[med-svn] [python-pysam] 01/05: Imported Upstream version 0.7.6
Charles Plessy
plessy at moszumanska.debian.org
Sat Apr 19 02:48:43 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository python-pysam.
commit 15fc052c4cc165d27403584aa51010a057e62245
Author: Charles Plessy <plessy at debian.org>
Date: Sat Apr 19 11:39:04 2014 +0900
Imported Upstream version 0.7.6
---
PKG-INFO | 2 +-
distribute_setup.py | 546 --
doc/faq.rst | 68 +
doc/release.rst | 8 +
doc/usage.rst | 7 +-
pysam.egg-info/PKG-INFO | 2 +-
pysam.egg-info/SOURCES.txt | 1 -
pysam/TabProxies.c | 52 +-
pysam/TabProxies.pyx | 2 +-
pysam/csamtools.c | 12573 +++++++++++++++++++++++++------------------
pysam/csamtools.pxd | 31 +
pysam/csamtools.pyx | 260 +-
pysam/ctabix.c | 304 +-
pysam/cvcf.c | 396 +-
pysam/pysam_util.c | 3 +
pysam/pysam_util.h | 6 +
pysam/tabix_util.c | 22 +
pysam/version.py | 2 +-
setup.py | 11 +-
tests/Makefile | 3 +-
tests/pysam_test.py | 49 +
21 files changed, 8088 insertions(+), 6260 deletions(-)
diff --git a/PKG-INFO b/PKG-INFO
index 8d8f7c5..dbb2aed 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.5
+Version: 0.7.6
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
diff --git a/distribute_setup.py b/distribute_setup.py
deleted file mode 100644
index a1cc2a1..0000000
--- a/distribute_setup.py
+++ /dev/null
@@ -1,546 +0,0 @@
-#!python
-"""Bootstrap distribute installation
-
-If you want to use setuptools in your package's setup.py, just include this
-file in the same directory with it, and add this to the top of your setup.py::
-
- from distribute_setup import use_setuptools
- use_setuptools()
-
-If you want to require a specific version of setuptools, set a download
-mirror, or use an alternate download directory, you can do so by supplying
-the appropriate options to ``use_setuptools()``.
-
-This file can also be run as a script to install or upgrade setuptools.
-"""
-import os
-import shutil
-import sys
-import time
-import fnmatch
-import tempfile
-import tarfile
-import optparse
-
-from distutils import log
-
-try:
- from site import USER_SITE
-except ImportError:
- USER_SITE = None
-
-try:
- import subprocess
-
- def _python_cmd(*args):
- args = (sys.executable,) + args
- return subprocess.call(args) == 0
-
-except ImportError:
- # will be used for python 2.3
- def _python_cmd(*args):
- args = (sys.executable,) + args
- # quoting arguments if windows
- if sys.platform == 'win32':
- def quote(arg):
- if ' ' in arg:
- return '"%s"' % arg
- return arg
- args = [quote(arg) for arg in args]
- return os.spawnl(os.P_WAIT, sys.executable, *args) == 0
-
-DEFAULT_VERSION = "0.6.34"
-DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/"
-SETUPTOOLS_FAKED_VERSION = "0.6c11"
-
-SETUPTOOLS_PKG_INFO = """\
-Metadata-Version: 1.0
-Name: setuptools
-Version: %s
-Summary: xxxx
-Home-page: xxx
-Author: xxx
-Author-email: xxx
-License: xxx
-Description: xxx
-""" % SETUPTOOLS_FAKED_VERSION
-
-
-def _install(tarball, install_args=()):
- # extracting the tarball
- tmpdir = tempfile.mkdtemp()
- log.warn('Extracting in %s', tmpdir)
- old_wd = os.getcwd()
- try:
- os.chdir(tmpdir)
- tar = tarfile.open(tarball)
- _extractall(tar)
- tar.close()
-
- # going in the directory
- subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
- os.chdir(subdir)
- log.warn('Now working in %s', subdir)
-
- # installing
- log.warn('Installing Distribute')
- if not _python_cmd('setup.py', 'install', *install_args):
- log.warn('Something went wrong during the installation.')
- log.warn('See the error message above.')
- # exitcode will be 2
- return 2
- finally:
- os.chdir(old_wd)
- shutil.rmtree(tmpdir)
-
-
-def _build_egg(egg, tarball, to_dir):
- # extracting the tarball
- tmpdir = tempfile.mkdtemp()
- log.warn('Extracting in %s', tmpdir)
- old_wd = os.getcwd()
- try:
- os.chdir(tmpdir)
- tar = tarfile.open(tarball)
- _extractall(tar)
- tar.close()
-
- # going in the directory
- subdir = os.path.join(tmpdir, os.listdir(tmpdir)[0])
- os.chdir(subdir)
- log.warn('Now working in %s', subdir)
-
- # building an egg
- log.warn('Building a Distribute egg in %s', to_dir)
- _python_cmd('setup.py', '-q', 'bdist_egg', '--dist-dir', to_dir)
-
- finally:
- os.chdir(old_wd)
- shutil.rmtree(tmpdir)
- # returning the result
- log.warn(egg)
- if not os.path.exists(egg):
- raise IOError('Could not build the egg.')
-
-
-def _do_download(version, download_base, to_dir, download_delay):
- egg = os.path.join(to_dir, 'distribute-%s-py%d.%d.egg'
- % (version, sys.version_info[0], sys.version_info[1]))
- if not os.path.exists(egg):
- tarball = download_setuptools(version, download_base,
- to_dir, download_delay)
- _build_egg(egg, tarball, to_dir)
- sys.path.insert(0, egg)
- import setuptools
- setuptools.bootstrap_install_from = egg
-
-
-def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, download_delay=15, no_fake=True):
- # making sure we use the absolute path
- to_dir = os.path.abspath(to_dir)
- was_imported = 'pkg_resources' in sys.modules or \
- 'setuptools' in sys.modules
- try:
- try:
- import pkg_resources
- if not hasattr(pkg_resources, '_distribute'):
- if not no_fake:
- _fake_setuptools()
- raise ImportError
- except ImportError:
- return _do_download(version, download_base, to_dir, download_delay)
- try:
- pkg_resources.require("distribute>=" + version)
- return
- except pkg_resources.VersionConflict:
- e = sys.exc_info()[1]
- if was_imported:
- sys.stderr.write(
- "The required version of distribute (>=%s) is not available,\n"
- "and can't be installed while this script is running. Please\n"
- "install a more recent version first, using\n"
- "'easy_install -U distribute'."
- "\n\n(Currently using %r)\n" % (version, e.args[0]))
- sys.exit(2)
- else:
- del pkg_resources, sys.modules['pkg_resources'] # reload ok
- return _do_download(version, download_base, to_dir,
- download_delay)
- except pkg_resources.DistributionNotFound:
- return _do_download(version, download_base, to_dir,
- download_delay)
- finally:
- if not no_fake:
- _create_fake_setuptools_pkg_info(to_dir)
-
-
-def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
- to_dir=os.curdir, delay=15):
- """Download distribute from a specified location and return its filename
-
- `version` should be a valid distribute version number that is available
- as an egg for download under the `download_base` URL (which should end
- with a '/'). `to_dir` is the directory where the egg will be downloaded.
- `delay` is the number of seconds to pause before an actual download
- attempt.
- """
- # making sure we use the absolute path
- to_dir = os.path.abspath(to_dir)
- try:
- from urllib.request import urlopen
- except ImportError:
- from urllib2 import urlopen
- tgz_name = "distribute-%s.tar.gz" % version
- url = download_base + tgz_name
- saveto = os.path.join(to_dir, tgz_name)
- src = dst = None
- if not os.path.exists(saveto): # Avoid repeated downloads
- try:
- log.warn("Downloading %s", url)
- src = urlopen(url)
- # Read/write all in one block, so we don't create a corrupt file
- # if the download is interrupted.
- data = src.read()
- dst = open(saveto, "wb")
- dst.write(data)
- finally:
- if src:
- src.close()
- if dst:
- dst.close()
- return os.path.realpath(saveto)
-
-
-def _no_sandbox(function):
- def __no_sandbox(*args, **kw):
- try:
- from setuptools.sandbox import DirectorySandbox
- if not hasattr(DirectorySandbox, '_old'):
- def violation(*args):
- pass
- DirectorySandbox._old = DirectorySandbox._violation
- DirectorySandbox._violation = violation
- patched = True
- else:
- patched = False
- except ImportError:
- patched = False
-
- try:
- return function(*args, **kw)
- finally:
- if patched:
- DirectorySandbox._violation = DirectorySandbox._old
- del DirectorySandbox._old
-
- return __no_sandbox
-
-
-def _patch_file(path, content):
- """Will backup the file then patch it"""
- f = open(path)
- existing_content = f.read()
- f.close()
- if existing_content == content:
- # already patched
- log.warn('Already patched.')
- return False
- log.warn('Patching...')
- _rename_path(path)
- f = open(path, 'w')
- try:
- f.write(content)
- finally:
- f.close()
- return True
-
-_patch_file = _no_sandbox(_patch_file)
-
-
-def _same_content(path, content):
- f = open(path)
- existing_content = f.read()
- f.close()
- return existing_content == content
-
-
-def _rename_path(path):
- new_name = path + '.OLD.%s' % time.time()
- log.warn('Renaming %s to %s', path, new_name)
- os.rename(path, new_name)
- return new_name
-
-
-def _remove_flat_installation(placeholder):
- if not os.path.isdir(placeholder):
- log.warn('Unkown installation at %s', placeholder)
- return False
- found = False
- for file in os.listdir(placeholder):
- if fnmatch.fnmatch(file, 'setuptools*.egg-info'):
- found = True
- break
- if not found:
- log.warn('Could not locate setuptools*.egg-info')
- return
-
- log.warn('Moving elements out of the way...')
- pkg_info = os.path.join(placeholder, file)
- if os.path.isdir(pkg_info):
- patched = _patch_egg_dir(pkg_info)
- else:
- patched = _patch_file(pkg_info, SETUPTOOLS_PKG_INFO)
-
- if not patched:
- log.warn('%s already patched.', pkg_info)
- return False
- # now let's move the files out of the way
- for element in ('setuptools', 'pkg_resources.py', 'site.py'):
- element = os.path.join(placeholder, element)
- if os.path.exists(element):
- _rename_path(element)
- else:
- log.warn('Could not find the %s element of the '
- 'Setuptools distribution', element)
- return True
-
-_remove_flat_installation = _no_sandbox(_remove_flat_installation)
-
-
-def _after_install(dist):
- log.warn('After install bootstrap.')
- placeholder = dist.get_command_obj('install').install_purelib
- _create_fake_setuptools_pkg_info(placeholder)
-
-
-def _create_fake_setuptools_pkg_info(placeholder):
- if not placeholder or not os.path.exists(placeholder):
- log.warn('Could not find the install location')
- return
- pyver = '%s.%s' % (sys.version_info[0], sys.version_info[1])
- setuptools_file = 'setuptools-%s-py%s.egg-info' % \
- (SETUPTOOLS_FAKED_VERSION, pyver)
- pkg_info = os.path.join(placeholder, setuptools_file)
- if os.path.exists(pkg_info):
- log.warn('%s already exists', pkg_info)
- return
-
- log.warn('Creating %s', pkg_info)
- try:
- f = open(pkg_info, 'w')
- except EnvironmentError:
- log.warn("Don't have permissions to write %s, skipping", pkg_info)
- return
- try:
- f.write(SETUPTOOLS_PKG_INFO)
- finally:
- f.close()
-
- pth_file = os.path.join(placeholder, 'setuptools.pth')
- log.warn('Creating %s', pth_file)
- f = open(pth_file, 'w')
- try:
- f.write(os.path.join(os.curdir, setuptools_file))
- finally:
- f.close()
-
-_create_fake_setuptools_pkg_info = _no_sandbox(
- _create_fake_setuptools_pkg_info
-)
-
-
-def _patch_egg_dir(path):
- # let's check if it's already patched
- pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
- if os.path.exists(pkg_info):
- if _same_content(pkg_info, SETUPTOOLS_PKG_INFO):
- log.warn('%s already patched.', pkg_info)
- return False
- _rename_path(path)
- os.mkdir(path)
- os.mkdir(os.path.join(path, 'EGG-INFO'))
- pkg_info = os.path.join(path, 'EGG-INFO', 'PKG-INFO')
- f = open(pkg_info, 'w')
- try:
- f.write(SETUPTOOLS_PKG_INFO)
- finally:
- f.close()
- return True
-
-_patch_egg_dir = _no_sandbox(_patch_egg_dir)
-
-
-def _before_install():
- log.warn('Before install bootstrap.')
- _fake_setuptools()
-
-
-def _under_prefix(location):
- if 'install' not in sys.argv:
- return True
- args = sys.argv[sys.argv.index('install') + 1:]
- for index, arg in enumerate(args):
- for option in ('--root', '--prefix'):
- if arg.startswith('%s=' % option):
- top_dir = arg.split('root=')[-1]
- return location.startswith(top_dir)
- elif arg == option:
- if len(args) > index:
- top_dir = args[index + 1]
- return location.startswith(top_dir)
- if arg == '--user' and USER_SITE is not None:
- return location.startswith(USER_SITE)
- return True
-
-
-def _fake_setuptools():
- log.warn('Scanning installed packages')
- try:
- import pkg_resources
- except ImportError:
- # we're cool
- log.warn('Setuptools or Distribute does not seem to be installed.')
- return
- ws = pkg_resources.working_set
- try:
- setuptools_dist = ws.find(
- pkg_resources.Requirement.parse('setuptools', replacement=False)
- )
- except TypeError:
- # old distribute API
- setuptools_dist = ws.find(
- pkg_resources.Requirement.parse('setuptools')
- )
-
- if setuptools_dist is None:
- log.warn('No setuptools distribution found')
- return
- # detecting if it was already faked
- setuptools_location = setuptools_dist.location
- log.warn('Setuptools installation detected at %s', setuptools_location)
-
- # if --root or --preix was provided, and if
- # setuptools is not located in them, we don't patch it
- if not _under_prefix(setuptools_location):
- log.warn('Not patching, --root or --prefix is installing Distribute'
- ' in another location')
- return
-
- # let's see if its an egg
- if not setuptools_location.endswith('.egg'):
- log.warn('Non-egg installation')
- res = _remove_flat_installation(setuptools_location)
- if not res:
- return
- else:
- log.warn('Egg installation')
- pkg_info = os.path.join(setuptools_location, 'EGG-INFO', 'PKG-INFO')
- if (os.path.exists(pkg_info) and
- _same_content(pkg_info, SETUPTOOLS_PKG_INFO)):
- log.warn('Already patched.')
- return
- log.warn('Patching...')
- # let's create a fake egg replacing setuptools one
- res = _patch_egg_dir(setuptools_location)
- if not res:
- return
- log.warn('Patching complete.')
- _relaunch()
-
-
-def _relaunch():
- log.warn('Relaunching...')
- # we have to relaunch the process
- # pip marker to avoid a relaunch bug
- _cmd1 = ['-c', 'install', '--single-version-externally-managed']
- _cmd2 = ['-c', 'install', '--record']
- if sys.argv[:3] == _cmd1 or sys.argv[:3] == _cmd2:
- sys.argv[0] = 'setup.py'
- args = [sys.executable] + sys.argv
- sys.exit(subprocess.call(args))
-
-
-def _extractall(self, path=".", members=None):
- """Extract all members from the archive to the current working
- directory and set owner, modification time and permissions on
- directories afterwards. `path' specifies a different directory
- to extract to. `members' is optional and must be a subset of the
- list returned by getmembers().
- """
- import copy
- import operator
- from tarfile import ExtractError
- directories = []
-
- if members is None:
- members = self
-
- for tarinfo in members:
- if tarinfo.isdir():
- # Extract directories with a safe mode.
- directories.append(tarinfo)
- tarinfo = copy.copy(tarinfo)
- tarinfo.mode = 448 # decimal for oct 0700
- self.extract(tarinfo, path)
-
- # Reverse sort directories.
- if sys.version_info < (2, 4):
- def sorter(dir1, dir2):
- return cmp(dir1.name, dir2.name)
- directories.sort(sorter)
- directories.reverse()
- else:
- directories.sort(key=operator.attrgetter('name'), reverse=True)
-
- # Set correct owner, mtime and filemode on directories.
- for tarinfo in directories:
- dirpath = os.path.join(path, tarinfo.name)
- try:
- self.chown(tarinfo, dirpath)
- self.utime(tarinfo, dirpath)
- self.chmod(tarinfo, dirpath)
- except ExtractError:
- e = sys.exc_info()[1]
- if self.errorlevel > 1:
- raise
- else:
- self._dbg(1, "tarfile: %s" % e)
-
-
-def _build_install_args(options):
- """
- Build the arguments to 'python setup.py install' on the distribute package
- """
- install_args = []
- if options.user_install:
- if sys.version_info < (2, 6):
- log.warn("--user requires Python 2.6 or later")
- raise SystemExit(1)
- install_args.append('--user')
- return install_args
-
-def _parse_args():
- """
- Parse the command line for options
- """
- parser = optparse.OptionParser()
- parser.add_option(
- '--user', dest='user_install', action='store_true', default=False,
- help='install in user site package (requires Python 2.6 or later)')
- parser.add_option(
- '--download-base', dest='download_base', metavar="URL",
- default=DEFAULT_URL,
- help='alternative URL from where to download the distribute package')
- options, args = parser.parse_args()
- # positional arguments are ignored
- return options
-
-def main(version=DEFAULT_VERSION):
- """Install or upgrade setuptools and EasyInstall"""
- options = _parse_args()
- tarball = download_setuptools(download_base=options.download_base)
- return _install(tarball, _build_install_args(options))
-
-if __name__ == '__main__':
- sys.exit(main())
diff --git a/doc/faq.rst b/doc/faq.rst
index cd4b4c5..a674e8f 100644
--- a/doc/faq.rst
+++ b/doc/faq.rst
@@ -38,3 +38,71 @@ avoid this, use::
This will iterate through reads as they appear in the file.
+Weirdness with spliced reads in samfile.pileup(chr,start,end) given spliced alignments from an RNA-seq bam file
+===============================================================================================================
+
+Spliced reads are reported within samfile.pileup. To ignore these
+in your analysis, test the flags ``is_del == True and indel=0``
+in the :class:`~.PileupRead` object.
+
+I can't edit quality scores in place
+====================================
+
+Editing reads in-place generally works, though there is some
+quirk to be aware of. Assigning to AlignedRead.seq will invalidate
+any quality scores in AlignedRead.qual. The reason is that samtools
+manages the memory of the sequence and quality scores together
+and thus requires them to always be of the same length or 0.
+
+Thus, to in-place edit the sequence and quality scores, copies of
+the quality scores need to be taken. Consider trimming for example::
+
+ q = read.qual
+ read.seq = read.seq[5:10]
+ read.qual = q[5:10]
+
+
+Why is there no SNPCaller class anymore?
+=========================================
+
+SNP calling is highly complex and heavily parameterized. There was a
+danger that the pysam implementations might show different behaviour from the
+samtools implementation, which would have caused a lot of confusion.
+
+The best way to use samtools SNP calling from python is to use the
+:meth:`pysam.mpileup` command and parse the output directly.
+
+I get an error 'PileupProxy accessed after iterator finished'
+=============================================================
+
+Pysam works by providing proxy objects to objects defined within
+the C-samtools package. Thus, some attention must be paid at the
+lifetime of objects. The following to code snippets will cause an
+error::
+
+ s = Samfile( 'ex1.bam' )
+ for p in s.pileup('chr1', 1000,1010):
+ pass
+
+ for pp in p.pileups:
+ print pp
+
+The iteration has finished, thus the contents of p are invalid. A
+variation of this::
+
+ p = Samfile( 'ex1.bam' ).pileup( 'chr1', 1000, 1010).next()
+ for pp in p.pileups:
+ print pp
+
+Again, the iteration finishes as the temporary iterator created
+by pileup goes out of scope. The solution is to keep a handle
+to the iterator that remains alive::
+
+ i = Samfile( 'ex1.bam' ).pileup( 'chr1', 1000, 1010)
+ p = i.next()
+ for pp in p.pileups:
+ print pp
+
+
+
+
diff --git a/doc/release.rst b/doc/release.rst
index 58a58aa..3413c1f 100644
--- a/doc/release.rst
+++ b/doc/release.rst
@@ -2,6 +2,14 @@
Release notes
=============
+Release 0.7.6
+=============
+
+ * added inferred_length property
+ * issue 122: MACOSX getline missing, now it works?
