[med-svn] [pysam] 05/13: Imported Upstream version 0.7.3
Charles Plessy
plessy at alioth.debian.org
Fri Aug 9 09:47:29 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch master
in repository pysam.
commit 14c14ac0fd1811c9ee22b51f501a5a66b279e509
Author: Charles Plessy <plessy at debian.org>
Date: Fri Aug 9 18:34:33 2013 +0900
Imported Upstream version 0.7.3
---
MANIFEST.in | 5 +-
PKG-INFO | 6 +-
distribute_setup.py | 107 +-
pysam.egg-info/PKG-INFO | 6 +-
pysam.egg-info/SOURCES.txt | 8 +
pysam.egg-info/requires.txt | 2 +-
pysam.egg-info/top_level.txt | 4 -
pysam/__init__.py | 5 +-
pysam/alternatives.py | 82 +
pysam/ctabix.c | 3822 +++++++--------
pysam/ctabix.pyx | 2 +-
pysam/cvcf.c |10447 +++++++++++++++++++++++-------------------
pysam/cvcf.pyx | 4 +-
pysam/version.py | 2 +-
setup.py | 36 +-
tabix/bedidx.c | 156 +
tabix/bgzf.c | 555 +++
tabix/bgzip.c | 206 +
tabix/index.c | 967 ++++
tabix/knetfile.c | 632 +++
tabix/kstring.c | 165 +
tests/example_btag.bam | Bin 0 -> 771 bytes
tests/pysam_test.py | 10 +
23 files changed, 10486 insertions(+), 6743 deletions(-)
diff --git a/MANIFEST.in b/MANIFEST.in
index f613856..a0c9889 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -21,9 +21,12 @@ include pysam/TabProxies.pxd
include pysam/cvcf.pyx
include pysam/cvcf.pxd
include pysam/cvcf.c
+include pysam/*.c
+include pysam/*.h
include pysam/pysam_util.h
include samtools/*.h
include samtools/*/*.h
+include tabix/*.c
include tabix/*.h
# pysam tests
@@ -44,6 +47,7 @@ include tests/example.py
include tests/pysam_test.py
include tests/segfault_tests.py
include tests/example_*.sam
+include tests/example_btag.bam
include tests/tag_bug.bam
include tests/example.vcf40
include tests/example_empty_header.bam
@@ -56,4 +60,3 @@ include tests/example.gtf.gz.tbi
include tests/example.bed.gz
include tests/example.bed.gz.tbi
include tests/vcf-examples/*.vcf
-
diff --git a/PKG-INFO b/PKG-INFO
index cc28edb..905bd25 100644
--- a/PKG-INFO
+++ b/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.2
+Version: 0.7.3
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
@@ -11,8 +11,6 @@ Description:
pysam
*****
- For more information, see http://code.google.com/p/pysam.
-
Platform: ALL
-Requires: cython (>=0.16)
+Requires: cython (>=0.17)
diff --git a/distribute_setup.py b/distribute_setup.py
index b204902..a1cc2a1 100644
--- a/distribute_setup.py
+++ b/distribute_setup.py
@@ -14,11 +14,14 @@ 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:
@@ -46,7 +49,7 @@ except ImportError:
args = [quote(arg) for arg in args]
return os.spawnl(os.P_WAIT, sys.executable, *args) == 0
-DEFAULT_VERSION = "0.6.24"
+DEFAULT_VERSION = "0.6.34"
DEFAULT_URL = "http://pypi.python.org/packages/source/d/distribute/"
SETUPTOOLS_FAKED_VERSION = "0.6c11"
@@ -63,7 +66,7 @@ Description: xxx
""" % SETUPTOOLS_FAKED_VERSION
-def _install(tarball):
+def _install(tarball, install_args=()):
# extracting the tarball
tmpdir = tempfile.mkdtemp()
log.warn('Extracting in %s', tmpdir)
@@ -81,11 +84,14 @@ def _install(tarball):
# installing
log.warn('Installing Distribute')
- if not _python_cmd('setup.py', 'install'):
+ 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):
@@ -110,6 +116,7 @@ def _build_egg(egg, tarball, to_dir):
finally:
os.chdir(old_wd)
+ shutil.rmtree(tmpdir)
# returning the result
log.warn(egg)
if not os.path.exists(egg):
@@ -144,7 +151,7 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
except ImportError:
return _do_download(version, download_base, to_dir, download_delay)
try:
- pkg_resources.require("distribute>="+version)
+ pkg_resources.require("distribute>=" + version)
return
except pkg_resources.VersionConflict:
e = sys.exc_info()[1]
@@ -167,6 +174,7 @@ def use_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
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
@@ -203,6 +211,7 @@ def download_setuptools(version=DEFAULT_VERSION, download_base=DEFAULT_URL,
dst.close()
return os.path.realpath(saveto)
+
def _no_sandbox(function):
def __no_sandbox(*args, **kw):
try:
@@ -227,9 +236,12 @@ def _no_sandbox(function):
return __no_sandbox
+
def _patch_file(path, content):
"""Will backup the file then patch it"""
- existing_content = open(path).read()
+ f = open(path)
+ existing_content = f.read()
+ f.close()
if existing_content == content:
# already patched
log.warn('Already patched.')
@@ -245,15 +257,21 @@ def _patch_file(path, content):
_patch_file = _no_sandbox(_patch_file)
+
def _same_content(path, content):
- return open(path).read() == 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 into %s', path, new_name)
+ 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)
@@ -267,7 +285,7 @@ def _remove_flat_installation(placeholder):
log.warn('Could not locate setuptools*.egg-info')
return
- log.warn('Removing elements out of the way...')
+ 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)
@@ -289,11 +307,13 @@ def _remove_flat_installation(placeholder):
_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')
@@ -307,7 +327,11 @@ def _create_fake_setuptools_pkg_info(placeholder):
return
log.warn('Creating %s', pkg_info)
- f = open(pkg_info, 'w')
+ 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:
@@ -321,7 +345,10 @@ def _create_fake_setuptools_pkg_info(placeholder):
finally:
f.close()
-_create_fake_setuptools_pkg_info = _no_sandbox(_create_fake_setuptools_pkg_info)
+_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
@@ -343,6 +370,7 @@ def _patch_egg_dir(path):
_patch_egg_dir = _no_sandbox(_patch_egg_dir)
+
def _before_install():
log.warn('Before install bootstrap.')
_fake_setuptools()
@@ -351,7 +379,7 @@ def _before_install():
def _under_prefix(location):
if 'install' not in sys.argv:
return True
- args = sys.argv[sys.argv.index('install')+1:]
+ args = sys.argv[sys.argv.index('install') + 1:]
for index, arg in enumerate(args):
for option in ('--root', '--prefix'):
if arg.startswith('%s=' % option):
@@ -359,7 +387,7 @@ def _under_prefix(location):
return location.startswith(top_dir)
elif arg == option:
if len(args) > index:
- top_dir = args[index+1]
+ top_dir = args[index + 1]
return location.startswith(top_dir)
if arg == '--user' and USER_SITE is not None:
return location.startswith(USER_SITE)
@@ -376,11 +404,14 @@ def _fake_setuptools():
return
ws = pkg_resources.working_set
try:
- setuptools_dist = ws.find(pkg_resources.Requirement.parse('setuptools',
- replacement=False))
+ 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'))
+ setuptools_dist = ws.find(
+ pkg_resources.Requirement.parse('setuptools')
+ )
if setuptools_dist is None:
log.warn('No setuptools distribution found')
@@ -414,7 +445,7 @@ def _fake_setuptools():
res = _patch_egg_dir(setuptools_location)
if not res:
return
- log.warn('Patched done.')
+ log.warn('Patching complete.')
_relaunch()
@@ -422,7 +453,9 @@ def _relaunch():
log.warn('Relaunching...')
# we have to relaunch the process
# pip marker to avoid a relaunch bug
- if sys.argv[:3] == ['-c', 'install', '--single-version-externally-managed']:
+ _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))
@@ -448,7 +481,7 @@ def _extractall(self, path=".", members=None):
# Extract directories with a safe mode.
directories.append(tarinfo)
tarinfo = copy.copy(tarinfo)
- tarinfo.mode = 448 # decimal for oct 0700
+ tarinfo.mode = 448 # decimal for oct 0700
self.extract(tarinfo, path)
# Reverse sort directories.
@@ -475,11 +508,39 @@ def _extractall(self, path=".", members=None):
self._dbg(1, "tarfile: %s" % e)
-def main(argv, version=DEFAULT_VERSION):
+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"""
- tarball = download_setuptools()
- _install(tarball)
-
+ options = _parse_args()
+ tarball = download_setuptools(download_base=options.download_base)
+ return _install(tarball, _build_install_args(options))
if __name__ == '__main__':
- main(sys.argv[1:])
+ sys.exit(main())
diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO
index cc28edb..905bd25 100644
--- a/pysam.egg-info/PKG-INFO
+++ b/pysam.egg-info/PKG-INFO
@@ -1,6 +1,6 @@
Metadata-Version: 1.1
Name: pysam
-Version: 0.7.2
+Version: 0.7.3
Summary: pysam
Home-page: http://code.google.com/p/pysam/
Author: Andreas Heger
@@ -11,8 +11,6 @@ Description:
pysam
*****
- For more information, see http://code.google.com/p/pysam.
-
Platform: ALL
-Requires: cython (>=0.16)
+Requires: cython (>=0.17)
diff --git a/pysam.egg-info/SOURCES.txt b/pysam.egg-info/SOURCES.txt
index b59e914..8a914d5 100644
--- a/pysam.egg-info/SOURCES.txt
+++ b/pysam.egg-info/SOURCES.txt
@@ -12,6 +12,7 @@ pysam/TabProxies.pxd
pysam/TabProxies.pyx
pysam/VCF.py
pysam/__init__.py
+pysam/alternatives.py
pysam/csamtools.c
pysam/csamtools.pxd
pysam/csamtools.pyx
@@ -108,16 +109,22 @@ samtools/win32/xcurses.h
samtools/win32/zconf.h
samtools/win32/zlib.h
tabix/bam_endian.h
+tabix/bedidx.c
tabix/bedidx.c.pysam.c
+tabix/bgzf.c
tabix/bgzf.c.pysam.c
tabix/bgzf.h
+tabix/bgzip.c
tabix/bgzip.c.pysam.c
+tabix/index.c
tabix/index.c.pysam.c
tabix/khash.h
+tabix/knetfile.c
tabix/knetfile.c.pysam.c
tabix/knetfile.h
tabix/kseq.h
tabix/ksort.h
+tabix/kstring.c
tabix/kstring.c.pysam.c
tabix/kstring.h
tabix/pysam.h
@@ -141,6 +148,7 @@ tests/example.gtf.gz
tests/example.gtf.gz.tbi
tests/example.py
tests/example.vcf40
+tests/example_btag.bam
tests/example_btag.sam
tests/example_empty_header.bam
tests/example_unmapped_reads_no_sq.sam
diff --git a/pysam.egg-info/requires.txt b/pysam.egg-info/requires.txt
index 3c6d9e8..9410b7b 100644
--- a/pysam.egg-info/requires.txt
+++ b/pysam.egg-info/requires.txt
@@ -1 +1 @@
-cython>=0.16
\ No newline at end of file
+cython>=0.17
\ No newline at end of file
diff --git a/pysam.egg-info/top_level.txt b/pysam.egg-info/top_level.txt
index b030ff1..23f03da 100644
--- a/pysam.egg-info/top_level.txt
+++ b/pysam.egg-info/top_level.txt
@@ -1,5 +1 @@
-pysam/Pileup
pysam
-pysam/__init__
-pysam/version
-pysam/namedtuple
diff --git a/pysam/__init__.py b/pysam/__init__.py
index c3a1266..e1d87ee 100644
--- a/pysam/__init__.py
+++ b/pysam/__init__.py
@@ -125,11 +125,10 @@ __all__ = \
[ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
["Pileup" ]
-from version import __version__, __samtools_version__
+from pysam.version import __version__, __samtools_version__
def get_include():
- base = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'include'))
- return [os.path.join(base, 'samtools'), os.path.join(base, 'pysam')]
+ return [os.path.abspath(os.path.join(os.path.dirname(__file__), 'include'))]
def get_defines():
return [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')]
diff --git a/pysam/alternatives.py b/pysam/alternatives.py
new file mode 100644
index 0000000..fd76802
--- /dev/null
+++ b/pysam/alternatives.py
@@ -0,0 +1,82 @@
+# This file contains an alternative implementation
+# to call samtools functions. These are direct calls.
