2u);
+ for (i = 0; i < N_TMPSTR; ++i) free(t[i].s);
+ return 0;
+}
diff --git a/samtools/misc/seqtk.c.pysam.c b/samtools/misc/seqtk.c.pysam.c
deleted file mode 100644
index 46b3c56..0000000
--- a/samtools/misc/seqtk.c.pysam.c
+++ /dev/null
@@ -1,785 +0,0 @@
-#include "pysam.h"
-
-#include <stdio.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <stdint.h>
-#include <zlib.h>
-#include <string.h>
-#include <unistd.h>
-#include <limits.h>
-
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
-
-typedef struct {
- int n, m;
- uint64_t *a;
-} reglist_t;
-
-#include "khash.h"
-KHASH_MAP_INIT_STR(reg, reglist_t)
-
-typedef kh_reg_t reghash_t;
-
-reghash_t *stk_reg_read(const char *fn)
-{
- reghash_t *h = kh_init(reg);
- gzFile fp;
- kstream_t *ks;
- int dret;
- kstring_t *str;
- // read the list
- str = calloc(1, sizeof(kstring_t));
- fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
- ks = ks_init(fp);
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
- int beg = -1, end = -1;
- reglist_t *p;
- khint_t k = kh_get(reg, h, str->s);
- if (k == kh_end(h)) {
- int ret;
- char *s = strdup(str->s);
- k = kh_put(reg, h, s, &ret);
- memset(&kh_val(h, k), 0, sizeof(reglist_t));
- }
- p = &kh_val(h, k);
- if (dret != '\n') {
- if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
- beg = atoi(str->s);
- if (dret != '\n') {
- if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
- end = atoi(str->s);
- if (end < 0) end = -1;
- }
- }
- }
- }
- // skip the rest of the line
- if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
- if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
- if (beg < 0) beg = 0, end = INT_MAX;
- if (p->n == p->m) {
- p->m = p->m? p->m<<1 : 4;
- p->a = realloc(p->a, p->m * 8);
- }
- p->a[p->n++] = (uint64_t)beg<<32 | end;
- }
- ks_destroy(ks);
- gzclose(fp);
- free(str->s); free(str);
- return h;
-}
-
-void stk_reg_destroy(reghash_t *h)
-{
- khint_t k;
- for (k = 0; k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- free(kh_val(h, k).a);
- free((char*)kh_key(h, k));
- }
- }
- kh_destroy(reg, h);
-}
-
-/* constant table */
-
-unsigned char seq_nt16_table[256] = {
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15 /*'-'*/,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
- 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
- 15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
- 15,15, 5, 6, 8,15, 7, 9, 0,10,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
- 15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
-};
-
-char *seq_nt16_rev_table = "XACMGRSVTWYHKDBN";
-unsigned char seq_nt16to4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
-int bitcnt_table[] = { 4, 1, 1, 2, 1, 2, 2, 3, 1, 2, 2, 3, 2, 3, 3, 4 };
-
-/* composition */
-int stk_comp(int argc, char *argv[])
-{
- gzFile fp;
- kseq_t *seq;
- int l, c, upper_only = 0;
- reghash_t *h = 0;
- reglist_t dummy;
- while ((c = getopt(argc, argv, "ur:")) >= 0) {
- switch (c) {
- case 'u': upper_only = 1; break;
- case 'r': h = stk_reg_read(optarg); break;
- }
- }
- if (argc == optind) {
- fprintf(pysamerr, "Usage: seqtk comp [-u] [-r in.bed] <in.fa>\n\n");
- fprintf(pysamerr, "Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts\n");
- return 1;
- }
- fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
- seq = kseq_init(fp);
- dummy.n= dummy.m = 1; dummy.a = calloc(1, 8);
- while ((l = kseq_read(seq)) >= 0) {
- int i, k;
- reglist_t *p = 0;
- if (h) {
- khint_t k = kh_get(reg, h, seq->name.s);
- if (k != kh_end(h)) p = &kh_val(h, k);
- } else {
- p = &dummy;
- dummy.a[0] = l;
- }
- for (k = 0; p && k < p->n; ++k) {
- int beg = p->a[k]>>32, end = p->a[k]&0xffffffff;
- int la, lb, lc, na, nb, nc, cnt[11];
- if (beg > 0) la = seq->seq.s[beg-1], lb = seq_nt16_table[la], lc = bitcnt_table[lb];
- else la = 'a', lb = -1, lc = 0;
- na = seq->seq.s[beg]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
- memset(cnt, 0, 11 * sizeof(int));
- for (i = beg; i < end; ++i) {
- int is_CpG = 0, a, b, c;
- a = na; b = nb; c = nc;
- na = seq->seq.s[i+1]; nb = seq_nt16_table[na]; nc = bitcnt_table[nb];
- if (b == 2 || b == 10) { // C or Y
- if (nb == 4 || nb == 5) is_CpG = 1;
- } else if (b == 4 || b == 5) { // G or R
- if (lb == 2 || lb == 10) is_CpG = 1;
- }
- if (upper_only == 0 || isupper(a)) {
- if (c > 1) ++cnt[c+2];
- if (c == 1) ++cnt[seq_nt16to4_table[b]];
- if (b == 10 || b == 5) ++cnt[9];
- else if (c == 2) {
- ++cnt[8];
- }
- if (is_CpG) {
- ++cnt[7];
- if (b == 10 || b == 5) ++cnt[10];
- }
- }
- la = a; lb = b; lc = c;
- }
- if (h) printf("%s\t%d\t%d", seq->name.s, beg, end);
- else printf("%s\t%d", seq->name.s, l);
- for (i = 0; i < 11; ++i) printf("\t%d", cnt[i]);
- putchar('\n');
- }
- fflush(stdout);
- }
- free(dummy.a);
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
-
-int stk_randbase(int argc, char *argv[])
-{
- gzFile fp;
- kseq_t *seq;
- int l;
- if (argc == 1) {
- fprintf(pysamerr, "Usage: seqtk randbase <in.fa>\n");
- return 1;
- }
- fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- int i;
- printf(">%s", seq->name.s);
- for (i = 0; i < l; ++i) {
- int c, b, a, j, k, m;
- b = seq->seq.s[i];
- c = seq_nt16_table[b];
- a = bitcnt_table[c];
- if (a == 2) {
- m = (drand48() < 0.5);
- for (j = k = 0; j < 4; ++j) {
- if ((1<<j & c) == 0) continue;
- if (k == m) break;
- ++k;
- }
- seq->seq.s[i] = islower(b)? "acgt"[j] : "ACGT"[j];
- }
- if (i%60 == 0) putchar('\n');
- putchar(seq->seq.s[i]);
- }
- putchar('\n');
- }
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
-
-int stk_hety(int argc, char *argv[])
-{
- gzFile fp;
- kseq_t *seq;
- int l, c, win_size = 50000, n_start = 5, win_step, is_lower_mask = 0;
- char *buf;
- uint32_t cnt[3];
- if (argc == 1) {
- fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Usage: seqtk hety [options] <in.fa>\n\n");
- fprintf(pysamerr, "Options: -w INT window size [%d]\n", win_size);
- fprintf(pysamerr, " -t INT # start positions in a window [%d]\n", n_start);
- fprintf(pysamerr, " -m treat lowercases as masked\n");
- fprintf(pysamerr, "\n");
- return 1;
- }
- while ((c = getopt(argc, argv, "w:t:m")) >= 0) {
- switch (c) {
- case 'w': win_size = atoi(optarg); break;
- case 't': n_start = atoi(optarg); break;
- case 'm': is_lower_mask = 1; break;
- }
- }
- fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
- seq = kseq_init(fp);
- win_step = win_size / n_start;
- buf = calloc(win_size, 1);
- while ((l = kseq_read(seq)) >= 0) {
- int x, i, y, z, next = 0;
- cnt[0] = cnt[1] = cnt[2] = 0;
- for (i = 0; i <= l; ++i) {
- if ((i >= win_size && i % win_step == 0) || i == l) {
- if (i == l && l >= win_size) {
- for (y = l - win_size; y < next; ++y) --cnt[(int)buf[y % win_size]];
- }
- if (cnt[1] + cnt[2] > 0)
- printf("%s\t%d\t%d\t%.2lf\t%d\t%d\n", seq->name.s, next, i,
- (double)cnt[2] / (cnt[1] + cnt[2]) * win_size, cnt[1] + cnt[2], cnt[2]);
- next = i;
- }
- if (i < l) {
- y = i % win_size;
- c = seq->seq.s[i];
- if (is_lower_mask && islower(c)) c = 'N';
- c = seq_nt16_table[c];
- x = bitcnt_table[c];
- if (i >= win_size) --cnt[(int)buf[y]];
- buf[y] = z = x > 2? 0 : x == 2? 2 : 1;
- ++cnt[z];
- }
- }
- }
- free(buf);
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
-
-/* fq2fa */
-int stk_fq2fa(int argc, char *argv[])
-{
- gzFile fp;
- kseq_t *seq;
- char *buf;
- int l, i, c, qual_thres = 0, linelen = 60;
- while ((c = getopt(argc, argv, "q:l:")) >= 0) {
- switch (c) {
- case 'q': qual_thres = atoi(optarg); break;
- case 'l': linelen = atoi(optarg); break;
- }
- }
- if (argc == optind) {
- fprintf(pysamerr, "Usage: seqtk fq2fa [-q qualThres=0] [-l lineLen=60] <in.fq>\n");
- return 1;
- }
- buf = linelen > 0? malloc(linelen + 1) : 0;
- fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- if (seq->qual.l && qual_thres > 0) {
- for (i = 0; i < l; ++i)
- if (seq->qual.s[i] - 33 < qual_thres)