+ * seq and qual can be set None
+ * added Fastqfile
+
Release 0.7.5
=============
diff --git a/doc/usage.rst b/doc/usage.rst
index e438015..a3bc1c9 100644
--- a/doc/usage.rst
+++ b/doc/usage.rst
@@ -267,11 +267,8 @@ and consists of three files:
return Extension(name = modname,
sources=[pyxfilename],
extra_link_args=[ os.path.join( dirname, "csamtools.so")],
- include_dirs = ['../samtools',
- '../pysam',
- ] )
-
-
+ include_dirs = pysam.get_include(),
+ define_macros = pysam.get_defines() )
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
diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO
index 8d8f7c5..dbb2aed 100644
--- a/pysam.egg-info/PKG-INFO
+++ b/pysam.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.5
+Version: 0.7.6
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 dcf1ced..49dc1f3 100644
--- a/pysam.egg-info/SOURCES.txt
+++ b/pysam.egg-info/SOURCES.txt
@@ -3,7 +3,6 @@ INSTALL
KNOWN_BUGS
MANIFEST.in
THANKS
-distribute_setup.py
pysam.py
setup.cfg
setup.py
diff --git a/pysam/TabProxies.c b/pysam/TabProxies.c
index 7c87ba2..099e19e 100644
--- a/pysam/TabProxies.c
+++ b/pysam/TabProxies.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
+/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -342,8 +342,8 @@ 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_10TabProxies_VCFProxy;
struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
/* "pysam/TabProxies.pxd":41
* ctypedef int uint64_t
@@ -393,31 +393,31 @@ struct __pyx_obj_5pysam_10TabProxies_BedProxy {
};
-/* "pysam/TabProxies.pxd":83
+/* "pysam/TabProxies.pxd":60
* cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
-/* "pysam/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_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_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;
};
@@ -454,32 +454,32 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
-/* "pysam/TabProxies.pyx":656
- * TupleProxy._setindex(self, idx, str(value) )
+/* "pysam/TabProxies.pyx":590
+ * return f( self.fields[idx] )
*
- * cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
- * '''Proxy class for access to VCF fields.
+ * cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
+ * '''Proxy class for access to Bed fields.
*
*/
-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;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
-/* "pysam/TabProxies.pyx":590
- * return f( self.fields[idx] )
+/* "pysam/TabProxies.pyx":656
+ * TupleProxy._setindex(self, idx, str(value) )
*
- * cdef class BedProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
- * '''Proxy class for access to Bed fields.
+ * cdef class VCFProxy( NamedTupleProxy ): # <<<<<<<<<<<<<<
+ * '''Proxy class for access to VCF fields.
*
*/
-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;
/* "pysam/TabProxies.pyx":326
diff --git a/pysam/TabProxies.pyx b/pysam/TabProxies.pyx
index 396445b..b83e58b 100644
--- a/pysam/TabProxies.pyx
+++ b/pysam/TabProxies.pyx
@@ -169,7 +169,7 @@ cdef class TupleProxy:
cdef char * old_pos
cdef int field
cdef int max_fields, x
-
+
assert strlen(buffer) == nbytes
if buffer[nbytes] != 0:
diff --git a/pysam/csamtools.c b/pysam/csamtools.c
index 99a0350..66c8778 100644
--- a/pysam/csamtools.c
+++ b/pysam/csamtools.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
+/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -347,30 +347,32 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-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_IteratorRowAllRefs;
+struct __pyx_obj_5pysam_9csamtools_SNPCall;
+struct __pyx_obj_5pysam_9csamtools_AlignedRead;
+struct __pyx_obj_5pysam_9csamtools_Fastqfile;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection;
+struct __pyx_obj_5pysam_9csamtools_IndexedReads;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowAll;
struct __pyx_obj_5pysam_9csamtools_IteratorColumn;
+struct __pyx_obj_5pysam_9csamtools_IteratorColumnRegion;
+struct __pyx_obj_5pysam_9csamtools_Samfile;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr;
struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs;
struct __pyx_obj_5pysam_9csamtools_Fastafile;
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr;
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_obj_5pysam_9csamtools_PileupRead;
+struct __pyx_obj_5pysam_9csamtools_FastqProxy;
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion;
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
+/* "pysam/csamtools.pxd":414
* # Utility types
*
* ctypedef struct __iterdata: # <<<<<<<<<<<<<<
@@ -386,7 +388,7 @@ struct __pyx_t_5pysam_9csamtools___iterdata {
int seq_len;
};
-/* "pysam/csamtools.pxd":523
+/* "pysam/csamtools.pxd":554
* cdef char * getSequence( self )
* cdef setMask( self, mask )
* cdef setupIteratorData( self, # <<<<<<<<<<<<<<
@@ -398,7 +400,7 @@ struct __pyx_opt_args_5pysam_9csamtools_14IteratorColumn_setupIteratorData {
int reopen;
};
-/* "pysam/csamtools.pyx":518
+/* "pysam/csamtools.pyx":644
* counter[0] += 1;
*
* ctypedef struct MateData: # <<<<<<<<<<<<<<
@@ -411,113 +413,133 @@ struct __pyx_t_5pysam_9csamtools_MateData {
uint32_t flag;
};
-/* "pysam/csamtools.pxd":455
- * cdef int n_pu
+/* "pysam/csamtools.pxd":495
+ * cdef uint32_t _is_tail
+ *
+ * cdef class IteratorRow: # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class PileupRead: # <<<<<<<<<<<<<<
- * cdef AlignedRead _alignment
- * cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_PileupRead {
+struct __pyx_obj_5pysam_9csamtools_IteratorRow {
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) )
+/* "pysam/csamtools.pxd":518
+ * cdef int cnext(self)
+ *
+ * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef int tid
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
+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;
+};
+
+
+/* "pysam/csamtools.pyx":3467
+ * return retval, out_stderr, out_stdout
+ *
+ * cdef class SNPCall: # <<<<<<<<<<<<<<
+ * '''the results of a SNP call.'''
+ * cdef int _tid
+ */
+struct __pyx_obj_5pysam_9csamtools_SNPCall {
PyObject_HEAD
- PyObject *__pyx_v_x;
- PyObject *__pyx_v_y;
- PyObject *__pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ int _tid;
+ int _pos;
+ char _reference_base;
+ char _genotype;
+ int _consensus_quality;
+ int _snp_quality;
+ int _rms_mapping_quality;
+ int _coverage;
};
-/* "pysam/csamtools.pxd":464
- * cdef uint32_t _is_tail
+/* "pysam/csamtools.pxd":446
+ * cdef int cnext(self)
*
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * pass
+ * cdef class AlignedRead: # <<<<<<<<<<<<<<
*
+ * # object that this AlignedRead represents
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRow {
+struct __pyx_obj_5pysam_9csamtools_AlignedRead {
PyObject_HEAD
+ bam1_t *_delegate;
};
-/* "pysam/csamtools.pxd":467
- * pass
+/* "pysam/csamtools.pxd":438
+ * cdef kseq_t * _delegate
*
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam_iter_t iter # iterator state object
- * cdef bam1_t * b
+ * cdef class Fastqfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * cdef gzFile fastqfile
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
+struct __pyx_obj_5pysam_9csamtools_Fastqfile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtab;
+ char *_filename;
+ gzFile fastqfile;
+ kseq_t *entry;
+};
+
+
+/* "pysam/csamtools.pxd":523
+ * cdef IteratorRowRegion rowiter
+ *
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef int current_pos
+ */
+struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
- bam_iter_t iter;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtab;
bam1_t *b;
- int retval;
- struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
+ int current_pos;
samfile_t *fp;
+ PyObject *positions;
int owns_samfile;
};
-/* "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])" )
+/* "pysam/csamtools.pxd":570
+ * pass
*
+ * cdef class IndexedReads: # <<<<<<<<<<<<<<
+ * cdef Samfile samfile
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
+struct __pyx_obj_5pysam_9csamtools_IndexedReads {
PyObject_HEAD
- 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_Samfile *samfile;
+ samfile_t *fp;
+ PyObject *index;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":420
- * cdef bam1_t * _delegate
+/* "pysam/csamtools.pxd":511
+ * cdef int cnext(self)
*
- * cdef class Samfile: # <<<<<<<<<<<<<<
- * cdef char * _filename
- * # pointer to samfile
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam1_t * b
+ * cdef samfile_t * fp
*/
-struct __pyx_obj_5pysam_9csamtools_Samfile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtab;
- char *_filename;
- samfile_t *samfile;
- bam_index_t *index;
- int isbam;
- int isstream;
- int isremote;
+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;
- char *mode;
- int64_t start_offset;
+ samfile_t *fp;
+ int owns_samfile;
};
-/* "pysam/csamtools.pxd":504
+/* "pysam/csamtools.pxd":535
* cdef int cnext(self)
*
* cdef class IteratorColumn: # <<<<<<<<<<<<<<
@@ -542,7 +564,61 @@ struct __pyx_obj_5pysam_9csamtools_IteratorColumn {
};
-/* "pysam/csamtools.pxd":536
+/* "pysam/csamtools.pxd":562
+ * 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":451
+ * cdef bam1_t * _delegate
+ *
+ * cdef class Samfile: # <<<<<<<<<<<<<<
+ * cdef char * _filename
+ * # pointer to samfile
+ */
+struct __pyx_obj_5pysam_9csamtools_Samfile {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_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;
+};
+
+
+/* "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])" )
+ *
+ */
+struct __pyx_obj_5pysam_9csamtools___pyx_scope_struct_1_genexpr {
+ PyObject_HEAD
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "pysam/csamtools.pxd":567
* cdef int truncate
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
@@ -554,7 +630,7 @@ struct __pyx_obj_5pysam_9csamtools_IteratorColumnAllRefs {
};
-/* "pysam/csamtools.pxd":408
+/* "pysam/csamtools.pxd":428
* # Note: need to declare all C fields and methods here
* #
* cdef class Fastafile: # <<<<<<<<<<<<<<
@@ -569,7 +645,24 @@ struct __pyx_obj_5pysam_9csamtools_Fastafile {
};
-/* "pysam/csamtools.pxd":449
+/* "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_obj_5pysam_9csamtools___pyx_scope_struct__genexpr {
+ PyObject_HEAD
+ PyObject *__pyx_v_x;
+ PyObject *__pyx_v_y;
+ PyObject *__pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
+};
+
+
+/* "pysam/csamtools.pxd":480
* cdef char * _getrname( self, int tid )
*
* cdef class PileupProxy: # <<<<<<<<<<<<<<
@@ -585,154 +678,91 @@ struct __pyx_obj_5pysam_9csamtools_PileupProxy {
};
-/* "pysam/csamtools.pxd":539
- * pass
+/* "pysam/csamtools.pxd":486
+ * cdef int n_pu
*
- * cdef class IndexedReads: # <<<<<<<<<<<<<<
- * cdef Samfile samfile
- * cdef samfile_t * fp
+ * cdef class PileupRead: # <<<<<<<<<<<<<<
+ * cdef AlignedRead _alignment
+ * cdef int32_t _qpos
*/
-struct __pyx_obj_5pysam_9csamtools_IndexedReads {
+struct __pyx_obj_5pysam_9csamtools_PileupRead {
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;
- samfile_t *fp;
- int owns_samfile;
-};
-
-
-/* "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_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;
+ 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.pxd":415
+/* "pysam/csamtools.pxd":435
* cdef char * _fetch( self, char * reference, int start, int end, int * length )
*
- * cdef class AlignedRead: # <<<<<<<<<<<<<<
+ * cdef class FastqProxy: # <<<<<<<<<<<<<<
+ * cdef kseq_t * _delegate
*
- * # object that this AlignedRead represents
*/
-struct __pyx_obj_5pysam_9csamtools_AlignedRead {
+struct __pyx_obj_5pysam_9csamtools_FastqProxy {
PyObject_HEAD
- bam1_t *_delegate;
+ kseq_t *_delegate;
};
-/* "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_5pysam_9csamtools_SNPCall {
- PyObject_HEAD
- int _tid;
- int _pos;
- char _reference_base;
- char _genotype;
- int _consensus_quality;
- int _snp_quality;
- int _rms_mapping_quality;
- int _coverage;
-};
-
-
-/* "pysam/csamtools.pxd":492
- * cdef IteratorRowRegion rowiter
+/* "pysam/csamtools.pxd":498
+ * pass
*
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * b
- * cdef int current_pos
+ * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
+ * cdef bam_iter_t iter # iterator state object
+ * cdef bam1_t * b
*/
-struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection {
+struct __pyx_obj_5pysam_9csamtools_IteratorRowRegion {
struct __pyx_obj_5pysam_9csamtools_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtab;
+ bam_iter_t iter;
bam1_t *b;
- int current_pos;
+ int retval;
+ struct __pyx_obj_5pysam_9csamtools_Samfile *samfile;
samfile_t *fp;
- PyObject *positions;
int owns_samfile;
};
-/* "pysam/csamtools.pyx":545
+/* "pysam/csamtools.pyx":1921
+ * return ret
*
+ * cdef class IteratorColumn: # <<<<<<<<<<<<<<
+ * '''abstract base class for iterators over columns.
*
- * 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_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);
+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_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
-/* "pysam/csamtools.pyx":1545
- * if self.owns_samfile: samclose( self.fp )
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * """*(Samfile samfile, int reopen = True)*
+/* "pysam/csamtools.pyx":2083
+ * self.iterdata.seq = NULL
*
+ * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
+ * '''iterates over a region only.
+ * '''
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowAll *);
+struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion {
+ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
-/* "pysam/csamtools.pyx":1466
+/* "pysam/csamtools.pyx":1597
*
*
* cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
@@ -747,39 +777,51 @@ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion {
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion;
-/* "pysam/csamtools.pyx":1771
- * return ret
+/* "pysam/csamtools.pyx":1792
+ * raise StopIteration
*
- * cdef class IteratorColumn: # <<<<<<<<<<<<<<
- * '''abstract base class for iterators over columns.
+ * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile)*
*
*/
-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 *);
+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_5pysam_9csamtools_IteratorColumn *__pyx_vtabptr_5pysam_9csamtools_IteratorColumn;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
-/* "pysam/csamtools.pyx":1936
- * self.iterdata.seq = NULL
+/* "pysam/csamtools.pyx":382
+ * ## Public methods
+ * ######################################################################
+ * cdef class Fastafile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
*
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * '''iterates over a region only.
- * '''
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion {
- struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumn __pyx_base;
+struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
+ char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
};
-static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnRegion *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
+
+
+/* "pysam/csamtools.pyx":546
+ * else: return None
+ *
+ * cdef class Fastqfile: # <<<<<<<<<<<<<<
+ * '''*(filename)*
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile {
+ kseq_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *);
+ int (*cnext)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *);
+};
+static struct __pyx_vtabstruct_5pysam_9csamtools_Fastqfile *__pyx_vtabptr_5pysam_9csamtools_Fastqfile;
-/* "pysam/csamtools.pyx":1973
+/* "pysam/csamtools.pyx":2120
* self.n_plp )
*
* cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
@@ -793,33 +835,37 @@ struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs {
static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorColumnAllRefs *__pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs;
-/* "pysam/csamtools.pyx":1646
- * raise StopIteration
+/* "pysam/csamtools.pyx":671
*
- * 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_5pysam_9csamtools_IteratorRowSelection {
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
- int (*cnext)(struct __pyx_obj_5pysam_9csamtools_IteratorRowSelection *);
+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_IteratorRowSelection *__pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection;
+static struct __pyx_vtabstruct_5pysam_9csamtools_Samfile *__pyx_vtabptr_5pysam_9csamtools_Samfile;
-/* "pysam/csamtools.pyx":375
- * ## Public methods
- * ######################################################################
- * cdef class Fastafile: # <<<<<<<<<<<<<<
- * '''*(filename)*
+/* "pysam/csamtools.pyx":1681
+ * if self.owns_samfile: samclose( self.fp )
+ *
+ * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
+ * """*(Samfile samfile, int reopen = True)*
*
*/
-struct __pyx_vtabstruct_5pysam_9csamtools_Fastafile {
- char *(*_fetch)(struct __pyx_obj_5pysam_9csamtools_Fastafile *, char *, int, int, int *);
+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_5pysam_9csamtools_Fastafile *__pyx_vtabptr_5pysam_9csamtools_Fastafile;
+static struct __pyx_vtabstruct_5pysam_9csamtools_IteratorRowAll *__pyx_vtabptr_5pysam_9csamtools_IteratorRowAll;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -1441,6 +1487,8 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'pysam.csamtools' */
static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastafile = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_FastqProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_9csamtools_Fastqfile = 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;
@@ -1470,6 +1518,7 @@ 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_makeFastqProxy(kseq_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*/
@@ -1493,6 +1542,7 @@ static PyObject *__pyx_builtin_ord;
static PyObject *__pyx_builtin_map;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_IOError;
+static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_OverflowError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_OSError;
@@ -1500,7 +1550,6 @@ static PyObject *__pyx_builtin_AttributeError;
static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_sorted;
static PyObject *__pyx_builtin_KeyError;
-static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_min;
static PyObject *__pyx_builtin_max;
static PyObject *__pyx_builtin_chr;
@@ -1524,6 +1573,20 @@ static PyObject *__pyx_pf_5pysam_9csamtools_9Fastafile_8close(struct __pyx_obj_5
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_10FastqProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_4name___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_8sequence___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_7comment___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_10FastqProxy_7quality___get__(struct __pyx_obj_5pysam_9csamtools_FastqProxy *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_9csamtools_9Fastqfile___cinit__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_2_isOpen(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_4_open(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_6close(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_9csamtools_9Fastqfile_8__dealloc__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_8filename___get__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_10__iter__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_12__next__(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_9csamtools_9Fastqfile_14test(struct __pyx_obj_5pysam_9csamtools_Fastqfile *__pyx_v_self); /* 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 */
@@ -1652,6 +1715,7 @@ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_9is_qcfail_2__set__(struct _
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_15inferred_length___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 */
@@ -1704,42 +1768,45 @@ static char __pyx_k_16[] = "";
static char __pyx_k_17[] = "start out of range (%i)";
static char __pyx_k_18[] = "end out of range (%i)";
static char __pyx_k_19[] = "%s:%i-%i";
-static char __pyx_k_24[] = "invalid file opening mode `%s`";
-static char __pyx_k_26[] = "-";
-static char __pyx_k_27[] = "http:";
-static char __pyx_k_28[] = "ftp:";
-static char __pyx_k_29[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
-static char __pyx_k_30[] = "unequal names and lengths of reference sequences";
-static char __pyx_k_31[] = "@SQ\tSN:%s\tLN:%s\n";
-static char __pyx_k_32[] = "file `%s` not found";
-static char __pyx_k_33[] = "could not open file (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_34[] = "file does not have valid header (mode='%s') - is it BAM format?";
-static char __pyx_k_35[] = "file does not have valid header (mode='%s') - is it SAM format?";
-static char __pyx_k_36[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
-static char __pyx_k_37[] = ".bai";
-static char __pyx_k_38[] = "error while opening index `%s` ";
-static char __pyx_k_41[] = "tid %i out of range 0<=tid<%i";
-static char __pyx_k_43[] = "[:-]";
-static char __pyx_k_45[] = "invalid reference `%s`";
-static char __pyx_k_46[] = "invalid coordinates: start (%i) > end (%i)";
-static char __pyx_k_48[] = "seek only available in bam files";
-static char __pyx_k_50[] = "seek no available in streams";
-static char __pyx_k_56[] = "fetch called on bamfile without index";
-static char __pyx_k_58[] = "callback functionality requires a region/reference";
-static char __pyx_k_60[] = "no index available for fetch";
-static char __pyx_k_62[] = "fetching by region is not available for sam files";
-static char __pyx_k_64[] = "callback not implemented yet";
-static char __pyx_k_66[] = "fetch called for samfile without header";
-static char __pyx_k_69[] = "read %s: is unpaired";
-static char __pyx_k_70[] = "mate %s: is unmapped";
-static char __pyx_k_71[] = "mate not found";
-static char __pyx_k_76[] = "counting functionality requires a region/reference";
-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_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_21[] = "No such file or directory: %s";
+static char __pyx_k_24[] = "name: %s\n";
+static char __pyx_k_25[] = "comment: %s\n";
+static char __pyx_k_26[] = "seq: %s\n";
+static char __pyx_k_27[] = "qual: %s\n";
+static char __pyx_k_28[] = "return value: %d\n";
+static char __pyx_k_32[] = "invalid file opening mode `%s`";
+static char __pyx_k_34[] = "-";
+static char __pyx_k_35[] = "http:";
+static char __pyx_k_36[] = "ftp:";
+static char __pyx_k_37[] = "either supply options `template`, `header` or both `referencenames` and `referencelengths` for writing";
+static char __pyx_k_38[] = "unequal names and lengths of reference sequences";
+static char __pyx_k_39[] = "@SQ\tSN:%s\tLN:%s\n";
+static char __pyx_k_40[] = "file `%s` not found";
+static char __pyx_k_41[] = "could not open file (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_42[] = "file does not have valid header (mode='%s') - is it BAM format?";
+static char __pyx_k_43[] = "file does not have valid header (mode='%s') - is it SAM format?";
+static char __pyx_k_44[] = "file header is empty (mode='%s') - is it SAM/BAM format?";
+static char __pyx_k_45[] = ".bai";
+static char __pyx_k_46[] = "error while opening index `%s` ";
+static char __pyx_k_49[] = "tid %i out of range 0<=tid<%i";
+static char __pyx_k_51[] = "[:-]";
+static char __pyx_k_53[] = "invalid reference `%s`";
+static char __pyx_k_54[] = "invalid coordinates: start (%i) > end (%i)";
+static char __pyx_k_56[] = "seek only available in bam files";
+static char __pyx_k_58[] = "seek no available in streams";
+static char __pyx_k_64[] = "fetch called on bamfile without index";
+static char __pyx_k_66[] = "callback functionality requires a region/reference";
+static char __pyx_k_68[] = "no index available for fetch";
+static char __pyx_k_70[] = "fetching by region is not available for sam files";
+static char __pyx_k_72[] = "callback not implemented yet";
+static char __pyx_k_74[] = "fetch called for samfile without header";
+static char __pyx_k_77[] = "read %s: is unpaired";
+static char __pyx_k_78[] = "mate %s: is unmapped";
+static char __pyx_k_79[] = "mate not found";
+static char __pyx_k_84[] = "counting functionality requires a region/reference";
+static char __pyx_k_87[] = "count for a region is not available for sam files";
+static char __pyx_k_90[] = "no index available for pileup";
+static char __pyx_k_93[] = "pileup of samfiles not implemented yet";
static char __pyx_k__A[] = "A";
static char __pyx_k__B[] = "B";
static char __pyx_k__C[] = "C";
@@ -1760,147 +1827,151 @@ 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_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_100[] = "Samfile.mapped only available in bam files";
+static char __pyx_k_102[] = "mapping information not recorded in index or index not available";
+static char __pyx_k_105[] = "Samfile.unmapped only available in bam files";
+static char __pyx_k_110[] = "@";
+static char __pyx_k_112[] = "header line without '@': '%s'";
+static char __pyx_k_114[] = "header line with invalid type '%s': '%s'";
+static char __pyx_k_115[] = ":";
+static char __pyx_k_116[] = "malformatted header: no ':' in field";
+static char __pyx_k_119[] = "unknown field code '%s' in record '%s'";
+static char __pyx_k_120[] = "multiple '%s' lines are not permitted";
+static char __pyx_k_121[] = "@%s";
+static char __pyx_k_122[] = "%s:%s";
+static char __pyx_k_123[] = "invalid type for record %s: %s, expected %s";
+static char __pyx_k_125[] = "incomplete sequence information in '%s'";
+static char __pyx_k_128[] = "can not iterate over samfile without header";
+static char __pyx_k_131[] = "no index available for iteration";
+static char __pyx_k_137[] = "can only use this iterator on bam files";
+static char __pyx_k_138[] = "reference sequence for '%s' (tid=%i) not found";
+static char __pyx_k_139[] = "unknown stepper option `%s` in IteratorColumn";
+static char __pyx_k_141[] = "error during iteration";
+static char __pyx_k_144[] = "Invalid clipping in CIGAR string";
+static char __pyx_k_147[] = "%i%c";
+static char __pyx_k_148[] = "quality and sequence mismatch: %i != %i";
+static char __pyx_k_149[] = "%c";
+static char __pyx_k_150[] = "<";
+static char __pyx_k_152[] = "integer %i out of range of BAM/SAM specification";
+static char __pyx_k_153[] = "2sccI%i%s";
+static char __pyx_k_157[] = "2sc%is";
+static char __pyx_k_159[] = "create_string_buffer";
+static char __pyx_k_160[] = "tag '%s' not present";
+static char __pyx_k_161[] = "unknown auxilliary type '%s'";
+static char __pyx_k_162[] = "Contig index";
+static char __pyx_k_163[] = "Mapped position on contig";
+static char __pyx_k_164[] = "Contig index for mate pair";
+static char __pyx_k_165[] = "Position of mate pair";
+static char __pyx_k_166[] = "Insert size";
+static char __pyx_k_167[] = "Binary flag";
+static char __pyx_k_168[] = "Count of cigar entries";
+static char __pyx_k_169[] = "Cigar entries";
+static char __pyx_k_170[] = "Mapping quality";
+static char __pyx_k_171[] = "Bam index bin number";
+static char __pyx_k_172[] = "Length of query name";
+static char __pyx_k_173[] = "Query name";
+static char __pyx_k_174[] = "Length of query sequence";
+static char __pyx_k_175[] = "Query sequence";
+static char __pyx_k_176[] = "Quality scores";
+static char __pyx_k_177[] = "Length of auxilary data";
+static char __pyx_k_178[] = "Maximum data length";
+static char __pyx_k_179[] = "Current data length";
+static char __pyx_k_180[] = "%-30s %-10s= %s";
+static char __pyx_k_181[] = "(";
+static char __pyx_k_182[] = ")";
+static char __pyx_k_183[] = "This class cannot be instantiated from Python";
+static char __pyx_k_185[] = "PileupProxy accessed after iterator finished";
+static char __pyx_k_189[] = "No such file or directory: '%s'";
+static char __pyx_k_190[] = "-o";
+static char __pyx_k_191[] = "option -o is forbidden in samtools view";
+static char __pyx_k_197[] = "can only IndexReads on bam files";
+static char __pyx_k_198[] = "read %s not found";
+static char __pyx_k_199[] = "number of :term:`filename` associated with this object.";
+static char __pyx_k_200[] = "the query name (None if not present)";
+static char __pyx_k_201[] = "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_202[] = "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_203[] = "read sequence bases, including :term:`soft clipped` bases \n (None if not present).\n\n In Python 3, this property is of type bytes and assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n Note that assigning to seq will invalidate any quality scores.\n Thus, to in-place edit the sequence and quality scores, copies of\n the quality scores need to be taken. [...]