+# Plus: less overhead
+# Minus: more trouble in maintaining
+
+#in csamtools.pxd
+ # samtools toolkit functions
+ ctypedef int (*pysam_samtools_f)(int argc, char *argv[])
+
+ int bam_taf2baf(int argc, char *argv[])
+ int bam_pileup(int argc, char *argv[])
+ int bam_merge(int argc, char *argv[])
+ int bam_index(int argc, char *argv[])
+ int bam_sort(int argc, char *argv[])
+ int bam_tview_main(int argc, char *argv[])
+ int bam_mating(int argc, char *argv[])
+ int bam_rmdup(int argc, char *argv[])
+ int bam_rmdupse(int argc, char *argv[])
+ int bam_flagstat(int argc, char *argv[])
+ int bam_fillmd(int argc, char *argv[])
+ int main_samview(int argc, char *argv[])
+ int main_import(int argc, char *argv[])
+ int faidx_main(int argc, char *argv[])
+ int glf3_view_main(int argc, char *argv[])
+
+
+## Alternative code in csamtools.pyx
+cdef class SamtoolsWrapper:
+ '''generic wrapper around samtools functions'''
+ cdef pysam_samtools_f f
+
+ def __init__(self): self.f = NULL
+
+ def call(self, *args ):
+
+ if self.f == NULL: raise NotImplementedError("invalid call to base class" )
+
+ cdef char ** cargs
+ cdef int i, n, retval
+ n = len(args)
+ # allocate one more for first (dummy) argument (contains command)
+ cargs = <char**>calloc( n+1, sizeof( char *) )
+ cargs[0] = "method"
+ for i from 0 <= i < n:
+ cargs[i+1] = args[i]
+ for i from 0 <= i < n+1:
+ print cargs[i]
+ retval = self.f(n+1, cargs)
+ free( cargs )
+ return retval
+
+cdef class SamtoolsWrapperImport( SamtoolsWrapper ):
+ def __init__(self): self.f = main_import
+cdef class SamtoolsWrapperPileup( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_pileup
+cdef class SamtoolsWrapperMerge( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_merge
+cdef class SamtoolsWrapperSort( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_sort
+cdef class SamtoolsWrapperIndex( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_index
+cdef class SamtoolsWrapperFaidx( SamtoolsWrapper ):
+ def __init__(self): self.f = faidx_main
+cdef class SamtoolsWrapperFixMate( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_mating
+cdef class SamtoolsWrapperRmDup( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_rmdup
+cdef class SamtoolsWrapperRmDupSe( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_rmdupse
+cdef class SamtoolsWrapperGlf3Viwen( SamtoolsWrapper ):
+ def __init__(self): self.f = glf3_view_main
+cdef class SamtoolsWrapperFlagStat( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_flagstat
+cdef class SamtoolsWrapperFillMd( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_fillmd
+cdef class SamtoolsWrapperCalMd( SamtoolsWrapper ):
+ def __init__(self): self.f = bam_fillmd
+
+automatic creation of these functions does not work
+due to pyrex/cython
+
+def sort( *args, **kwargs ): return SamtoolsWrapperSort().call(*args, **kwargs)
diff --git a/pysam/ctabix.c b/pysam/ctabix.c
index 8ed84fc..2a1ce55 100644
--- a/pysam/ctabix.c
+++ b/pysam/ctabix.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Fri Nov 30 11:02:40 2012 */
+/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,7 +11,6 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -23,22 +22,18 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
-
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,28 +41,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
-#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -75,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -89,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -101,11 +94,9 @@
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -115,31 +106,30 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
-
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
-
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -147,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -166,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -174,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -193,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -206,7 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -225,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -239,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -248,6 +228,7 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
@@ -268,8 +249,8 @@
#define _USE_MATH_DEFINES
#endif
#include <math.h>
-#define __PYX_HAVE__ctabix
-#define __PYX_HAVE_API__ctabix
+#define __PYX_HAVE__pysam__ctabix
+#define __PYX_HAVE_API__pysam__ctabix
#include "string.h"
#include "stdlib.h"
#include "stdio.h"
@@ -336,7 +317,11 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
@@ -366,51 +351,28 @@ static const char *__pyx_filename;
static const char *__pyx_f[] = {
"ctabix.pyx",
"TabProxies.pxd",
+ "type.pxd",
"bool.pxd",
"complex.pxd",
};
/*--- Type declarations ---*/
-struct __pyx_obj_6ctabix_Parser;
-struct __pyx_obj_6ctabix_asVCF;
-struct __pyx_obj_10TabProxies_TupleProxy;
-struct __pyx_obj_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_10TabProxies_BedProxy;
-struct __pyx_obj_6ctabix_tabix_copy_iterator;
-struct __pyx_obj_10TabProxies_VCFProxy;
-struct __pyx_obj_10TabProxies_GTFProxy;
-struct __pyx_obj_6ctabix_TabixIterator;
-struct __pyx_obj_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_6ctabix_TabixHeaderIterator;
-struct __pyx_obj_6ctabix_Tabixfile;
-struct __pyx_obj_6ctabix_asGTF;
-struct __pyx_obj_6ctabix_asBed;
-struct __pyx_obj_6ctabix_tabix_inplace_iterator;
-struct __pyx_obj_6ctabix_asTuple;
-
-/* "ctabix.pxd":190
- * cdef tabix_t * tabixfile
- *
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_6ctabix_Parser {
- PyObject_HEAD
-};
-
-
-/* "ctabix.pxd":202
- * pass
- *
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_6ctabix_asVCF {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
-};
-
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator;
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_5pysam_6ctabix_Parser;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile;
+struct __pyx_obj_5pysam_6ctabix_asBed;
+struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
/* "TabProxies.pxd":41
* ctypedef int uint64_t
@@ -419,9 +381,9 @@ struct __pyx_obj_6ctabix_asVCF {
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_TupleProxy {
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
PyObject_HEAD
- struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
char *data;
char **fields;
int nfields;
@@ -439,8 +401,8 @@ struct __pyx_obj_10TabProxies_TupleProxy {
* pass
*
*/
-struct __pyx_obj_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
};
@@ -451,8 +413,8 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy {
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_BedProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
char *contig;
uint32_t start;
uint32_t end;
@@ -460,100 +422,110 @@ struct __pyx_obj_10TabProxies_BedProxy {
};
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "pysam/ctabix.pxd":186
+ * cdef tabix_t * tabixfile
*
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_6ctabix_tabix_copy_iterator {
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
- struct __pyx_obj_6ctabix_Parser *parser;
-};
-
-
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_10TabProxies_VCFProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+/* "pysam/ctabix.pxd":205
+ * pass
*
- * cdef:
+ * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_10TabProxies_GTFProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "ctabix.pxd":182
+/* "pysam/ctabix.pxd":182
* cdef char * _filename
*
* cdef class TabixIterator: # <<<<<<<<<<<<<<
* cdef ti_iter_t iterator
* cdef tabix_t * tabixfile
*/
-struct __pyx_obj_6ctabix_TabixIterator {
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
PyObject_HEAD
ti_iter_t iterator;
tabix_t *tabixfile;
};
-/* "ctabix.pxd":205
- * pass
+/* "pysam/ctabix.pxd":210
+ * cdef Parser parser
*
- * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
*/
-struct __pyx_obj_6ctabix_TabixIteratorParsed {
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
- struct __pyx_obj_6ctabix_Parser *parser;
+ 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":186
+/* "pysam/ctabix.pxd":190
* cdef tabix_t * tabixfile
*
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
+ *
*/
-struct __pyx_obj_6ctabix_TabixHeaderIterator {
+struct __pyx_obj_5pysam_6ctabix_Parser {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
};
-/* "ctabix.pxd":172
+/* "pysam/ctabix.pxd":193
+ * pass
+ *
+ * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+};
+
+
+/* "pysam/ctabix.pxd":202
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asVCF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
+};
+
+
+/* "pysam/ctabix.pxd":172
* # char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
*
* cdef class Tabixfile: # <<<<<<<<<<<<<<
*
* # pointer to tabixfile
*/
-struct __pyx_obj_6ctabix_Tabixfile {
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
PyObject_HEAD
tabix_t *tabixfile;
int isremote;
@@ -561,72 +533,72 @@ struct __pyx_obj_6ctabix_Tabixfile {
};
-/* "ctabix.pxd":196
+/* "pysam/ctabix.pxd":199
* pass
*
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_asGTF {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_asBed {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pxd":199
+/* "pysam/ctabix.pxd":196
* pass
*
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_asBed {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_asGTF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
-struct __pyx_obj_6ctabix_tabix_inplace_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab;
- FILE *infile;
- char *buffer;
- size_t size;
- struct __pyx_obj_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
};
-/* "ctabix.pxd":193
- * pass
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * pass
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_obj_6ctabix_asTuple {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
};
-
-/* "ctabix.pyx":771
- * return self.__cnext__()
+/* "pysam/ctabix.pxd":218
+ * cdef __cnext__(self)
*
* ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
- *
+ * cdef FILE * infile
+ * cdef Parser parser
*/
-
-struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *);
+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;
};
-static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator;
+
/* "TabProxies.pxd":41
@@ -637,14 +609,14 @@ static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabi
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_TupleProxy {
- int (*getMaxFields)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t);
- PyObject *(*take)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*present)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*copy)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*update)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
+struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy {
+ int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t);
+ PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
};
-static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
/* "TabProxies.pxd":69
@@ -655,10 +627,10 @@ static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxi
*
*/
-struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
/* "TabProxies.pxd":83
@@ -669,10 +641,24 @@ static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10Tab
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_VCFProxy {
- struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
+
+
+/* "pysam/ctabix.pyx":709
+ * ## Iterators for parsing through unindexed files.
+ * #########################################################
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
+};
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
/* "TabProxies.pxd":60
@@ -683,39 +669,39 @@ static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_GTFProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
- char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *);
+struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
-static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
-/* "TabProxies.pxd":72
- * pass
+/* "pysam/ctabix.pyx":771
+ * return self.__cnext__()
*
- * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * '''iterate over ``infile``.
*
- * cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_BedProxy {
- struct __pyx_vtabstruct_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_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
-/* "ctabix.pyx":709
- * ## Iterators for parsing through unindexed files.
- * #########################################################
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * '''iterate over ``infile``.
+/* "TabProxies.pxd":72
+ * pass
+ *
+ * cdef class BedProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
*
+ * cdef:
*/
-struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *);
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -772,6 +758,11 @@ static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ct
static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+
static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
@@ -799,42 +790,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -850,34 +846,39 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_GetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
return m->sq_item(o, i);
}
}
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
const char *name, int exact); /*proto*/
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
- if (unlikely(d == Py_None)) {
- __Pyx_RaiseNoneIndexingError();
- return NULL;
- }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -945,16 +946,6 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
PyObject *tuple);
static int __Pyx_CyFunction_init(void);
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject *);
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
@@ -1001,10 +992,10 @@ static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
#endif
#endif
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
typedef struct {
@@ -1027,12 +1018,14 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from 'TabProxies' */
-static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
+/* Module declarations from 'pysam' */
+
+/* Module declarations from 'pysam.TabProxies' */
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0;
/* Module declarations from 'cpython.version' */
@@ -1058,7 +1051,10 @@ static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
/* Module declarations from 'cpython.iterator' */
+/* Module declarations from '__builtin__' */
+
/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
/* Module declarations from 'cpython.number' */
@@ -1112,26 +1108,26 @@ static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
/* Module declarations from 'cpython' */
-/* Module declarations from 'ctabix' */
-static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_tabix_inplace_iterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_tabix_copy_iterator = 0;
-static PyObject *__pyx_v_6ctabix__FILENAME_ENCODING = 0;
-static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *); /*proto*/
-static PyObject *__pyx_f_6ctabix__force_bytes(PyObject *); /*proto*/
-static PyObject *__pyx_f_6ctabix__charptr_to_str(char *); /*proto*/
-#define __Pyx_MODULE_NAME "ctabix"
-int __pyx_module_is_main_ctabix = 0;
-
-/* Implementation of 'ctabix' */
+/* Module declarations from 'pysam.ctabix' */
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0;
+static PyObject *__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = 0;
+static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *); /*proto*/
+static PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *); /*proto*/
+#define __Pyx_MODULE_NAME "pysam.ctabix"
+int __pyx_module_is_main_pysam__ctabix = 0;
+
+/* Implementation of 'pysam.ctabix' */
static PyObject *__pyx_builtin_TypeError;
static PyObject *__pyx_builtin_NotImplementedError;
static PyObject *__pyx_builtin_IOError;
@@ -1141,46 +1137,46 @@ static PyObject *__pyx_builtin_OSError;
static PyObject *__pyx_builtin_ord;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_MemoryError;
-static int __pyx_pf_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_4_open(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_9Tabixfile_10close(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
-static void __pyx_pf_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_self); /* proto */
-static int __pyx_pf_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */
-static PyObject *__pyx_pf_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */
-static void __pyx_pf_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixIterator *__pyx_v_self); /* proto */
-static int __pyx_pf_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */
-static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
-static void __pyx_pf_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static int __pyx_pf_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
-static void __pyx_pf_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */
-static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */
-static int __pyx_pf_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
-static void __pyx_pf_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
-static int __pyx_pf_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_6ctabix_Parser *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
+static int __pyx_pf_5pysam_6ctabix_9Tabixfile___cinit__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_2_isOpen(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_4_open(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6_parseRegion(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8filename___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_6header___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_10close(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_6ctabix_9Tabixfile_12__dealloc__(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_6ctabix_13TabixIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_6ctabix_13TabixIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_7asTuple___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asTuple *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_5asGTF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asGTF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_5asBed___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asBed *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_5asVCF___call__(CYTHON_UNUSED struct __pyx_obj_5pysam_6ctabix_asVCF *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___cinit__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_tabixfile, int __pyx_v_tid, int __pyx_v_start, int __pyx_v_end, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__iter__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_6__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_tabix_compress(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename_in, PyObject *__pyx_v_filename_out, PyObject *__pyx_v_force); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_force, PyObject *__pyx_v_seq_col, PyObject *__pyx_v_start_col, PyObject *__pyx_v_end_col, PyObject *__pyx_v_preset, PyObject *__pyx_v_meta_char, PyObject *__pyx_v_zerobased); /* proto */