- seq->seq.s[i] = tolower(seq->seq.s[i]);
- }
- putchar('>');
- if (seq->comment.l) {
- fputs(seq->name.s, stdout);
- putchar(' ');
- puts(seq->comment.s);
- } else puts(seq->name.s);
- if (buf) { // multi-line
- for (i = 0; i < l; i += linelen) {
- int x = i + linelen < l? linelen : l - i;
- memcpy(buf, seq->seq.s + i, x);
- buf[x] = 0;
- puts(buf);
- }
- } else puts(seq->seq.s);
- }
- free(buf);
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
-
-int stk_maskseq(int argc, char *argv[])
-{
- khash_t(reg) *h = kh_init(reg);
- gzFile fp;
- kseq_t *seq;
- int l, i, j, c, is_complement = 0, is_lower = 0;
- khint_t k;
- while ((c = getopt(argc, argv, "cl")) >= 0) {
- switch (c) {
- case 'c': is_complement = 1; break;
- case 'l': is_lower = 1; break;
- }
- }
- if (argc - optind < 2) {
- fprintf(pysamerr, "Usage: seqtk maskseq [-cl] <in.fa> <in.bed>\n\n");
- fprintf(pysamerr, "Options: -c mask the complement regions\n");
- fprintf(pysamerr, " -l soft mask (to lower cases)\n");
- return 1;
- }
- h = stk_reg_read(argv[optind+1]);
- // maskseq
- fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- k = kh_get(reg, h, seq->name.s);
- if (k == kh_end(h)) { // not found in the hash table
- if (is_complement) {
- for (j = 0; j < l; ++j)
- seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
- }
- } else {
- reglist_t *p = &kh_val(h, k);
- if (!is_complement) {
- for (i = 0; i < p->n; ++i) {
- int beg = p->a[i]>>32, end = p->a[i];
- if (beg >= seq->seq.l) {
- fprintf(pysamerr, "[maskseq] start position >= the sequence length.\n");
- continue;
- }
- if (end >= seq->seq.l) end = seq->seq.l;
- if (is_lower) for (j = beg; j < end; ++j) seq->seq.s[j] = tolower(seq->seq.s[j]);
- else for (j = beg; j < end; ++j) seq->seq.s[j] = 'N';
- }
- } else {
- int8_t *mask = calloc(seq->seq.l, 1);
- for (i = 0; i < p->n; ++i) {
- int beg = p->a[i]>>32, end = p->a[i];
- if (end >= seq->seq.l) end = seq->seq.l;
- for (j = beg; j < end; ++j) mask[j] = 1;
- }
- for (j = 0; j < l; ++j)
- if (mask[j] == 0) seq->seq.s[j] = is_lower? tolower(seq->seq.s[j]) : 'N';
- free(mask);
- }
- }
- printf(">%s", seq->name.s);
- for (j = 0; j < seq->seq.l; ++j) {
- if (j%60 == 0) putchar('\n');
- putchar(seq->seq.s[j]);
- }
- putchar('\n');
- }
- // free
- kseq_destroy(seq);
- gzclose(fp);
- stk_reg_destroy(h);
- return 0;
-}
-
-/* subseq */
-
-int stk_subseq(int argc, char *argv[])
-{
- khash_t(reg) *h = kh_init(reg);
- gzFile fp;
- kseq_t *seq;
- int l, i, j, c, is_tab = 0;
- khint_t k;
- while ((c = getopt(argc, argv, "t")) >= 0) {
- switch (c) {
- case 't': is_tab = 1; break;
- }
- }
- if (optind + 2 > argc) {
- fprintf(pysamerr, "Usage: seqtk subseq [-t] <in.fa> <in.bed>\n\n");
- fprintf(pysamerr, "Note: Use 'samtools faidx' if only a few regions are intended.\n");
- return 1;
- }
- h = stk_reg_read(argv[optind+1]);
- // subseq
- fp = strcmp(argv[optind], "-")? gzopen(argv[optind], "r") : gzdopen(fileno(stdin), "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- reglist_t *p;
- k = kh_get(reg, h, seq->name.s);
- if (k == kh_end(h)) continue;
- p = &kh_val(h, k);
- for (i = 0; i < p->n; ++i) {
- int beg = p->a[i]>>32, end = p->a[i];
- if (beg >= seq->seq.l) {
- fprintf(pysamerr, "[subseq] %s: %d >= %ld\n", seq->name.s, beg, seq->seq.l);
- continue;
- }
- if (end > seq->seq.l) end = seq->seq.l;
- if (is_tab == 0) {
- printf("%c%s", seq->qual.l == seq->seq.l? '@' : '>', seq->name.s);
- if (end == INT_MAX) {
- if (beg) printf(":%d", beg+1);
- } else printf(":%d-%d", beg+1, end);
- } else printf("%s\t%d\t", seq->name.s, beg + 1);
- if (end > seq->seq.l) end = seq->seq.l;
- for (j = 0; j < end - beg; ++j) {
- if (is_tab == 0 && j % 60 == 0) putchar('\n');
- putchar(seq->seq.s[j + beg]);
- }
- putchar('\n');
- if (seq->qual.l != seq->seq.l || is_tab) continue;
- printf("+");
- for (j = 0; j < end - beg; ++j) {
- if (j % 60 == 0) putchar('\n');
- putchar(seq->qual.s[j + beg]);
- }
- putchar('\n');
- }
- }
- // free
- kseq_destroy(seq);
- gzclose(fp);
- stk_reg_destroy(h);
- return 0;
-}
-
-/* mergefa */
-int stk_mergefa(int argc, char *argv[])
-{
- gzFile fp[2];
- kseq_t *seq[2];
- int i, l, c, is_intersect = 0, is_haploid = 0, qual = 0, is_mask = 0;
- while ((c = getopt(argc, argv, "himq:")) >= 0) {
- switch (c) {
- case 'i': is_intersect = 1; break;
- case 'h': is_haploid = 1; break;
- case 'm': is_mask = 1; break;
- case 'q': qual = atoi(optarg); break;
- }
- }
- if (is_mask && is_intersect) {
- fprintf(pysamerr, "[%s] `-i' and `-h' cannot be applied at the same time.\n", __func__);
- return 1;
- }
- if (optind + 2 > argc) {
- fprintf(pysamerr, "\nUsage: seqtk mergefa [options] <in1.fa> <in2.fa>\n\n");
- fprintf(pysamerr, "Options: -q INT quality threshold [0]\n");
- fprintf(pysamerr, " -i take intersection\n");
- fprintf(pysamerr, " -m convert to lowercase when one of the input base is N.\n");
- fprintf(pysamerr, " -h suppress hets in the input\n\n");
- return 1;
- }
- for (i = 0; i < 2; ++i) {
- fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
- seq[i] = kseq_init(fp[i]);
- }
- while (kseq_read(seq[0]) >= 0) {
- int min_l, c[2], is_upper;
- kseq_read(seq[1]);
- if (strcmp(seq[0]->name.s, seq[1]->name.s))
- fprintf(pysamerr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
- if (seq[0]->seq.l != seq[1]->seq.l)
- fprintf(pysamerr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
- min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
- printf(">%s", seq[0]->name.s);
- for (l = 0; l < min_l; ++l) {
- c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
- if (seq[0]->qual.l && seq[0]->qual.s[l] - 33 < qual) c[0] = tolower(c[0]);
- if (seq[1]->qual.l && seq[1]->qual.s[l] - 33 < qual) c[1] = tolower(c[1]);
- if (is_intersect) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
- else if (is_mask) is_upper = (isupper(c[0]) || isupper(c[1]))? 1 : 0;
- else is_upper = (isupper(c[0]) && isupper(c[1]))? 1 : 0;
- c[0] = seq_nt16_table[c[0]]; c[1] = seq_nt16_table[c[1]];
- if (c[0] == 0) c[0] = 15;
- if (c[1] == 0) c[1] = 15;
- if (is_haploid && (bitcnt_table[c[0]] > 1 || bitcnt_table[c[1]] > 1)) is_upper = 0;
- if (is_intersect) {
- c[0] = c[0] & c[1];
- if (c[0] == 0) is_upper = 0;
- } else if (is_mask) {
- if (c[0] == 15 || c[1] == 15) is_upper = 0;
- c[0] = c[0] & c[1];
- if (c[0] == 0) is_upper = 0;
- } else c[0] = c[0] | c[1];
- c[0] = seq_nt16_rev_table[c[0]];
- if (!is_upper) c[0] = tolower(c[0]);
- if (l%60 == 0) putchar('\n');
- putchar(c[0]);
- }
- putchar('\n');
- }
- return 0;
-}
-
-int stk_famask(int argc, char *argv[])
-{
- gzFile fp[2];
- kseq_t *seq[2];
- int i, l;
- if (argc < 3) {
- fprintf(pysamerr, "Usage: seqtk famask <src.fa> <mask.fa>\n");
- return 1;
- }
- for (i = 0; i < 2; ++i) {
- fp[i] = strcmp(argv[optind+i], "-")? gzopen(argv[optind+i], "r") : gzdopen(fileno(stdin), "r");
- seq[i] = kseq_init(fp[i]);
- }
- while (kseq_read(seq[0]) >= 0) {
- int min_l, c[2];
- kseq_read(seq[1]);
- if (strcmp(seq[0]->name.s, seq[1]->name.s))
- fprintf(pysamerr, "[%s] Different sequence names: %s != %s\n", __func__, seq[0]->name.s, seq[1]->name.s);
- if (seq[0]->seq.l != seq[1]->seq.l)
- fprintf(pysamerr, "[%s] Unequal sequence length: %ld != %ld\n", __func__, seq[0]->seq.l, seq[1]->seq.l);
- min_l = seq[0]->seq.l < seq[1]->seq.l? seq[0]->seq.l : seq[1]->seq.l;
- printf(">%s", seq[0]->name.s);
- for (l = 0; l < min_l; ++l) {
- c[0] = seq[0]->seq.s[l]; c[1] = seq[1]->seq.s[l];
- if (c[1] == 'x') c[0] = tolower(c[0]);
- else if (c[1] != 'X') c[0] = c[1];
- if (l%60 == 0) putchar('\n');
- putchar(c[0]);
- }
- putchar('\n');
- }
- return 0;
-}
-
-int stk_mutfa(int argc, char *argv[])
-{
- khash_t(reg) *h = kh_init(reg);
- gzFile fp;
- kseq_t *seq;
- kstream_t *ks;
- int l, i, dret;
- kstring_t *str;
- khint_t k;
- if (argc < 3) {
- fprintf(pysamerr, "Usage: seqtk mutfa <in.fa> <in.snp>\n\n");