+static char __pyx_k_204[] = "read sequence base qualities, including :term:`soft\n clipped` bases (None if not present).\n\n In Python 3, this property is of type bytes and assigning a\n unicode string to it consisting of ASCII characters only will\n work, but is inefficient.\n\n Note that to set quality scores the sequence has to be set\n previously as this will determine the permitted length of\n the quality score array.\n\n This [...]
+static char __pyx_k_205[] = "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_206[] = "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_207[] = "start index of the aligned query portion of the sequence (0-based, inclusive)";
+static char __pyx_k_208[] = "end index of the aligned query portion of the sequence (0-based, exclusive)";
+static char __pyx_k_209[] = "Length of the aligned query sequence";
+static char __pyx_k_210[] = "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_211[] = "properties flag";
+static char __pyx_k_212[] = "\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_213[] = "\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_214[] = "0-based leftmost coordinate";
+static char __pyx_k_215[] = "properties bin";
+static char __pyx_k_216[] = "length of the read (read only). Returns 0 if not given.";
+static char __pyx_k_217[] = "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_218[] = "aligned length of the read on the reference genome. Returns None if\n not available.";
+static char __pyx_k_219[] = "mapping quality";
+static char __pyx_k_220[] = "the :term:`reference` id of the mate\n deprecated, use RNEXT instead.\n ";
+static char __pyx_k_221[] = "the :term:`reference` id of the mate ";
+static char __pyx_k_222[] = "the position of the mate\n deprecated, use PNEXT instead.";
+static char __pyx_k_223[] = "the position of the mate";
+static char __pyx_k_224[] = "the insert size\n deprecated: use tlen instead";
+static char __pyx_k_225[] = "the insert size";
+static char __pyx_k_226[] = "true if read is paired in sequencing";
+static char __pyx_k_227[] = "true if read is mapped in a proper pair";
+static char __pyx_k_228[] = "true if read itself is unmapped";
+static char __pyx_k_229[] = "true if the mate is unmapped";
+static char __pyx_k_230[] = "true if read is mapped to reverse strand";
+static char __pyx_k_231[] = "true is read is mapped to reverse strand";
+static char __pyx_k_232[] = "true if this is read1";
+static char __pyx_k_233[] = "true if this is read2";
+static char __pyx_k_234[] = "true if not primary alignment";
+static char __pyx_k_235[] = "true if QC failure";
+static char __pyx_k_236[] = "true if optical or PCR duplicate";
+static char __pyx_k_237[] = "a list of reference positions that this read aligns to.";
+static char __pyx_k_238[] = "inferred read length from CIGAR string.\n\n Returns 0 if CIGAR string is not present.\n ";
+static char __pyx_k_239[] = "a list of aligned read and reference positions.\n\n Unaligned position are marked by None.\n ";
+static char __pyx_k_240[] = "number of :term:`reference` sequences in the file.";
+static char __pyx_k_241[] = "tuple with the names of :term:`reference` sequences.";
+static char __pyx_k_242[] = "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_243[] = "total number of mapped reads in file.\n ";
+static char __pyx_k_244[] = "total number of unmapped reads in file.\n ";
+static char __pyx_k_245[] = "full contents of the :term:`sam file` header as a string.";
+static char __pyx_k_246[] = "header information within the :term:`sam file`. The records and fields are returned as\n a two-level dictionary.\n ";
+static char __pyx_k_247[] = "the chromosome ID as is defined in the header";
+static char __pyx_k_248[] = "number of reads mapping to this column.";
+static char __pyx_k_249[] = "list of reads (:class:`pysam.PileupRead`) aligned to this column";
+static char __pyx_k_250[] = "a :class:`pysam.AlignedRead` object of the aligned read";
+static char __pyx_k_251[] = "position of the read base at the pileup site, 0-based";
+static char __pyx_k_252[] = "indel length; 0 for no indel, positive for ins and negative for del";
+static char __pyx_k_253[] = "1 iff the base on the padded read is a deletion";
+static char __pyx_k_254[] = "current sequence length.";
+static char __pyx_k_255[] = "nucleotide position of SNP.";
+static char __pyx_k_256[] = "reference base at pos. ``N`` if no reference sequence supplied.";
+static char __pyx_k_257[] = "the genotype called.";
+static char __pyx_k_258[] = "the genotype quality (Phred-scaled).";
+static char __pyx_k_259[] = "the snp quality (Phred scaled) - probability of consensus being identical to reference sequence.";
+static char __pyx_k_260[] = "the root mean square (rms) of the mapping quality of all reads involved in the call.";
+static char __pyx_k_261[] = "coverage or read depth - the number of reads involved in the call.";
+static char __pyx_k_262[] = "getfilesystemencoding";
+static char __pyx_k_263[] = "MIDNSHP=X";
+static char __pyx_k_264[] = "(\\d+)([MIDNSHP=X])";
+static char __pyx_k_266[] = "=ACMGRSVTWYHKDBN";
+static char __pyx_k_269[] = "/home/andreas/devel/pysam/pysam/csamtools.pyx";
+static char __pyx_k_270[] = "PileupColumn.__str__";
+static char __pyx_k_271[] = "pysam.csamtools";
+static char __pyx_k_272[] = "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_275[] = "StderrStore.__init__";
+static char __pyx_k_278[] = "StderrStore.readAndRelease";
+static char __pyx_k_281[] = "StderrStore.release";
+static char __pyx_k_284[] = "StderrStore.__del__";
+static char __pyx_k_285[] = "\n stderr is captured.\n ";
+static char __pyx_k_288[] = "StderrStoreWindows.__init__";
+static char __pyx_k_291[] = "StderrStoreWindows.readAndRelease";
+static char __pyx_k_294[] = "StderrStoreWindows.release";
+static char __pyx_k_295[] = "does nothing. stderr can't be redirected on windows";
+static char __pyx_k_304[] = "Outs.__init__";
+static char __pyx_k_307[] = "Outs.setdevice";
+static char __pyx_k_310[] = "Outs.setfile";
+static char __pyx_k_313[] = "Outs.setfd";
+static char __pyx_k_316[] = "Outs.restore";
+static char __pyx_k_317[] = "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";
@@ -2089,6 +2160,7 @@ static char __pyx_k__template[] = "template";
static char __pyx_k__truncate[] = "truncate";
static char __pyx_k__warnings[] = "warnings";
static char __pyx_k__Fastafile[] = "Fastafile";
+static char __pyx_k__Fastqfile[] = "Fastqfile";
static char __pyx_k__TypeError[] = "TypeError";
static char __pyx_k____enter__[] = "__enter__";
static char __pyx_k___hasIndex[] = "_hasIndex";
@@ -2153,41 +2225,36 @@ 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_106;
-static PyObject *__pyx_kp_s_107;
-static PyObject *__pyx_kp_s_108;
-static PyObject *__pyx_kp_s_111;
+static PyObject *__pyx_kp_s_105;
+static PyObject *__pyx_kp_s_110;
static PyObject *__pyx_kp_s_112;
-static PyObject *__pyx_kp_s_113;
static PyObject *__pyx_kp_s_114;
static PyObject *__pyx_kp_s_115;
-static PyObject *__pyx_kp_s_117;
+static PyObject *__pyx_kp_s_116;
+static PyObject *__pyx_kp_s_119;
static PyObject *__pyx_kp_s_120;
+static PyObject *__pyx_kp_s_121;
+static PyObject *__pyx_kp_s_122;
static PyObject *__pyx_kp_s_123;
-static PyObject *__pyx_kp_s_129;
+static PyObject *__pyx_kp_s_125;
+static PyObject *__pyx_kp_s_128;
static PyObject *__pyx_kp_s_13;
-static PyObject *__pyx_kp_s_130;
static PyObject *__pyx_kp_s_131;
-static PyObject *__pyx_kp_s_133;
+static PyObject *__pyx_kp_s_137;
+static PyObject *__pyx_kp_s_138;
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_kp_s_147;
+static PyObject *__pyx_kp_s_148;
static PyObject *__pyx_kp_s_149;
static PyObject *__pyx_kp_s_15;
-static PyObject *__pyx_n_s_151;
+static PyObject *__pyx_kp_s_150;
static PyObject *__pyx_kp_s_152;
static PyObject *__pyx_kp_s_153;
-static PyObject *__pyx_kp_s_154;
-static PyObject *__pyx_kp_s_155;
-static PyObject *__pyx_kp_s_156;
static PyObject *__pyx_kp_s_157;
-static PyObject *__pyx_kp_s_158;
-static PyObject *__pyx_kp_s_159;
+static PyObject *__pyx_n_s_159;
static PyObject *__pyx_kp_b_16;
static PyObject *__pyx_kp_s_16;
static PyObject *__pyx_kp_s_160;
@@ -2207,73 +2274,79 @@ 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_176;
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_180;
static PyObject *__pyx_kp_s_181;
static PyObject *__pyx_kp_s_182;
static PyObject *__pyx_kp_s_183;
+static PyObject *__pyx_kp_s_185;
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_253;
-static PyObject *__pyx_kp_s_255;
-static PyObject *__pyx_kp_s_260;
-static PyObject *__pyx_n_s_261;
+static PyObject *__pyx_kp_s_191;
+static PyObject *__pyx_kp_s_197;
+static PyObject *__pyx_kp_s_198;
+static PyObject *__pyx_kp_s_21;
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_kp_s_264;
+static PyObject *__pyx_kp_s_269;
+static PyObject *__pyx_n_s_270;
+static PyObject *__pyx_n_s_271;
+static PyObject *__pyx_kp_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_n_s_278;
+static PyObject *__pyx_n_s_281;
+static PyObject *__pyx_n_s_284;
+static PyObject *__pyx_kp_s_285;
+static PyObject *__pyx_n_s_288;
+static PyObject *__pyx_n_s_291;
+static PyObject *__pyx_n_s_294;
+static PyObject *__pyx_kp_s_295;
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_n_s_310;
+static PyObject *__pyx_n_s_313;
+static PyObject *__pyx_n_s_316;
+static PyObject *__pyx_kp_s_317;
static PyObject *__pyx_kp_s_32;
-static PyObject *__pyx_kp_s_33;
-static PyObject *__pyx_kp_s_34;
-static PyObject *__pyx_kp_s_35;
-static PyObject *__pyx_kp_s_36;
-static PyObject *__pyx_kp_b_37;
+static PyObject *__pyx_kp_s_37;
static PyObject *__pyx_kp_s_38;
+static PyObject *__pyx_kp_s_39;
+static PyObject *__pyx_kp_s_40;
static PyObject *__pyx_kp_s_41;
+static PyObject *__pyx_kp_s_42;
static PyObject *__pyx_kp_s_43;
-static PyObject *__pyx_kp_s_45;
+static PyObject *__pyx_kp_s_44;
+static PyObject *__pyx_kp_b_45;
static PyObject *__pyx_kp_s_46;
-static PyObject *__pyx_kp_s_48;
+static PyObject *__pyx_kp_s_49;
static PyObject *__pyx_kp_s_5;
-static PyObject *__pyx_kp_s_50;
+static PyObject *__pyx_kp_s_51;
+static PyObject *__pyx_kp_s_53;
+static PyObject *__pyx_kp_s_54;
static PyObject *__pyx_kp_s_56;
static PyObject *__pyx_kp_s_58;
static PyObject *__pyx_kp_s_6;
-static PyObject *__pyx_kp_s_60;
-static PyObject *__pyx_kp_s_62;
static PyObject *__pyx_kp_s_64;
static PyObject *__pyx_kp_s_66;
-static PyObject *__pyx_kp_s_69;
+static PyObject *__pyx_kp_s_68;
static PyObject *__pyx_kp_s_7;
static PyObject *__pyx_kp_s_70;
-static PyObject *__pyx_kp_s_71;
-static PyObject *__pyx_kp_s_76;
+static PyObject *__pyx_kp_s_72;
+static PyObject *__pyx_kp_s_74;
+static PyObject *__pyx_kp_s_77;
+static PyObject *__pyx_kp_s_78;
static PyObject *__pyx_kp_s_79;
-static PyObject *__pyx_kp_s_82;
-static PyObject *__pyx_kp_s_85;
+static PyObject *__pyx_kp_s_84;
+static PyObject *__pyx_kp_s_87;
static PyObject *__pyx_kp_s_9;
-static PyObject *__pyx_kp_s_92;
-static PyObject *__pyx_kp_s_94;
-static PyObject *__pyx_kp_s_97;
+static PyObject *__pyx_kp_s_90;
+static PyObject *__pyx_kp_s_93;
static PyObject *__pyx_kp_s__2scB;
static PyObject *__pyx_kp_s__2scH;
static PyObject *__pyx_kp_s__2scI;
@@ -2299,6 +2372,7 @@ static PyObject *__pyx_n_s__DT;
static PyObject *__pyx_n_s__F;
static PyObject *__pyx_n_s__FO;
static PyObject *__pyx_n_s__Fastafile;
+static PyObject *__pyx_n_s__Fastqfile;
static PyObject *__pyx_n_s__GO;
static PyObject *__pyx_n_s__H;
static PyObject *__pyx_n_s__HD;
@@ -2568,13 +2642,13 @@ static PyObject *__pyx_int_neg_32767;
static PyObject *__pyx_int_536870912;
static PyObject *__pyx_int_4294967295;
static PyObject *__pyx_int_neg_2147483648;
-static PyObject *__pyx_k_21;
-static PyObject *__pyx_k_22;
-static PyObject *__pyx_k_23;
-static PyObject *__pyx_k_54;
-static PyObject *__pyx_k_73;
-static int __pyx_k_132;
-static PyObject *__pyx_k_180;
+static PyObject *__pyx_k_29;
+static PyObject *__pyx_k_30;
+static PyObject *__pyx_k_31;
+static PyObject *__pyx_k_62;
+static PyObject *__pyx_k_81;
+static int __pyx_k_140;
+static PyObject *__pyx_k_188;
static PyObject *__pyx_k_tuple_2;
static PyObject *__pyx_k_tuple_4;
static PyObject *__pyx_k_tuple_8;
@@ -2582,112 +2656,114 @@ static PyObject *__pyx_k_tuple_11;
static PyObject *__pyx_k_tuple_12;
static PyObject *__pyx_k_tuple_14;
static PyObject *__pyx_k_tuple_20;
-static PyObject *__pyx_k_tuple_25;
-static PyObject *__pyx_k_tuple_39;
-static PyObject *__pyx_k_tuple_40;
-static PyObject *__pyx_k_tuple_42;
-static PyObject *__pyx_k_tuple_44;
+static PyObject *__pyx_k_tuple_22;
+static PyObject *__pyx_k_tuple_23;
+static PyObject *__pyx_k_tuple_33;
static PyObject *__pyx_k_tuple_47;
-static PyObject *__pyx_k_tuple_49;
-static PyObject *__pyx_k_tuple_51;
+static PyObject *__pyx_k_tuple_48;
+static PyObject *__pyx_k_tuple_50;
static PyObject *__pyx_k_tuple_52;
-static PyObject *__pyx_k_tuple_53;
static PyObject *__pyx_k_tuple_55;
static PyObject *__pyx_k_tuple_57;
static PyObject *__pyx_k_tuple_59;
+static PyObject *__pyx_k_tuple_60;
static PyObject *__pyx_k_tuple_61;
static PyObject *__pyx_k_tuple_63;
static PyObject *__pyx_k_tuple_65;
static PyObject *__pyx_k_tuple_67;
-static PyObject *__pyx_k_tuple_68;
-static PyObject *__pyx_k_tuple_72;
-static PyObject *__pyx_k_tuple_74;
+static PyObject *__pyx_k_tuple_69;
+static PyObject *__pyx_k_tuple_71;
+static PyObject *__pyx_k_tuple_73;
static PyObject *__pyx_k_tuple_75;
-static PyObject *__pyx_k_tuple_77;
-static PyObject *__pyx_k_tuple_78;
+static PyObject *__pyx_k_tuple_76;
static PyObject *__pyx_k_tuple_80;
-static PyObject *__pyx_k_tuple_81;
+static PyObject *__pyx_k_tuple_82;
static PyObject *__pyx_k_tuple_83;
-static PyObject *__pyx_k_tuple_84;
+static PyObject *__pyx_k_tuple_85;
static PyObject *__pyx_k_tuple_86;
-static PyObject *__pyx_k_tuple_87;
static PyObject *__pyx_k_tuple_88;
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_92;
+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_105;
+static PyObject *__pyx_k_tuple_104;
+static PyObject *__pyx_k_tuple_106;
+static PyObject *__pyx_k_tuple_107;
+static PyObject *__pyx_k_tuple_108;
static PyObject *__pyx_k_tuple_109;
-static PyObject *__pyx_k_tuple_110;
-static PyObject *__pyx_k_tuple_116;
+static PyObject *__pyx_k_tuple_111;
+static PyObject *__pyx_k_tuple_113;
+static PyObject *__pyx_k_tuple_117;
static PyObject *__pyx_k_tuple_118;
-static PyObject *__pyx_k_tuple_119;
-static PyObject *__pyx_k_tuple_121;
-static PyObject *__pyx_k_tuple_122;
static PyObject *__pyx_k_tuple_124;
-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_129;
+static PyObject *__pyx_k_tuple_130;
+static PyObject *__pyx_k_tuple_132;
+static PyObject *__pyx_k_tuple_133;
static PyObject *__pyx_k_tuple_134;
static PyObject *__pyx_k_tuple_135;
-static PyObject *__pyx_k_tuple_137;
-static PyObject *__pyx_k_tuple_138;
+static PyObject *__pyx_k_tuple_136;
+static PyObject *__pyx_k_tuple_142;
static PyObject *__pyx_k_tuple_143;
+static PyObject *__pyx_k_tuple_145;
static PyObject *__pyx_k_tuple_146;
-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_151;
+static PyObject *__pyx_k_tuple_154;
+static PyObject *__pyx_k_tuple_155;
+static PyObject *__pyx_k_tuple_156;
+static PyObject *__pyx_k_tuple_158;
static PyObject *__pyx_k_tuple_184;
-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_264;
+static PyObject *__pyx_k_tuple_192;
+static PyObject *__pyx_k_tuple_193;
+static PyObject *__pyx_k_tuple_194;
+static PyObject *__pyx_k_tuple_195;
+static PyObject *__pyx_k_tuple_196;
+static PyObject *__pyx_k_tuple_265;
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_276;
+static PyObject *__pyx_k_tuple_279;
+static PyObject *__pyx_k_tuple_282;
+static PyObject *__pyx_k_tuple_286;
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_297;
+static PyObject *__pyx_k_tuple_298;
static PyObject *__pyx_k_tuple_299;
-static PyObject *__pyx_k_tuple_302;
+static PyObject *__pyx_k_tuple_300;
+static PyObject *__pyx_k_tuple_301;
+static PyObject *__pyx_k_tuple_303;
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_tuple_308;
+static PyObject *__pyx_k_tuple_311;
+static PyObject *__pyx_k_tuple_314;
+static PyObject *__pyx_k_tuple_318;
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_277;
+static PyObject *__pyx_k_codeobj_280;
+static PyObject *__pyx_k_codeobj_283;
+static PyObject *__pyx_k_codeobj_287;
+static PyObject *__pyx_k_codeobj_290;
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_302;
static PyObject *__pyx_k_codeobj_306;
-static PyObject *__pyx_k_codeobj_310;
+static PyObject *__pyx_k_codeobj_309;
+static PyObject *__pyx_k_codeobj_312;
+static PyObject *__pyx_k_codeobj_315;
+static PyObject *__pyx_k_codeobj_319;
static PyObject *__pyx_gb_5pysam_9csamtools_4generator(__pyx_GeneratorObject *__pyx_generator, PyObject *__pyx_sent_value); /* proto */
/* "pysam/csamtools.pyx":140
@@ -3887,7 +3963,7 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
* dest._is_tail = src.is_tail
* return dest # <<<<<<<<<<<<<<
*
- * cdef convertBinaryTagToList( uint8_t * s ):
+ * cdef class FastqProxy
*/
__Pyx_XDECREF(__pyx_r);
__Pyx_INCREF(((PyObject *)__pyx_v_dest));
@@ -3908,7 +3984,75 @@ static PyObject *__pyx_f_5pysam_9csamtools_makePileupRead(bam_pileup1_t *__pyx_v
return __pyx_r;
}
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*/
__pyx_v_counter = ((int *)__pyx_v_f);
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return __pyx_r;
}
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__pyx_v_d = ((__pyx_t_5pysam_9csamtools_MateData *)__pyx_v_f);
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__pyx_t_1 = (__pyx_v_d->mate == NULL);
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return __pyx_r;
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return __pyx_r;
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*/
__pyx_v_ctext = NULL;
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*
* if mode[0] == 'w': # <<<<<<<<<<<<<<
* # open file for writing
*
*/
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+ __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 = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":681
+ /* "pysam/csamtools.pyx":807
*
* # header structure (used for writing)
* if template: # <<<<<<<<<<<<<<
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* header_to_write = template.samfile.header
*/
- __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;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(((PyObject *)__pyx_v_template)); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":683
+ /* "pysam/csamtools.pyx":809
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@@ -7465,17 +8829,17 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
goto __pyx_L17;
}
- /* "pysam/csamtools.pyx":685
+ /* "pysam/csamtools.pyx":811
* header_to_write = template.samfile.header
*
* elif header: # <<<<<<<<<<<<<<
* header_to_write = self._buildHeader( header )
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*/
- __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;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_header); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 811; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_11) {
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*
* elif header:
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@@ -7487,7 +8851,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
}
/*else*/ {
- /* "pysam/csamtools.pyx":690
+ /* "pysam/csamtools.pyx":816
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*/
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- __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;}
+ __pyx_t_11 = __Pyx_PyObject_IsTrue(__pyx_v_referencenames); if (unlikely(__pyx_t_11 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __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_1 = __Pyx_PyObject_IsTrue(__pyx_v_referencelengths); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_10 = __pyx_t_1;
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__pyx_t_10 = __pyx_t_11;
}
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;}
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_37));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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- /* "pysam/csamtools.pyx":691
+ /* "pysam/csamtools.pyx":817
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* # allocate and fill header
*/
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- __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;}
+ __pyx_t_13 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_13 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_15 = PyObject_Length(__pyx_v_referencelengths); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __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;}
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_38));
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 817; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
#endif
- /* "pysam/csamtools.pyx":694
+ /* "pysam/csamtools.pyx":820
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* # allocate and fill header
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__Pyx_GOTREF(__pyx_t_5);
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__pyx_t_8 = __pyx_v_referencenames; __Pyx_INCREF(__pyx_t_8); __pyx_t_15 = 0;
__pyx_t_16 = NULL;
} else {
- __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_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); 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);
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if (__pyx_t_15 >= PyList_GET_SIZE(__pyx_t_8)) break;
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- __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;}
+ __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 = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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;}
+ __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 = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else if (!__pyx_t_16 && PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_15 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
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+ __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 = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 694; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF(__pyx_v_ref);
__pyx_v_ref = __pyx_t_7;
__pyx_t_7 = 0;
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+ __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 = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (unlikely(__Pyx_PyList_Append(__pyx_t_5, (PyObject*)__pyx_t_7))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 820; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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__pyx_v_referencenames = __pyx_t_8;
__pyx_t_8 = 0;
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+ /* "pysam/csamtools.pyx":821
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*/
__pyx_v_header_to_write = bam_header_init();
- /* "pysam/csamtools.pyx":696
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+ __pyx_t_15 = PyObject_Length(__pyx_v_referencenames); if (unlikely(__pyx_t_15 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 822; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_header_to_write->n_targets = __pyx_t_15;
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__Pyx_INCREF(__pyx_int_0);
__pyx_v_n = __pyx_int_0;
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+ __pyx_t_15 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_v_referencenames); 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);
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+ __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 = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 824; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 698; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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break;
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@@ -8108,42 +9472,42 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
}
if (__pyx_t_10) {
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+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_40), __pyx_v_filename); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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;}
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__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_t_5 = PyObject_Call(__pyx_builtin_IOError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __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;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 867; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L29;
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__pyx_L29:;
- /* "pysam/csamtools.pyx":744
+ /* "pysam/csamtools.pyx":870
*
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* if self.samfile == NULL:
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+ __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 = 870; __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 = 870; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- /* "pysam/csamtools.pyx":745
+ /* "pysam/csamtools.pyx":871
* # try to detect errors
* self.samfile = samopen( filename, bmode, NULL )
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@@ -8153,31 +9517,31 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
__pyx_t_10 = (__pyx_v_self->samfile == NULL);
if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":746
+ /* "pysam/csamtools.pyx":872
* self.samfile = samopen( filename, bmode, NULL )
* if self.samfile == NULL:
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+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_41), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __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_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