+static int __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self, PyObject *__pyx_v_infile, int __pyx_v_buffer_size); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
+static void __pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_inplace_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *__pyx_v_self); /* proto */
+static int __pyx_pf_5pysam_6ctabix_19tabix_copy_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_copy_iterator_4__next__(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_2__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_22tabix_generic_iterator_6next(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_6ctabix_4tabix_iterator(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_infile, PyObject *__pyx_v_parser); /* proto */
static char __pyx_k_1[] = "Argument must be string or unicode.";
static char __pyx_k_3[] = "Argument must be string, bytes or unicode.";
static char __pyx_k_5[] = "invalid file opening mode `%s`";
@@ -1218,8 +1214,9 @@ static char __pyx_k_60[] = "the file header.\n \n .. note::\n
static char __pyx_k_61[] = "chromosome names";
static char __pyx_k_62[] = "getfilesystemencoding";
static char __pyx_k_65[] = "/ifs/devel/pysam/pysam/ctabix.pyx";
-static char __pyx_k_76[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
-static char __pyx_k_79[] = "tabix_inplace_iterator";
+static char __pyx_k_66[] = "pysam.ctabix";
+static char __pyx_k_77[] = "iterate over ``infile``.\n \n Permits the use of file-like objects for example from the gzip module.\n ";
+static char __pyx_k_80[] = "tabix_inplace_iterator";
static char __pyx_k__b[] = "b";
static char __pyx_k__c[] = "c";
static char __pyx_k__r[] = "r";
@@ -1259,7 +1256,6 @@ static char __pyx_k__types[] = "types";
static char __pyx_k__Parser[] = "Parser";
static char __pyx_k__buffer[] = "buffer";
static char __pyx_k__closed[] = "closed";
-static char __pyx_k__ctabix[] = "ctabix";
static char __pyx_k__ctypes[] = "ctypes";
static char __pyx_k__decode[] = "decode";
static char __pyx_k__encode[] = "encode";
@@ -1350,9 +1346,10 @@ static PyObject *__pyx_n_s_58;
static PyObject *__pyx_kp_s_6;
static PyObject *__pyx_n_s_62;
static PyObject *__pyx_kp_s_65;
+static PyObject *__pyx_n_s_66;
static PyObject *__pyx_kp_s_7;
-static PyObject *__pyx_kp_s_76;
-static PyObject *__pyx_n_s_79;
+static PyObject *__pyx_kp_s_77;
+static PyObject *__pyx_n_s_80;
static PyObject *__pyx_kp_s_9;
static PyObject *__pyx_n_s__IOError;
static PyObject *__pyx_n_s__KeyError;
@@ -1391,7 +1388,6 @@ static PyObject *__pyx_n_s__closed;
static PyObject *__pyx_n_s__conf;
static PyObject *__pyx_n_s__conf_data;
static PyObject *__pyx_n_s__cpy;
-static PyObject *__pyx_n_s__ctabix;
static PyObject *__pyx_n_s__ctypes;
static PyObject *__pyx_n_s__decode;
static PyObject *__pyx_n_s__encode;
@@ -1491,21 +1487,21 @@ static PyObject *__pyx_k_tuple_55;
static PyObject *__pyx_k_tuple_56;
static PyObject *__pyx_k_tuple_57;
static PyObject *__pyx_k_tuple_63;
-static PyObject *__pyx_k_tuple_66;
-static PyObject *__pyx_k_tuple_68;
-static PyObject *__pyx_k_tuple_70;
-static PyObject *__pyx_k_tuple_72;
-static PyObject *__pyx_k_tuple_74;
-static PyObject *__pyx_k_tuple_77;
+static PyObject *__pyx_k_tuple_67;
+static PyObject *__pyx_k_tuple_69;
+static PyObject *__pyx_k_tuple_71;
+static PyObject *__pyx_k_tuple_73;
+static PyObject *__pyx_k_tuple_75;
+static PyObject *__pyx_k_tuple_78;
static PyObject *__pyx_k_codeobj_64;
-static PyObject *__pyx_k_codeobj_67;
-static PyObject *__pyx_k_codeobj_69;
-static PyObject *__pyx_k_codeobj_71;
-static PyObject *__pyx_k_codeobj_73;
-static PyObject *__pyx_k_codeobj_75;
-static PyObject *__pyx_k_codeobj_78;
-
-/* "ctabix.pyx":19
+static PyObject *__pyx_k_codeobj_68;
+static PyObject *__pyx_k_codeobj_70;
+static PyObject *__pyx_k_codeobj_72;
+static PyObject *__pyx_k_codeobj_74;
+static PyObject *__pyx_k_codeobj_76;
+static PyObject *__pyx_k_codeobj_79;
+
+/* "pysam/ctabix.pyx":19
* from cpython.version cimport PY_MAJOR_VERSION
*
* cdef from_string_and_size(char* s, size_t length): # <<<<<<<<<<<<<<
@@ -1513,7 +1509,7 @@ static PyObject *__pyx_k_codeobj_78;
* return s[:length]
*/
-static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
+static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1523,7 +1519,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("from_string_and_size", 0);
- /* "ctabix.pyx":20
+ /* "pysam/ctabix.pyx":20
*
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3: # <<<<<<<<<<<<<<
@@ -1533,7 +1529,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
__pyx_t_1 = (PY_MAJOR_VERSION < 3);
if (__pyx_t_1) {
- /* "ctabix.pyx":21
+ /* "pysam/ctabix.pyx":21
* cdef from_string_and_size(char* s, size_t length):
* if PY_MAJOR_VERSION < 3:
* return s[:length] # <<<<<<<<<<<<<<
@@ -1541,7 +1537,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
* return s[:length].decode("ascii")
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = PyBytes_FromStringAndSize(__pyx_v_s + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = PyBytes_FromStringAndSize(((const char*)__pyx_v_s) + 0, __pyx_v_length - 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 21; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1550,7 +1546,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
}
/*else*/ {
- /* "ctabix.pyx":23
+ /* "pysam/ctabix.pyx":23
* return s[:length]
* else:
* return s[:length].decode("ascii") # <<<<<<<<<<<<<<
@@ -1558,7 +1554,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
* # filename encoding (copied from lxml.etree.pyx)
*/
__Pyx_XDECREF(__pyx_r);
- __pyx_t_2 = ((PyObject *)PyUnicode_DecodeASCII(__pyx_v_s, __pyx_v_length, NULL)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_2 = ((PyObject *)__Pyx_decode_c_string(__pyx_v_s, 0, __pyx_v_length, NULL, NULL, PyUnicode_DecodeASCII)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(((PyObject *)__pyx_t_2));
__pyx_r = ((PyObject *)__pyx_t_2);
__pyx_t_2 = 0;
@@ -1570,7 +1566,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
goto __pyx_L0;
__pyx_L1_error:;
__Pyx_XDECREF(__pyx_t_2);
- __Pyx_AddTraceback("ctabix.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("pysam.ctabix.from_string_and_size", __pyx_clineno, __pyx_lineno, __pyx_filename);
__pyx_r = 0;
__pyx_L0:;
__Pyx_XGIVEREF(__pyx_r);
@@ -1578,7 +1574,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
return __pyx_r;
}
-/* "ctabix.pyx":36
+/* "pysam/ctabix.pyx":36
* #_C_FILENAME_ENCODING = <char*>_FILENAME_ENCODING
*
* cdef bytes _my_encodeFilename(object filename): # <<<<<<<<<<<<<<
@@ -1586,7 +1582,7 @@ static PyObject *__pyx_f_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __
* """
*/
-static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) {
+static PyObject *__pyx_f_5pysam_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename) {
PyObject *__pyx_r = NULL;
__Pyx_RefNannyDeclarations
int __pyx_t_1;
@@ -1598,7 +1594,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename)
int __pyx_clineno = 0;
__Pyx_RefNannySetupContext("_my_encodeFilename", 0);
- /* "ctabix.pyx":39
+ /* "pysam/ctabix.pyx":39
* u"""Make sure a filename is 8-bit encoded (or None).
* """
* if filename is None: # <<<<<<<<<<<<<<
@@ -1608,7 +1604,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename)
__pyx_t_1 = (__pyx_v_filename == Py_None);
if (__pyx_t_1) {
- /* "ctabix.pyx":40
+ /* "pysam/ctabix.pyx":40
* """
* if filename is None:
* return None # <<<<<<<<<<<<<<
@@ -1622,7 +1618,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename)
goto __pyx_L3;
}
- /* "ctabix.pyx":41
+ /* "pysam/ctabix.pyx":41
* if filename is None:
* return None
* elif PyBytes_Check(filename): # <<<<<<<<<<<<<<
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__pyx_t_1 = PyBytes_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "ctabix.pyx":42
+ /* "pysam/ctabix.pyx":42
* return None
* elif PyBytes_Check(filename):
* return filename # <<<<<<<<<<<<<<
@@ -1647,7 +1643,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename)
goto __pyx_L3;
}
- /* "ctabix.pyx":43
+ /* "pysam/ctabix.pyx":43
* elif PyBytes_Check(filename):
* return filename
* elif PyUnicode_Check(filename): # <<<<<<<<<<<<<<
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__pyx_t_1 = PyUnicode_Check(__pyx_v_filename);
if (__pyx_t_1) {
- /* "ctabix.pyx":44
+ /* "pysam/ctabix.pyx":44
* return filename
* elif PyUnicode_Check(filename):
* return filename.encode(_FILENAME_ENCODING) # <<<<<<<<<<<<<<
@@ -1669,9 +1665,9 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename)
__Pyx_GOTREF(__pyx_t_2);
__pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
- __Pyx_INCREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING));
- PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING));
- __Pyx_GIVEREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING));
+ __Pyx_INCREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
+ PyTuple_SET_ITEM(__pyx_t_3, 0, ((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
+ __Pyx_GIVEREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
__pyx_t_4 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_4);
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
@@ -1684,7 +1680,7 @@ static PyObject *__pyx_f_6ctabix__my_encodeFilename(PyObject *__pyx_v_filename)
}
/*else*/ {
- /* "ctabix.pyx":46
+ /* "pysam/ctabix.pyx":46
* return filename.encode(_FILENAME_ENCODING)
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goto __pyx_L0;
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*/
values[1] = ((PyObject *)Py_None);
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values[2] = ((PyObject *)Py_None);
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int __pyx_v_rstart;
int __pyx_v_rend;
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*/
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}
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goto __pyx_L4;
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}
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goto __pyx_L4;
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}
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* if rstart > rend: raise ValueError( 'invalid region: start (%i) > end (%i)' % (rstart, rend) )
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}
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}
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}
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-static PyObject *__pyx_pw_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
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+static PyObject *__pyx_pw_5pysam_6ctabix_9Tabixfile_9fetch(PyObject *__pyx_v_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_reference = 0;
PyObject *__pyx_v_start = 0;
PyObject *__pyx_v_end = 0;
PyObject *__pyx_v_region = 0;
PyObject *__pyx_v_parser = 0;
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PyObject *__pyx_r = 0;
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__Pyx_RefNannySetupContext("fetch (wrapper)", 0);
{
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PyObject* values[5] = {0,0,0,0,0};
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*/
values[0] = ((PyObject *)Py_None);
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+ /* "pysam/ctabix.pyx":192
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values[1] = ((PyObject *)Py_None);
- /* "ctabix.pyx":193
+ /* "pysam/ctabix.pyx":193
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*/
values[2] = ((PyObject *)Py_None);
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+ /* "pysam/ctabix.pyx":194
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*/
values[3] = ((PyObject *)Py_None);
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+ /* "pysam/ctabix.pyx":195
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__pyx_L3_error:;
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__Pyx_RefNannyFinishContext();
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+ __pyx_r = __pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)__pyx_v_self), __pyx_v_reference, __pyx_v_start, __pyx_v_end, __pyx_v_region, __pyx_v_parser);
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*/
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+static PyObject *__pyx_pf_5pysam_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_5pysam_6ctabix_Tabixfile *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region, PyObject *__pyx_v_parser) {
PyObject *__pyx_v_rtid = NULL;
PyObject *__pyx_v_rstart = NULL;
PyObject *__pyx_v_rend = NULL;
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__Pyx_RefNannySetupContext("fetch", 0);
__Pyx_INCREF(__pyx_v_region);
- /* "ctabix.pyx":209
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*/
ti_lazy_index_load(__pyx_v_self->tabixfile);
- /* "ctabix.pyx":211
+ /* "pysam/ctabix.pyx":211
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__pyx_t_4 = (!__pyx_t_3);
if (__pyx_t_4) {
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+ /* "pysam/ctabix.pyx":212
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}
__pyx_L3:;
- /* "ctabix.pyx":214
+ /* "pysam/ctabix.pyx":214
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if ((likely(PyTuple_CheckExact(__pyx_t_5))) || (PyList_CheckExact(__pyx_t_5))) {
PyObject* sequence = __pyx_t_5;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ Py_ssize_t size = Py_SIZE(sequence);
+ #else
+ Py_ssize_t size = PySequence_Size(sequence);
+ #endif
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+ if (size > 4) __Pyx_RaiseTooManyValuesError(4);
+ else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size);
+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ #if CYTHON_COMPILING_IN_CPYTHON
if (likely(PyTuple_CheckExact(sequence))) {
- if (unlikely(PyTuple_GET_SIZE(sequence) != 4)) {
- if (PyTuple_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
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- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_1 = PyTuple_GET_ITEM(sequence, 0);
__pyx_t_2 = PyTuple_GET_ITEM(sequence, 1);
__pyx_t_6 = PyTuple_GET_ITEM(sequence, 2);
__pyx_t_7 = PyTuple_GET_ITEM(sequence, 3);
} else {
- if (unlikely(PyList_GET_SIZE(sequence) != 4)) {
- if (PyList_GET_SIZE(sequence) > 4) __Pyx_RaiseTooManyValuesError(4);
- else __Pyx_RaiseNeedMoreValuesError(PyList_GET_SIZE(sequence));
- {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- }
__pyx_t_1 = PyList_GET_ITEM(sequence, 0);
__pyx_t_2 = PyList_GET_ITEM(sequence, 1);
__pyx_t_6 = PyList_GET_ITEM(sequence, 2);
@@ -3616,28 +3611,36 @@ static PyObject *__pyx_pf_6ctabix_9Tabixfile_8fetch(struct __pyx_obj_6ctabix_Tab
__Pyx_INCREF(__pyx_t_2);
__Pyx_INCREF(__pyx_t_6);
__Pyx_INCREF(__pyx_t_7);
+ #else
+ Py_ssize_t i;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
+ for (i=0; i < 4; i++) {
+ PyObject* item = PySequence_ITEM(sequence, i); if (unlikely(!item)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ *(temps[i]) = item;
+ }
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- } else {
+ } else
+ {
Py_ssize_t index = -1;
+ PyObject** temps[4] = {&__pyx_t_1,&__pyx_t_2,&__pyx_t_6,&__pyx_t_7};
__pyx_t_8 = PyObject_GetIter(__pyx_t_5); if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_9 = Py_TYPE(__pyx_t_8)->tp_iternext;
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- __Pyx_GOTREF(__pyx_t_7);
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__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
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__Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 214; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_v_rend = __pyx_t_7;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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+ __pyx_t_7 = PyObject_Call(((PyObject *)((PyObject*)__pyx_ptype_5pysam_6ctabix_TabixIterator)), ((PyObject *)__pyx_t_5), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_RefNannySetupContext("__cinit__ (wrapper)", 0);
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PyObject* values[4] = {0,0,0,0};
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Py_ssize_t kw_args;
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switch (pos_args) {
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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case 2:
- values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__start);
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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values[3] = PyTuple_GET_ITEM(__pyx_args, 3);
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}
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bgzf_seek(__pyx_v_self->tabixfile->fp, 0, 0);
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}
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while (1) {
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__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
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switch (pos_args) {
case 0:
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} else {
values[0] = PyTuple_GET_ITEM(__pyx_args, 0);
}
- __pyx_v_tabixfile = ((struct __pyx_obj_6ctabix_Tabixfile *)values[0]);
+ __pyx_v_tabixfile = ((struct __pyx_obj_5pysam_6ctabix_Tabixfile *)values[0]);
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return __pyx_r;
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int __pyx_t_3;
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const char *__pyx_filename = NULL;
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#endif
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__pyx_v_self->iterator = ti_query(__pyx_v_self->tabixfile, NULL, 0, 0);
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+ __pyx_r = __pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__(((struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator *)__pyx_v_self));
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*
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__pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len));
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-static void __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_v_self) {
+static void __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(PyObject *__pyx_v_self); /*proto*/
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int __pyx_v_len;
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int __pyx_v_start;
int __pyx_v_end;
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__Pyx_RaiseArgtupleInvalid("__cinit__", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 516; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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values[4] = PyTuple_GET_ITEM(__pyx_args, 4);
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__Pyx_XDECREF(__pyx_t_4);
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-static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
+static PyObject *__pyx_pw_5pysam_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
+static char __pyx_doc_5pysam_6ctabix_2tabix_index[] = "tabix_index(filename, force=False, seq_col=None, start_col=None, end_col=None, preset=None, meta_char='#', zerobased=False)\n\n index tab-separated *filename* using tabix.\n\n An existing index will not be overwritten unless\n *force* is set.\n\n The index will be built from coordinates\n in columns *seq_col*, *start_col* and *end_col*.\n\n The contents of *filename* have to be sorted by \n contig and position - [...]