- fprintf(pysamerr, "Note: <in.snp> contains at least four columns per line which are:\n");
- fprintf(pysamerr, " 'chr 1-based-pos any base-changed-to'.\n");
- return 1;
- }
- // read the list
- str = calloc(1, sizeof(kstring_t));
- fp = strcmp(argv[2], "-")? gzopen(argv[2], "r") : gzdopen(fileno(stdin), "r");
- ks = ks_init(fp);
- while (ks_getuntil(ks, 0, str, &dret) >= 0) {
- char *s = strdup(str->s);
- int beg = 0, ret;
- reglist_t *p;
- k = kh_get(reg, h, s);
- if (k == kh_end(h)) {
- k = kh_put(reg, h, s, &ret);
- memset(&kh_val(h, k), 0, sizeof(reglist_t));
- }
- p = &kh_val(h, k);
- if (ks_getuntil(ks, 0, str, &dret) > 0) beg = atol(str->s) - 1; // 2nd col
- ks_getuntil(ks, 0, str, &dret); // 3rd col
- ks_getuntil(ks, 0, str, &dret); // 4th col
- // skip the rest of the line
- if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n');
- if (isalpha(str->s[0]) && str->l == 1) {
- if (p->n == p->m) {
- p->m = p->m? p->m<<1 : 4;
- p->a = realloc(p->a, p->m * 8);
- }
- p->a[p->n++] = (uint64_t)beg<<32 | str->s[0];
- }
- }
- ks_destroy(ks);
- gzclose(fp);
- free(str->s); free(str);
- // mutfa
- fp = strcmp(argv[1], "-")? gzopen(argv[1], "r") : gzdopen(fileno(stdin), "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- reglist_t *p;
- k = kh_get(reg, h, seq->name.s);
- if (k != kh_end(h)) {
- p = &kh_val(h, k);
- for (i = 0; i < p->n; ++i) {
- int beg = p->a[i]>>32;
- if (beg < seq->seq.l)
- seq->seq.s[beg] = (int)p->a[i];
- }
- }
- printf(">%s", seq->name.s);
- for (i = 0; i < l; ++i) {
- if (i%60 == 0) putchar('\n');
- putchar(seq->seq.s[i]);
- }
- putchar('\n');
- }
- // free
- kseq_destroy(seq);
- gzclose(fp);
- for (k = 0; k < kh_end(h); ++k) {
- if (kh_exist(h, k)) {
- free(kh_val(h, k).a);
- free((char*)kh_key(h, k));
- }
- }
- kh_destroy(reg, h);
- return 0;
-}
-
-int stk_listhet(int argc, char *argv[])
-{
- gzFile fp;
- kseq_t *seq;
- int i, l;
- if (argc == 1) {
- fprintf(pysamerr, "Usage: seqtk listhet <in.fa>\n");
- return 1;
- }
- fp = (strcmp(argv[1], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[1], "r");
- seq = kseq_init(fp);
- while ((l = kseq_read(seq)) >= 0) {
- for (i = 0; i < l; ++i) {
- int b = seq->seq.s[i];
- if (bitcnt_table[seq_nt16_table[b]] == 2)
- printf("%s\t%d\t%c\n", seq->name.s, i+1, b);
- }
- }
- kseq_destroy(seq);
- gzclose(fp);
- return 0;
-}
-
-/* cutN */
-static int cutN_min_N_tract = 1000;
-static int cutN_nonN_penalty = 10;
-
-static int find_next_cut(const kseq_t *ks, int k, int *begin, int *end)
-{
- int i, b, e;
- while (k < ks->seq.l) {
- if (seq_nt16_table[(int)ks->seq.s[k]] == 15) {
- int score, max;
- score = 0; e = max = -1;
- for (i = k; i < ks->seq.l && score >= 0; ++i) { /* forward */
- if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
- else score -= cutN_nonN_penalty;
- if (score > max) max = score, e = i;
- }
- score = 0; b = max = -1;
- for (i = e; i >= 0 && score >= 0; --i) { /* backward */
- if (seq_nt16_table[(int)ks->seq.s[i]] == 15) ++score;
- else score -= cutN_nonN_penalty;
- if (score > max) max = score, b = i;
- }
- if (e + 1 - b >= cutN_min_N_tract) {
- *begin = b;
- *end = e + 1;
- return *end;
- }
- k = e + 1;
- } else ++k;
- }
- return -1;
-}
-static void print_seq(FILE *fpout, const kseq_t *ks, int begin, int end)
-{
- int i;
- if (begin >= end) return; // FIXME: why may this happen? Understand it!
- fprintf(fpout, ">%s:%d-%d", ks->name.s, begin+1, end);
- for (i = begin; i < end && i < ks->seq.l; ++i) {
- if ((i - begin)%60 == 0) fputc('\n', fpout);
- fputc(ks->seq.s[i], fpout);
- }
- fputc('\n', fpout);
-}
-int stk_cutN(int argc, char *argv[])
-{
- int c, l, gap_only = 0;
- gzFile fp;
- kseq_t *ks;
- while ((c = getopt(argc, argv, "n:p:g")) >= 0) {
- switch (c) {
- case 'n': cutN_min_N_tract = atoi(optarg); break;
- case 'p': cutN_nonN_penalty = atoi(optarg); break;
- case 'g': gap_only = 1; break;
- default: return 1;
- }
- }
- if (argc == optind) {
- fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Usage: seqtk cutN [options] <in.fa>\n\n");
- fprintf(pysamerr, "Options: -n INT min size of N tract [%d]\n", cutN_min_N_tract);
- fprintf(pysamerr, " -p INT penalty for a non-N [%d]\n", cutN_nonN_penalty);
- fprintf(pysamerr, " -g print gaps only, no sequence\n\n");
- return 1;
- }
- fp = (strcmp(argv[optind], "-") == 0)? gzdopen(fileno(stdin), "r") : gzopen(argv[optind], "r");
- ks = kseq_init(fp);
- while ((l = kseq_read(ks)) >= 0) {
- int k = 0, begin = 0, end = 0;
- while (find_next_cut(ks, k, &begin, &end) >= 0) {
- if (begin != 0) {
- if (gap_only) printf("%s\t%d\t%d\n", ks->name.s, begin, end);
- else print_seq(stdout, ks, k, begin);
- }
- k = end;
- }
- if (!gap_only) print_seq(stdout, ks, k, l);
- }
- kseq_destroy(ks);
- gzclose(fp);
- return 0;
-}
-
-/* main function */
-static int usage()
-{
- fprintf(pysamerr, "\n");
- fprintf(pysamerr, "Usage: seqtk <command> <arguments>\n\n");
- fprintf(pysamerr, "Command: comp get the nucleotide composite of FASTA/Q\n");
- fprintf(pysamerr, " hety regional heterozygosity\n");
- fprintf(pysamerr, " fq2fa convert FASTQ to FASTA\n");
- fprintf(pysamerr, " subseq extract subsequences from FASTA/Q\n");
- fprintf(pysamerr, " maskseq mask sequences\n");
- fprintf(pysamerr, " mutfa point mutate FASTA at specified positions\n");
- fprintf(pysamerr, " mergefa merge two FASTA/Q files\n");
- fprintf(pysamerr, " randbase choose a random base from hets\n");
- fprintf(pysamerr, " cutN cut sequence at long N\n");
- fprintf(pysamerr, " listhet extract the position of each het\n");
- fprintf(pysamerr, "\n");
- return 1;
-}
-
-int main(int argc, char *argv[])
-{
- if (argc == 1) return usage();
- if (strcmp(argv[1], "comp") == 0) stk_comp(argc-1, argv+1);
- else if (strcmp(argv[1], "hety") == 0) stk_hety(argc-1, argv+1);
- else if (strcmp(argv[1], "fq2fa") == 0) stk_fq2fa(argc-1, argv+1);
- else if (strcmp(argv[1], "subseq") == 0) stk_subseq(argc-1, argv+1);
- else if (strcmp(argv[1], "maskseq") == 0) stk_maskseq(argc-1, argv+1);
- else if (strcmp(argv[1], "mutfa") == 0) stk_mutfa(argc-1, argv+1);
- else if (strcmp(argv[1], "mergefa") == 0) stk_mergefa(argc-1, argv+1);
- else if (strcmp(argv[1], "randbase") == 0) stk_randbase(argc-1, argv+1);
- else if (strcmp(argv[1], "cutN") == 0) stk_cutN(argc-1, argv+1);
- else if (strcmp(argv[1], "listhet") == 0) stk_listhet(argc-1, argv+1);
- else if (strcmp(argv[1], "famask") == 0) stk_famask(argc-1, argv+1);
- else {
- fprintf(pysamerr, "[main] unrecognized commad '%s'. Abort!\n", argv[1]);
- return 1;
- }
- return 0;
-}
diff --git a/samtools/padding.c.pysam.c b/samtools/padding.c.pysam.c
new file mode 100644
index 0000000..b736dcd
--- /dev/null
+++ b/samtools/padding.c.pysam.c
@@ -0,0 +1,481 @@
+#include "pysam.h"
+
+#include <string.h>
+#include <assert.h>
+#include <unistd.h>
+#include "kstring.h"
+#include "sam_header.h"
+#include "sam.h"
+#include "bam.h"
+#include "faidx.h"
+
+bam_header_t *bam_header_dup(const bam_header_t *h0); /*in sam.c*/
+
+static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
+{
+ if (n != b->core.n_cigar) {
+ int o = b->core.l_qname + b->core.n_cigar * 4;
+ if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
+ b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
+ memcpy(b->data + b->core.l_qname, cigar, n * 4);
+ b->data_len += (n - b->core.n_cigar) * 4;
+ b->core.n_cigar = n;
+ } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
+}
+
+#define write_cigar(_c, _n, _m, _v) do { \
+ if (_n == _m) { \
+ _m = _m? _m<<1 : 4; \
+ _c = (uint32_t*)realloc(_c, _m * 4); \
+ } \
+ _c[_n++] = (_v); \
+ } while (0)
+
+static void unpad_seq(bam1_t *b, kstring_t *s)
+{
+ int k, j, i;
+ int length;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *seq = bam1_seq(b);
+ // b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
+ // We need the padded length after alignment from the CIGAR (excluding