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_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __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;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 872; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L30;
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__pyx_L30:;
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+ /* "pysam/csamtools.pyx":875
*
* # bam files require a valid header
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@@ -8186,7 +9550,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
*/
if (__pyx_v_self->isbam) {
- /* "pysam/csamtools.pyx":750
+ /* "pysam/csamtools.pyx":876
* # bam files require a valid header
* if self.isbam:
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@@ -8196,26 +9560,26 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
__pyx_t_10 = (__pyx_v_self->samfile->header == NULL);
if (__pyx_t_10) {
- /* "pysam/csamtools.pyx":751
+ /* "pysam/csamtools.pyx":877
* if self.isbam:
* if self.samfile.header == NULL:
* raise ValueError( "file does not have valid header (mode='%s') - is it BAM format?" % mode ) # <<<<<<<<<<<<<<
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+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_42), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __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_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
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_t_5 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_t_8), NULL); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __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;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 877; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L32;
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__pyx_L32:;
@@ -8223,14 +9587,14 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
}
/*else*/ {
- /* "pysam/csamtools.pyx":754
+ /* "pysam/csamtools.pyx":880
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- __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;}
+ __pyx_t_10 = __Pyx_PyObject_IsTrue(__pyx_v_check_header); if (unlikely(__pyx_t_10 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 880; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_10) {
__pyx_t_11 = (__pyx_v_self->samfile->header == NULL);
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@@ -8239,40 +9603,40 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
}
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":755
+ /* "pysam/csamtools.pyx":881
* # in sam files it is optional (samfile full of unmapped reads)
* if check_header and self.samfile.header == NULL:
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* # disabled for autodetection to work
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- __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_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_43), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 881; __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_t_8 = PyTuple_New(1); 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);
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
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+ __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 = 881; __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;}
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goto __pyx_L33;
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__pyx_L33:;
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__pyx_L31:;
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+ /* "pysam/csamtools.pyx":885
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+ __pyx_t_1 = __Pyx_PyObject_IsTrue(__pyx_v_check_sq); if (unlikely(__pyx_t_1 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_1) {
__pyx_t_10 = (__pyx_v_self->samfile->header->n_targets == 0);
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@@ -8281,26 +9645,26 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
}
if (__pyx_t_11) {
- /* "pysam/csamtools.pyx":760
+ /* "pysam/csamtools.pyx":886
* # needs to be disabled so that reading from sam-files without headers works
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+ __pyx_t_5 = PyNumber_Remainder(((PyObject *)__pyx_kp_s_44), __pyx_v_mode); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
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+ __pyx_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
PyTuple_SET_ITEM(__pyx_t_8, 0, ((PyObject *)__pyx_t_5));
__Pyx_GIVEREF(((PyObject *)__pyx_t_5));
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+ __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 = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(((PyObject *)__pyx_t_8)); __pyx_t_8 = 0;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L34;
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__pyx_L34:;
@@ -8308,7 +9672,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_6_open(struct __pyx_obj_5py
}
__pyx_L16:;
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__pyx_t_11 = (__pyx_v_self->samfile == NULL);
if (__pyx_t_11) {
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__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_t_8 = PyTuple_New(1); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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*/
values[3] = ((PyObject *)Py_None);
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* '''
*/
values[4] = ((PyObject *)Py_None);
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if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
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int __pyx_clineno = 0;
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__Pyx_RefNannySetupContext("fetch", 0);
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+ __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 = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
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PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
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+ __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 = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 928; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -10366,7 +11730,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_20fetch(struct __pyx_obj_5p
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+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
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+ __pyx_t_6 = PyObject_Call(__pyx_builtin_NotImplementedError, ((PyObject *)__pyx_k_tuple_73), NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1088; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_read), __pyx_ptype_5pysam_9csamtools_AlignedRead, 1, "read", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1101; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L3;
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goto __pyx_L4;
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__pyx_L4:;
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__pyx_v_mate_data.name = ((char *)bam1_qname(__pyx_v_read->_delegate));
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- /* "pysam/csamtools.pyx":1010
+ /* "pysam/csamtools.pyx":1136
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*
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@@ -11034,36 +12398,36 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_22mate(struct __pyx_obj_5py
__pyx_t_2 = (__pyx_v_mate_data.mate == NULL);
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":1011
+ /* "pysam/csamtools.pyx":1137
*
* if mate_data.mate == NULL:
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*
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+ __pyx_t_3 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_80), NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1011; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1137; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
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__pyx_L5:;
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+ /* "pysam/csamtools.pyx":1139
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+ if (!(likely(__Pyx_TypeTest(__pyx_t_3, __pyx_ptype_5pysam_9csamtools_AlignedRead)))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1139; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_3 = 0;
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+ /* "pysam/csamtools.pyx":1140
*
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__pyx_t_5 = __pyx_v_mate_data.mate;
__pyx_v_dest->_delegate = __pyx_t_5;
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+ /* "pysam/csamtools.pyx":1141
* cdef AlignedRead dest = AlignedRead.__new__(AlignedRead)
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PyObject* values[5] = {0,0,0,0,0};
- /* "pysam/csamtools.pyx":1018
+ /* "pysam/csamtools.pyx":1144
*
* def count( self,
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*/
values[0] = ((PyObject *)Py_None);
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+ /* "pysam/csamtools.pyx":1145
* def count( self,
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*/
values[1] = ((PyObject *)Py_None);
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+ /* "pysam/csamtools.pyx":1146
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*/
values[2] = ((PyObject *)Py_None);
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+ /* "pysam/csamtools.pyx":1147
* start = None,
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* region = None, # <<<<<<<<<<<<<<
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*/
values[3] = ((PyObject *)Py_None);
- values[4] = __pyx_k_73;
+ values[4] = __pyx_k_81;
if (unlikely(__pyx_kwds)) {
Py_ssize_t kw_args;
const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args);
@@ -11193,7 +12557,7 @@ static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_25count(PyObject *__pyx_v_s
}
}
if (unlikely(kw_args > 0)) {
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@@ -11214,7 +12578,7 @@ static PyObject *__pyx_pw_5pysam_9csamtools_7Samfile_25count(PyObject *__pyx_v_s
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goto __pyx_L4_argument_unpacking_done;
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+ __Pyx_RaiseArgtupleInvalid("count", 0, 0, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1143; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":1017
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("count", 0);
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__Pyx_INCREF(__pyx_v_region);
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- /* "pysam/csamtools.pyx":1036
+ /* "pysam/csamtools.pyx":1162
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__pyx_L3:;
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+ /* "pysam/csamtools.pyx":1164
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+ __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 = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_1 = PyTuple_New(4); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1164; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_reference);
@@ -11318,7 +12682,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
__Pyx_INCREF(__pyx_v_region);
PyTuple_SET_ITEM(__pyx_t_1, 3, __pyx_v_region);
__Pyx_GIVEREF(__pyx_v_region);
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__Pyx_GOTREF(__pyx_t_5);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
@@ -11332,7 +12696,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1038; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -11354,7 +12718,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_24count(struct __pyx_obj_5p
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__Pyx_GOTREF(item);
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/*else*/ {
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+ __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 = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (size > 4) __Pyx_RaiseTooManyValuesError(4);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -11839,7 +13203,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
Py_ssize_t i;
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+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(item);
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{
Py_ssize_t index = -1;
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+ __pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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@@ -11858,7 +13222,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
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- 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;}
+ if (__Pyx_IternextUnpackEndCheck(__pyx_t_9(__pyx_t_8), 4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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+ __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 = 1246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_rtid = __pyx_t_11;
__pyx_v_rstart = __pyx_t_12;
__pyx_v_rend = __pyx_t_13;
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*/
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* if callback:
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+ __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 = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ __pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1249; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_7);
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goto __pyx_L7;
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+ __pyx_t_3 = __Pyx_PyObject_IsTrue(__pyx_v_callback); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
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+ __pyx_t_7 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_92), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1252; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_Raise(__pyx_t_7, 0, 0, 0);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1126; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L9;
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@@ -11953,7 +13317,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_7Samfile_26pileup(struct __pyx_obj_5
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__pyx_L8:;
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+ __pyx_t_9 = PyDict_New(); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1406; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_10 = -1; __pyx_t_8 = PyObject_GetIter(__pyx_t_9); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_8);
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+ __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 = 1407; __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;}
+ __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 = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else if (!__pyx_t_11 && PyTuple_CheckExact(__pyx_t_8)) {
if (__pyx_t_10 >= PyTuple_GET_SIZE(__pyx_t_8)) break;
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+ __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 = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#else
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+ __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 = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else {
__pyx_t_9 = __pyx_t_11(__pyx_t_8);
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if (PyErr_Occurred()) {
if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) PyErr_Clear();
- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1281; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1407; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_field = __pyx_t_9;
__pyx_t_9 = 0;
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- __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;}
+ __pyx_t_3 = (__Pyx_PySequence_Contains(((PyObject *)__pyx_kp_s_115), __pyx_v_field, Py_NE)); if (unlikely(__pyx_t_3 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1408; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
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+ /* "pysam/csamtools.pyx":1409
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__Pyx_Raise(__pyx_t_9, 0, 0, 0);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_7);
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- __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;}
+ __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 = 1436; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (size > 2) __Pyx_RaiseTooManyValuesError(2);
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+ __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 = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1452; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1326; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_2 = 0;
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+ /* "pysam/csamtools.pyx":1453
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PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_t_2);
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PyTuple_SET_ITEM(__pyx_t_7, 0, __pyx_v_key);
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+ __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 = 1453; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
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}
/*else*/ {
- /* "pysam/csamtools.pyx":1331
+ /* "pysam/csamtools.pyx":1457
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+ __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 = 1457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else if (!__pyx_t_6 && PyTuple_CheckExact(__pyx_t_1)) {
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+ __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 = 1457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 1457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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} else {
__pyx_t_2 = __pyx_t_6(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
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break;
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+ __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 = 1458; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (__pyx_t_3) {
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+ __pyx_t_2 = PyObject_GetItem(__pyx_v_fields, __pyx_v_key); if (!__pyx_t_2) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1459; __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;
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- /* "pysam/csamtools.pyx":1376
+ /* "pysam/csamtools.pyx":1502
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__Pyx_GOTREF(__pyx_t_6);
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PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_fields);
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PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)__pyx_v_lines));
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+ 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 = 1508; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_btext = ((PyObject*)__pyx_t_7);
__pyx_t_7 = 0;
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+ __pyx_t_13 = PyBytes_AsString(((PyObject *)__pyx_v_btext)); if (unlikely((!__pyx_t_13) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1509; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
strncpy(__pyx_v_dest->text, __pyx_t_13, __pyx_v_dest->l_text);
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if (__pyx_t_5) {
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__pyx_v_seqs = ((PyObject*)__pyx_t_7);
__pyx_t_7 = 0;
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@@ -15541,23 +16905,23 @@ static bam_header_t *__pyx_f_5pysam_9csamtools_7Samfile__buildHeader(struct __py
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+ __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 = 1515; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_t_7);
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PyTuple_SET_ITEM(__pyx_t_18, 0, ((PyObject *)__pyx_t_11));
__Pyx_GIVEREF(((PyObject *)__pyx_t_11));
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}
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*/
__pyx_v_dest->target_name = ((char **)calloc(__pyx_v_dest->n_targets, (sizeof(char *))));
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* dest.n_targets = len(seqs)
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__pyx_v_dest->target_len = ((uint32_t *)calloc(__pyx_v_dest->n_targets, (sizeof(uint32_t))));
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strncpy((__pyx_v_dest->target_name[__pyx_v_x]), __pyx_t_13, (__pyx_t_3 + 1));
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__pyx_v_self->b = ((bam1_t *)calloc(1, (sizeof(bam1_t))));
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bam_seek(__pyx_v_self->fp->x.bam, __pyx_t_4, 0);
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__pyx_v_self->current_pos = (__pyx_v_self->current_pos + 1);
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bam_destroy1(__pyx_v_self->b);
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* d.tid))
*
*/
- __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_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 = 1896; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_5));
- /* "pysam/csamtools.pyx":1747
+ /* "pysam/csamtools.pyx":1897
* raise ValueError( "reference sequence for '%s' (tid=%i) not found" % \
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*
*
*/
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+ __pyx_t_6 = PyInt_FromLong(__pyx_v_d->tid); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1897; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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_t_7 = PyTuple_New(2); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1896; __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));
@@ -18647,20 +20011,20 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__Pyx_GIVEREF(__pyx_t_6);
__pyx_t_5 = 0;
__pyx_t_6 = 0;
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__Pyx_DECREF(((PyObject *)__pyx_t_7)); __pyx_t_7 = 0;
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+ __pyx_t_7 = PyTuple_New(1); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_7, 0, ((PyObject *)__pyx_t_6));
__Pyx_GIVEREF(((PyObject *)__pyx_t_6));
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1895; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
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__pyx_L5:;
@@ -18668,7 +20032,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":1750
+ /* "pysam/csamtools.pyx":1900
*
*
* while ret >= 0: # <<<<<<<<<<<<<<
@@ -18679,7 +20043,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
__pyx_t_3 = (__pyx_v_ret >= 0);
if (!__pyx_t_3) break;
- /* "pysam/csamtools.pyx":1752
+ /* "pysam/csamtools.pyx":1902
* while ret >= 0:
*
* skip = 0 # <<<<<<<<<<<<<<
@@ -18688,7 +20052,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_skip = 0;
- /* "pysam/csamtools.pyx":1755
+ /* "pysam/csamtools.pyx":1905
*
* # realign read - changes base qualities
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@@ -18713,7 +20077,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L8:;
- /* "pysam/csamtools.pyx":1757
+ /* "pysam/csamtools.pyx":1907
* 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: # <<<<<<<<<<<<<<
@@ -18729,7 +20093,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":1758
+ /* "pysam/csamtools.pyx":1908
*
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres) # <<<<<<<<<<<<<<
@@ -18738,7 +20102,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
*/
__pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres);
- /* "pysam/csamtools.pyx":1759
+ /* "pysam/csamtools.pyx":1909
* if d.seq != NULL and capQ_thres > 10:
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1 # <<<<<<<<<<<<<<
@@ -18751,7 +20115,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
goto __pyx_L10;
}
- /* "pysam/csamtools.pyx":1760
+ /* "pysam/csamtools.pyx":1910
* q = bam_cap_mapQ(b, d.seq, capQ_thres)
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q # <<<<<<<<<<<<<<
@@ -18768,7 +20132,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L9:;
- /* "pysam/csamtools.pyx":1761
+ /* "pysam/csamtools.pyx":1911
* if q < 0: skip = 1
* elif b.core.qual > q: b.core.qual = q
* if b.core.flag & BAM_FUNMAP: skip = 1 # <<<<<<<<<<<<<<
@@ -18781,7 +20145,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
goto __pyx_L11;
}
- /* "pysam/csamtools.pyx":1762
+ /* "pysam/csamtools.pyx":1912
* 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 # <<<<<<<<<<<<<<
@@ -18800,7 +20164,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L11:;
- /* "pysam/csamtools.pyx":1764
+ /* "pysam/csamtools.pyx":1914
* elif b.core.flag & 1 and not b.core.flag & 2: skip = 1
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* if not skip: break # <<<<<<<<<<<<<<
@@ -18814,7 +20178,7 @@ static int __pyx_f_5pysam_9csamtools___advance_snpcalls(void *__pyx_v_data, bam1
}
__pyx_L12:;
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+ /* "pysam/csamtools.pyx":1917
* # additional filters
*
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b ) # <<<<<<<<<<<<<<
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}
__pyx_L7_break:;
- /* "pysam/csamtools.pyx":1769
+ /* "pysam/csamtools.pyx":1919
* ret = bam_iter_read( d.samfile.x.bam, d.iter, b )
*
* return ret # <<<<<<<<<<<<<<
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else goto __pyx_L5_argtuple_error;
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+ if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, __pyx_v_kwargs, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
}
} else if (PyTuple_GET_SIZE(__pyx_args) != 1) {
goto __pyx_L5_argtuple_error;
@@ -18888,14 +20252,14 @@ static int __pyx_pw_5pysam_9csamtools_14IteratorColumn_1__cinit__(PyObject *__py
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