+static PyMethodDef __pyx_mdef_5pysam_6ctabix_3tabix_index = {__Pyx_NAMESTR("tabix_index"), (PyCFunction)__pyx_pw_5pysam_6ctabix_3tabix_index, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_2tabix_index)};
+static PyObject *__pyx_pw_5pysam_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) {
PyObject *__pyx_v_filename = 0;
PyObject *__pyx_v_force = 0;
PyObject *__pyx_v_seq_col = 0;
@@ -6373,16 +6366,15 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_
PyObject *__pyx_v_preset = 0;
PyObject *__pyx_v_meta_char = 0;
PyObject *__pyx_v_zerobased = 0;
- static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0};
PyObject *__pyx_r = 0;
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("tabix_index (wrapper)", 0);
- __pyx_self = __pyx_self;
{
+ static PyObject **__pyx_pyargnames[] = {&__pyx_n_s__filename,&__pyx_n_s__force,&__pyx_n_s__seq_col,&__pyx_n_s__start_col,&__pyx_n_s__end_col,&__pyx_n_s__preset,&__pyx_n_s__meta_char,&__pyx_n_s__zerobased,0};
PyObject* values[8] = {0,0,0,0,0,0,0,0};
values[1] = __pyx_k_39;
- /* "ctabix.pyx":613
+ /* "pysam/ctabix.pyx":613
* def tabix_index( filename,
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* seq_col = None, # <<<<<<<<<<<<<<
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*/
values[2] = ((PyObject *)Py_None);
- /* "ctabix.pyx":614
+ /* "pysam/ctabix.pyx":614
* force = False,
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* start_col = None, # <<<<<<<<<<<<<<
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*/
values[3] = ((PyObject *)Py_None);
- /* "ctabix.pyx":615
+ /* "pysam/ctabix.pyx":615
* seq_col = None,
* start_col = None,
* end_col = None, # <<<<<<<<<<<<<<
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*/
values[4] = ((PyObject *)Py_None);
- /* "ctabix.pyx":616
+ /* "pysam/ctabix.pyx":616
* start_col = None,
* end_col = None,
* preset = None, # <<<<<<<<<<<<<<
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kw_args = PyDict_Size(__pyx_kwds);
switch (pos_args) {
case 0:
- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename);
- if (likely(values[0])) kw_args--;
+ if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__filename)) != 0)) kw_args--;
else goto __pyx_L5_argtuple_error;
case 1:
if (kw_args > 0) {
@@ -6506,16 +6497,16 @@ static PyObject *__pyx_pw_6ctabix_3tabix_index(PyObject *__pyx_self, PyObject *_
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__pyx_L3_error:;
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__Pyx_RefNannyFinishContext();
return NULL;
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* seq_col = None,
*/
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PyObject *__pyx_v_preset2conf = NULL;
PyObject *__pyx_v_conf_data = NULL;
ti_conf_t __pyx_v_conf;
@@ -6562,7 +6553,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
__Pyx_INCREF(__pyx_v_end_col);
__Pyx_INCREF(__pyx_v_preset);
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+ /* "pysam/ctabix.pyx":653
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*
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@@ -6607,30 +6598,26 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
}
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- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_seq_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (!__pyx_t_4) {
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- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_start_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
if (!__pyx_t_6) {
- __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_3);
+ __pyx_t_3 = PyObject_RichCompare(__pyx_v_end_col, Py_None, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 655; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
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@@ -6647,7 +6634,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
}
if (__pyx_t_4) {
- /* "ctabix.pyx":656
+ /* "pysam/ctabix.pyx":656
*
* if preset == None and (seq_col == None or start_col == None or end_col == None):
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@@ -6663,7 +6650,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
}
__pyx_L4:;
- /* "ctabix.pyx":658
+ /* "pysam/ctabix.pyx":658
* raise ValueError("neither preset nor seq_col,start_col and end_col given" )
*
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@@ -6680,7 +6667,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
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if (__pyx_t_5) {
- /* "ctabix.pyx":659
+ /* "pysam/ctabix.pyx":659
*
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__Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0;
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+ /* "pysam/ctabix.pyx":660
* if not filename.endswith(".gz"):
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* os.unlink( filename ) # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":661
+ /* "pysam/ctabix.pyx":661
* tabix_compress( filename, filename + ".gz", force = force )
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* filename += ".gz" # <<<<<<<<<<<<<<
@@ -6748,7 +6735,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
}
__pyx_L5:;
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* filename += ".gz"
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@@ -6785,7 +6772,7 @@ static PyObject *__pyx_pf_6ctabix_2tabix_index(CYTHON_UNUSED PyObject *__pyx_sel
}
if (__pyx_t_6) {
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+ /* "pysam/ctabix.pyx":664
*
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}
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* # preset-code, contig, start, end, metachar for commends, lines to ignore at beginning
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__Pyx_GOTREF(((PyObject *)__pyx_t_9));
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* # 0 is a missing column
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__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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* preset2conf = {
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__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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* 'gff' : ( 0, 1, 4, 5, ord('#'), 0 ),
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__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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* 'bed' : ( 0x10000, 1, 2, 3, ord('#'), 0 ),
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__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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* 'psltbl' : ( 0x10000, 15, 17, 18, ord('#'), 0 ),
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__Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0;
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if (__pyx_t_6) {
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/*try:*/ {
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}
/*else*/ {
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}
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__Pyx_DECREF(__pyx_v_preset);
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}
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}
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PyObject* sequence = __pyx_v_conf_data;
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__pyx_v_self->infile = fdopen(__pyx_v_fd, __pyx_k__r);
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+ {__Pyx_NAMESTR("close"), (PyCFunction)__pyx_pw_5pysam_6ctabix_9Tabixfile_11close, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_9Tabixfile_10close)},
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#endif
};
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PyObject *o = (*t->tp_alloc)(t, 0);
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Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TabixIterator(PyObject *o) {
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PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_6ctabix_13TabixIterator_7__dealloc__(o);
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--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
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#endif
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- sizeof(struct __pyx_obj_6ctabix_TabixIterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TabixIterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9435,9 +9411,9 @@ static PyTypeObject __pyx_type_6ctabix_TabixIterator = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/
- __pyx_pw_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TabixIterator, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_13TabixIterator_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_TabixIterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9447,7 +9423,7 @@ static PyTypeObject __pyx_type_6ctabix_TabixIterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TabixIterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9461,21 +9437,21 @@ static PyTypeObject __pyx_type_6ctabix_TabixIterator = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator(PyTypeObject *t, PyObject *a, PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- if (__pyx_pw_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) {
+ if (__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator(PyObject *o) {
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_6ctabix_19TabixHeaderIterator_7__dealloc__(o);
+ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
@@ -9483,8 +9459,8 @@ static void __pyx_tp_dealloc_6ctabix_TabixHeaderIterator(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_6ctabix_TabixHeaderIterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixHeaderIterator_4__next__)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixHeaderIterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixHeaderIterator_4__next__)},
{0, 0, 0, 0}
};
@@ -9586,12 +9562,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixHeaderIterator = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_TabixHeaderIterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.TabixHeaderIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.TabixHeaderIterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_TabixHeaderIterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9616,9 +9592,9 @@ static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
0, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/
- __pyx_pw_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TabixHeaderIterator, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_19TabixHeaderIterator_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_TabixHeaderIterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9628,7 +9604,7 @@ static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TabixHeaderIterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_TabixHeaderIterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9642,17 +9618,17 @@ static PyTypeObject __pyx_type_6ctabix_TabixHeaderIterator = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k) {
+static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
return o;
}
-static void __pyx_tp_dealloc_6ctabix_Parser(PyObject *o) {
+static void __pyx_tp_dealloc_5pysam_6ctabix_Parser(PyObject *o) {
(*Py_TYPE(o)->tp_free)(o);
}
-static PyMethodDef __pyx_methods_6ctabix_Parser[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_Parser[] = {
{0, 0, 0, 0}
};
@@ -9754,12 +9730,12 @@ static PyBufferProcs __pyx_tp_as_buffer_Parser = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_Parser = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_Parser = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.Parser"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_Parser), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.Parser"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9786,7 +9762,7 @@ static PyTypeObject __pyx_type_6ctabix_Parser = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_Parser, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_Parser, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9796,7 +9772,7 @@ static PyTypeObject __pyx_type_6ctabix_Parser = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_Parser, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_Parser, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9810,13 +9786,13 @@ static PyTypeObject __pyx_type_6ctabix_Parser = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asTuple[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asTuple[] = {
{0, 0, 0, 0}
};
@@ -9918,12 +9894,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asTuple = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asTuple = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asTuple = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asTuple"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asTuple), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asTuple"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -9937,7 +9913,7 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = {
&__pyx_tp_as_sequence_asTuple, /*tp_as_sequence*/
&__pyx_tp_as_mapping_asTuple, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_6ctabix_7asTuple_1__call__, /*tp_call*/
+ __pyx_pw_5pysam_6ctabix_7asTuple_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -9950,7 +9926,7 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asTuple, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_asTuple, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -9960,7 +9936,7 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asTuple, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asTuple, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -9974,13 +9950,13 @@ static PyTypeObject __pyx_type_6ctabix_asTuple = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asGTF[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asGTF[] = {
{0, 0, 0, 0}
};
@@ -10082,12 +10058,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asGTF = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asGTF = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asGTF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asGTF"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asGTF), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asGTF"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10101,7 +10077,7 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = {
&__pyx_tp_as_sequence_asGTF, /*tp_as_sequence*/
&__pyx_tp_as_mapping_asGTF, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_6ctabix_5asGTF_1__call__, /*tp_call*/
+ __pyx_pw_5pysam_6ctabix_5asGTF_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -10114,7 +10090,7 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asGTF, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_asGTF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10124,7 +10100,7 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asGTF, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asGTF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10138,13 +10114,13 @@ static PyTypeObject __pyx_type_6ctabix_asGTF = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asBed[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asBed[] = {
{0, 0, 0, 0}
};
@@ -10246,12 +10222,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asBed = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asBed = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asBed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asBed"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asBed), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asBed"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10265,7 +10241,7 @@ static PyTypeObject __pyx_type_6ctabix_asBed = {
&__pyx_tp_as_sequence_asBed, /*tp_as_sequence*/
&__pyx_tp_as_mapping_asBed, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_6ctabix_5asBed_1__call__, /*tp_call*/
+ __pyx_pw_5pysam_6ctabix_5asBed_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -10278,7 +10254,7 @@ static PyTypeObject __pyx_type_6ctabix_asBed = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asBed, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_asBed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10288,7 +10264,7 @@ static PyTypeObject __pyx_type_6ctabix_asBed = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asBed, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asBed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10302,13 +10278,13 @@ static PyTypeObject __pyx_type_6ctabix_asBed = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
- PyObject *o = __pyx_tp_new_6ctabix_Parser(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k) {
+ PyObject *o = __pyx_tp_new_5pysam_6ctabix_Parser(t, a, k);
if (!o) return 0;
return o;
}
-static PyMethodDef __pyx_methods_6ctabix_asVCF[] = {
+static PyMethodDef __pyx_methods_5pysam_6ctabix_asVCF[] = {
{0, 0, 0, 0}
};
@@ -10410,12 +10386,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCF = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_asVCF = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_asVCF = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.asVCF"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_asVCF), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.asVCF"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_Parser, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_Parser, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10429,7 +10405,7 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = {
&__pyx_tp_as_sequence_asVCF, /*tp_as_sequence*/
&__pyx_tp_as_mapping_asVCF, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_6ctabix_5asVCF_1__call__, /*tp_call*/
+ __pyx_pw_5pysam_6ctabix_5asVCF_1__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -10442,7 +10418,7 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = {
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_6ctabix_asVCF, /*tp_methods*/
+ __pyx_methods_5pysam_6ctabix_asVCF, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10452,7 +10428,7 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_asVCF, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_asVCF, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10466,53 +10442,55 @@ static PyTypeObject __pyx_type_6ctabix_asVCF = {
#endif
};
-static PyObject *__pyx_tp_new_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p;
+static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_6ctabix_TabixIteratorParsed *)o);
- p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o);
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_TabixIteratorParsed(PyObject *o) {
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+static void __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_6ctabix_19TabixIteratorParsed_7__dealloc__(o);
+ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_7__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->parser));
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
if (p->parser) {
e = (*v)(((PyObject*)p->parser), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_6ctabix_TabixIteratorParsed(PyObject *o) {
- struct __pyx_obj_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_6ctabix_TabixIteratorParsed *)o;
+static int __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
PyObject* tmp;
tmp = ((PyObject*)p->parser);
- p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_6ctabix_TabixIteratorParsed[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_6ctabix_19TabixIteratorParsed_4__next__)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIteratorParsed[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__)},
{0, 0, 0, 0}
};
@@ -10614,12 +10592,12 @@ static PyBufferProcs __pyx_tp_as_buffer_TabixIteratorParsed = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.TabixIteratorParsed"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.TabixIteratorParsed"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10640,13 +10618,13 @@ static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
&__pyx_tp_as_buffer_TabixIteratorParsed, /*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 mapped reads in a region.\n\n Returns parsed data.\n "), /*tp_doc*/
- __pyx_tp_traverse_6ctabix_TabixIteratorParsed, /*tp_traverse*/
- __pyx_tp_clear_6ctabix_TabixIteratorParsed, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/
- __pyx_pw_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_TabixIteratorParsed, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_TabixIteratorParsed, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10656,7 +10634,7 @@ static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_TabixIteratorParsed, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10669,56 +10647,58 @@ static PyTypeObject __pyx_type_6ctabix_TabixIteratorParsed = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator __pyx_vtable_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator __pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator;
-static PyObject *__pyx_tp_new_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_6ctabix_tabix_inplace_iterator *p;
+static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o);
- p->__pyx_vtab = __pyx_vtabptr_6ctabix_tabix_inplace_iterator;
- p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator(PyObject *o) {
- struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
+ PyObject_GC_UnTrack(o);
{
PyObject *etype, *eval, *etb;
PyErr_Fetch(&etype, &eval, &etb);
++Py_REFCNT(o);
- __pyx_pw_6ctabix_22tabix_inplace_iterator_5__dealloc__(o);
+ __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_5__dealloc__(o);
if (PyErr_Occurred()) PyErr_WriteUnraisable(o);
--Py_REFCNT(o);
PyErr_Restore(etype, eval, etb);
}
- Py_XDECREF(((PyObject *)p->parser));
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+ struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
if (p->parser) {
e = (*v)(((PyObject*)p->parser), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_6ctabix_tabix_inplace_iterator(PyObject *o) {
- struct __pyx_obj_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_6ctabix_tabix_inplace_iterator *)o;
+static int __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *)o;
PyObject* tmp;
tmp = ((PyObject*)p->parser);
- p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_6ctabix_tabix_inplace_iterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
@@ -10820,12 +10800,12 @@ static PyBufferProcs __pyx_tp_as_buffer_tabix_inplace_iterator = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_inplace_iterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.tabix_inplace_iterator"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.tabix_inplace_iterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_tabix_inplace_iterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_tabix_inplace_iterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -10846,13 +10826,13 @@ static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = {
&__pyx_tp_as_buffer_tabix_inplace_iterator, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not safe. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/
- __pyx_tp_traverse_6ctabix_tabix_inplace_iterator, /*tp_traverse*/
- __pyx_tp_clear_6ctabix_tabix_inplace_iterator, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_6ctabix_tabix_inplace_iterator, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_6ctabix_tabix_inplace_iterator, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/
- __pyx_pw_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_tabix_inplace_iterator, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_22tabix_inplace_iterator_7__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_tabix_inplace_iterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -10862,7 +10842,7 @@ static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_tabix_inplace_iterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_tabix_inplace_iterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -10875,47 +10855,49 @@ static PyTypeObject __pyx_type_6ctabix_tabix_inplace_iterator = {
0, /*tp_version_tag*/
#endif
};
-static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator __pyx_vtable_6ctabix_tabix_copy_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator __pyx_vtable_5pysam_6ctabix_tabix_copy_iterator;
-static PyObject *__pyx_tp_new_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_6ctabix_tabix_copy_iterator *p;
+static PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_6ctabix_tabix_copy_iterator *)o);
- p->__pyx_vtab = __pyx_vtabptr_6ctabix_tabix_copy_iterator;
- p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- if (__pyx_pw_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) {
+ p = ((struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o);
+ p->__pyx_vtab = __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ if (__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_1__cinit__(o, a, k) < 0) {
Py_DECREF(o); o = 0;
}
return o;
}
-static void __pyx_tp_dealloc_6ctabix_tabix_copy_iterator(PyObject *o) {
- struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
- Py_XDECREF(((PyObject *)p->parser));
+static void __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->parser);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
+ struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
if (p->parser) {
e = (*v)(((PyObject*)p->parser), a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_6ctabix_tabix_copy_iterator(PyObject *o) {
- struct __pyx_obj_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_6ctabix_tabix_copy_iterator *)o;
+static int __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator(PyObject *o) {
+ struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *p = (struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *)o;
PyObject* tmp;
tmp = ((PyObject*)p->parser);
- p->parser = ((struct __pyx_obj_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
+ p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_6ctabix_tabix_copy_iterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
+static PyMethodDef __pyx_methods_5pysam_6ctabix_tabix_copy_iterator[] = {
+ {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(0)},
{0, 0, 0, 0}
};
@@ -11017,12 +10999,12 @@ static PyBufferProcs __pyx_tp_as_buffer_tabix_copy_iterator = {
#endif
};
-static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = {
+static PyTypeObject __pyx_type_5pysam_6ctabix_tabix_copy_iterator = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("ctabix.tabix_copy_iterator"), /*tp_name*/
- sizeof(struct __pyx_obj_6ctabix_tabix_copy_iterator), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.ctabix.tabix_copy_iterator"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_6ctabix_tabix_copy_iterator, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_6ctabix_tabix_copy_iterator, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -11043,13 +11025,13 @@ static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = {
&__pyx_tp_as_buffer_tabix_copy_iterator, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("iterate over ``infile``.\n\n This iterator is not save. If the :meth:`__next__()` method is called \n after ``infile`` is closed, the result is undefined (see ``fclose()``).\n\n The iterator might either raise a StopIteration or segfault.\n "), /*tp_doc*/
- __pyx_tp_traverse_6ctabix_tabix_copy_iterator, /*tp_traverse*/
- __pyx_tp_clear_6ctabix_tabix_copy_iterator, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_6ctabix_tabix_copy_iterator, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_6ctabix_tabix_copy_iterator, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
- __pyx_pw_6ctabix_19tabix_copy_iterator_3__iter__, /*tp_iter*/
- __pyx_pw_6ctabix_19tabix_copy_iterator_5__next__, /*tp_iternext*/
- __pyx_methods_6ctabix_tabix_copy_iterator, /*tp_methods*/
+ __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_3__iter__, /*tp_iter*/
+ __pyx_pw_5pysam_6ctabix_19tabix_copy_iterator_5__next__, /*tp_iternext*/
+ __pyx_methods_5pysam_6ctabix_tabix_copy_iterator, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -11059,7 +11041,7 @@ static PyTypeObject __pyx_type_6ctabix_tabix_copy_iterator = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_6ctabix_tabix_copy_iterator, /*tp_new*/
+ __pyx_tp_new_5pysam_6ctabix_tabix_copy_iterator, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -11124,9 +11106,10 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_6, __pyx_k_6, sizeof(__pyx_k_6), 0, 0, 1, 0},
{&__pyx_n_s_62, __pyx_k_62, sizeof(__pyx_k_62), 0, 0, 1, 1},
{&__pyx_kp_s_65, __pyx_k_65, sizeof(__pyx_k_65), 0, 0, 1, 0},
+ {&__pyx_n_s_66, __pyx_k_66, sizeof(__pyx_k_66), 0, 0, 1, 1},
{&__pyx_kp_s_7, __pyx_k_7, sizeof(__pyx_k_7), 0, 0, 1, 0},
- {&__pyx_kp_s_76, __pyx_k_76, sizeof(__pyx_k_76), 0, 0, 1, 0},
- {&__pyx_n_s_79, __pyx_k_79, sizeof(__pyx_k_79), 0, 0, 1, 1},
+ {&__pyx_kp_s_77, __pyx_k_77, sizeof(__pyx_k_77), 0, 0, 1, 0},
+ {&__pyx_n_s_80, __pyx_k_80, sizeof(__pyx_k_80), 0, 0, 1, 1},
{&__pyx_kp_s_9, __pyx_k_9, sizeof(__pyx_k_9), 0, 0, 1, 0},
{&__pyx_n_s__IOError, __pyx_k__IOError, sizeof(__pyx_k__IOError), 0, 0, 1, 1},
{&__pyx_n_s__KeyError, __pyx_k__KeyError, sizeof(__pyx_k__KeyError), 0, 0, 1, 1},
@@ -11165,7 +11148,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__conf, __pyx_k__conf, sizeof(__pyx_k__conf), 0, 0, 1, 1},
{&__pyx_n_s__conf_data, __pyx_k__conf_data, sizeof(__pyx_k__conf_data), 0, 0, 1, 1},
{&__pyx_n_s__cpy, __pyx_k__cpy, sizeof(__pyx_k__cpy), 0, 0, 1, 1},
- {&__pyx_n_s__ctabix, __pyx_k__ctabix, sizeof(__pyx_k__ctabix), 0, 0, 1, 1},
{&__pyx_n_s__ctypes, __pyx_k__ctypes, sizeof(__pyx_k__ctypes), 0, 0, 1, 1},
{&__pyx_n_s__decode, __pyx_k__decode, sizeof(__pyx_k__decode), 0, 0, 1, 1},
{&__pyx_n_s__encode, __pyx_k__encode, sizeof(__pyx_k__encode), 0, 0, 1, 1},
@@ -11247,7 +11229,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "ctabix.pyx":58
+ /* "pysam/ctabix.pyx":58
* return s
* elif PyUnicode_Check(s):
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_2));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_4));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_9));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
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__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_11));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_12));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_22));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_22));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_27));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_36));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_37));
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_45));
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/*--- Module creation code ---*/
#if PY_MAJOR_VERSION < 3
- __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION);
+ __pyx_m = Py_InitModule4(__Pyx_NAMESTR("ctabix"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m);
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__pyx_m = PyModule_Create(&__pyx_moduledef);
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- #if PY_MAJOR_VERSION < 3
- Py_INCREF(__pyx_m);
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+ #if PY_MAJOR_VERSION >= 3
+ {
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+ if (!PyDict_GetItemString(modules, "pysam.ctabix")) {
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+ }
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+ #if CYTHON_COMPILING_IN_PYPY
+ Py_INCREF(__pyx_b);
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- if (__pyx_module_is_main_ctabix) {
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/*--- Global init code ---*/
- __pyx_v_6ctabix__FILENAME_ENCODING = ((PyObject*)Py_None); Py_INCREF(Py_None);
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/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
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{
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+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 279; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_13TabixIterator_4__next__;
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}
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+ #endif
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{
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}
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+ #endif
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+ __pyx_type_5pysam_6ctabix_asGTF.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asGTF", (PyObject *)&__pyx_type_5pysam_6ctabix_asGTF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 394; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asGTF = &__pyx_type_5pysam_6ctabix_asGTF;
+ __pyx_type_5pysam_6ctabix_asBed.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asBed", (PyObject *)&__pyx_type_5pysam_6ctabix_asBed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asBed = &__pyx_type_5pysam_6ctabix_asBed;
+ __pyx_type_5pysam_6ctabix_asVCF.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asVCF", (PyObject *)&__pyx_type_5pysam_6ctabix_asVCF) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 471; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asVCF = &__pyx_type_5pysam_6ctabix_asVCF;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ #if CYTHON_COMPILING_IN_CPYTHON
{
- PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ PyObject *wrapper = __Pyx_GetAttrString((PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed, "__next__"); if (unlikely(!wrapper)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
if (Py_TYPE(wrapper) == &PyWrapperDescr_Type) {
- __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
- __pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__.doc = __pyx_doc_6ctabix_19TabixIteratorParsed_4__next__;
- ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_6ctabix_19TabixIteratorParsed_4__next__;
+ __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__ = *((PyWrapperDescrObject *)wrapper)->d_base;
+ __pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__.doc = __pyx_doc_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
+ ((PyWrapperDescrObject *)wrapper)->d_base = &__pyx_wrapperbase_5pysam_6ctabix_19TabixIteratorParsed_4__next__;
}
}
- if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_TabixIteratorParsed = &__pyx_type_6ctabix_TabixIteratorParsed;
- __pyx_vtabptr_6ctabix_tabix_inplace_iterator = &__pyx_vtable_6ctabix_tabix_inplace_iterator;
- __pyx_vtable_6ctabix_tabix_inplace_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *))__pyx_f_6ctabix_22tabix_inplace_iterator___cnext__;
- if (PyType_Ready(&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_tabix_inplace_iterator = &__pyx_type_6ctabix_tabix_inplace_iterator;
- __pyx_vtabptr_6ctabix_tabix_copy_iterator = &__pyx_vtable_6ctabix_tabix_copy_iterator;
- __pyx_vtable_6ctabix_tabix_copy_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_6ctabix_tabix_copy_iterator *))__pyx_f_6ctabix_19tabix_copy_iterator___cnext__;
- if (PyType_Ready(&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_tabix_copy_iterator = &__pyx_type_6ctabix_tabix_copy_iterator;
+ #endif
+ if (__Pyx_SetAttrString(__pyx_m, "TabixIteratorParsed", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIteratorParsed) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 510; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = &__pyx_type_5pysam_6ctabix_TabixIteratorParsed;
+ __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator;