+ // soft clips S, but including pads from CIGAR D operations)
+ length = 0;
+ for (k = 0; k < b->core.n_cigar; ++k) {
+ int op, ol;
+ op= bam_cigar_op(cigar[k]);
+ ol = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
+ length += ol;
+ }
+ ks_resize(s, length);
+ for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
+ int op, ol;
+ op = bam_cigar_op(cigar[k]);
+ ol = bam_cigar_oplen(cigar[k]);
+ if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+ for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
+ } else if (op == BAM_CSOFT_CLIP) {
+ j += ol;
+ } else if (op == BAM_CHARD_CLIP) {
+ /* do nothing */
+ } else if (op == BAM_CDEL) {
+ for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+ } else {
+ fprintf(pysamerr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+ assert(-1);
+ }
+ }
+ assert(length == s->l);
+}
+
+int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
+{
+ char base;
+ char *fai_ref = 0;
+ int fai_ref_len = 0, k;
+
+ fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+ if (fai_ref_len != ref_len) {
+ fprintf(pysamerr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
+ free(fai_ref);
+ return -1;
+ }
+ ks_resize(seq, ref_len);
+ seq->l = 0;
+ for (k = 0; k < ref_len; ++k) {
+ base = fai_ref[k];
+ if (base == '-' || base == '*') {
+ // Map gaps to null to match unpad_seq function
+ seq->s[seq->l++] = 0;
+ } else {
+ int i = bam_nt16_table[(int)base];
+ if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+ fprintf(pysamerr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
+ free(fai_ref);
+ return -1;
+ }
+ seq->s[seq->l++] = i;
+ }
+ }
+ assert(ref_len == seq->l);
+ free(fai_ref);
+ return 0;
+}
+
+int get_unpadded_len(faidx_t *fai, char *ref_name, int padded_len)
+{
+ char base;
+ char *fai_ref = 0;
+ int fai_ref_len = 0, k;
+ int bases=0, gaps=0;
+
+ fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+ if (fai_ref_len != padded_len) {
+ fprintf(pysamerr, "[depad] ERROR: FASTA sequence '%s' length %i, expected %i\n", ref_name, fai_ref_len, padded_len);
+ free(fai_ref);
+ return -1;
+ }
+ for (k = 0; k < padded_len; ++k) {
+ //fprintf(pysamerr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
+ base = fai_ref[k];
+ if (base == '-' || base == '*') {
+ gaps += 1;
+ } else {
+ int i = bam_nt16_table[(int)base];
+ if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
+ fprintf(pysamerr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence '%s'\n", base, (int)base, ref_name);
+ free(fai_ref);
+ return -1;
+ }
+ bases += 1;
+ }
+ }
+ free(fai_ref);
+ assert (padded_len == bases + gaps);
+ return bases;
+}
+
+inline int * update_posmap(int *posmap, kstring_t ref)
+{
+ int i, k;
+ posmap = realloc(posmap, ref.m * sizeof(int));
+ for (i = k = 0; i < ref.l; ++i) {
+ posmap[i] = k;
+ if (ref.s[i]) ++k;
+ }
+ return posmap;
+}
+
+int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
+{
+ bam_header_t *h = 0;
+ bam1_t *b = 0;
+ kstring_t r, q;
+ int r_tid = -1;
+ uint32_t *cigar2 = 0;
+ int ret = 0, n2 = 0, m2 = 0, *posmap = 0;
+
+ b = bam_init1();
+ r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
+ int read_ret;
+ h = in->header;
+ while ((read_ret = samread(in, b)) >= 0) { // read one alignment from `in'
+ uint32_t *cigar = bam1_cigar(b);
+ n2 = 0;
+ if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
+ // fprintf(pysamerr, "[depad] Found embedded reference '%s'\n", bam1_qname(b));
+ r_tid = b->core.tid;
+ unpad_seq(b, &r);
+ if (h->target_len[r_tid] != r.l) {
+ fprintf(pysamerr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+ return -1;
+ }
+ if (fai) {
+ // Check the embedded reference matches the FASTA file
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) {
+ fprintf(pysamerr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]);
+ return -1;
+ }
+ assert(r.l == q.l);
+ int i;
+ for (i = 0; i < r.l; ++i) {
+ if (r.s[i] != q.s[i]) {
+ // Show gaps as ASCII 45
+ fprintf(pysamerr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+ h->target_name[b->core.tid], i+1,
+ r.s[i] ? bam_nt16_rev_table[(int)r.s[i]] : 45,
+ q.s[i] ? bam_nt16_rev_table[(int)q.s[i]] : 45);
+ return -1;
+ }
+ }
+ }
+ write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
+ replace_cigar(b, n2, cigar2);
+ posmap = update_posmap(posmap, r);
+ } else if (b->core.n_cigar > 0) {
+ int i, k, op;
+ if (b->core.tid < 0) {
+ fprintf(pysamerr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam1_qname(b));
+ return -1;
+ } else if (b->core.tid == r_tid) {
+ ; // good case, reference available
+ //fprintf(pysamerr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b));
+ } else if (fai) {
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+ fprintf(pysamerr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ r_tid = b->core.tid;
+ // fprintf(pysamerr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+ } else {
+ fprintf(pysamerr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
+ return -1;
+ }
+ unpad_seq(b, &q);
+ if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[0]);
+ } else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[0]);
+ if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[1]);
+ }
+ }
+ /* Determine CIGAR operator for each base in the aligned read */
+ for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
+ q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+ /* Include any pads if starts with an insert */
+ if (q.s[0] == BAM_CINS) {
+ for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+ if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+ }
+ /* Count consecutive CIGAR operators to turn into a CIGAR string */
+ for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
+ if (op != q.s[i]) {
+ write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+ op = q.s[i]; k = 1;
+ } else ++k;
+ }
+ write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
+ if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+ if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+ }
+ write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ }
+ /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
+ int pre_op, post_op;
+ for (i = 2; i < n2; ++i)
+ if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+ pre_op = bam_cigar_op(cigar2[i-2]);
+ post_op = bam_cigar_op(cigar2[i]);
+ /* Note don't need to check for X/= as code above will use M only */
+ if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
+ /* This is a redundant P operator */
+ cigar2[i-1] = 0; // i.e. 0M
+ /* If had same operator either side, combine them in post_op */
+ if (pre_op == post_op) {
+ /* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+ cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+ cigar2[i-2] = 0; // i.e. 0M
+ }
+ }
+ }
+ /* Remove the zero'd operators (0M) */
+ for (i = k = 0; i < n2; ++i)
+ if (cigar2[i]) cigar2[k++] = cigar2[i];
+ n2 = k;
+ replace_cigar(b, n2, cigar2);
+ b->core.pos = posmap[b->core.pos];
+ if (b->core.mtid < 0 || b->core.mpos < 0) {
+ /* Nice case, no mate to worry about*/
+ // fprintf(pysamerr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+ /* TODO - Warning if FLAG says mate should be mapped? */
+ /* Clean up funny input where mate position is given but mate reference is missing: */
+ b->core.mtid = -1;
+ b->core.mpos = -1;
+ } else if (b->core.mtid == b->core.tid) {
+ /* Nice case, same reference */
+ // fprintf(pysamerr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
+ b->core.mpos = posmap[b->core.mpos];
+ } else {
+ /* Nasty case, Must load alternative posmap */
+ // fprintf(pysamerr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+ if (!fai) {
+ fprintf(pysamerr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
+ return -1;
+ }
+ /* Temporarily load the other reference sequence */
+ if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+ fprintf(pysamerr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ b->core.mpos = posmap[b->core.mpos];