__pyx_L3_error:;
__Pyx_DECREF(__pyx_v_kwargs); __pyx_v_kwargs = 0;
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L0;
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return __pyx_r;
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+ /* "pysam/csamtools.pyx":1969
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__pyx_v_self->samfile = __pyx_v_samfile;
- /* "pysam/csamtools.pyx":1820
+ /* "pysam/csamtools.pyx":1970
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+ __pyx_t_1 = PyInt_FromLong(BAM_DEF_MASK); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_self->mask = __pyx_t_3;
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__Pyx_GIVEREF(__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;
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_GIVEREF(__pyx_t_2);
__Pyx_GOTREF(__pyx_v_self->stepper);
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__pyx_v_self->stepper = __pyx_t_2;
__pyx_t_2 = 0;
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+ __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 = 1973; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_self->max_depth = __pyx_t_3;
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* self.stepper = kwargs.get( "stepper", None )
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*/
__pyx_v_self->iterdata.seq = NULL;
- /* "pysam/csamtools.pyx":1825
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*/
__pyx_v_self->tid = 0;
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+ /* "pysam/csamtools.pyx":1976
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__pyx_v_self->iterdata.tid = -1;
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}
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}
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*/
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return __pyx_r;
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bam_plp_reset(__pyx_v_self->pileup_iter);
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bam_plp_destroy(__pyx_v_self->pileup_iter);
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__pyx_v_self->pileup_iter = NULL;
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free(__pyx_v_self->iterdata.seq);
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+ __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 1, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_AddTraceback("pysam.csamtools.IteratorColumnRegion.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename);
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+ if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_samfile), __pyx_ptype_5pysam_9csamtools_Samfile, 1, "samfile", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2086; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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goto __pyx_L0;
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@@ -20042,7 +21415,7 @@ static int __pyx_pw_5pysam_9csamtools_20IteratorColumnRegion_1__cinit__(PyObject
return __pyx_r;
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__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__cinit__", 0);
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+ __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 = 2094; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_self->start = __pyx_v_start;
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__pyx_v_self->end = __pyx_v_end;
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return __pyx_r;
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((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));
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__pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
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goto __pyx_L5_argtuple_error;
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return __pyx_r;
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int __pyx_clineno = 0;
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__Pyx_RefNannySetupContext("__next__", 0);
- __Pyx_TraceCall("__next__", __pyx_f[0], 1987);
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* while 1: # <<<<<<<<<<<<<<
@@ -20466,7 +21839,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
while (1) {
if (!1) break;
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*
* while 1:
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((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));
- /* "pysam/csamtools.pyx":1994
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* self.cnext()
*
* if self.n_plp < 0: # <<<<<<<<<<<<<<
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__pyx_t_1 = (__pyx_v_self->__pyx_base.n_plp < 0);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1995
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+ __pyx_t_2 = PyObject_Call(__pyx_builtin_ValueError, ((PyObject *)__pyx_k_tuple_143), NULL); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1995; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2142; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
goto __pyx_L5;
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__pyx_L5:;
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@@ -20511,7 +21884,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
__pyx_t_1 = (__pyx_v_self->__pyx_base.plp != NULL);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":1999
+ /* "pysam/csamtools.pyx":2146
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@@ -20520,14 +21893,14 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
*/
__Pyx_XDECREF(__pyx_r);
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+ __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 = 2146; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_2 = 0;
@@ -20536,7 +21909,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
}
__pyx_L6:;
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* # otherwise, proceed to next reference or stop
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@@ -20545,25 +21918,25 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
*/
__pyx_v_self->__pyx_base.tid = (__pyx_v_self->__pyx_base.tid + 1);
- /* "pysam/csamtools.pyx":2006
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* self.tid += 1
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- __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_t_2 = PyInt_FromLong(__pyx_v_self->__pyx_base.tid); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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_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 = 2153; __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); __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_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 = 2153; __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 = 2006; __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 = 2153; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2007
+ /* "pysam/csamtools.pyx":2154
* self.tid += 1
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* self.setupIteratorData( self.tid, 0, max_pos, 0 ) # <<<<<<<<<<<<<<
@@ -20572,14 +21945,14 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
*/
__pyx_t_5.__pyx_n = 1;
__pyx_t_5.reopen = 0;
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+ __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 = 2154; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
goto __pyx_L7;
}
/*else*/ {
- /* "pysam/csamtools.pyx":2009
+ /* "pysam/csamtools.pyx":2156
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__Pyx_Raise(__pyx_builtin_StopIteration, 0, 0, 0);
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2009; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
__pyx_L7:;
}
@@ -20607,7 +21980,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_21IteratorColumnAllRefs_2__next__(st
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2014
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* ##-------------------------------------------------------------------
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__Pyx_RefNannySetupContext("query_start", 0);
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* cdef uint32_t * cigar_p, op
* cdef uint32_t k
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*/
__pyx_v_start_offset = 0;
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* cdef uint32_t start_offset = 0
*
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*/
if (__pyx_v_src->core.n_cigar) {
- /* "pysam/csamtools.pyx":2020
+ /* "pysam/csamtools.pyx":2167
*
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* cigar_p = bam1_cigar(src); # <<<<<<<<<<<<<<
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*/
__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2021
+ /* "pysam/csamtools.pyx":2168
* if src.core.n_cigar:
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar: # <<<<<<<<<<<<<<
@@ -20667,7 +22040,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_start(bam1_t *__pyx
__pyx_t_1 = __pyx_v_src->core.n_cigar;
for (__pyx_v_k = 0; __pyx_v_k < __pyx_t_1; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2022
+ /* "pysam/csamtools.pyx":2169
* cigar_p = bam1_cigar(src);
* for k from 0 <= k < src.core.n_cigar:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
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*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2027
+ /* "pysam/csamtools.pyx":2174
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
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*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2023
+ /* "pysam/csamtools.pyx":2170
* for k from 0 <= k < src.core.n_cigar:
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*/
case 5:
- /* "pysam/csamtools.pyx":2024
+ /* "pysam/csamtools.pyx":2171
* op = cigar_p[k] & BAM_CIGAR_MASK
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}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2025
+ /* "pysam/csamtools.pyx":2172
* if op==BAM_CHARD_CLIP:
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* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string') # <<<<<<<<<<<<<<
* return -1
* elif op==BAM_CSOFT_CLIP:
*/
- PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_136);
+ PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_144);
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* if start_offset!=0 and start_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
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__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2027
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* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
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case 4:
- /* "pysam/csamtools.pyx":2028
+ /* "pysam/csamtools.pyx":2175
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break;
default:
- /* "pysam/csamtools.pyx":2030
+ /* "pysam/csamtools.pyx":2177
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* break # <<<<<<<<<<<<<<
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}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2032
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2037
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* ##-------------------------------------------------------------------
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* cdef inline int32_t query_end(bam1_t *src) except -1: # <<<<<<<<<<<<<<
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int __pyx_t_4;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("query_end", 0);
- __Pyx_TraceCall("query_end", __pyx_f[0], 2037);
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- /* "pysam/csamtools.pyx":2040
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* cdef uint32_t * cigar_p, op
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__pyx_t_1 = __pyx_v_src->core.l_qseq;
__pyx_v_end_offset = __pyx_t_1;
- /* "pysam/csamtools.pyx":2042
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__pyx_t_2 = (__pyx_v_src->core.n_cigar > 1);
if (__pyx_t_2) {
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__pyx_v_cigar_p = bam1_cigar(__pyx_v_src);
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* if src.core.n_cigar>1:
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for (__pyx_v_k = __pyx_v_src->core.n_cigar-1; __pyx_v_k >= 1; __pyx_v_k--) {
- /* "pysam/csamtools.pyx":2045
+ /* "pysam/csamtools.pyx":2192
* cigar_p = bam1_cigar(src);
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK # <<<<<<<<<<<<<<
@@ -20856,7 +22229,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
__pyx_v_op = ((__pyx_v_cigar_p[__pyx_v_k]) & 15);
- /* "pysam/csamtools.pyx":2050
+ /* "pysam/csamtools.pyx":2197
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -20865,7 +22238,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
switch (__pyx_v_op) {
- /* "pysam/csamtools.pyx":2046
+ /* "pysam/csamtools.pyx":2193
* for k from src.core.n_cigar > k >= 1:
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP: # <<<<<<<<<<<<<<
@@ -20874,7 +22247,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
case 5:
- /* "pysam/csamtools.pyx":2047
+ /* "pysam/csamtools.pyx":2194
* op = cigar_p[k] & BAM_CIGAR_MASK
* if op==BAM_CHARD_CLIP:
* if end_offset!=0 and end_offset!=src.core.l_qseq: # <<<<<<<<<<<<<<
@@ -20890,16 +22263,16 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
}
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2048
+ /* "pysam/csamtools.pyx":2195
* 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:
*/
- PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_136);
+ PyErr_SetString(__pyx_builtin_ValueError, __pyx_k_144);
- /* "pysam/csamtools.pyx":2049
+ /* "pysam/csamtools.pyx":2196
* if end_offset!=0 and end_offset!=src.core.l_qseq:
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1 # <<<<<<<<<<<<<<
@@ -20913,7 +22286,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_L6:;
break;
- /* "pysam/csamtools.pyx":2050
+ /* "pysam/csamtools.pyx":2197
* PyErr_SetString(ValueError, 'Invalid clipping in CIGAR string')
* return -1
* elif op==BAM_CSOFT_CLIP: # <<<<<<<<<<<<<<
@@ -20922,7 +22295,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
*/
case 4:
- /* "pysam/csamtools.pyx":2051
+ /* "pysam/csamtools.pyx":2198
* return -1
* elif op==BAM_CSOFT_CLIP:
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT # <<<<<<<<<<<<<<
@@ -20933,7 +22306,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
break;
default:
- /* "pysam/csamtools.pyx":2053
+ /* "pysam/csamtools.pyx":2200
* end_offset -= cigar_p[k] >> BAM_CIGAR_SHIFT
* else:
* break # <<<<<<<<<<<<<<
@@ -20949,7 +22322,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2055
+ /* "pysam/csamtools.pyx":2202
* break
*
* if end_offset==0: # <<<<<<<<<<<<<<
@@ -20959,7 +22332,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
__pyx_t_4 = (__pyx_v_end_offset == 0);
if (__pyx_t_4) {
- /* "pysam/csamtools.pyx":2056
+ /* "pysam/csamtools.pyx":2203
*
* if end_offset==0:
* end_offset = src.core.l_qseq # <<<<<<<<<<<<<<
@@ -20972,7 +22345,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
}
__pyx_L7:;
- /* "pysam/csamtools.pyx":2058
+ /* "pysam/csamtools.pyx":2205
* end_offset = src.core.l_qseq
*
* return end_offset # <<<<<<<<<<<<<<
@@ -20989,7 +22362,7 @@ static CYTHON_INLINE int32_t __pyx_f_5pysam_9csamtools_query_end(bam1_t *__pyx_v
return __pyx_r;
}
-/* "pysam/csamtools.pyx":2061
+/* "pysam/csamtools.pyx":2208
*
*
* cdef inline object get_seq_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
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- /* "pysam/csamtools.pyx":2066
+ /* "pysam/csamtools.pyx":2213
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__pyx_t_1 = (!__pyx_v_src->core.l_qseq);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2067
+ /* "pysam/csamtools.pyx":2214
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* if not src.core.l_qseq:
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}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2069
+ /* "pysam/csamtools.pyx":2216
* return None
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+ __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 = 2216; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_seq = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
- /* "pysam/csamtools.pyx":2070
+ /* "pysam/csamtools.pyx":2217
*
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq # <<<<<<<<<<<<<<
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*
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+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_seq)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2217; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_s = ((char *)__pyx_t_3);
- /* "pysam/csamtools.pyx":2071
+ /* "pysam/csamtools.pyx":2218
* seq = PyBytes_FromStringAndSize(NULL, end - start)
* s = <char*>seq
* p = bam1_seq(src) # <<<<<<<<<<<<<<
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*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "pysam/csamtools.pyx":2073
+ /* "pysam/csamtools.pyx":2220
* p = bam1_seq(src)
*
* for k from start <= k < end: # <<<<<<<<<<<<<<
@@ -21081,7 +22454,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
__pyx_t_4 = __pyx_v_end;
for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2076
+ /* "pysam/csamtools.pyx":2223
* # 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
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@@ -21091,7 +22464,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_seq_range(bam1_t *_
(__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)]);
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- /* "pysam/csamtools.pyx":2078
+ /* "pysam/csamtools.pyx":2225
* s[k-start] = bam_nt16_rev_table[p[k/2] >> 4 * (1 - k%2) & 0xf]
*
* return seq # <<<<<<<<<<<<<<
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2081
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*
*
* cdef inline object get_qual_range(bam1_t *src, uint32_t start, uint32_t end): # <<<<<<<<<<<<<<
@@ -21141,9 +22514,9 @@ static CYTHON_INLINE PyObject *__pyx_f_5pysam_9csamtools_get_qual_range(bam1_t *
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- /* "pysam/csamtools.pyx":2086
+ /* "pysam/csamtools.pyx":2233
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*/
__pyx_v_p = bam1_qual(__pyx_v_src);
- /* "pysam/csamtools.pyx":2087
+ /* "pysam/csamtools.pyx":2234
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* p = bam1_qual(src)
* if p[0] == 0xff: # <<<<<<<<<<<<<<
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__pyx_t_1 = ((__pyx_v_p[0]) == 0xff);
if (__pyx_t_1) {
- /* "pysam/csamtools.pyx":2088
+ /* "pysam/csamtools.pyx":2235
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}
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- /* "pysam/csamtools.pyx":2090
+ /* "pysam/csamtools.pyx":2237
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+ __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 = 2237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_qual = ((PyObject*)__pyx_t_2);
__pyx_t_2 = 0;
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+ /* "pysam/csamtools.pyx":2238
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+ __pyx_t_3 = PyBytes_AsString(((PyObject *)__pyx_v_qual)); if (unlikely((!__pyx_t_3) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2238; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_q = ((char *)__pyx_t_3);
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for (__pyx_v_k = __pyx_v_start; __pyx_v_k < __pyx_t_4; __pyx_v_k++) {
- /* "pysam/csamtools.pyx":2095
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__pyx_v_self->_delegate->m_data = 40;
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__pyx_v_self->_delegate->data = ((uint8_t *)calloc(__pyx_v_self->_delegate->m_data, 1));
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__pyx_v_src = __pyx_t_1;
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__pyx_v_src = __pyx_t_6;
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__pyx_v_l = __pyx_t_3;
__pyx_t_3 = 0;
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*
*/
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+ __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2437; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_op);
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__Pyx_INCREF(__pyx_v_l);
PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_v_l);
__Pyx_GIVEREF(__pyx_v_l);
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+ __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 = 2437; __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;
}
- /* "pysam/csamtools.pyx":2287
+ /* "pysam/csamtools.pyx":2438
* l = cigar_p[k] >> BAM_CIGAR_SHIFT
* cigar.append((op, l))
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2289
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* return cigar
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int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__set__", 0);
- __Pyx_TraceCall("__set__", __pyx_f[0], 2289);
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- /* "pysam/csamtools.pyx":2290
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* def __set__(self, values ):
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+ __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 = 2441; __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 = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (!__pyx_t_2) {
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+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2441; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = (__pyx_t_3 == 0);
__pyx_t_5 = __pyx_t_4;
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@@ -22375,7 +23748,7 @@ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2296
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*/
__pyx_v_k = 0;
- /* "pysam/csamtools.pyx":2298
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* k = 0
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__pyx_t_6 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_6;
- /* "pysam/csamtools.pyx":2301
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*
* # get location of cigar string
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*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2306
+ /* "pysam/csamtools.pyx":2457
* pysam_bam_update( src,
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*/
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+ __pyx_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2457; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":2307
+ /* "pysam/csamtools.pyx":2458
* src.core.n_cigar * 4,
* len(values) * 4,
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*/
pysam_bam_update(__pyx_v_src, (__pyx_v_src->core.n_cigar * 4), (__pyx_t_3 * 4), ((uint8_t *)__pyx_v_p));
- /* "pysam/csamtools.pyx":2310
+ /* "pysam/csamtools.pyx":2461
*
* # length is number of cigar operations, not bytes
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*/
- __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_t_3 = PyObject_Length(__pyx_v_values); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2461; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_src->core.n_cigar = __pyx_t_3;
- /* "pysam/csamtools.pyx":2314
+ /* "pysam/csamtools.pyx":2465
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*/
__pyx_v_p = bam1_cigar(__pyx_v_src);
- /* "pysam/csamtools.pyx":2317
+ /* "pysam/csamtools.pyx":2468
*
* # insert cigar operations
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__pyx_t_1 = __pyx_v_values; __Pyx_INCREF(__pyx_t_1); __pyx_t_3 = 0;
__pyx_t_7 = NULL;
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- __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_t_3 = -1; __pyx_t_1 = PyObject_GetIter(__pyx_v_values); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
__pyx_t_7 = Py_TYPE(__pyx_t_1)->tp_iternext;
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+ __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 = 2468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- __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;}
+ __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 = 2468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 2468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __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 = 2468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- else {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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break;
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@@ -22491,7 +23864,7 @@ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx
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if (size > 2) __Pyx_RaiseTooManyValuesError(2);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_11 = PyObject_GetIter(__pyx_t_8); if (unlikely(!__pyx_t_11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_12 = NULL;
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goto __pyx_L7_unpacking_done;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2317; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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@@ -22539,23 +23912,23 @@ static int __pyx_pf_5pysam_9csamtools_11AlignedRead_5cigar_2__set__(struct __pyx
__pyx_v_l = __pyx_t_10;
__pyx_t_10 = 0;
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}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "pysam/csamtools.pyx":2322
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return __pyx_r;
}
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*
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PyObject *__pyx_t_1 = NULL;
int __pyx_t_2;
Py_ssize_t __pyx_t_3;
- int __pyx_t_4;
+ bam1_t *__pyx_t_4;
int __pyx_t_5;
- bam1_t *__pyx_t_6;
- int __pyx_t_7;
- char *__pyx_t_8;
- long __pyx_t_9;
+ char *__pyx_t_6;
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int __pyx_lineno = 0;
const char *__pyx_filename = NULL;
int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__set__", 0);