+ __pyx_vtable_5pysam_6ctabix_tabix_inplace_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *))__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_inplace_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_inplace_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_inplace_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = &__pyx_type_5pysam_6ctabix_tabix_inplace_iterator;
+ __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator = &__pyx_vtable_5pysam_6ctabix_tabix_copy_iterator;
+ __pyx_vtable_5pysam_6ctabix_tabix_copy_iterator.__pyx___cnext__ = (PyObject *(*)(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator *))__pyx_f_5pysam_6ctabix_19tabix_copy_iterator___cnext__;
+ if (PyType_Ready(&__pyx_type_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_6ctabix_tabix_copy_iterator.tp_dict, __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "tabix_copy_iterator", (PyObject *)&__pyx_type_5pysam_6ctabix_tabix_copy_iterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = &__pyx_type_5pysam_6ctabix_tabix_copy_iterator;
/*--- Type import code ---*/
- __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy = __Pyx_ImportType("pysam.TabProxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_GTFProxy = __Pyx_ImportType("pysam.TabProxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = __Pyx_ImportType("pysam.TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_BedProxy = __Pyx_ImportType("pysam.TabProxies", "BedProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_BedProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_VCFProxy = __Pyx_ImportType("pysam.TabProxies", "VCFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type",
+ #if CYTHON_COMPILING_IN_PYPY
+ sizeof(PyTypeObject),
+ #else
+ sizeof(PyHeapTypeObject),
+ #endif
+ 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_4bool_bool = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "bool", sizeof(PyBoolObject), 0); if (unlikely(!__pyx_ptype_7cpython_4bool_bool)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 8; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_7cpython_7complex_complex = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "complex", sizeof(PyComplexObject), 0); if (unlikely(!__pyx_ptype_7cpython_7complex_complex)) {__pyx_filename = __pyx_f[4]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "ctabix.pyx":6
+ /* "pysam/ctabix.pyx":6
* # Helper functions for python 3 compatibility - taken
* # from csamtools.pyx
* import tempfile, os, sys, types, itertools, struct, ctypes, gzip # <<<<<<<<<<<<<<
* import io
- * cimport TabProxies
+ * from pysam cimport TabProxies
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__tempfile), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -11970,11 +11972,11 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gzip, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 6; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":7
+ /* "pysam/ctabix.pyx":7
* # from csamtools.pyx
* import tempfile, os, sys, types, itertools, struct, ctypes, gzip
* import io # <<<<<<<<<<<<<<
- * cimport TabProxies
+ * from pysam cimport TabProxies
*
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__io), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -11982,7 +11984,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__io, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 7; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":14
+ /* "pysam/ctabix.pyx":14
* PyObject_AsFileDescriptor
*
* PYTHON3 = PY_MAJOR_VERSION >= 3 # <<<<<<<<<<<<<<
@@ -11994,7 +11996,7 @@ PyMODINIT_FUNC PyInit_ctabix(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__PYTHON3, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "ctabix.pyx":27
+ /* "pysam/ctabix.pyx":27
* # filename encoding (copied from lxml.etree.pyx)
* cdef str _FILENAME_ENCODING
* _FILENAME_ENCODING = sys.getfilesystemencoding() # <<<<<<<<<<<<<<
@@ -12010,23 +12012,23 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__Pyx_GOTREF(__pyx_t_1);
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__Pyx_GIVEREF(__pyx_t_1);
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* if _FILENAME_ENCODING is None:
*/
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__Pyx_GIVEREF(__pyx_t_1);
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__pyx_t_1 = 0;
goto __pyx_L2;
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*
*/
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- __Pyx_DECREF(((PyObject *)__pyx_v_6ctabix__FILENAME_ENCODING));
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+ __Pyx_DECREF(((PyObject *)__pyx_v_5pysam_6ctabix__FILENAME_ENCODING));
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__ascii));
- __pyx_v_6ctabix__FILENAME_ENCODING = __pyx_n_s__ascii;
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goto __pyx_L3;
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__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
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*
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*/
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if (PyObject_SetAttr(__pyx_m, __pyx_n_s__tabix_compress, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 564; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/ctabix.pyx":612
*
* def tabix_index( filename,
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__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
- /* "ctabix.pyx":618
+ /* "pysam/ctabix.pyx":618
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__Pyx_GIVEREF(__pyx_t_1);
__pyx_t_1 = 0;
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+ /* "pysam/ctabix.pyx":611
* if r < 0: raise OSError("writing failed")
*
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*/
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* def __init__(self, infile, parser ): # <<<<<<<<<<<<<<
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* self.infile = infile
*/
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+ __pyx_t_2 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_22tabix_generic_iterator_1__init__, 0, NULL, __pyx_n_s_66, ((PyObject *)__pyx_k_codeobj_70)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ /* "pysam/ctabix.pyx":842
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* def __iter__(self): # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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+ /* "pysam/ctabix.pyx":880
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* class tabix_generic_iterator: # <<<<<<<<<<<<<<
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*/
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+ if (PyDict_SetItemString(((PyObject *)__pyx_t_1), "__doc__", ((PyObject *)__pyx_kp_s_77)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
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+ __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_5pysam_6ctabix_5tabix_iterator, NULL, __pyx_n_s_66); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 883; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/ctabix.pyx":899
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- PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_79));
- __Pyx_GIVEREF(((PyObject *)__pyx_n_s_79));
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+ PyList_SET_ITEM(__pyx_t_1, 8, ((PyObject *)__pyx_n_s_80));
+ __Pyx_GIVEREF(((PyObject *)__pyx_n_s_80));
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
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@@ -12277,10 +12279,10 @@ PyMODINIT_FUNC PyInit_ctabix(void)
__Pyx_XDECREF(__pyx_t_1);
__Pyx_XDECREF(__pyx_t_2);
if (__pyx_m) {
- __Pyx_AddTraceback("init ctabix", __pyx_clineno, __pyx_lineno, __pyx_filename);
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Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init ctabix");
+ PyErr_SetString(PyExc_ImportError, "init pysam.ctabix");
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__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -12323,6 +12325,32 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) {
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}
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
+ Py_ssize_t length;
+ if (unlikely((start < 0) | (stop < 0))) {
+ length = strlen(cstring);
+ if (start < 0) {
+ start += length;
+ if (start < 0)
+ start = 0;
+ }
+ if (stop < 0)
+ stop += length;
+ }
+ length = stop - start;
+ if (unlikely(length <= 0))
+ return PyUnicode_FromUnicode(NULL, 0);
+ cstring += start;
+ if (decode_func) {
+ return decode_func(cstring, length, errors);
+ } else {
+ return PyUnicode_Decode(cstring, length, encoding, errors);
+ }
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static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
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PyObject *tmp_type, *tmp_value, *tmp_tb;
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- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
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- }
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+ value = NULL;
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Py_INCREF(value);
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- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
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+ Py_INCREF(Py_None);
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PyErr_SetString(PyExc_TypeError,
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static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
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tb = 0;
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}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -12456,9 +12514,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -12472,6 +12527,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
@@ -12485,7 +12541,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -12506,48 +12562,72 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
}
}
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -12586,22 +12666,54 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
-
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
+}
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
@@ -12609,13 +12721,8 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else if (PyErr_Occurred()) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
+ } else {
+ return __Pyx_IterFinish();
}
return 0;
}
@@ -12640,12 +12747,9 @@ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed
return 0;
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
-}
-
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -12654,19 +12758,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -12674,10 +12786,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
@@ -12690,6 +12805,7 @@ bad:
}
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -12697,8 +12813,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -12710,6 +12830,9 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
@@ -12783,7 +12906,6 @@ bad:
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
- /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -12813,7 +12935,6 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
- /* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -13105,6 +13226,56 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
PyString_AsString(func_name), (void *)op);
#endif
}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyCFunctionObject* f = (PyCFunctionObject*)func;
+ PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+ PyObject *self = PyCFunction_GET_SELF(func);
+ Py_ssize_t size;
+ switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ case METH_VARARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ return (*meth)(self, arg);
+ break;
+ case METH_VARARGS | METH_KEYWORDS:
+ return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+ case METH_NOARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 0)
+ return (*meth)(self, NULL);
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes no arguments (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ case METH_O:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 1)
+ return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes exactly one argument (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ default:
+ PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+ "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+ "longer supported!");
+ return NULL;
+ }
+ PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+ f->m_ml->ml_name);
+ return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ return PyCFunction_Call(func, arg, kw);
+}
+#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -13124,7 +13295,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_PyCFunction_Call, /*tp_call*/
+ __Pyx_CyFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -13160,15 +13331,16 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void)
-{
+static int __Pyx_CyFunction_init(void) {
+#if !CYTHON_COMPILING_IN_PYPY
+ __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
-{
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults = PyMem_Malloc(size);
if (!m->defaults)
@@ -13177,85 +13349,12 @@ void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
-{
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults_tuple = tuple;
Py_INCREF(tuple);
}
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyBytes_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
- else
- return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
- } else {
- int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
const int32_t neg_one = (int32_t)-1, const_zero = (int32_t)0;
const int is_unsigned = const_zero < neg_one;
@@ -13285,6 +13384,10 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
else
return (int32_t)__Pyx_PyInt_AsSignedLongLong(x);
} else {
+ #if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+ #else
int32_t val;
PyObject *v = __Pyx_PyNumber_Int(x);
#if PY_VERSION_HEX < 0x03000000
@@ -13304,6 +13407,7 @@ static CYTHON_INLINE int32_t __Pyx_PyInt_from_py_int32_t(PyObject* x) {
if (likely(!ret))
return val;
}
+ #endif
return (int32_t)-1;
}
}
@@ -13744,6 +13848,23 @@ bad:
return -1;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -13796,23 +13917,6 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx
index 6a19541..67e8514 100644
--- a/pysam/ctabix.pyx
+++ b/pysam/ctabix.pyx
@@ -5,7 +5,7 @@
# from csamtools.pyx
import tempfile, os, sys, types, itertools, struct, ctypes, gzip
import io
-cimport TabProxies
+from pysam cimport TabProxies
from cpython cimport PyErr_SetString, PyBytes_Check, \
PyUnicode_Check, PyBytes_FromStringAndSize, \
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
index 6caaba0..1754ba8 100644
--- a/pysam/cvcf.c
+++ b/pysam/cvcf.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.16 on Mon Nov 19 08:44:41 2012 */
+/* Generated by Cython 0.17.4 on Wed Jan 23 22:59:29 2013 */
#define PY_SSIZE_T_CLEAN
#include "Python.h"
@@ -11,7 +11,6 @@
#ifndef offsetof
#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
#endif
-
#if !defined(WIN32) && !defined(MS_WINDOWS)
#ifndef __stdcall
#define __stdcall
@@ -23,22 +22,18 @@
#define __fastcall
#endif
#endif
-
#ifndef DL_IMPORT
#define DL_IMPORT(t) t
#endif
#ifndef DL_EXPORT
#define DL_EXPORT(t) t
#endif
-
#ifndef PY_LONG_LONG
#define PY_LONG_LONG LONG_LONG
#endif
-
#ifndef Py_HUGE_VAL
#define Py_HUGE_VAL HUGE_VAL
#endif
-
#ifdef PYPY_VERSION
#define CYTHON_COMPILING_IN_PYPY 1
#define CYTHON_COMPILING_IN_CPYTHON 0
@@ -46,28 +41,28 @@
#define CYTHON_COMPILING_IN_PYPY 0
#define CYTHON_COMPILING_IN_CPYTHON 1
#endif
-
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyCFunction_Call PyObject_Call
-#else
- #define __Pyx_PyCFunction_Call PyCFunction_Call
-#endif
-
#if PY_VERSION_HEX < 0x02050000
typedef int Py_ssize_t;
#define PY_SSIZE_T_MAX INT_MAX
#define PY_SSIZE_T_MIN INT_MIN
#define PY_FORMAT_SIZE_T ""
+ #define CYTHON_FORMAT_SSIZE_T ""
#define PyInt_FromSsize_t(z) PyInt_FromLong(z)
#define PyInt_AsSsize_t(o) __Pyx_PyInt_AsInt(o)
- #define PyNumber_Index(o) PyNumber_Int(o)
- #define PyIndex_Check(o) PyNumber_Check(o)
+ #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
+ (PyErr_Format(PyExc_TypeError, \
+ "expected index value, got %.200s", Py_TYPE(o)->tp_name), \
+ (PyObject*)0))
+ #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \
+ !PyComplex_Check(o))
+ #define PyIndex_Check __Pyx_PyIndex_Check
#define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message)
#define __PYX_BUILD_PY_SSIZE_T "i"
#else
#define __PYX_BUILD_PY_SSIZE_T "n"
+ #define CYTHON_FORMAT_SSIZE_T "z"
+ #define __Pyx_PyIndex_Check PyIndex_Check
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt)
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
@@ -75,7 +70,6 @@
#define PyVarObject_HEAD_INIT(type, size) \
PyObject_HEAD_INIT(type) size,
#define PyType_Modified(t)
-
typedef struct {
void *buf;
PyObject *obj;
@@ -89,7 +83,6 @@
Py_ssize_t *suboffsets;
void *internal;
} Py_buffer;
-
#define PyBUF_SIMPLE 0
#define PyBUF_WRITABLE 0x0001
#define PyBUF_FORMAT 0x0004
@@ -101,11 +94,9 @@
#define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
#define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
#define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
-
typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
#endif
-
#if PY_MAJOR_VERSION < 3
#define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
@@ -115,31 +106,30 @@
#define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
#endif
-
#if PY_MAJOR_VERSION < 3 && PY_MINOR_VERSION < 6
#define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict")
#endif
-
#if PY_MAJOR_VERSION >= 3
#define Py_TPFLAGS_CHECKTYPES 0
#define Py_TPFLAGS_HAVE_INDEX 0
#endif
-
#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3)
#define Py_TPFLAGS_HAVE_NEWBUFFER 0
#endif
-
-
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_GET_LENGTH)
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
#define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