+ /* Restore the reference and posmap*/
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
+ fprintf(pysamerr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ }
+ }
+ samwrite(out, b);
+ }
+ if (read_ret < -1) {
+ fprintf(pysamerr, "[depad] truncated file.\n");
+ ret = 1;
+ }
+ free(r.s); free(q.s); free(posmap);
+ bam_destroy1(b);
+ return ret;
+}
+
+bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
+{
+ int i = 0, unpadded_len = 0;
+ bam_header_t *header = 0 ;
+
+ header = bam_header_dup(old);
+ for (i = 0; i < old->n_targets; ++i) {
+ unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]);
+ if (unpadded_len < 0) {
+ fprintf(pysamerr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]);
+ } else {
+ header->target_len[i] = unpadded_len;
+ //fprintf(pysamerr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+ }
+ }
+ /* Duplicating the header allocated new buffer for header string */
+ /* After modifying the @SQ lines it will only get smaller, since */
+ /* the LN entries will be the same or shorter, and we'll remove */
+ /* any MD entries (MD5 checksums). */
+ assert(strlen(old->text) == strlen(header->text));
+ assert (0==strcmp(old->text, header->text));
+ const char *text;
+ text = old->text;
+ header->text[0] = '\0'; /* Resuse the allocated buffer */
+ char * newtext = header->text;
+ char * end=NULL;
+ while (text[0]=='@') {
+ end = strchr(text, '\n');
+ assert(end != 0);
+ if (text[1]=='S' && text[2]=='Q' && text[3]=='\t') {
+ /* TODO - edit the @SQ line here to remove MD and fix LN. */
+ /* For now just remove the @SQ line, and samtools will */
+ /* automatically generate a minimal replacement with LN. */
+ /* However, that discards any other tags like AS, SP, UR. */
+ //fprintf(pysamerr, "[depad] Removing @SQ line\n");
+ } else {
+ /* Copy this line to the new header */
+ strncat(newtext, text, end - text + 1);
+ }
+ text = end + 1;
+ }
+ assert (text[0]=='\0');
+ /* Check we didn't overflow the buffer */
+ assert (strlen(header->text) <= strlen(old->text));
+ if (strlen(header->text) < header->l_text) {
+ //fprintf(pysamerr, "[depad] Reallocating header buffer\n");
+ assert (newtext == header->text);
+ newtext = malloc(strlen(header->text) + 1);
+ strcpy(newtext, header->text);
+ free(header->text);
+ header->text = newtext;
+ header->l_text = strlen(newtext);
+ }
+ //fprintf(pysamerr, "[depad] Here is the new header (pending @SQ lines),\n\n%s\n(end)\n", header->text);
+ return header;
+}
+
+static int usage(int is_long_help);
+
+int main_pad2unpad(int argc, char *argv[])
+{
+ samfile_t *in = 0, *out = 0;
+ bam_header_t *h = 0;
+ faidx_t *fai = 0;
+ int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
+ int ret=0;
+
+ /* parse command-line options */
+ strcpy(in_mode, "r"); strcpy(out_mode, "w");
+ while ((c = getopt(argc, argv, "Sso:u1T:?")) >= 0) {
+ switch (c) {
+ case 'S': is_bamin = 0; break;
+ case 's': assert(compress_level == -1); is_bamout = 0; break;
+ case 'o': fn_out = strdup(optarg); break;
+ case 'u': assert(is_bamout == 1); compress_level = 0; break;
+ case '1': assert(is_bamout == 1); compress_level = 1; break;
+ case 'T': fn_ref = strdup(optarg); break;
+ case '?': is_long_help = 1; break;
+ default: return usage(is_long_help);
+ }
+ }
+ if (argc == optind) return usage(is_long_help);
+
+ if (is_bamin) strcat(in_mode, "b");
+ if (is_bamout) strcat(out_mode, "b");
+ strcat(out_mode, "h");
+ if (compress_level >= 0) {
+ char tmp[2];
+ tmp[0] = compress_level + '0'; tmp[1] = '\0';
+ strcat(out_mode, tmp);
+ }
+
+ // Load FASTA reference (also needed for SAM -> BAM if missing header)
+ if (fn_ref) {
+ fn_list = samfaipath(fn_ref);
+ fai = fai_load(fn_ref);
+ }
+ // open file handlers
+ if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) {
+ fprintf(pysamerr, "[depad] failed to open \"%s\" for reading.\n", argv[optind]);
+ ret = 1;
+ goto depad_end;
+ }
+ if (in->header == 0) {
+ fprintf(pysamerr, "[depad] failed to read the header from \"%s\".\n", argv[optind]);
+ ret = 1;
+ goto depad_end;
+ }
+ if (in->header->text == 0 || in->header->l_text == 0) {
+ fprintf(pysamerr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]);
+ assert (0 == in->header->l_text);
+ assert (0 == in->header->text);
+ }
+ if (fn_ref) {
+ h = fix_header(in->header, fai);
+ } else {
+ fprintf(pysamerr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+ h = in->header;
+ }
+ if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) {
+ fprintf(pysamerr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
+ ret = 1;
+ goto depad_end;
+ }
+
+ // Do the depad
+ ret = bam_pad2unpad(in, out, fai);
+
+depad_end:
+ // close files, free and return
+ if (fai) fai_destroy(fai);
+ if (h != in->header) bam_header_destroy(h);
+ samclose(in);
+ samclose(out);
+ free(fn_list); free(fn_out);
+ return ret;
+}
+
+static int usage(int is_long_help)
+{
+ fprintf(pysamerr, "\n");
+ fprintf(pysamerr, "Usage: samtools depad <in.bam>\n\n");
+ fprintf(pysamerr, "Options: -s output is SAM (default is BAM)\n");
+ fprintf(pysamerr, " -S input is SAM (default is BAM)\n");
+ fprintf(pysamerr, " -u uncompressed BAM output (can't use with -s)\n");
+ fprintf(pysamerr, " -1 fast compression BAM output (can't use with -s)\n");
+ fprintf(pysamerr, " -T FILE reference sequence file [null]\n");
+ fprintf(pysamerr, " -o FILE output file name [stdout]\n");
+ fprintf(pysamerr, " -? longer help\n");
+ fprintf(pysamerr, "\n");
+ if (is_long_help)
+ fprintf(pysamerr, "Notes:\n\
+\n\
+ 1. Requires embedded reference sequences (before the reads for that reference),\n\
+ with the future aim to also support a FASTA padded reference sequence file.\n\
+\n\
+ 2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
+\n");
+ return 1;
+}
diff --git a/samtools/sam.c.pysam.c b/samtools/sam.c.pysam.c
index 7f71f7a..a65fc0c 100644
--- a/samtools/sam.c.pysam.c
+++ b/samtools/sam.c.pysam.c
@@ -38,6 +38,13 @@ static void append_header_text(bam_header_t *header, char* text, int len)
header->text[header->l_text] = 0;
}
+int samthreads(samfile_t *fp, int n_threads, int n_sub_blks)
+{
+ if (!(fp->type&1) || (fp->type&2)) return -1;
+ bgzf_mt(fp->x.bam, n_threads, n_sub_blks);
+ return 0;
+}
+
samfile_t *samopen(const char *fn, const char *mode, const void *aux)
{
samfile_t *fp;
@@ -81,7 +88,7 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
} else { // text
// open file
fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
- if (fp->x.tamr == 0) goto open_err_ret;
+ if (fp->x.tamw == 0) goto open_err_ret;
if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2;
else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2;
else fp->type |= BAM_OFDEC<<2;
diff --git a/samtools/sam.h b/samtools/sam.h
index 0b87194..0495501 100644
--- a/samtools/sam.h
+++ b/samtools/sam.h
@@ -90,6 +90,7 @@ extern "C" {
int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
char *samfaipath(const char *fn_ref);
+ int samthreads(samfile_t *fp, int n_threads, int n_sub_blks);
#ifdef __cplusplus
}
diff --git a/samtools/sam_header.c.pysam.c b/samtools/sam_header.c.pysam.c
index 2178047..dcfc99d 100644
--- a/samtools/sam_header.c.pysam.c
+++ b/samtools/sam_header.c.pysam.c
@@ -368,6 +368,7 @@ static HeaderLine *sam_header_line_parse(const char *headerLine)
while (*to && *to=='\t') to++;
if ( to-from != 1 ) {
debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ free(hline);
return 0;
}
from = to;
@@ -436,8 +437,14 @@ static int sam_header_line_validate(HeaderLine *hline)
tag = tags->data;
if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
{
- debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
- return 0;
+ // Lower case tags are user-defined values.
+ if( !(islower(tag->key[0]) || islower(tag->key[1])) )
+ {
+ // Neither is lower case, but tag was not recognized.
+ debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
+ // return 0; // Even unknown tags are allowed - for forward compatibility with new attributes
+ }
+ // else - allow user defined tag
}
tags = tags->next;
}
@@ -665,6 +672,36 @@ char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n
return ret;
}
+void *sam_header2key_val(void *iter, const char type[2], const char key_tag[2], const char value_tag[2], const char **_key, const char **_value)
+{
+ list_t *l = iter;
+ if ( !l ) return NULL;
+
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+
+ HeaderTag *key, *value;
+ key = header_line_has_tag(hline,key_tag);
+ value = header_line_has_tag(hline,value_tag);
+ if ( !key && !value )
+ {
+ l = l->next;
+ continue;
+ }
+
+ *_key = key->value;
+ *_value = value->value;
+ return l->next;
+ }
+ return l;
+}
+
const char *sam_tbl_get(void *h, const char *key)
{
khash_t(str) *tbl = (khash_t(str)*)h;
@@ -735,4 +772,41 @@ void *sam_header_merge(int n, const void **_dicts)
return out_dict;
}
+char **sam_header2tbl_n(const void *dict, const char type[2], const char *tags[], int *n)
+{
+ int nout = 0;
+ char **out = NULL;
+
+ *n = 0;
+ list_t *l = (list_t *)dict;
+ if ( !l ) return NULL;
+
+ int i, ntags = 0;
+ while ( tags[ntags] ) ntags++;
+
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+ out = (char**) realloc(out, sizeof(char*)*(nout+1)*ntags);
+ for (i=0; i<ntags; i++)
+ {
+ HeaderTag *key = header_line_has_tag(hline, tags[i]);
+ if ( !key )
+ {
+ out[nout*ntags+i] = NULL;
+ continue;
+ }
+ out[nout*ntags+i] = key->value;
+ }
+ nout++;
+ l = l->next;
+ }
+ *n = nout;
+ return out;
+}
diff --git a/samtools/sam_header.h b/samtools/sam_header.h
index e5c754f..4b0cb03 100644
--- a/samtools/sam_header.h
+++ b/samtools/sam_header.h
@@ -10,8 +10,32 @@ extern "C" {
void sam_header_free(void *header);
char *sam_header_write(const void *headerDict); // returns a newly allocated string
+ /*
+ // Usage example
+ const char *key, *val;
+ void *iter = sam_header_parse2(bam->header->text);
+ while ( iter = sam_header_key_val(iter, "RG","ID","SM" &key,&val) ) printf("%s\t%s\n", key,val);
+ */
+ void *sam_header2key_val(void *iter, const char type[2], const char key_tag[2], const char value_tag[2], const char **key, const char **value);
char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n);
+ /*
+ // Usage example
+ int i, j, n;
+ const char *tags[] = {"SN","LN","UR","M5",NULL};
+ void *dict = sam_header_parse2(bam->header->text);
+ char **tbl = sam_header2tbl_n(h->dict, "SQ", tags, &n);
+ for (i=0; i<n; i++)
+ {
+ for (j=0; j<4; j++)
+ if ( tbl[4*i+j] ) printf("\t%s", tbl[4*i+j]);
+ else printf("-");
+ printf("\n");
+ }
+ if (tbl) free(tbl);
+ */
+ char **sam_header2tbl_n(const void *dict, const char type[2], const char *tags[], int *n);
+
void *sam_header2tbl(const void *dict, char type[2], char key_tag[2], char value_tag[2]);
const char *sam_tbl_get(void *h, const char *key);
int sam_tbl_size(void *h);
diff --git a/samtools/sam_view.c.pysam.c b/samtools/sam_view.c.pysam.c
index 05da8e3..8622aa1 100644
--- a/samtools/sam_view.c.pysam.c
+++ b/samtools/sam_view.c.pysam.c
@@ -5,6 +5,7 @@
#include <stdio.h>
#include <unistd.h>
#include <math.h>
+#include <inttypes.h>
#include "sam_header.h"
#include "sam.h"
#include "faidx.h"
@@ -16,15 +17,16 @@ KHASH_SET_INIT_STR(rg)
// data passed to the bam_fetch callback is encapsulated in this struct.
typedef struct {
bam_header_t *header;
- int *count;
+ int64_t *count; // int does overflow for very big BAMs
} count_func_data_t;
typedef khash_t(rg) *rghash_t;
// FIXME: we'd better use no global variables...
static rghash_t g_rghash = 0;
-static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0;
-static float g_subsam = -1;
+static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0, g_qual_scale = 0, g_min_qlen = 0;
+static uint32_t g_subsam_seed = 0;
+static double g_subsam_frac = -1.;
static char *g_library, *g_rg;
static void *g_bed;
@@ -32,16 +34,31 @@ void *bed_read(const char *fn);
void bed_destroy(void *_h);
int bed_overlap(const void *_h, const char *chr, int beg, int end);
-static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b)
+static int process_aln(const bam_header_t *h, bam1_t *b)
{
+ if (g_qual_scale > 1) {
+ int i;
+ uint8_t *qual = bam1_qual(b);
+ for (i = 0; i < b->core.l_qseq; ++i) {
+ int c = qual[i] * g_qual_scale;
+ qual[i] = c < 93? c : 93;
+ }
+ }
+ if (g_min_qlen > 0) {
+ int k, qlen = 0;
+ uint32_t *cigar = bam1_cigar(b);
+ for (k = 0; k < b->core.n_cigar; ++k)
+ if ((bam_cigar_type(bam_cigar_op(cigar[k]))&1) || bam_cigar_op(cigar[k]) == BAM_CHARD_CLIP)
+ qlen += bam_cigar_oplen(cigar[k]);
+ if (qlen < g_min_qlen) return 1;
+ }
if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off))
return 1;
if (g_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b))))
return 1;
- if (g_subsam > 0.) {
- int x = (int)(g_subsam + .499);
- uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + x;
- if (k%1024 / 1024.0 >= g_subsam - x) return 1;
+ if (g_subsam_frac > 0.) {
+ uint32_t k = __ac_X31_hash_string(bam1_qname(b)) + g_subsam_seed;
+ if ((double)(k&0xffffff) / 0x1000000 >= g_subsam_frac) return 1;
}
if (g_rg || g_rghash) {
uint8_t *s = bam_aux_get(b, "RG");
@@ -94,7 +111,7 @@ static char *drop_rg(char *hdtxt, rghash_t h, int *len)
// callback function for bam_fetch() that prints nonskipped records
static int view_func(const bam1_t *b, void *data)
{
- if (!__g_skip_aln(((samfile_t*)data)->header, b))
+ if (!process_aln(((samfile_t*)data)->header, (bam1_t*)b))
samwrite((samfile_t*)data, b);
return 0;
}
@@ -102,7 +119,7 @@ static int view_func(const bam1_t *b, void *data)
// callback function for bam_fetch() that counts nonskipped records
static int count_func(const bam1_t *b, void *data)
{
- if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) {
+ if (!process_aln(((count_func_data_t*)data)->header, (bam1_t*)b)) {
(*((count_func_data_t*)data)->count)++;
}
return 0;
@@ -113,16 +130,23 @@ static int usage(int is_long_help);
int main_samview(int argc, char *argv[])
{
int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0;
- int of_type = BAM_OFDEC, is_long_help = 0;
- int count = 0;
+ int of_type = BAM_OFDEC, is_long_help = 0, n_threads = 0;
+ int64_t count = 0;
samfile_t *in = 0, *out = 0;
- char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0;
+ char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0, *fn_rg = 0, *q;
/* parse command-line options */
strcpy(in_mode, "r"); strcpy(out_mode, "w");
- while ((c = getopt(argc, argv, "Sbct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:")) >= 0) {
+ while ((c = getopt(argc, argv, "SbBct:h1Ho:q:f:F:ul:r:xX?T:R:L:s:Q:@:m:")) >= 0) {
switch (c) {
- case 's': g_subsam = atof(optarg); break;
+ case 's':
+ if ((g_subsam_seed = strtol(optarg, &q, 10)) != 0) {
+ srand(g_subsam_seed);
+ g_subsam_seed = rand();
+ }
+ g_subsam_frac = strtod(q, &q);
+ break;
+ case 'm': g_min_qlen = atoi(optarg); break;
case 'c': is_count = 1; break;
case 'S': is_bamin = 0; break;
case 'b': is_bamout = 1; break;
@@ -143,6 +167,9 @@ int main_samview(int argc, char *argv[])
case 'X': of_type = BAM_OFSTR; break;
case '?': is_long_help = 1; break;
case 'T': fn_ref = strdup(optarg); is_bamin = 0; break;
+ case 'B': bam_no_B = 1; break;
+ case 'Q': g_qual_scale = atoi(optarg); break;
+ case '@': n_threads = strtol(optarg, 0, 0); break;
default: return usage(is_long_help);
}
}
@@ -200,13 +227,14 @@ int main_samview(int argc, char *argv[])
ret = 1;
goto view_end;
}
+ if (n_threads > 1) samthreads(out, n_threads, 256);
if (is_header_only) goto view_end; // no need to print alignments
if (argc == optind + 1) { // convert/print the entire file
bam1_t *b = bam_init1();
int r;
while ((r = samread(in, b)) >= 0) { // read one alignment from `in'
- if (!__g_skip_aln(in->header, b)) {
+ if (!process_aln(in->header, b)) {
if (!is_count) samwrite(out, b); // write the alignment to `out'
count++;
}
@@ -248,9 +276,9 @@ int main_samview(int argc, char *argv[])