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__Pyx_INCREF(__pyx_v_seq);
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- if (__pyx_t_5) {
- __pyx_r = 0;
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goto __pyx_L3;
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- __pyx_L3:;
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- __Pyx_DECREF(__pyx_v_seq);
- __pyx_v_seq = __pyx_t_1;
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- * cdef int l, k, nbytes_new, nbytes_old
- *
- * src = self._delegate # <<<<<<<<<<<<<<
+ /* "pysam/csamtools.pyx":2539
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*
- * l = len(seq)
+ * src = self._delegate
*/
- __pyx_t_6 = __pyx_v_self->_delegate;
- __pyx_v_src = __pyx_t_6;
+ __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 = 2539; __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;
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- * src = self._delegate
+ /* "pysam/csamtools.pyx":2541
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*
- * l = len(seq) # <<<<<<<<<<<<<<
+ * src = self._delegate # <<<<<<<<<<<<<<
*
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*/
- __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;
+ __pyx_t_4 = __pyx_v_self->_delegate;
+ __pyx_v_src = __pyx_t_4;
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+ /* "pysam/csamtools.pyx":2545
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- * # acquire pointer to location in memory
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*/
__pyx_v_nbytes_new = (__Pyx_div_long((__pyx_v_l + 1), 2) + __pyx_v_l);
- /* "pysam/csamtools.pyx":2381
+ /* "pysam/csamtools.pyx":2546
* # 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 # <<<<<<<<<<<<<<
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* # acquire pointer to location in memory
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*/
__pyx_v_nbytes_old = (__Pyx_div_long((__pyx_v_src->core.l_qseq + 1), 2) + __pyx_v_src->core.l_qseq);
- /* "pysam/csamtools.pyx":2383
- * nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
+ /* "pysam/csamtools.pyx":2549
+ *
* # acquire pointer to location in memory
* p = bam1_seq( src ) # <<<<<<<<<<<<<<
* src.core.l_qseq = l
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*/
__pyx_v_p = bam1_seq(__pyx_v_src);
- /* "pysam/csamtools.pyx":2384
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* # acquire pointer to location in memory
* p = bam1_seq( src )
* src.core.l_qseq = l # <<<<<<<<<<<<<<
*
- * pysam_bam_update( src,
+ * # change length of data field
*/
__pyx_v_src->core.l_qseq = __pyx_v_l;
- /* "pysam/csamtools.pyx":2389
+ /* "pysam/csamtools.pyx":2556
* nbytes_old,
* nbytes_new,
* p) # <<<<<<<<<<<<<<
- * # re-acquire pointer to location in memory
- * # as it might have moved
+ *
+ * if l > 0:
*/
pysam_bam_update(__pyx_v_src, __pyx_v_nbytes_old, __pyx_v_nbytes_new, __pyx_v_p);
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- * # re-acquire pointer to location in memory
- * # as it might have moved
- * p = bam1_seq( src ) # <<<<<<<<<<<<<<
- * for k from 0 <= k < nbytes_new: p[k] = 0
- * # convert to C string
+ /* "pysam/csamtools.pyx":2558
+ * p)
+ *
+ * if l > 0: # <<<<<<<<<<<<<<
+ * # re-acquire pointer to location in memory
+ * # as it might have moved
*/
- __pyx_v_p = bam1_seq(__pyx_v_src);
+ __pyx_t_2 = (__pyx_v_l > 0);
+ if (__pyx_t_2) {
- /* "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
+ /* "pysam/csamtools.pyx":2561
+ * # re-acquire pointer to location in memory
+ * # as it might have moved
+ * p = bam1_seq( src ) # <<<<<<<<<<<<<<
+ * for k from 0 <= k < nbytes_new: p[k] = 0
+ * # convert to C string
*/
- __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;
- }
+ __pyx_v_p = bam1_seq(__pyx_v_src);
- /* "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)
+ /* "pysam/csamtools.pyx":2562
+ * # as it might have moved
+ * p = bam1_seq( src )
+ * for k from 0 <= k < nbytes_new: p[k] = 0 # <<<<<<<<<<<<<<
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+ * s = seq
*/
- __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;
+ __pyx_t_5 = __pyx_v_nbytes_new;
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+ }
- /* "pysam/csamtools.pyx":2396
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- * s = seq
- * for k from 0 <= k < l: # <<<<<<<<<<<<<<
- * p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
+ /* "pysam/csamtools.pyx":2564
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+ * # convert to C string
+ * s = seq # <<<<<<<<<<<<<<
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+ __pyx_t_6 = PyBytes_AsString(__pyx_v_seq); if (unlikely((!__pyx_t_6) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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*
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- * p = bam1_qual( src ) # <<<<<<<<<<<<<<
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*
*/
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- * # erase qualities
- * p = bam1_qual( src )
- * p[0] = 0xff # <<<<<<<<<<<<<<
- *
+ /* "pysam/csamtools.pyx":2570
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*/
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+ (__pyx_v_p[0]) = 0xff;
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return __pyx_r;
}
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* def __get__(self): # <<<<<<<<<<<<<<
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* cdef bam1_t * src
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__pyx_v_src = __pyx_t_1;
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
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__pyx_v_p = bam1_qual(__pyx_v_src);
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+ __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 = 2607; __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 = 2607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ __pyx_t_4 = PyObject_Length(__pyx_v_qual); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2607; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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*/
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* # if absent - set to 0xff
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* return # <<<<<<<<<<<<<<
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}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2432
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+ __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 = 2611; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_v_qual);
__pyx_v_qual = __pyx_t_2;
__pyx_t_2 = 0;
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* cdef int l
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- __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_t_7 = PyBytes_AsString(__pyx_v_qual); if (unlikely((!__pyx_t_7) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* # convert to C string
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__pyx_t_6 = (__pyx_v_src->core.l_qseq != __pyx_v_l);
if (__pyx_t_6) {
- /* "pysam/csamtools.pyx":2438
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__Pyx_GIVEREF(__pyx_t_2);
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__Pyx_GOTREF(((PyObject *)__pyx_t_8));
__Pyx_DECREF(((PyObject *)__pyx_t_9)); __pyx_t_9 = 0;
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PyTuple_SET_ITEM(__pyx_t_9, 0, ((PyObject *)__pyx_t_8));
__Pyx_GIVEREF(((PyObject *)__pyx_t_8));
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__Pyx_GOTREF(__pyx_t_8);
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__pyx_L4:;
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* if src.core.l_qseq != l:
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2439; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2618; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
}
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* assert src.core.l_qseq == l
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return __pyx_r;
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__pyx_v_src = __pyx_t_1;
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__pyx_v_start = __pyx_t_3;
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+ __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 = 2644; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_v_end = __pyx_t_3;
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* property qlen:
*/
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+ __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 = 2673; __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 = 2673; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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return __pyx_r;
}
-/* "pysam/csamtools.pyx":2498
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int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2498);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2677);
- /* "pysam/csamtools.pyx":2500
+ /* "pysam/csamtools.pyx":2679
* def __get__(self):
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* src = self._delegate # <<<<<<<<<<<<<<
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
- /* "pysam/csamtools.pyx":2501
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* cdef bam1_t * src
* src = self._delegate
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* property tags:
*/
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- __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;}
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+ __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 = 2680; __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 = 2680; __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 = 2680; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_r = __pyx_t_4;
__pyx_t_4 = 0;
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return __pyx_r;
}
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* multiple times.
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* def __get__(self): # <<<<<<<<<<<<<<
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int __pyx_clineno = 0;
__Pyx_TraceDeclarations
__Pyx_RefNannySetupContext("__get__", 0);
- __Pyx_TraceCall("__get__", __pyx_f[0], 2518);
+ __Pyx_TraceCall("__get__", __pyx_f[0], 2697);
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+ /* "pysam/csamtools.pyx":2706
* cdef int32_t nvalues
*
* src = self._delegate # <<<<<<<<<<<<<<
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__pyx_t_1 = __pyx_v_self->_delegate;
__pyx_v_src = __pyx_t_1;
- /* "pysam/csamtools.pyx":2528
+ /* "pysam/csamtools.pyx":2707
*
* src = self._delegate
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@@ -24203,7 +25589,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct _
__pyx_t_2 = (__pyx_v_src->l_aux == 0);
if (__pyx_t_2) {
__Pyx_XDECREF(__pyx_r);
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2707; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_r = ((PyObject *)__pyx_t_3);
__pyx_t_3 = 0;
@@ -24212,7 +25598,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct _
}
__pyx_L3:;
- /* "pysam/csamtools.pyx":2529
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*/
__pyx_v_s = bam1_aux(__pyx_v_src);
- /* "pysam/csamtools.pyx":2530
+ /* "pysam/csamtools.pyx":2709
* if src.l_aux == 0: return []
* s = bam1_aux( src )
* result = [] # <<<<<<<<<<<<<<
* auxtag[2] = 0
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*/
- __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_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_result = ((PyObject*)__pyx_t_3);
__pyx_t_3 = 0;
- /* "pysam/csamtools.pyx":2531
+ /* "pysam/csamtools.pyx":2710
* s = bam1_aux( src )
* result = []
* auxtag[2] = 0 # <<<<<<<<<<<<<<
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*/
(__pyx_v_auxtag[2]) = 0;
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+ /* "pysam/csamtools.pyx":2711
* result = []
* auxtag[2] = 0
* while s < (src.data + src.data_len): # <<<<<<<<<<<<<<
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__pyx_t_2 = (__pyx_v_s < (__pyx_v_src->data + __pyx_v_src->data_len));
if (!__pyx_t_2) break;
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+ /* "pysam/csamtools.pyx":2713
* while s < (src.data + src.data_len):
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* auxtag[0] = s[0] # <<<<<<<<<<<<<<
@@ -24262,7 +25648,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools_11AlignedRead_4tags___get__(struct _
*/
(__pyx_v_auxtag[0]) = (__pyx_v_s[0]);
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+ /* "pysam/csamtools.pyx":2714
* # get tag
* auxtag[0] = s[0]
* auxtag[1] = s[1] # <<<<<<<<<<<<<<
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*/
(__pyx_v_auxtag[1]) = (__pyx_v_s[1]);
- /* "pysam/csamtools.pyx":2536
+ /* "pysam/csamtools.pyx":2715
* auxtag[0] = s[0]
* auxtag[1] = s[1]
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*/
__pyx_v_s = (__pyx_v_s + 2);
- /* "pysam/csamtools.pyx":2537
+ /* "pysam/csamtools.pyx":2716
* auxtag[1] = s[1]
* s += 2
* auxtype = s[0] # <<<<<<<<<<<<<<
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*/
__pyx_v_auxtype = (__pyx_v_s[0]);
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+ /* "pysam/csamtools.pyx":2717
* s += 2
* auxtype = s[0]
* if auxtype in ('c', 'C'): # <<<<<<<<<<<<<<
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__pyx_t_2 = __pyx_t_6;
if (__pyx_t_2) {
- /* "pysam/csamtools.pyx":2539
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+ __pyx_t_3 = PyInt_FromLong(((int)bam_aux2i(__pyx_v_s))); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2718; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
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goto __pyx_L6;
}
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__pyx_t_2 = __pyx_t_5;
if (__pyx_t_2) {
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__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
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goto __pyx_L6;
}
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__pyx_t_2 = __pyx_t_6;
if (__pyx_t_2) {
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__Pyx_XDECREF(__pyx_v_value);
__pyx_v_value = __pyx_t_3;
__pyx_t_3 = 0;
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goto __pyx_L6;
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if (__pyx_t_2) {
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goto __pyx_L6;
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goto __pyx_L6;
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__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
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case 3:
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+ __Pyx_RaiseArgtupleInvalid("overlap", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3148; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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}
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__pyx_v_inf = __pyx_t_4;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ /* "pysam/csamtools.pyx":3442
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+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3442; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
__Pyx_GOTREF(__pyx_t_4);
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+ __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 = 3442; __pyx_clineno = __LINE__; goto __pyx_L41_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/csamtools.pyx":3441
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PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
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__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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__Pyx_GOTREF(__pyx_t_19);
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if (__pyx_t_2) {
__Pyx_GIVEREF(__pyx_t_1);
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__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;
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__Pyx_GOTREF(__pyx_t_18);
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__Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0;
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if (__pyx_t_8) {
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__Pyx_GOTREF(__pyx_t_4);
__Pyx_GOTREF(__pyx_t_1);
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+ __pyx_t_6 = PyTuple_New(2); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3444; __pyx_clineno = __LINE__; goto __pyx_L29_except_error;}
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__Pyx_INCREF(__pyx_v_stdout_f);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_v_stdout_f);
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PyTuple_SET_ITEM(__pyx_t_6, 1, ((PyObject *)__pyx_n_s__rb));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__rb));
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__Pyx_GOTREF(__pyx_t_20);
__Pyx_DECREF(((PyObject *)__pyx_t_6)); __pyx_t_6 = 0;
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+ __pyx_t_15 = PyObject_GetAttr(__pyx_t_20, __pyx_n_s____exit__); if (unlikely(!__pyx_t_15)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3444; __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 = 3227; __pyx_clineno = __LINE__; goto __pyx_L56_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 = 3444; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
__Pyx_GOTREF(__pyx_t_6);
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+ __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 = 3444; __pyx_clineno = __LINE__; goto __pyx_L56_error;}
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__Pyx_DECREF(__pyx_t_20); __pyx_t_20 = 0;
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__pyx_v_inf = __pyx_t_21;
__Pyx_DECREF(__pyx_t_21); __pyx_t_21 = 0;
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+ __pyx_t_21 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__read); if (unlikely(!__pyx_t_21)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3446; __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_t_20 = PyObject_Call(__pyx_t_21, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_20)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3446; __pyx_clineno = __LINE__; goto __pyx_L62_error;}
__Pyx_GOTREF(__pyx_t_20);
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__Pyx_XDECREF(__pyx_v_out_stdout);
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__Pyx_XDECREF(__pyx_t_20); __pyx_t_20 = 0;
- /* "pysam/csamtools.pyx":3227
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/*except:*/ {
__Pyx_AddTraceback("pysam.csamtools._samtools_dispatch", __pyx_clineno, __pyx_lineno, __pyx_filename);
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__Pyx_GOTREF(__pyx_t_20);
__Pyx_GOTREF(__pyx_t_21);
__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_t_22 = PyTuple_New(3); if (unlikely(!__pyx_t_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3444; __pyx_clineno = __LINE__; goto __pyx_L64_except_error;}
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__Pyx_INCREF(__pyx_t_20);
PyTuple_SET_ITEM(__pyx_t_22, 0, __pyx_t_20);
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__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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__Pyx_GOTREF(__pyx_t_19);
__pyx_t_2 = __Pyx_PyObject_IsTrue(__pyx_t_19);
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if (__pyx_t_5) {
__Pyx_GIVEREF(__pyx_t_20);
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__Pyx_GIVEREF(__pyx_t_6);
__Pyx_ErrRestore(__pyx_t_20, __pyx_t_21, __pyx_t_6);
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goto __pyx_L73;
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+ __pyx_t_4 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__remove); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3447; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
/*else*/ {
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+ /* "pysam/csamtools.pyx":3449
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+ __pyx_t_3 = PyList_New(0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3449; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__pyx_v_out_stdout = ((PyObject *)__pyx_t_3);
__pyx_t_3 = 0;
}
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+ /* "pysam/csamtools.pyx":3452
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*/
pysam_unset_stderr();
- /* "pysam/csamtools.pyx":3236
+ /* "pysam/csamtools.pyx":3453
* # get error messages
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@@ -33736,7 +35283,7 @@ static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyO
__Pyx_XGOTREF(__pyx_t_11);
/*try:*/ {
- /* "pysam/csamtools.pyx":3237
+ /* "pysam/csamtools.pyx":3454
* pysam_unset_stderr()
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__Pyx_GOTREF(__pyx_t_3);
__Pyx_INCREF(__pyx_v_stderr_f);
PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_v_stderr_f);
@@ -33752,14 +35299,14 @@ static PyObject *__pyx_pf_5pysam_9csamtools__samtools_dispatch(CYTHON_UNUSED PyO
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PyTuple_SET_ITEM(__pyx_t_3, 1, ((PyObject *)__pyx_n_s__r));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__r));
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+ __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 = 3454; __pyx_clineno = __LINE__; goto __pyx_L78_error;}
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__Pyx_GOTREF(__pyx_t_15);
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__pyx_v_inf = __pyx_t_4;
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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+ /* "pysam/csamtools.pyx":3455
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+ __pyx_t_4 = PyObject_GetAttr(__pyx_v_inf, __pyx_n_s__readlines); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3455; __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_t_1 = PyObject_Call(__pyx_t_4, ((PyObject *)__pyx_empty_tuple), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3455; __pyx_clineno = __LINE__; goto __pyx_L92_error;}
__Pyx_GOTREF(__pyx_t_1);
__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0;
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__Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0;
__Pyx_XDECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/csamtools.pyx":3454
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__Pyx_INCREF(__pyx_t_1);
PyTuple_SET_ITEM(__pyx_t_6, 0, __pyx_t_1);
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__Pyx_DECREF(__pyx_t_15); __pyx_t_15 = 0;
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__Pyx_GOTREF(__pyx_t_19);
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__Pyx_GIVEREF(__pyx_t_1);
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}
/*else:*/ {
- /* "pysam/csamtools.pyx":3244
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+ __pyx_t_2 = PyObject_GetAttr(__pyx_v_store, __pyx_n_s__release); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4042; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3826; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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}
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}
/*else*/ {
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__pyx_t_4 = __pyx_v_samfile->samfile;
__pyx_v_self->fp = __pyx_t_4;
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3832; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyErr_SetObject(PyExc_AssertionError, ((PyObject *)__pyx_kp_s_197));
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return __pyx_r;
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PyTuple_SET_ITEM(__pyx_t_1, 0, ((PyObject *)((PyObject*)(&PyList_Type))));
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+ __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 = 4067; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+}
+
+static void __pyx_tp_dealloc_5pysam_9csamtools_FastqProxy(PyObject *o) {
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+static PyObject *__pyx_getprop_5pysam_9csamtools_10FastqProxy_name(PyObject *o, CYTHON_UNUSED void *x) {
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+static PyObject *__pyx_getprop_5pysam_9csamtools_10FastqProxy_sequence(PyObject *o, CYTHON_UNUSED void *x) {
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0, /*mp_ass_subscript*/
};
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};
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- __Pyx_NAMESTR("pysam.csamtools.Fastafile"), /*tp_name*/
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0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_9csamtools_Fastafile, /*tp_dealloc*/
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0, /*tp_getattro*/
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- &__pyx_tp_as_buffer_Fastafile, /*tp_as_buffer*/
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- __pyx_getsets_5pysam_9csamtools_Fastafile, /*tp_getset*/
+ __pyx_getsets_5pysam_9csamtools_Fastqfile, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
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0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_5pysam_9csamtools_Fastafile, /*tp_new*/
+ __pyx_tp_new_5pysam_9csamtools_Fastqfile, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
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return __pyx_pw_5pysam_9csamtools_11AlignedRead_9positions_1__get__(o);
}
+static PyObject *__pyx_getprop_5pysam_9csamtools_11AlignedRead_inferred_length(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_9csamtools_11AlignedRead_15inferred_length_1__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);
}
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};
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};
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@@ -37089,7 +39031,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRow = {
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 [...]