#else
#define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
#define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((k=k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBaseString_Type PyUnicode_Type
#define PyStringObject PyUnicodeObject
@@ -147,7 +137,6 @@
#define PyString_Check PyUnicode_Check
#define PyString_CheckExact PyUnicode_CheckExact
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PyBytesObject PyStringObject
#define PyBytes_Type PyString_Type
@@ -166,7 +155,6 @@
#define PyBytes_Concat PyString_Concat
#define PyBytes_ConcatAndDel PyString_ConcatAndDel
#endif
-
#if PY_VERSION_HEX < 0x02060000
#define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
#define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
@@ -174,9 +162,7 @@
#ifndef PySet_CheckExact
#define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
#endif
-
#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
-
#if PY_MAJOR_VERSION >= 3
#define PyIntObject PyLongObject
#define PyInt_Type PyLong_Type
@@ -193,11 +179,9 @@
#define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
#define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyBoolObject PyLongObject
#endif
-
#if PY_VERSION_HEX < 0x03020000
typedef long Py_hash_t;
#define __Pyx_PyInt_FromHash_t PyInt_FromLong
@@ -206,7 +190,6 @@
#define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
#define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
#endif
-
#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300)
#define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b)
#define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value)
@@ -225,11 +208,9 @@
(likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \
(PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1)))
#endif
-
#if PY_MAJOR_VERSION >= 3
#define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n)))
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a))
@@ -239,7 +220,6 @@
#define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a))
#define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n))
#endif
-
#if PY_VERSION_HEX < 0x02050000
#define __Pyx_NAMESTR(n) ((char *)(n))
#define __Pyx_DOCSTR(n) ((char *)(n))
@@ -248,6 +228,7 @@
#define __Pyx_DOCSTR(n) (n)
#endif
+
#if PY_MAJOR_VERSION >= 3
#define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
#define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
@@ -268,8 +249,8 @@
#define _USE_MATH_DEFINES
#endif
#include <math.h>
-#define __PYX_HAVE__cvcf
-#define __PYX_HAVE_API__cvcf
+#define __PYX_HAVE__pysam__cvcf
+#define __PYX_HAVE_API__pysam__cvcf
#include "stdlib.h"
#include "string.h"
#include "stdint.h"
@@ -335,7 +316,11 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*);
+#if CYTHON_COMPILING_IN_CPYTHON
#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
#ifdef __GNUC__
@@ -369,27 +354,27 @@ static const char *__pyx_f[] = {
};
/*--- Type declarations ---*/
-struct __pyx_obj_6ctabix_Parser;
-struct __pyx_obj_6ctabix_asVCF;
-struct __pyx_obj_10TabProxies_TupleProxy;
-struct __pyx_obj_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_10TabProxies_BedProxy;
-struct __pyx_obj_6ctabix_tabix_copy_iterator;
-struct __pyx_obj_4cvcf_VCFRecord;
-struct __pyx_obj_10TabProxies_VCFProxy;
-struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse;
-struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data;
-struct __pyx_obj_6ctabix_TabixIterator;
-struct __pyx_obj_4cvcf_asVCFRecord;
-struct __pyx_obj_10TabProxies_GTFProxy;
-struct __pyx_obj_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_6ctabix_TabixHeaderIterator;
-struct __pyx_obj_6ctabix_Tabixfile;
-struct __pyx_obj_6ctabix_asGTF;
-struct __pyx_obj_6ctabix_asBed;
-struct __pyx_obj_6ctabix_tabix_inplace_iterator;
-struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_6ctabix_asTuple;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data;
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy;
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
+struct __pyx_obj_5pysam_6ctabix_TabixIterator;
+struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse;
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator;
+struct __pyx_obj_5pysam_6ctabix_Parser;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
+struct __pyx_obj_5pysam_6ctabix_Tabixfile;
+struct __pyx_obj_5pysam_6ctabix_asBed;
+struct __pyx_obj_5pysam_6ctabix_asGTF;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
+struct __pyx_obj_5pysam_4cvcf_VCFRecord;
+struct __pyx_obj_5pysam_6ctabix_asTuple;
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
+struct __pyx_obj_5pysam_6ctabix_asVCF;
struct __pyx_defaults;
typedef struct __pyx_defaults __pyx_defaults;
struct __pyx_defaults1;
@@ -417,27 +402,16 @@ struct __pyx_defaults4 {
PyObject *__pyx_arg_lineparse;
};
-/* "ctabix.pxd":190
- * cdef tabix_t * tabixfile
- *
- * cdef class Parser: # <<<<<<<<<<<<<<
- * pass
+/* "pysam/cvcf.pyx":647
+ * return False
*
+ * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
+ * cols = line.split('\t')
+ * if len(cols) != len(self._samples)+9:
*/
-struct __pyx_obj_6ctabix_Parser {
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data {
PyObject_HEAD
-};
-
-
-/* "ctabix.pxd":202
- * pass
- *
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_6ctabix_asVCF {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+ PyObject *__pyx_v_alt;
};
@@ -448,9 +422,9 @@ struct __pyx_obj_6ctabix_asVCF {
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_TupleProxy {
+struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
PyObject_HEAD
- struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtab;
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
char *data;
char **fields;
int nfields;
@@ -468,8 +442,8 @@ struct __pyx_obj_10TabProxies_TupleProxy {
* pass
*
*/
-struct __pyx_obj_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
};
@@ -480,8 +454,8 @@ struct __pyx_obj_10TabProxies_NamedTupleProxy {
*
* cdef:
*/
-struct __pyx_obj_10TabProxies_BedProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_obj_5pysam_10TabProxies_BedProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
char *contig;
uint32_t start;
uint32_t end;
@@ -489,58 +463,91 @@ struct __pyx_obj_10TabProxies_BedProxy {
};
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "ctabix.pxd":186
+ * cdef tabix_t * tabixfile
*
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
+ * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_6ctabix_tabix_copy_iterator {
+struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator {
PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtab;
- FILE *infile;
- struct __pyx_obj_6ctabix_Parser *parser;
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
};
-/* "cvcf.pyx":94
- * ###########################################################################################################
- *
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
+/* "ctabix.pxd":205
+ * pass
*
+ * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
*/
-struct __pyx_obj_4cvcf_VCFRecord {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
- PyObject *vcf;
- char *contig;
- uint32_t pos;
+struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "TabProxies.pxd":83
- * cdef update( self, char * buffer, size_t nbytes )
+/* "ctabix.pxd":182
+ * cdef char * _filename
*
- * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ * cdef class TabixIterator: # <<<<<<<<<<<<<<
+ * cdef ti_iter_t iterator
+ * cdef tabix_t * tabixfile
+ */
+struct __pyx_obj_5pysam_6ctabix_TabixIterator {
+ PyObject_HEAD
+ ti_iter_t iterator;
+ tabix_t *tabixfile;
+};
+
+
+/* "ctabix.pxd":210
+ * cdef Parser parser
*
- * cdef:
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
*/
-struct __pyx_obj_10TabProxies_VCFProxy {
- struct __pyx_obj_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
+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/cvcf.pyx":790
+ * if alt:
+ * for i in range(1,min(len(ref),min(map(len,alt)))):
+ * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<<
+ * break
+ * ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+ */
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr {
+ PyObject_HEAD
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope;
+ PyObject *__pyx_v_allele;
+ PyObject *__pyx_t_0;
+ Py_ssize_t __pyx_t_1;
+ PyObject *(*__pyx_t_2)(PyObject *);
};
-/* "cvcf.pyx":899
+/* "pysam/cvcf.pyx":899
* return line
*
* def _parse(self, line, stream): # <<<<<<<<<<<<<<
* # deal with files with header only
* if line.startswith("##"): return
*/
-struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse {
+struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse {
PyObject_HEAD
PyObject *__pyx_v_d;
PyObject *__pyx_v_line;
@@ -552,89 +559,46 @@ struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse {
};
-/* "cvcf.pyx":647
- * return False
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
*
- * def parse_data( self, line, lineparse=False ): # <<<<<<<<<<<<<<
- * cols = line.split('\t')
- * if len(cols) != len(self._samples)+9:
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
*/
-struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data {
+struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator {
PyObject_HEAD
- PyObject *__pyx_v_alt;
+ struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtab;
+ FILE *infile;
+ struct __pyx_obj_5pysam_6ctabix_Parser *parser;
};
-/* "ctabix.pxd":182
- * cdef char * _filename
- *
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
+/* "ctabix.pxd":190
* cdef tabix_t * tabixfile
+ *
+ * cdef class Parser: # <<<<<<<<<<<<<<
+ * pass
+ *
*/
-struct __pyx_obj_6ctabix_TabixIterator {
+struct __pyx_obj_5pysam_6ctabix_Parser {
PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
};
-/* "cvcf.pyx":226
+/* "pysam/cvcf.pyx":226
*
*
* cdef class asVCFRecord( ctabix.Parser ): # <<<<<<<<<<<<<<
* '''converts a :term:`tabix row` into a VCF record.'''
* cdef vcffile
*/
-struct __pyx_obj_4cvcf_asVCFRecord {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_4cvcf_asVCFRecord {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
PyObject *vcffile;
};
-/* "TabProxies.pxd":60
- * cdef update( self, char * buffer, size_t nbytes )
- *
- * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_10TabProxies_GTFProxy {
- struct __pyx_obj_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
-};
-
-
-/* "ctabix.pxd":205
- * pass
- *
- * cdef class TabixIteratorParsed: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
- */
-struct __pyx_obj_6ctabix_TabixIteratorParsed {
- PyObject_HEAD
- ti_iter_t iterator;
- tabix_t *tabixfile;
- struct __pyx_obj_6ctabix_Parser *parser;
-};
-
-
-/* "ctabix.pxd":186
- * cdef tabix_t * tabixfile
- *
- * cdef class TabixHeaderIterator: # <<<<<<<<<<<<<<
- * cdef ti_iter_t iterator
- * cdef tabix_t * tabixfile
- */
-struct __pyx_obj_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)
*
@@ -642,7 +606,7 @@ struct __pyx_obj_6ctabix_TabixHeaderIterator {
*
* # pointer to tabixfile
*/
-struct __pyx_obj_6ctabix_Tabixfile {
+struct __pyx_obj_5pysam_6ctabix_Tabixfile {
PyObject_HEAD
tabix_t *tabixfile;
int isremote;
@@ -650,61 +614,56 @@ struct __pyx_obj_6ctabix_Tabixfile {
};
-/* "ctabix.pxd":196
+/* "ctabix.pxd":199
* pass
*
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
+ * cdef class asBed(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_asGTF {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_asBed {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pxd":199
+/* "ctabix.pxd":196
* pass
*
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
+ * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
* pass
*
*/
-struct __pyx_obj_6ctabix_asBed {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_asGTF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "TabProxies.pxd":83
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
+ * cdef class VCFProxy( NamedTupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
-struct __pyx_obj_6ctabix_tabix_inplace_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtab;
- FILE *infile;
- char *buffer;
- size_t size;
- struct __pyx_obj_6ctabix_Parser *parser;
+struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
+ char *contig;
+ uint32_t pos;
};
-/* "cvcf.pyx":790
- * if alt:
- * for i in range(1,min(len(ref),min(map(len,alt)))):
- * if len(set(allele[-1].upper() for allele in alt)) > 1 or ref[-1].upper() != alt[0][-1].upper(): # <<<<<<<<<<<<<<
- * break
- * ref, alt = ref[:-1], [allele[:-1] for allele in alt]
+/* "pysam/cvcf.pyx":94
+ * ###########################################################################################################
+ *
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
*/
-struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr {
- PyObject_HEAD
- struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *__pyx_outer_scope;
- PyObject *__pyx_v_allele;
- PyObject *__pyx_t_0;
- Py_ssize_t __pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
+struct __pyx_obj_5pysam_4cvcf_VCFRecord {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ PyObject *vcf;
+ char *contig;
+ uint32_t pos;
};
@@ -715,24 +674,36 @@ struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr {
* pass
*
*/
-struct __pyx_obj_6ctabix_asTuple {
- struct __pyx_obj_6ctabix_Parser __pyx_base;
+struct __pyx_obj_5pysam_6ctabix_asTuple {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-
-/* "ctabix.pxd":218
- * cdef __cnext__(self)
+/* "TabProxies.pxd":60
+ * cdef update( self, char * buffer, size_t nbytes )
*
- * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef Parser parser
+ * cdef class GTFProxy( TupleProxy) : # <<<<<<<<<<<<<<
+ *
+ * cdef:
*/
+struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *_attributes;
+ int hasOwnAttributes;
+};
+
-struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_copy_iterator *);
+/* "ctabix.pxd":202
+ * pass
+ *
+ * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
+ * pass
+ *
+ */
+struct __pyx_obj_5pysam_6ctabix_asVCF {
+ struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
};
-static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabix_tabix_copy_iterator;
+
/* "TabProxies.pxd":41
@@ -743,14 +714,14 @@ static struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator *__pyx_vtabptr_6ctabi
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_TupleProxy {
- int (*getMaxFields)(struct __pyx_obj_10TabProxies_TupleProxy *, size_t);
- PyObject *(*take)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*present)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*copy)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
- PyObject *(*update)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t);
+struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy {
+ int (*getMaxFields)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, size_t);
+ PyObject *(*take)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*copy)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
+ PyObject *(*update)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
};
-static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxies_TupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
/* "TabProxies.pxd":69
@@ -761,10 +732,10 @@ static struct __pyx_vtabstruct_10TabProxies_TupleProxy *__pyx_vtabptr_10TabProxi
*
*/
-struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10TabProxies_NamedTupleProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy *__pyx_vtabptr_5pysam_10TabProxies_NamedTupleProxy;
/* "TabProxies.pxd":83
@@ -775,24 +746,38 @@ static struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy *__pyx_vtabptr_10Tab
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_VCFProxy {
- struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_VCFProxy *__pyx_vtabptr_10TabProxies_VCFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy *__pyx_vtabptr_5pysam_10TabProxies_VCFProxy;
-/* "ctabix.pxd":210
- * cdef Parser parser
+/* "pysam/cvcf.pyx":94
+ * ###########################################################################################################
*
- * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
- * cdef FILE * infile
- * cdef char * buffer
+ * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
+ * '''vcf record.
+ *
+ */
+
+struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+};
+static struct __pyx_vtabstruct_5pysam_4cvcf_VCFRecord *__pyx_vtabptr_5pysam_4cvcf_VCFRecord;
+
+
+/* "ctabix.pxd":210
+ * cdef Parser parser
+ *
+ * ctypedef class tabix_inplace_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef char * buffer
*/
-struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator {
- PyObject *(*__pyx___cnext__)(struct __pyx_obj_6ctabix_tabix_inplace_iterator *);
+struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator {
+ PyObject *(*__pyx___cnext__)(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator *);
};
-static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ctabix_tabix_inplace_iterator;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator;
/* "TabProxies.pxd":60
@@ -803,25 +788,25 @@ static struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator *__pyx_vtabptr_6ct
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_GTFProxy {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __pyx_base;
- char *(*getAttributes)(struct __pyx_obj_10TabProxies_GTFProxy *);
+struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy __pyx_base;
+ char *(*getAttributes)(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *);
};
-static struct __pyx_vtabstruct_10TabProxies_GTFProxy *__pyx_vtabptr_10TabProxies_GTFProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_GTFProxy *__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
-/* "cvcf.pyx":94
- * ###########################################################################################################
- *
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
- * '''vcf record.