}
view_end:
- if (is_count && ret == 0) {
- printf("%d\n", count);
- }
+ if (is_count && ret == 0)
+ printf("%" PRId64 "\n", count);
+
// close files, free and return
free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); free(fn_rg);
if (g_bed) bed_destroy(g_bed);
@@ -279,6 +307,8 @@ static int usage(int is_long_help)
fprintf(pysamerr, " -x output FLAG in HEX (samtools-C specific)\n");
fprintf(pysamerr, " -X output FLAG in string (samtools-C specific)\n");
fprintf(pysamerr, " -c print only the count of matching records\n");
+ fprintf(pysamerr, " -B collapse the backward CIGAR operation\n");
+ fprintf(pysamerr, " -@ INT number of BAM compression threads [0]\n");
fprintf(pysamerr, " -L FILE output alignments overlapping the input BED FILE [null]\n");
fprintf(pysamerr, " -t FILE list of reference names and lengths (force -S) [null]\n");
fprintf(pysamerr, " -T FILE reference sequence file (force -S) [null]\n");
@@ -349,12 +379,14 @@ int main_bam2fq(int argc, char *argv[])
bam_header_t *h;
bam1_t *b;
int8_t *buf;
- int max_buf;
+ int max_buf, c, no12 = 0;
+ while ((c = getopt(argc, argv, "n")) > 0)
+ if (c == 'n') no12 = 1;
if (argc == 1) {
fprintf(pysamerr, "Usage: samtools bam2fq <in.bam>\n");
return 1;
}
- fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+ fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
if (fp == 0) return 1;
h = bam_header_read(fp);
b = bam_init1();
@@ -364,9 +396,12 @@ int main_bam2fq(int argc, char *argv[])
int i, qlen = b->core.l_qseq;
uint8_t *seq;
putchar('@'); fputs(bam1_qname(b), stdout);
- if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
- else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
- else putchar('\n');
+ if (no12) putchar('\n');
+ else {
+ if ((b->core.flag & 0x40) && !(b->core.flag & 0x80)) puts("/1");
+ else if ((b->core.flag & 0x80) && !(b->core.flag & 0x40)) puts("/2");
+ else putchar('\n');
+ }
if (max_buf < qlen + 1) {
max_buf = qlen + 1;
kroundup32(max_buf);
diff --git a/setup.py b/setup.py
index 0cc9c4b..1b4a325 100644
--- a/setup.py
+++ b/setup.py
@@ -11,6 +11,8 @@ import platform
name = "pysam"
+IS_PYTHON3 = sys.version_info[0] >= 3
+
# collect pysam version
sys.path.insert( 0, "pysam")
import version
@@ -19,7 +21,9 @@ version = version.__version__
samtools_exclude = ( "bamtk.c", "razip.c", "bgzip.c",
"main.c", "calDepth.c", "bam2bed.c",
- "wgsim.c", "md5fa.c", "maq2sam.c",)
+ "wgsim.c", "md5fa.c", "maq2sam.c",
+ "bamcheck.c",
+ "chk_indel.c" )
samtools_dest = os.path.abspath( "samtools" )
tabix_exclude = ( "main.c", )
tabix_dest = os.path.abspath( "tabix" )
@@ -140,6 +144,18 @@ except ImportError:
tabproxies_sources = ["pysam/TabProxies.c" ]
cvcf_sources = ["pysam/cvcf.c" ]
else:
+ # remove existing files to recompute
+ # necessary to be both compatible for python 2.7 and 3.3
+ if IS_PYTHON3:
+ for f in ( "pysam/csamtools.c",
+ "pysam/ctabix.c",
+ "pysam/TabProxies.c",
+ "pysam/cvcf.c" ):
+ try:
+ os.unlink( f )
+ except:
+ pass
+
cmdclass = { 'build_ext' : build_ext }
csamtools_sources = [ "pysam/csamtools.pyx" ]
tabix_sources = [ "pysam/ctabix.pyx" ]
diff --git a/tests/Makefile b/tests/Makefile
index 2b401e5..7774778 100644
--- a/tests/Makefile
+++ b/tests/Makefile
@@ -11,7 +11,9 @@ all: ex1.pileup.gz ex1.bam.bai \
ex10.bam ex10.bam.bai \
example_unmapped_reads_no_sq.bam \
example_user_header.bam \
- example_btag.bam
+ example_btag.bam \
+ example_bai.bam
+
ex2.sam.gz: ex1.bam ex1.bam.bai
samtools view -h ex1.bam | gzip > ex2.sam.gz
@@ -36,6 +38,14 @@ example_unmapped_reads_no_sq.bam: example_unmapped_reads_no_sq.sam
samtools import tmp.list $< $@
rm -f tmp.list
+example_bai.bam: ex1.bam
+ cp ex1.bam $@
+ samtools index $@
+ mv $@.bai example_bai.bai
+
+
+
+
clean:
rm -fr *.bam *.bai *.fai *.pileup* \
*~ calDepth *.dSYM pysam_*.sam \
diff --git a/tests/pysam_test.py b/tests/pysam_test.py
index c8acf83..5cfed74 100755
--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -53,7 +53,8 @@ def runSamtools( cmd ):
'''run a samtools command'''
try:
- retcode = subprocess.call(cmd, shell=True)
+ retcode = subprocess.call(cmd, shell=True,
+ stderr = subprocess.PIPE)
if retcode < 0:
print("Child was terminated by signal", -retcode)
except OSError as e:
@@ -78,7 +79,9 @@ class BinaryTest(unittest.TestCase):
first_time = True
- # a list of commands to test
+ # a dictionary of commands to test
+ # first entry: (samtools output file, samtools command)
+ # second entry: (pysam output file, (pysam function, pysam options) )
commands = \
{
"view" :
@@ -179,6 +182,21 @@ class BinaryTest(unittest.TestCase):
("ex1.bam2fq", "bam2fq ex1.bam > ex1.bam2fq" ),
("pysam_ex1.bam2fq", (pysam.bam2fq, "pysam_ex1.bam") ),
),
+ "pad2unpad":
+ (
+ ("ex2.unpad", "pad2unpad -T ex1.fa ex2.bam > ex2.unpad" ),
+ ("pysam_ex2.unpad", (pysam.pad2unpad, "-T ex1.fa ex2.bam") ),
+ ),
+ "bamshuf":
+ (
+ ("ex1.bamshuf.bam", "bamshuf ex1.bam ex1.bamshuf" ),
+ ("pysam_ex1.bamshuf.bam", (pysam.bamshuf, "ex1.bam pysam_ex1.bamshuf") ),
+ ),
+ "bedcov":
+ (
+ ("ex1.bedcov", "bedcov ex1.bed ex1.bam > ex1.bedcov" ),
+ ("pysam_ex1.bedcov", (pysam.bedcov, "ex1.bed ex1.bam") ),
+ ),
}
# some tests depend on others. The order specifies in which order
@@ -186,23 +204,26 @@ class BinaryTest(unittest.TestCase):
# The first three (faidx, import, index) need to be in that order,
# the rest is arbitrary.
order = ('faidx', 'import', 'index',
- # 'pileup1', 'pileup2', deprecated
- # 'glfview', deprecated
- 'view', 'view2',
- 'sort',
- 'mpileup',
- 'depth',
- 'idxstats',
- 'fixmate',
- 'flagstat',
- # 'calmd',
- 'merge',
- 'rmdup',
- 'reheader',
- 'cat',
- 'targetcut',
- 'phase',
- 'bam2fq',
+ # 'pileup1', 'pileup2', deprecated
+ # 'glfview', deprecated
+ 'view', 'view2',
+ 'sort',
+ 'mpileup',
+ 'depth',
+ 'idxstats',
+ 'fixmate',
+ 'flagstat',
+ ## 'calmd',
+ 'merge',
+ 'rmdup',
+ 'reheader',
+ 'cat',
+ 'bedcov',
+ 'targetcut',
+ 'phase',
+ 'bamshuf',
+ 'bam2fq',
+ 'pad2unpad',
)
def setUp( self ):
@@ -226,12 +247,14 @@ class BinaryTest(unittest.TestCase):
shutil.copy( "ex1.fa", os.path.join( WORKDIR, "ex1.fa" ) )
shutil.copy( "ex1.sam.gz", os.path.join( WORKDIR, "ex1.sam.gz" ) )
shutil.copy( "ex1.sam", os.path.join( WORKDIR, "ex1.sam" ) )
+ shutil.copy( "ex2.bam", os.path.join( WORKDIR, "ex2.bam" ) )
# cd to workdir
savedir = os.getcwd()
os.chdir( WORKDIR )
for label in self.order:
+ # print ("command=", label)
command = self.commands[label]
# build samtools command and target and run
samtools_target, samtools_command = command[0]
@@ -252,7 +275,6 @@ class BinaryTest(unittest.TestCase):
(label, pysam_options, msg) )
-
if ">" in samtools_command:
with open( pysam_target, "wb" ) as outfile:
if type(output) == list:
@@ -333,6 +355,15 @@ class BinaryTest(unittest.TestCase):
def testBam2fq( self ):
self.checkCommand( "bam2fq" )
+ def testBedcov( self ):
+ self.checkCommand( "bedcov" )
+
+ def testBamshuf( self ):
+ self.checkCommand( "bamshuf" )
+
+ def testPad2Unpad( self ):
+ self.checkCommand( "pad2unpad" )
+
# def testPileup1( self ):
# self.checkCommand( "pileup1" )
@@ -480,6 +511,18 @@ class IOTest(unittest.TestCase):
self.assertRaises( ValueError, pysam.Samfile, input_filename, "r",
check_header = False)
+ def testBAMWithoutAlignedReads( self ):
+ '''see issue 117'''
+ input_filename = "test_unaligned.bam"
+ samfile = pysam.Samfile( input_filename, "rb", check_sq = False )
+ samfile.fetch( until_eof = True )
+
+ def testBAMWithShortBAI( self ):
+ '''see issue 116'''
+ input_filename = "example_bai.bam"
+ samfile = pysam.Samfile( input_filename, "rb", check_sq = False )
+ samfile.fetch( 'chr2' )
+
def testFetchFromClosedFile( self ):
samfile = pysam.Samfile( "ex1.bam", "rb" )
@@ -545,9 +588,9 @@ class TestFloatTagBug( unittest.TestCase ):
'''see issue 71'''
def testFloatTagBug( self ):
- '''a float tag before another exposed a parsing bug in bam_aux_get - expected to fail
+ '''a float tag before another exposed a parsing bug in bam_aux_get.
- This test is expected to fail until samtools is fixed.