+ __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*/
@@ -37299,7 +39241,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowRegion = {
0, /*tp_setattro*/
&__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("*(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_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*/
@@ -37484,7 +39426,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAll = {
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*/
+ __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\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n \n\n "), /*tp_doc*/
0, /*tp_traverse*/
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@@ -37692,7 +39634,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowAllRefs = {
0, /*tp_setattro*/
&__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("iterates over all mapped reads by chaining iterators over each reference\n "), /*tp_doc*/
+ __Pyx_DOCSTR("iterates over all mapped reads by chaining iterators over each reference\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n "), /*tp_doc*/
__pyx_tp_traverse_5pysam_9csamtools_IteratorRowAllRefs, /*tp_traverse*/
__pyx_tp_clear_5pysam_9csamtools_IteratorRowAllRefs, /*tp_clear*/
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@@ -37902,7 +39844,7 @@ static PyTypeObject __pyx_type_5pysam_9csamtools_IteratorRowSelection = {
0, /*tp_setattro*/
&__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("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n "), /*tp_doc*/
+ __Pyx_DOCSTR("*(Samfile samfile)*\n\n iterate over reads in *samfile* at a given list of file positions.\n\n .. note::\n It is usually not necessary to create an object of this class\n explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.\n "), /*tp_doc*/
__pyx_tp_traverse_5pysam_9csamtools_IteratorRowSelection, /*tp_traverse*/
__pyx_tp_clear_5pysam_9csamtools_IteratorRowSelection, /*tp_clear*/
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};
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- {(char *)"seq_len", __pyx_getprop_5pysam_9csamtools_14IteratorColumn_seq_len, 0, __Pyx_DOCSTR(__pyx_k_245), 0},
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};
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- {(char *)"coverage", __pyx_getprop_5pysam_9csamtools_7SNPCall_coverage, 0, __Pyx_DOCSTR(__pyx_k_252), 0},
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+ {(char *)"reference_base", __pyx_getprop_5pysam_9csamtools_7SNPCall_reference_base, 0, __Pyx_DOCSTR(__pyx_k_256), 0},
+ {(char *)"genotype", __pyx_getprop_5pysam_9csamtools_7SNPCall_genotype, 0, __Pyx_DOCSTR(__pyx_k_257), 0},
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+ {(char *)"snp_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_snp_quality, 0, __Pyx_DOCSTR(__pyx_k_259), 0},
+ {(char *)"mapping_quality", __pyx_getprop_5pysam_9csamtools_7SNPCall_mapping_quality, 0, __Pyx_DOCSTR(__pyx_k_260), 0},
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{&__pyx_kp_s_64, __pyx_k_64, sizeof(__pyx_k_64), 0, 0, 1, 0},
{&__pyx_kp_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 0},
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{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
{&__pyx_kp_s_70, __pyx_k_70, sizeof(__pyx_k_70), 0, 0, 1, 0},
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{&__pyx_kp_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 0},
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{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
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{&__pyx_kp_s__2scB, __pyx_k__2scB, sizeof(__pyx_k__2scB), 0, 0, 1, 0},
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{&__pyx_kp_s__2scI, __pyx_k__2scI, sizeof(__pyx_k__2scI), 0, 0, 1, 0},
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{&__pyx_n_s__F, __pyx_k__F, sizeof(__pyx_k__F), 0, 0, 1, 1},
{&__pyx_n_s__FO, __pyx_k__FO, sizeof(__pyx_k__FO), 0, 0, 1, 1},
{&__pyx_n_s__Fastafile, __pyx_k__Fastafile, sizeof(__pyx_k__Fastafile), 0, 0, 1, 1},
+ {&__pyx_n_s__Fastqfile, __pyx_k__Fastqfile, sizeof(__pyx_k__Fastqfile), 0, 0, 1, 1},
{&__pyx_n_s__GO, __pyx_k__GO, sizeof(__pyx_k__GO), 0, 0, 1, 1},
{&__pyx_n_s__H, __pyx_k__H, sizeof(__pyx_k__H), 0, 0, 1, 1},
{&__pyx_n_s__HD, __pyx_k__HD, sizeof(__pyx_k__HD), 0, 0, 1, 1},
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{0, 0, 0, 0, 0, 0, 0}
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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 = 247; __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 = 254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __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 = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_builtin_ord = __Pyx_GetName(__pyx_b, __pyx_n_s__ord); if (!__pyx_builtin_ord) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 142; __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 = 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 = 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;}
+ __pyx_builtin_map = __Pyx_GetName(__pyx_b, __pyx_n_s__map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 268; __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 = 405; __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 = 424; __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 = 617; __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 = 966; __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 = 1004; __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 = 1006; __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 = 1351; __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 = 1436; __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 = 1452; __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 = 1518; __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 = 2776; __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 = 2776; __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 = 3186; __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 = 3441; __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 = 3443; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
return 0;
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return -1;
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__Pyx_GOTREF(__pyx_k_tuple_4);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
- /* "pysam/csamtools.pyx":398
+ /* "pysam/csamtools.pyx":405
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+ __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 = 405; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_8);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_8));
- /* "pysam/csamtools.pyx":431
+ /* "pysam/csamtools.pyx":438
* '''number of :term:`filename` associated with this object.'''
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+ __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 = 438; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_11);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
- /* "pysam/csamtools.pyx":456
+ /* "pysam/csamtools.pyx":463
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+ __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 = 463; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_12);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
- /* "pysam/csamtools.pyx":462
+ /* "pysam/csamtools.pyx":469
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+ __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 = 469; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_14);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_14));
- /* "pysam/csamtools.pyx":481
+ /* "pysam/csamtools.pyx":488
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* if PY_MAJOR_VERSION >= 3:
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+ __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 = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_k_tuple_20);
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_20));
- /* "pysam/csamtools.pyx":663
+ /* "pysam/csamtools.pyx":593
+ * '''number of :term:`filename` associated with this object.'''
+ * def __get__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
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+ __pyx_k_tuple_22 = PyTuple_Pack(1, ((PyObject *)__pyx_kp_s_10)); if (unlikely(!__pyx_k_tuple_22)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 593; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_22);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_22));
+
+ /* "pysam/csamtools.pyx":597
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+ * def __iter__(self):
+ * if not self._isOpen(): raise ValueError( "I/O operation on closed file" ) # <<<<<<<<<<<<<<
+ * return self
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_25));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
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- __Pyx_GOTREF(__pyx_k_tuple_75);
- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_75));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_80));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_81));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_83));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_84));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_116));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_119));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_126));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_135));
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- __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_146));
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+ __pyx_k_codeobj_312 = (PyObject*)__Pyx_PyCode_New(2, 0, 3, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_311, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s__setfd, 3350, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_312)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3350; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":3141
+ /* "pysam/csamtools.pyx":3358
* 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;}
+ __pyx_k_tuple_314 = PyTuple_Pack(1, ((PyObject *)__pyx_n_s__self)); if (unlikely(!__pyx_k_tuple_314)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __Pyx_GOTREF(__pyx_k_tuple_314);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_314));
+ __pyx_k_codeobj_315 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_314, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s__restore, 3358, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_315)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "pysam/csamtools.pyx":3152
+ /* "pysam/csamtools.pyx":3369
* 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_k_tuple_318 = 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_318);
+ __Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_318));
+ __pyx_k_codeobj_319 = (PyObject*)__Pyx_PyCode_New(3, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_k_tuple_318, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_269, __pyx_n_s___samtools_dispatch, 3369, __pyx_empty_bytes); if (unlikely(!__pyx_k_codeobj_319)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3369; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_RefNannyFinishContext();
return 0;
__pyx_L1_error:;
@@ -41043,14 +43009,34 @@ PyMODINIT_FUNC PyInit_csamtools(void)
/*--- Type init code ---*/
__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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastafile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 382; __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 = 382; __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 = 382; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_FastqProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "FastqProxy", (PyObject *)&__pyx_type_5pysam_9csamtools_FastqProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 523; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_FastqProxy = &__pyx_type_5pysam_9csamtools_FastqProxy;
+ __pyx_vtabptr_5pysam_9csamtools_Fastqfile = &__pyx_vtable_5pysam_9csamtools_Fastqfile;
+ __pyx_vtable_5pysam_9csamtools_Fastqfile.getCurrent = (kseq_t *(*)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *))__pyx_f_5pysam_9csamtools_9Fastqfile_getCurrent;
+ __pyx_vtable_5pysam_9csamtools_Fastqfile.cnext = (int (*)(struct __pyx_obj_5pysam_9csamtools_Fastqfile *))__pyx_f_5pysam_9csamtools_9Fastqfile_cnext;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Fastqfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
+ __pyx_wrapperbase_5pysam_9csamtools_9Fastqfile_12__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_9csamtools_9Fastqfile_12__next__.doc = __pyx_doc_5pysam_9csamtools_9Fastqfile_12__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_9csamtools_9Fastqfile_12__next__;
+ }
+ }
+ #endif
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Fastqfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "Fastqfile", (PyObject *)&__pyx_type_5pysam_9csamtools_Fastqfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 546; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_9csamtools_Fastqfile = &__pyx_type_5pysam_9csamtools_Fastqfile;
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
+ {
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead, "__str__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2246; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41058,7 +43044,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetAttrString(__pyx_m, "AlignedRead", (PyObject *)&__pyx_type_5pysam_9csamtools_AlignedRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2246; __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;
@@ -41066,10 +43052,10 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_Samfile, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41077,26 +43063,26 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_Samfile.tp_dict, __pyx_vtabptr_5pysam_9csamtools_Samfile) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 671; __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 = 671; __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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupProxy) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3246; __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 = 3246; __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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_PileupRead) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3298; __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 = 3298; __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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRow) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1572; __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 = 1572; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41104,17 +43090,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1597; __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 = 1597; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAll, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1681; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41122,14 +43108,14 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowAll.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowAll) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1681; __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 = 1681; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41137,16 +43123,16 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetAttrString(__pyx_m, "IteratorRowAllRefs", (PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1745; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorRowSelection, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41154,8 +43140,8 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorRowSelection.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorRowSelection) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1792; __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 = 1792; __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;
@@ -41163,17 +43149,17 @@ PyMODINIT_FUNC PyInit_csamtools(void)
__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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumn) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1921; __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 = 1921; __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 = 1921; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnRegion, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41181,16 +43167,16 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnRegion.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnRegion) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2083; __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 = 2083; __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 (PyType_Ready(&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
#if CYTHON_COMPILING_IN_CPYTHON
{
- 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;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
__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__;
@@ -41198,14 +43184,14 @@ PyMODINIT_FUNC PyInit_csamtools(void)
}
}
#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;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_9csamtools_IteratorColumnAllRefs.tp_dict, __pyx_vtabptr_5pysam_9csamtools_IteratorColumnAllRefs) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2120; __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 = 2120; __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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_IndexedReads) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 4021; __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 = 4021; __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;}
+ if (PyType_Ready(&__pyx_type_5pysam_9csamtools_SNPCall) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3467; __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 = 3467; __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;
@@ -41378,7 +43364,7 @@ PyMODINIT_FUNC PyInit_csamtools(void)
*/
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+ /* "pysam/csamtools.pyx":4081
* if self.owns_samfile: samclose( self.fp )
*
* __all__ = ["Samfile", # <<<<<<<<<<<<<<
* "Fastafile",
- * "IteratorRow",
+ * "Fastqfile",
*/
- __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;}
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/* "pysam/csamtools.pyx":1
diff --git a/pysam/csamtools.pxd b/pysam/csamtools.pxd
index a490283..8341814 100644
--- a/pysam/csamtools.pxd
+++ b/pysam/csamtools.pxd
@@ -388,6 +388,26 @@ cdef extern from "pysam_util.h":
# void pysam_dump_glf( glf1_t * g, bam_maqcns_t * c )
+ ctypedef struct gzFile:
+ pass
+
+ ctypedef struct kstring_t:
+ size_t l
+ size_t m
+ char *s
+
+ ctypedef struct kseq_t:
+ kstring_t name
+ kstring_t comment
+ kstring_t seq
+ kstring_t qual
+
+ gzFile gzopen( char *, char * )
+ kseq_t * kseq_init( gzFile )
+ int kseq_read( kseq_t * )
+ void kseq_destroy( kseq_t * )
+ void gzclose( gzFile )
+
####################################################################
# Utility types
@@ -412,6 +432,17 @@ cdef class Fastafile:
cdef char * _fetch( self, char * reference, int start, int end, int * length )
+cdef class FastqProxy:
+ cdef kseq_t * _delegate
+
+cdef class Fastqfile:
+ cdef char * _filename
+ cdef gzFile fastqfile
+ cdef kseq_t * entry
+
+ cdef kseq_t * getCurrent( self )
+ cdef int cnext(self)
+
cdef class AlignedRead:
# object that this AlignedRead represents
diff --git a/pysam/csamtools.pyx b/pysam/csamtools.pyx
index 58fed03..763798f 100644
--- a/pysam/csamtools.pyx
+++ b/pysam/csamtools.pyx
@@ -185,6 +185,13 @@ cdef makePileupRead( bam_pileup1_t * src ):
dest._is_tail = src.is_tail
return dest
+cdef class FastqProxy
+cdef makeFastqProxy( kseq_t * src):
+ '''enter src into AlignedRead.'''
+ cdef FastqProxy dest = FastqProxy.__new__(FastqProxy)
+ dest._delegate = src
+ return dest
+
cdef convertBinaryTagToList( uint8_t * s ):
"""return bytesize, number of values list of values in s."""
cdef char auxtype
@@ -506,6 +513,109 @@ cdef class Fastafile:
end-1,
length )
+
+######################################################################
+######################################################################
+######################################################################
+## Fastq file
+######################################################################
+
+cdef class FastqProxy:
+ def __init__(self): pass
+
+ property name:
+ def __get__(self):
+ return self._delegate.name.s
+
+ property sequence:
+ def __get__(self):
+ return self._delegate.seq.s
+
+ property comment:
+ def __get__(self):
+ if self._delegate.comment.l:
+ return self._delegate.comment.s
+ else: return None
+
+ property quality:
+ def __get__(self):
+ if self._delegate.qual.l:
+ return self._delegate.qual.s
+ else: return None
+
+cdef class Fastqfile:
+ '''*(filename)*
+
+ A *FASTQ* file. The file is automatically opened.
+
+ '''
+
+ def __cinit__(self, *args, **kwargs ):
+ # self.fastqfile = NULL
+ self._filename = NULL
+ self._open( *args, **kwargs )
+
+ def _isOpen( self ):
+ '''return true if samfile has been opened.'''
+ return self._filename != NULL
+
+ def _open( self,
+ filename ):
+ '''open an indexed fasta file.
+
+ This method expects an indexed fasta file.
+ '''
+
+ if not os.path.exists( filename ):
+ raise IOError( "No such file or directory: %s" % filename )
+
+ # close a previously opened file
+ # if self.fastqfile != NULL: self.close()
+ if self._filename != NULL: free(self._filename)
+ filename = _my_encodeFilename(filename)
+ self._filename = strdup(filename)
+ self.fastqfile = gzopen( filename, "r" )
+ self.entry = kseq_init( self.fastqfile )
+
+ def close( self ):
+ '''close file.'''
+ if self._filename != NULL:
+ gzclose( self.fastqfile )
+ free(self._filename)
+
+ def __dealloc__(self):
+ kseq_destroy(self.entry)
+ self.close()
+
+ property filename:
+ '''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
+
+ def __iter__(self):
+ if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
+ return self
+
+ cdef kseq_t * getCurrent( self ):
+ return self.entry
+
+ cdef int cnext(self):
+ '''C version of iterator
+ '''
+ return kseq_read(self.entry)
+
+ def __next__(self):
+ """
+ python version of next().
+ """
+ cdef int l
+ l = kseq_read( self.entry)
+ if (l > 0):
+ return makeFastqProxy( self.entry )
+ else:
+ raise StopIteration
+
#------------------------------------------------------------------------
#------------------------------------------------------------------------
#------------------------------------------------------------------------
@@ -1459,6 +1569,11 @@ cdef class IteratorRow:
iterate over all reads in all reference sequences.
The method :meth:`Samfile.fetch` returns an IteratorRow.
+
+ .. note::
+ It is usually not necessary to create an object of this class
+ explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.
+
'''
pass
@@ -1481,6 +1596,11 @@ cdef class IteratorRowRegion(IteratorRow):
Note that the index will be shared between
samfile and the iterator.
+
+ .. note::
+ It is usually not necessary to create an object of this class
+ explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.
+
"""
def __cinit__(self, Samfile samfile, int tid, int beg, int end, int reopen = True ):
@@ -1550,6 +1670,12 @@ cdef class IteratorRowAll(IteratorRow):
By default, the file is re-openend to avoid conflicts between
multiple iterators working on the same file. Set *reopen* = False
to not re-open *samfile*.
+
+ .. note::
+ It is usually not necessary to create an object of this class
+ explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.
+
+
"""
def __cinit__(self, Samfile samfile, int reopen = True ):
@@ -1602,6 +1728,10 @@ cdef class IteratorRowAll(IteratorRow):
cdef class IteratorRowAllRefs(IteratorRow):
"""iterates over all mapped reads by chaining iterators over each reference
+
+ .. note::
+ It is usually not necessary to create an object of this class
+ explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.
"""
def __cinit__(self, Samfile samfile):
@@ -1647,6 +1777,10 @@ cdef class IteratorRowSelection(IteratorRow):
"""*(Samfile samfile)*
iterate over reads in *samfile* at a given list of file positions.
+
+ .. note::
+ It is usually not necessary to create an object of this class
+ explicitely. It is returned as a result of call to a :meth:`Samfile.fetch`.
"""
def __cinit__(self, Samfile samfile, positions, int reopen = True ):
@@ -1828,15 +1962,11 @@ cdef class IteratorColumn:
self.plp = NULL
self.pileup_iter = <bam_plp_t>NULL
-
def __iter__(self):
return self
cdef int cnext(self):
'''perform next iteration.
-
- This method is analogous to the samtools bam_plp_auto method.
- It has been re-implemented to permit for filtering.
'''
self.plp = bam_plp_auto( self.pileup_iter,
&self.tid,
@@ -1922,12 +2052,13 @@ cdef class IteratorColumn:
bam_plp_reset(self.pileup_iter)
def __dealloc__(self):
- # reset in order to avoid memory leak messages for iterators that have
- # not been fully consumed
+ # 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)
self.pileup_iter = <bam_plp_t>NULL
+ self.plp = <const_bam_pileup1_t_ptr>NULL
if self.iterdata.seq != NULL:
free(self.iterdata.seq)
@@ -2203,6 +2334,10 @@ cdef class AlignedRead:
def __hash__(self):
return _Py_HashPointer(<void *>self)
+ #######################################################################
+ #######################################################################
+ ## Basic properties
+ #######################################################################
property qname:
"""the query name (None if not present)"""
def __get__(self):
@@ -2348,9 +2483,22 @@ cdef class AlignedRead:
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).
+ """read sequence bases, including :term:`soft clipped` bases
+ (None if not present).
+
+ 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.
- 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."""
+ Note that assigning to seq will invalidate any quality scores.
+ Thus, to in-place edit the sequence and quality scores, copies of
+ the quality scores need to be taken. Consider trimming for example::
+
+ q = read.qual
+ read.seq = read.seq[5:10]
+ read.qual = q[5:10]
+
+ """
def __get__(self):
cdef bam1_t * src
cdef char * s
@@ -2363,48 +2511,63 @@ cdef class AlignedRead:
def __set__(self,seq):
# samtools manages sequence and quality length memory together
# 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
cdef uint8_t * p
cdef char * s
cdef int l, k, nbytes_new, nbytes_old
- src = self._delegate
+ if seq == None:
+ l = 0
+ else:
+ l = len(seq)
+ seq = _force_bytes(seq)
- l = len(seq)
+ src = self._delegate
# 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
nbytes_old = (src.core.l_qseq+1)/2 + src.core.l_qseq
+
# acquire pointer to location in memory
p = bam1_seq( src )
src.core.l_qseq = l
+ # change length of data field
pysam_bam_update( src,
nbytes_old,
nbytes_new,
p)
- # re-acquire pointer to location in memory
- # 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
- for k from 0 <= k < l:
- p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
-
- # erase qualities
- p = bam1_qual( src )
- p[0] = 0xff
+ if l > 0:
+ # re-acquire pointer to location in memory
+ # 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
+ for k from 0 <= k < l:
+ p[k/2] |= pysam_translate_sequence(s[k]) << 4 * (1 - k % 2)
+
+ # erase qualities
+ p = bam1_qual( src )
+ p[0] = 0xff
property qual:
- """read sequence base qualities, including :term:`soft clipped` bases (None if not present).
+ """read sequence base qualities, including :term:`soft
+ clipped` bases (None if not present).
- 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."""
+ 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.
+
+ Note that to set quality scores the sequence has to be set
+ previously as this will determine the permitted length of
+ the quality score array.
+
+ This method raises a ValueError if the length of the
+ quality scores and the sequence are not the same.
+ """
def __get__(self):
cdef bam1_t * src
@@ -2784,6 +2947,10 @@ cdef class AlignedRead:
"""the position of the mate"""
def __get__(self): return self._delegate.core.mpos
def __set__(self, mpos): self._delegate.core.mpos = mpos
+ #######################################################################
+ #######################################################################
+ ## Flags
+ #######################################################################
property isize:
"""the insert size
deprecated: use tlen instead"""
@@ -2859,6 +3026,11 @@ cdef class AlignedRead:
def __set__(self,val):
if val: self._delegate.core.flag |= BAM_FDUP
else: self._delegate.core.flag &= ~BAM_FDUP
+
+ #######################################################################
+ #######################################################################
+ ## Derived properties
+ #######################################################################
property positions:
"""a list of reference positions that this read aligns to."""
def __get__(self):
@@ -2886,6 +3058,32 @@ cdef class AlignedRead:
return result
+ property inferred_length:
+ """inferred read length from CIGAR string.
+
+ Returns 0 if CIGAR string is not present.
+ """
+ def __get__(self):
+ cdef uint32_t k, qpos
+ cdef int op
+ cdef uint32_t * cigar_p
+ cdef bam1_t * src
+
+ src = self._delegate
+ if src.core.n_cigar == 0: return 0
+
+ qpos = 0
+ cigar_p = bam1_cigar(src)
+
+ for k from 0 <= k < src.core.n_cigar:
+ op = cigar_p[k] & BAM_CIGAR_MASK
+
+ if op == BAM_CMATCH or op == BAM_CINS or op == BAM_CSOFT_CLIP:
+ qpos += cigar_p[k] >> BAM_CIGAR_SHIFT
+
+ return qpos
+
+
property aligned_pairs:
"""a list of aligned read and reference positions.
@@ -2927,7 +3125,10 @@ cdef class AlignedRead:
return result
-
+ #######################################################################
+ #######################################################################
+ ##
+ #######################################################################
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.
@@ -3069,7 +3270,7 @@ cdef class PileupProxy:
cdef int x
pileups = []
- if self.plp[0] == NULL:
+ if self.plp == NULL or self.plp[0] == NULL:
raise ValueError("PileupProxy accessed after iterator finished")
# warning: there could be problems if self.n and self.buf are
@@ -3863,6 +4064,7 @@ cdef class IndexedReads:
__all__ = ["Samfile",
"Fastafile",
+ "Fastqfile",
"IteratorRow",
"IteratorColumn",
"AlignedRead",
diff --git a/pysam/ctabix.c b/pysam/ctabix.c
index 88603ad..3d639f2 100644
--- a/pysam/ctabix.c
+++ b/pysam/ctabix.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
+/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -348,163 +348,147 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_BedProxy;
struct __pyx_obj_5pysam_6ctabix_Parser;
-struct __pyx_obj_5pysam_6ctabix_asTuple;
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_Tabixfile;
-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_asVCF;
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
struct __pyx_obj_5pysam_6ctabix_TabixIterator;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
+struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
-/* "TabProxies.pxd":41
- * ctypedef int uint64_t
+/* "pysam/ctabix.pxd":190
+ * cdef tabix_t * tabixfile
*
- * cdef class TupleProxy: # <<<<<<<<<<<<<<
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
*
- * cdef:
*/
-struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
+struct __pyx_obj_5pysam_6ctabix_Parser {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
- char *data;
- char **fields;
- int nfields;
- int index;
- int nbytes;
- int offset;
- int is_modified;
};
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
+/* "pysam/ctabix.pxd":199
+ * pass
*
- * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
- * pass
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
+ * pass
*
*/
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_asBed {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":72
- * pass
+/* "pysam/ctabix.pxd":202
+ * pass
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef:
*/
-struct __pyx_obj_5pysam_10TabProxies_BedProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
+struct __pyx_obj_5pysam_6ctabix_asVCF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "pysam/ctabix.pxd":190
- * cdef tabix_t * tabixfile
- *
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
+/* "pysam/ctabix.pxd":210
+ * cdef Parser parser
*
+ * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
*/
-struct __pyx_obj_5pysam_6ctabix_Parser {
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
+ FILE *infile;
+ char *buffer;
+ size_t size;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "pysam/ctabix.pxd":193
- * pass
- *
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * pass
+/* "pysam/ctabix.pxd":182
+ * cdef char * _filename
*
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_asTuple {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "pysam/ctabix.pxd":205
- * pass
+/* "pysam/ctabix.pxd":186
+ * cdef tabix_t * tabixfile
*
- * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
* cdef ti_iter_t iterator
* cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
PyObject_HEAD
ti_iter_t iterator;
tabix_t *tabixfile;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "pysam/ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+/* "TabProxies.pxd":41
+ * ctypedef int uint64_t
*
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
+ * cdef class TupleProxy: # <<<<<<<<<<<<<<
*
- * # pointer to tabixfile
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_Tabixfile {
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
PyObject_HEAD
- tabix_t *tabixfile;
- int isremote;
- char *_filename;
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
+ char *data;
+ char **fields;
+ int nfields;
+ int index;
+ int nbytes;
+ int offset;
+ int is_modified;
};
-/* "pysam/ctabix.pxd":196
- * pass
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_asGTF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
-/* "pysam/ctabix.pxd":218
- * cdef __cnext__(self)
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( 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/ctabix.pxd":186
- * cdef tabix_t * tabixfile
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
*
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
- PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
};
@@ -522,75 +506,91 @@ struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
};
-/* "pysam/ctabix.pxd":202
+/* "pysam/ctabix.pxd":196
* pass
*
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_asVCF {
+struct __pyx_obj_5pysam_6ctabix_asGTF {
struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "pysam/ctabix.pxd":199
- * pass
+/* "pysam/ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
*
+ * # pointer to tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_asBed {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
+ PyObject_HEAD
+ tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
};
-/* "pysam/ctabix.pxd":182
- * cdef char * _filename
+/* "pysam/ctabix.pxd":205
+ * pass
*
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
* cdef ti_iter_t iterator
* cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
PyObject_HEAD
ti_iter_t iterator;
tabix_t *tabixfile;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
+/* "TabProxies.pxd":72
+ * pass
*
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t start;
+ uint32_t end;
+ int bedfields;
};
-/* "pysam/ctabix.pxd":210
- * cdef Parser parser
+/* "pysam/ctabix.pxd":218
+ * cdef __cnext__(self)
*
- * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * 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":193
+ * pass
+ *
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+};
+
+
/* "TabProxies.pxd":41
* ctypedef int uint64_t
@@ -638,19 +638,32 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
+/* "pysam/ctabix.pyx":709
+ * ## Iterators for parsing through unindexed files.
+ * #########################################################
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
*
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ */
+
+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":72
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
/* "pysam/ctabix.pyx":771
@@ -667,32 +680,19 @@ 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
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
* cdef:
*/
-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 *);
+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_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index 8456837..51f2cf0 100644
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.18 on Fri Jun 28 06:37:45 2013 */
+/* Generated by Cython 0.18 on Fri Sep 20 00:20:26 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -346,26 +346,26 @@ static const char *__pyx_f[] = {
/*--- Type declarations ---*/
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_4cvcf_VCFRecord;
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
-struct __pyx_obj_5pysam_6ctabix_Tabixfile;
+struct __pyx_obj_5pysam_6ctabix_asBed;
struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
-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_2__parse;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
+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_4cvcf_VCFRecord;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data;
struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile;
struct __pyx_obj_5pysam_6ctabix_TabixIterator;
-struct __pyx_obj_5pysam_6ctabix_asBed;
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
struct __pyx_defaults;
typedef struct __pyx_defaults __pyx_defaults;
struct __pyx_defaults1;
@@ -405,43 +405,49 @@ struct __pyx_obj_5pysam_6ctabix_Parser {
};
-/* "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;
};
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "ctabix.pxd":205
+ * pass
*
- * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
+ * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "pysam/cvcf.pyx":229
- *
+/* "pysam/cvcf.pyx":902
+ * return line
*
- * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
- * '''converts a :term:`tabix row` into a VCF record.'''
- * cdef vcffile
+ * def _parse(self, line, stream): # <<<<<<<<<<<<<<
+ * # deal with files with header only
+ * if line.startswith("##"): return
*/
-struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
- PyObject *vcffile;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse {
+ PyObject_HEAD
+ PyObject *__pyx_v_d;
+ PyObject *__pyx_v_line;
+ PyObject *__pyx_v_self;
+ PyObject *__pyx_v_stream;
+ Py_ssize_t __pyx_t_0;
+ PyObject *__pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
@@ -465,6 +471,32 @@ struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
};
+/* "TabProxies.pxd":69
+ * cdef char * getAttributes( self )
+ *
+ * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+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 )
+ *
+ * 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":95
* ###########################################################################################################
*
@@ -480,47 +512,28 @@ struct __pyx_obj_5pysam_4cvcf_VCFRecord {
};
-/* "ctabix.pxd":186
- * cdef tabix_t * tabixfile
- *
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
- */
-struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
- PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
-};
-
-
-/* "ctabix.pxd":172
- * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+/* "pysam/cvcf.pyx":229
*
- * cdef class Tabixfile: # <<<<<<<<<<<<<<
*
- * # pointer to tabixfile
+ * cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
+ * '''converts a :term:`tabix row` into a VCF record.'''
+ * cdef vcffile
*/
-struct __pyx_obj_5pysam_6ctabix_Tabixfile {
- PyObject_HEAD
- tabix_t *tabixfile;
- int isremote;
- char *_filename;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+ PyObject *vcffile;
};
-/* "ctabix.pxd":205
+/* "ctabix.pxd":202
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
* pass
*
- * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
- PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_6ctabix_asVCF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
@@ -537,93 +550,72 @@ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data {
};
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
- FILE *infile;
- char *buffer;
- size_t size;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
-/* "pysam/cvcf.pyx":902
- * return line
+/* "ctabix.pxd":186
+ * cdef tabix_t * tabixfile
*
- * def _parse(self, line, stream): # <<<<<<<<<<<<<<
- * # deal with files with header only
- * if line.startswith("##"): return
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse {
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
PyObject_HEAD
- PyObject *__pyx_v_d;
- PyObject *__pyx_v_line;
- PyObject *__pyx_v_self;
- PyObject *__pyx_v_stream;
- Py_ssize_t __pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "ctabix.pxd":202
+/* "ctabix.pxd":196
* pass
*
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_5pysam_6ctabix_asVCF {
+struct __pyx_obj_5pysam_6ctabix_asGTF {
struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "TabProxies.pxd":69
- * cdef char * getAttributes( self )
- *
- * cdef class NamedTupleProxy( TupleProxy) : # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
-};
-
-
-/* "TabProxies.pxd":72
- * pass
+/* "ctabix.pxd":172
+ * # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class Tabixfile: # <<<<<<<<<<<<<<
*
- * cdef:
+ * # pointer to tabixfile
*/
-struct __pyx_obj_5pysam_10TabProxies_BedProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
+ PyObject_HEAD
+ tabix_t *tabixfile;
+ int isremote;
+ char *_filename;
};
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+/* "ctabix.pxd":182
+ * cdef char * _filename
*
- * cdef:
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
@@ -644,55 +636,63 @@ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr {
};
-/* "ctabix.pxd":196
- * pass
- *
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
+/* "ctabix.pxd":210
+ * cdef Parser parser
*
+ * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
*/
-struct __pyx_obj_5pysam_6ctabix_asGTF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
+ PyObject_HEAD
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtab;
+ FILE *infile;
+ char *buffer;
+ size_t size;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "ctabix.pxd":182
- * cdef char * _filename
+/* "TabProxies.pxd":72
+ * pass
*
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
-struct __pyx_obj_5pysam_6ctabix_TabixIterator {
- PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
+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":199
- * pass
- *
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
*
+ * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
*/
-struct __pyx_obj_5pysam_6ctabix_asBed {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+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;
};
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
+/* "ctabix.pxd":193
+ * pass
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * pass
*
- * cdef:
*/
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
@@ -729,89 +729,89 @@ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
-/* "TabProxies.pxd":72
- * pass
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * 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;
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
+/* "pysam/cvcf.pyx":95
+ * ###########################################################################################################
*
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
*
- * cdef:
*/
-struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
+struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
+static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "ctabix.pxd":210
+ * cdef Parser parser
*
- * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
* cdef FILE * infile
- * cdef Parser parser
+ * cdef char * buffer
*/
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *);
+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_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
-/* "pysam/cvcf.pyx":95
- * ###########################################################################################################
+/* "TabProxies.pxd":72
+ * pass
*
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
*
- * cdef:
+ * cdef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
*/
-struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
- struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *);
};
-static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
-struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
+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_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
diff --git a/pysam/pysam_util.c b/pysam/pysam_util.c
index 4990e64..82c959c 100644
--- a/pysam/pysam_util.c
+++ b/pysam/pysam_util.c
@@ -8,6 +8,9 @@
#include "pysam_util.h"
#include "errmod.h" // for pysam_dump
+// for sequence parsing
+#include "kseq.h"
+
#ifndef inline
#define inline __inline
#endif
diff --git a/pysam/pysam_util.h b/pysam/pysam_util.h
index 90a9378..ce6c753 100644
--- a/pysam/pysam_util.h
+++ b/pysam/pysam_util.h
@@ -1,6 +1,12 @@
#ifndef PYSAM_UTIL_H
#define PYSAM_UTIL_H
+#include "kseq.h"
+
+// #######################################################
+// fastq parsing
+KSEQ_INIT(gzFile, gzread)
+
//////////////////////////////////////////////////////////////////
/*! set pysam standard error to point to file descriptor
diff --git a/pysam/tabix_util.c b/pysam/tabix_util.c
index b06a614..0305de1 100644
--- a/pysam/tabix_util.c
+++ b/pysam/tabix_util.c
@@ -2,3 +2,25 @@
#include "stdio.h"
FILE * pysamerr = NULL;
+#if !(_POSIX_C_SOURCE >= 200809L || _XOPEN_SOURCE >= 700)
+/*
+ * A rudimentary emulation of getline() for systems that dont support it
+ * natively. Since this is used for PPD file reading, it assumes (possibly
+ * falsely) that BUFSIZ is big enough.
+ */
+ssize_t
+getline(char **line, size_t *linelen, FILE *fp)
+{
+ if (*linelen == 0)
+ {
+ *linelen = BUFSIZ;
+ *line = malloc(*linelen);
+ }
+
+ memset(*line, 0, *linelen);
+ fgets(*line, *linelen, fp);
+
+ return (strlen(*line));
+
+}
+#endif
diff --git a/pysam/version.py b/pysam/version.py
index 52609de..0dfb2cf 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,6 +1,6 @@
# pysam versioning information
-__version__ = "0.7.5"
+__version__ = "0.7.6"
__samtools_version__ = "0.1.19"
diff --git a/setup.py b/setup.py
index 1b4a325..5fa876f 100644
--- a/setup.py
+++ b/setup.py
@@ -126,11 +126,12 @@ if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
# cp samtools/*.h pysam/*.h pysam/include
# cp samtools/win32/*.h pysam/include/win32
-
-from distribute_setup import use_setuptools
-use_setuptools()
-
-from setuptools import Extension, setup, find_packages
+try:
+ from setuptools import Extension, setup, find_packages
+except ImportError:
+ from ez_setup import use_setuptools
+ use_setuptools()
+ from setuptools import Extension, setup, find_packages
#######################################################
#######################################################
diff --git a/tests/Makefile b/tests/Makefile
index 7774778..05963e5 100644
--- a/tests/Makefile
+++ b/tests/Makefile
@@ -12,8 +12,7 @@ all: ex1.pileup.gz ex1.bam.bai \
example_unmapped_reads_no_sq.bam \
example_user_header.bam \
example_btag.bam \
- example_bai.bam
-
+ example_bai.bam \
ex2.sam.gz: ex1.bam ex1.bam.bai
samtools view -h ex1.bam | gzip > ex2.sam.gz
diff --git a/tests/pysam_test.py b/tests/pysam_test.py
index 5cfed74..67f205f 100755
--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -812,6 +812,14 @@ class TestIteratorColumn2(unittest.TestCase):
self.assertEqual( len(columns), 3)
self.assertEqual( columns, [169,170,171] )
+ def testAccessOnClosedIterator( self ):
+ '''see issue 131
+
+ Accessing pileup data after iterator has closed.
+ '''
+ pcolumn = self.samfile.pileup( 'chr1', 170, 180).__next__()
+ self.assertRaises( ValueError, getattr, pcolumn, "pileups" )
+
class TestAlignedReadFromBam(unittest.TestCase):
def setUp(self):
@@ -1163,6 +1171,30 @@ class TestFastaFile(unittest.TestCase):
def tearDown(self):
self.file.close()
+class TestFastqFile(unittest.TestCase):
+
+ def setUp(self):
+ self.file=pysam.Fastqfile( "ex1.fq" )
+
+ def testCounts( self ):
+ self.assertEqual( len( [ x for x in self.file ] ), 3270 )
+
+ def testMissingFile( self ):
+ self.assertRaises( IOError, pysam.Fastqfile, "nothere.fq" )
+
+ def testSequence( self ):
+ s = self.file.__next__()
+ # test first entry
+ self.assertEqual( s.sequence, b"GGGAACAGGGGGGTGCACTAATGCGCTCCACGCCC")
+ self.assertEqual( s.quality, b"<<86<<;<78<<<)<;4<67<;<;<74-7;,;8,;")
+ self.assertEqual( s.name, b"B7_589:1:101:825:28" )
+
+ for s in self.file: pass
+ # test last entry
+ self.assertEqual( s.sequence, b"TAATTGAAAAATTCATTTAAGAAATTACAAAATAT")
+ self.assertEqual( s.quality, b"<<<<<;<<<<<<<<<<<<<<<;;;<<<;<<8;<;<")
+ self.assertEqual( s.name, b"EAS56_65:8:64:507:478" )
+
class TestAlignedRead(unittest.TestCase):
'''tests to check if aligned read can be constructed
and manipulated.
@@ -1264,6 +1296,23 @@ class TestAlignedRead(unittest.TestCase):
self.assertEqual( getattr(b, x), False )
self.checkFieldEqual( a, b )
+ def testUpdate( self ):
+ '''issue 135: inplace update of sequence and quality score.
+
+ This does not work as setting the sequence will erase
+ the quality scores.
+ '''
+ a = self.buildRead()
+ a.seq = a.seq[5:10]
+ self.assertEqual( a.qual, None )
+
+ a = self.buildRead()
+ s = a.qual
+ a.seq = a.seq[5:10]
+ a.qual = s[5:10]
+
+ self.assertEqual( a.qual, s[5:10])
+
def testLargeRead( self ):
'''build an example read.'''
--
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