+ Fixed in 0.1.19
'''
samfile = pysam.Samfile("tag_bug.bam")
read = next(samfile.fetch(until_eof=True))
@@ -607,10 +650,23 @@ class TestTagParsing( unittest.TestCase ):
def testCigarString( self ):
r = self.makeRead()
- self.assertEqual( r.cigarstring, "M10D1M25" )
- r.cigarstring = "M20D10M20"
+ self.assertEqual( r.cigarstring, "10M1D25M" )
+ r.cigarstring = "20M10D20M"
self.assertEqual( r.cigar, [(0,20), (2,10), (0,20)])
+ def testLongTags( self ):
+ '''see issue 115'''
+
+ r = self.makeRead()
+ rg = 'HS2000-899_199.L3'
+ tags = [('XC', 85), ('XT', 'M'), ('NM', 5), ('SM', 29), ('AM', 29), ('XM', 1), ('XO', 1), ('XG', 4), ('MD', '37^ACCC29T18'), ('XA','5,+11707,36M1I48M,2;21,-48119779,46M1I38M,2;hs37d5,-10060835,40M1D45M,3;5,+11508,36M1I48M,3;hs37d5,+6743812,36M1I48M,3;19,-59118894,46M1I38M,3;4,-191044002,6M1I78M,3;')]
+
+ r.tags = tags
+ r.tags += [("RG",rg)] * 100
+ tags += [("RG",rg)] * 100
+
+ self.assertEqual( tags, r.tags )
+
class TestIteratorRow(unittest.TestCase):
def setUp(self):
@@ -670,7 +726,7 @@ class TestIteratorRowAll(unittest.TestCase):
self.samfile.close()
class TestIteratorColumn(unittest.TestCase):
- '''test iterator column against contents of ex3.bam.'''
+ '''test iterator column against contents of ex4.bam.'''
# note that samfile contains 1-based coordinates
# 1D means deletion with respect to reference sequence
@@ -728,12 +784,34 @@ class TestIteratorColumn(unittest.TestCase):
for start in range( 1, length, 90):
self.checkRange( contig, start, start + 90, truncate = True ) # this includes empty ranges
-
-
def tearDown(self):
self.samfile.close()
+class TestIteratorColumn2(unittest.TestCase):
+ '''test iterator column against contents of ex1.bam.'''
+
+ def setUp(self):
+ self.samfile=pysam.Samfile( "ex1.bam","rb" )
+
+ def testStart( self ):
+ #print self.samfile.fetch().next().pos
+ #print self.samfile.pileup().next().pos
+ pass
+
+ def testTruncate( self ):
+ '''see issue 107.'''
+ # note that ranges in regions start from 1
+ p = self.samfile.pileup(region='chr1:170:172', truncate=True)
+ columns = [ x.pos for x in p ]
+ self.assertEqual( len(columns), 3)
+ self.assertEqual( columns, [169,170,171] )
+
+ p = self.samfile.pileup( 'chr1', 169, 172, truncate=True)
+ columns = [ x.pos for x in p ]
+ self.assertEqual( len(columns), 3)
+ self.assertEqual( columns, [169,170,171] )
+
class TestAlignedReadFromBam(unittest.TestCase):
def setUp(self):
@@ -764,6 +842,10 @@ class TestAlignedReadFromBam(unittest.TestCase):
self.assertEqual( self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)], "read name length mismatch in read 1: %s != %s" % (self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)]) )
self.assertEqual( self.reads[1].cigar, [(0, 35)], "read name length mismatch in read 2: %s != %s" % (self.reads[1].cigar, [(0, 35)]) )
+ def testARcigarstring(self):
+ self.assertEqual( self.reads[0].cigarstring, '10M1D25M' )
+ self.assertEqual( self.reads[1].cigarstring, '35M' )
+
def testARmrnm(self):
self.assertEqual( self.reads[0].mrnm, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].mrnm, 0) )
self.assertEqual( self.reads[1].mrnm, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].mrnm, 1) )
@@ -893,7 +975,8 @@ class TestHeaderBam(TestHeaderSam):
class TestHeader1000Genomes( unittest.TestCase ):
- bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam"
+ # bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam"
+ bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase3_EX_or_LC_only_alignment/data/HG00104/alignment/HG00104.chrom11.ILLUMINA.bwa.GBR.low_coverage.20130415.bam"
def testRead( self ):
diff --git a/tests/tabix_test.py b/tests/tabix_test.py
index 5ff36ba..3477340 100644
--- a/tests/tabix_test.py
+++ b/tests/tabix_test.py
@@ -412,27 +412,34 @@ class TestBed( unittest.TestCase ):
self.assertEqual( int(c[2]) + 1, r.end )
self.assertEqual( str(int(c[2]) + 1), r[2].decode("ascii") )
-class TestVCFFromTabix( unittest.TestCase ):
+class TestVCF( unittest.TestCase ):
filename = "example.vcf40"
- columns = ("contig", "pos", "id",
- "ref", "alt", "qual",
- "filter", "info", "format" )
-
def setUp( self ):
self.tmpfilename = "tmp_%s.vcf" % id(self)
shutil.copyfile( self.filename, self.tmpfilename )
pysam.tabix_index( self.tmpfilename, preset = "vcf" )
- self.tabix = pysam.Tabixfile( self.tmpfilename + ".gz" )
- self.compare = loadAndConvert( self.filename )
-
def tearDown( self ):
-
os.unlink( self.tmpfilename + ".gz" )
- os.unlink( self.tmpfilename + ".gz.tbi" )
+ if os.path.exists( self.tmpfilename + ".gz.tbi" ):
+ os.unlink( self.tmpfilename + ".gz.tbi" )
+
+class TestVCFFromTabix( TestVCF ):
+
+ columns = ("contig", "pos", "id",
+ "ref", "alt", "qual",
+ "filter", "info", "format" )
+
+
+ def setUp( self ):
+
+ TestVCF.setUp( self )
+
+ self.tabix = pysam.Tabixfile( self.tmpfilename + ".gz" )
+ self.compare = loadAndConvert( self.filename )
def testRead( self ):
@@ -440,11 +447,9 @@ class TestVCFFromTabix( unittest.TestCase ):
for x, r in enumerate(self.tabix.fetch( parser = pysam.asVCF() )):
c = self.compare[x]
-
for y, field in enumerate( self.columns ):
# it is ok to have a missing format column
if y == 8 and y == len(c): continue
-
if field == "pos":
self.assertEqual( int(c[y]) - 1, getattr( r, field ) )
self.assertEqual( int(c[y]) - 1, r.pos )
@@ -456,10 +461,10 @@ class TestVCFFromTabix( unittest.TestCase ):
self.assertEqual( 0, len(r) )
else:
self.assertEqual( len(c), len( r ) + ncolumns )
-
+
for y in range(len(c) - ncolumns):
self.assertEqual( c[ncolumns+y], r[y] )
-
+
def testWrite( self ):
ncolumns = len(self.columns)
@@ -501,12 +506,9 @@ class TestVCFFromTabix( unittest.TestCase ):
r[y] = ("test_%i" % y).encode('ascii')
self.assertEqual( c[ncolumns+y], r[y] )
+class TestVCFFromVCF( TestVCF ):
-class TestVCFFromVCF( unittest.TestCase ):
-
- filename = "example.vcf40"
-
- columns = ("contig", "pos", "id",
+ columns = ("chrom", "pos", "id",
"ref", "alt", "qual",
"filter", "info", "format" )
@@ -520,14 +522,18 @@ class TestVCFFromVCF( unittest.TestCase ):
# tests failing on opening
fail_on_opening = ( (24, "Error HEADING_NOT_SEPARATED_BY_TABS" ),
)
-
def setUp( self ):
+ TestVCF.setUp( self )
+
self.vcf = pysam.VCF()
self.compare = loadAndConvert( self.filename )
def testParsing( self ):
+ # self.vcf.connect( self.tmpfilename + ".gz" )
+ ncolumns = len(self.columns)
+
fn = os.path.basename( self.filename )
with open(self.filename) as f:
@@ -545,10 +551,70 @@ class TestVCFFromVCF( unittest.TestCase ):
# python 2.7
# self.assertRaisesRegexp( ValueError, re.compile(msg), self.vcf.parse, f )
else:
- for ln in iter:
- pass
-
-############################################################################
+ # do the actual parsing
+ for x, r in enumerate(iter):
+ c = self.compare[x]
+ for y, field in enumerate( self.columns ):
+ # it is ok to have a missing format column
+ if y == 8 and y == len(c): continue
+
+ val = r[field]
+ if field == "pos":
+ self.assertEqual( int(c[y]) - 1, val )
+ elif field == "alt":
+ if c[y] == ".":
+ # convert . to empty list
+ self.assertEqual( [], val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+ else:
+ # convert to list
+ self.assertEqual( c[y].split(","), val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+
+ elif field == "filter":
+ if c[y] == "PASS" or c[y] == ".":
+ # convert PASS to empty list
+ self.assertEqual( [], val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+ else:
+ # convert to list
+ self.assertEqual( c[y].split(";"), val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+
+ elif field == "info":
+ # tests for info field not implemented
+ pass
+ elif field == "qual" and c[y] == ".":
+ self.assertEqual( -1, val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+ elif field == "format":
+ # format field converted to list
+ self.assertEqual( c[y].split(":"), val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+
+ elif type(val) in (int, float):
+ if c[y] == ".":
+ self.assertEqual( None, val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+
+ else:
+ self.assertEqual( float( c[y]), float(val),
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+
+ else:
+ self.assertEqual( c[y], val,
+ "mismatch in field %s: expected %s, got %s" %\
+ ( field,c[y], val ) )
+
+############################################################################
# create a test class for each example vcf file.
# Two samples are created -
# 1. Testing pysam/tabix access
diff --git a/tests/test_unaligned.bam b/tests/test_unaligned.bam
new file mode 100644
index 0000000..c71b01c
Binary files /dev/null and b/tests/test_unaligned.bam differ
--
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/pysam.git
More information about the debian-med-commit
mailing list