+/* "ctabix.pxd":218
+ * cdef __cnext__(self)
*
+ * ctypedef class tabix_copy_iterator: # <<<<<<<<<<<<<<
+ * cdef FILE * infile
+ * cdef Parser parser
*/
-struct __pyx_vtabstruct_4cvcf_VCFRecord {
- struct __pyx_vtabstruct_10TabProxies_TupleProxy __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_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
+static struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator *__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator;
/* "TabProxies.pxd":72
@@ -832,10 +817,10 @@ static struct __pyx_vtabstruct_4cvcf_VCFRecord *__pyx_vtabptr_4cvcf_VCFRecord;
* cdef:
*/
-struct __pyx_vtabstruct_10TabProxies_BedProxy {
- struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy __pyx_base;
+struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
+ struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
};
-static struct __pyx_vtabstruct_10TabProxies_BedProxy *__pyx_vtabptr_10TabProxies_BedProxy;
+static struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy *__pyx_vtabptr_5pysam_10TabProxies_BedProxy;
#ifndef CYTHON_REFNANNY
#define CYTHON_REFNANNY 0
#endif
@@ -912,42 +897,47 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j
__Pyx_GetItemInt_List_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Tuple_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) {
- if (likely(o != Py_None)) {
- if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
- PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
- Py_INCREF(r);
- return r;
- }
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) {
+ PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i);
+ Py_INCREF(r);
+ return r;
}
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
}
#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_GetItemInt_Fast(o, i) : \
__Pyx_GetItemInt_Generic(o, to_py_func(i)))
static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -963,13 +953,22 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i)
Py_INCREF(r);
return r;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_GetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return NULL;
+ i += l;
+ }
return m->sq_item(o, i);
}
}
+#else
+ if (PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
}
@@ -981,21 +980,22 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
+#if CYTHON_COMPILING_IN_PYPY
+#define __Pyx_PyObject_AsDouble(obj) \
+(likely(PyFloat_CheckExact(obj)) ? PyFloat_AS_DOUBLE(obj) : \
+ likely(PyInt_CheckExact(obj)) ? \
+ PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
+#else
#define __Pyx_PyObject_AsDouble(obj) \
((likely(PyFloat_CheckExact(obj))) ? \
PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
+#endif
static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void);
-
#if PY_MAJOR_VERSION >= 3
static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
PyObject *value;
- if (unlikely(d == Py_None)) {
- __Pyx_RaiseNoneIndexingError();
- return NULL;
- }
value = PyDict_GetItemWithError(d, key);
if (unlikely(!value)) {
if (!PyErr_Occurred())
@@ -1009,28 +1009,48 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
#define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
#endif
-static CYTHON_INLINE int __Pyx_NegateNonNeg(int b) {
- return unlikely(b < 0) ? b : !b;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) {
- return unlikely(b < 0) ? NULL : __Pyx_PyBool_FromLong(b);
+static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
+ int result = PySequence_Contains(seq, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
}
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/
+static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) {
+ int result = PyDict_Contains(dict, item);
+ return unlikely(result < 0) ? result : (result == (eq == Py_EQ));
+}
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len)) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
+ }
+ return PyList_Append(list, x);
+}
+#else
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#endif
+
static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */
static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
if (likely(PyList_CheckExact(L))) {
- if (PyList_Append(L, x) < 0) return NULL;
+ if (unlikely(PyList_Append(L, x) < 0)) return NULL;
Py_INCREF(Py_None);
return Py_None; /* this is just to have an accurate signature */
- }
- else {
+ } else {
PyObject *r, *m;
m = __Pyx_GetAttrString(L, "append");
if (!m) return NULL;
@@ -1040,6 +1060,18 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
}
}
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
+
+static void __Pyx_UnpackTupleError(PyObject *, Py_ssize_t index); /*proto*/
+
+static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** value1, PyObject** value2,
+ int is_tuple, int has_known_size, int decref_tuple);
+
+static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* dict, int is_dict, PyObject* method_name,
+ Py_ssize_t* p_orig_length, int* p_is_dict);
+static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* dict_or_iter, Py_ssize_t orig_length, Py_ssize_t* ppos,
+ PyObject** pkey, PyObject** pvalue, PyObject** pitem, int is_dict);
+
#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \
__Pyx_SetItemInt_Fast(o, i, v) : \
__Pyx_SetItemInt_Generic(o, to_py_func(i), v))
@@ -1051,6 +1083,7 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyOb
return r;
}
static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) {
+#if CYTHON_COMPILING_IN_CPYTHON
if (PyList_CheckExact(o)) {
Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
@@ -1060,13 +1093,26 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje
Py_DECREF(old);
return 1;
}
- }
- else if (likely(i >= 0)) {
+ } else { /* inlined PySequence_SetItem() */
PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
if (likely(m && m->sq_ass_item)) {
+ if (unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (unlikely(l < 0)) return -1;
+ i += l;
+ }
return m->sq_ass_item(o, i, v);
}
}
+#else
+#if CYTHON_COMPILING_IN_PYPY
+ if (PySequence_Check(o) && !PyDict_Check(o)) {
+#else
+ if (PySequence_Check(o)) {
+#endif
+ return PySequence_SetItem(o, i, v);
+ }
+#endif
return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
}
@@ -1105,6 +1151,12 @@ static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
#endif /* PyAnySet_CheckExact (<= Py2.4) */
#endif /* < Py2.5 */
+static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc);
+
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse);
+
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_dealloc);
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
@@ -1161,18 +1213,6 @@ static int __Pyx_CyFunction_init(void);
static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t);
-#include <string.h>
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
-
-#if PY_MAJOR_VERSION >= 3
-#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
-#else
-#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
-#endif
-
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *);
static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *);
@@ -1209,22 +1249,30 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
#define __Pyx_Generator_USED
#include <structmember.h>
+#include <frameobject.h>
typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
typedef struct {
PyObject_HEAD
__pyx_generator_body_t body;
PyObject *closure;
- int is_running;
- int resume_label;
PyObject *exc_type;
PyObject *exc_value;
PyObject *exc_traceback;
PyObject *gi_weakreflist;
PyObject *classobj;
+ PyObject *yieldfrom;
+ int resume_label;
+ char is_running; // using T_BOOL for property below requires char value
} __pyx_GeneratorObject;
static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject *closure);
static int __pyx_Generator_init(void);
+static int __Pyx_Generator_clear(PyObject* self);
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue);
+#else
+#define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue)
+#endif
static int __Pyx_check_binary_version(void);
@@ -1236,10 +1284,10 @@ static int __Pyx_check_binary_version(void);
#endif
#endif
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
+
static void* __Pyx_GetVtable(PyObject *dict); /*proto*/
static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
@@ -1264,36 +1312,38 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line,
static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-/* Module declarations from 'ctabix' */
-static PyTypeObject *__pyx_ptype_6ctabix_Tabixfile = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixHeaderIterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_Parser = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asTuple = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asGTF = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asBed = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_asVCF = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_TabixIteratorParsed = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_tabix_inplace_iterator = 0;
-static PyTypeObject *__pyx_ptype_6ctabix_tabix_copy_iterator = 0;
-
-/* Module declarations from 'TabProxies' */
-static PyTypeObject *__pyx_ptype_10TabProxies_TupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_GTFProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_NamedTupleProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_BedProxy = 0;
-static PyTypeObject *__pyx_ptype_10TabProxies_VCFProxy = 0;
-
-/* Module declarations from 'cvcf' */
-static PyTypeObject *__pyx_ptype_4cvcf_VCFRecord = 0;
-static PyTypeObject *__pyx_ptype_4cvcf_asVCFRecord = 0;
-static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct__parse_data = 0;
-static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr = 0;
-static PyTypeObject *__pyx_ptype_4cvcf___pyx_scope_struct_2__parse = 0;
-#define __Pyx_MODULE_NAME "cvcf"
-int __pyx_module_is_main_cvcf = 0;
-
-/* Implementation of 'cvcf' */
+/* Module declarations from 'pysam' */
+
+/* Module declarations from 'pysam.ctabix' */
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Parser = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asGTF = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asBed = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asVCF = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = 0;
+static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = 0;
+
+/* Module declarations from 'pysam.TabProxies' */
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_TupleProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_GTFProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_NamedTupleProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_BedProxy = 0;
+static PyTypeObject *__pyx_ptype_5pysam_10TabProxies_VCFProxy = 0;
+
+/* Module declarations from 'pysam.cvcf' */
+static PyTypeObject *__pyx_ptype_5pysam_4cvcf_VCFRecord = 0;
+static PyTypeObject *__pyx_ptype_5pysam_4cvcf_asVCFRecord = 0;
+static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = 0;
+static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = 0;
+static PyTypeObject *__pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = 0;
+#define __Pyx_MODULE_NAME "pysam.cvcf"
+int __pyx_module_is_main_pysam__cvcf = 0;
+
+/* Implementation of 'pysam.cvcf' */
static PyObject *__pyx_builtin_object;
static PyObject *__pyx_builtin_ValueError;
static PyObject *__pyx_builtin_range;
@@ -1304,73 +1354,73 @@ static PyObject *__pyx_builtin_zip;
static PyObject *__pyx_builtin_StopIteration;
static PyObject *__pyx_builtin_KeyError;
static PyObject *__pyx_builtin_NotImplementedError;
-static PyObject *__pyx_pf_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */
-static PyObject *__pyx_pf_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */
-static int __pyx_pf_4cvcf_9VCFRecord___init__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */
-static int __pyx_pf_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_4error(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */
-static Py_ssize_t __pyx_pf_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
-static int __pyx_pf_4cvcf_11asVCFRecord___init__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */
-static PyObject *__pyx_pf_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
-static PyObject *__pyx_pf_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_get_sequence(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_fa); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_2parse_regions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string); /* proto */
+static int __pyx_pf_5pysam_4cvcf_9VCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */
+static int __pyx_pf_5pysam_4cvcf_9VCFRecord_2__cinit__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_vcf); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4error(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */
+static Py_ssize_t __pyx_pf_5pysam_4cvcf_9VCFRecord_6__len__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6contig___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3pos___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_2id___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3ref___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_3alt___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4qual___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6filter___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_4info___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_6format___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_7samples___get__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_9VCFRecord_8__getitem__(struct __pyx_obj_5pysam_4cvcf_VCFRecord *__pyx_v_self, PyObject *__pyx_v_key); /* proto */
+static int __pyx_pf_5pysam_4cvcf_11asVCFRecord___init__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, PyObject *__pyx_v_vcffile); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_11asVCFRecord_2__call__(struct __pyx_obj_5pysam_4cvcf_asVCFRecord *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_len); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_85__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v__copy, PyObject *__pyx_v_reference, PyObject *__pyx_v_regions, PyObject *__pyx_v_lines, PyObject *__pyx_v_leftalign); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_2error(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_error, PyObject *__pyx_v_opt); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_87__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_format, PyObject *__pyx_v_filter); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_89__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_fmt, PyObject *__pyx_v_filter); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_8get_expected(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_alt); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10_add_definition(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_key, PyObject *__pyx_v_data, PyObject *__pyx_v_line); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_91__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_12format_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_data, PyObject *__pyx_v_format, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_separator); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_14enter_default_format(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_16parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_18write_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_20parse_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_22write_heading(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_24convertGT(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_GTstring); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_26convertGTback(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_GTdata); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_28parse_formatdata(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key, PyObject *__pyx_v_value, PyObject *__pyx_v_formatdict, PyObject *__pyx_v_line); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_30inregion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_chrom, PyObject *__pyx_v_pos); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_93__defaults__(CYTHON_UNUSED PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_10parse_data_genexpr(PyObject *__pyx_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_32parse_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_lineparse); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_34write_data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_data); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_36_parse_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_38_parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line, PyObject *__pyx_v_stream); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_41getsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_43setsamples(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_samples); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_45getheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_47setheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_header); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_49getinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_51setinfo(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_info); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_53getformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_55setformat(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_format); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_57getfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_59setfilter(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filter); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_61setversion(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_version); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_63setregions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_regions); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_65setreference(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_ref); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_67ignoreerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_69warnerror(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_errorstring); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_71parse(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_73write(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream, PyObject *__pyx_v_datagenerator); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_75writeheader(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_stream); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_77compare_calls(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, PyObject *__pyx_v_pos1, PyObject *__pyx_v_ref1, PyObject *__pyx_v_alt1, PyObject *__pyx_v_pos2, PyObject *__pyx_v_ref2, PyObject *__pyx_v_alt2); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_79connect(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_81fetch(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_reference, PyObject *__pyx_v_start, PyObject *__pyx_v_end, PyObject *__pyx_v_region); /* proto */
+static PyObject *__pyx_pf_5pysam_4cvcf_3VCF_83validate(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self, CYTHON_UNUSED PyObject *__pyx_v_record); /* proto */
static char __pyx_k_1[] = "";
static char __pyx_k_2[] = ",";
static char __pyx_k_4[] = ":";
@@ -1469,41 +1519,42 @@ static char __pyx_k_126[] = "needs to be checked";
static char __pyx_k_128[] = "[|/\\\\]";
static char __pyx_k_130[] = "^[ACGTN]+$";
static char __pyx_k_134[] = "/ifs/devel/pysam/pysam/cvcf.pyx";
-static char __pyx_k_137[] = "id numbertype number type description missingvalue";
-static char __pyx_k_139[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
-static char __pyx_k_140[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
-static char __pyx_k_141[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
-static char __pyx_k_142[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
-static char __pyx_k_143[] = "POS_NOT_NUMERICAL:Position column is not numerical";
-static char __pyx_k_144[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
-static char __pyx_k_145[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
-static char __pyx_k_146[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
-static char __pyx_k_147[] = "POS_NOT_POSITIVE:Position field must be >0";
-static char __pyx_k_148[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
-static char __pyx_k_149[] = "ERROR_INFO_STRING:Error while parsing info field";
-static char __pyx_k_150[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
-static char __pyx_k_151[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
-static char __pyx_k_152[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
-static char __pyx_k_153[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
-static char __pyx_k_154[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
-static char __pyx_k_155[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
-static char __pyx_k_156[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
-static char __pyx_k_157[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
-static char __pyx_k_158[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
-static char __pyx_k_159[] = "MISSING_REF:Reference allele missing";
-static char __pyx_k_160[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
-static char __pyx_k_161[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
-static char __pyx_k_162[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
-static char __pyx_k_163[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
-static char __pyx_k_164[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
-static char __pyx_k_165[] = "WRONG_REF:Wrong reference %s";
-static char __pyx_k_166[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
-static char __pyx_k_167[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
-static char __pyx_k_168[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
-static char __pyx_k_169[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
-static char __pyx_k_170[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'";
-static char __pyx_k_171[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s";
-static char __pyx_k_172[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value";
+static char __pyx_k_135[] = "pysam.cvcf";
+static char __pyx_k_138[] = "id numbertype number type description missingvalue";
+static char __pyx_k_140[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
+static char __pyx_k_141[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
+static char __pyx_k_142[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
+static char __pyx_k_143[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
+static char __pyx_k_144[] = "POS_NOT_NUMERICAL:Position column is not numerical";
+static char __pyx_k_145[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
+static char __pyx_k_146[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
+static char __pyx_k_147[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
+static char __pyx_k_148[] = "POS_NOT_POSITIVE:Position field must be >0";
+static char __pyx_k_149[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
+static char __pyx_k_150[] = "ERROR_INFO_STRING:Error while parsing info field";
+static char __pyx_k_151[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
+static char __pyx_k_152[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
+static char __pyx_k_153[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
+static char __pyx_k_154[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
+static char __pyx_k_155[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
+static char __pyx_k_156[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
+static char __pyx_k_157[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
+static char __pyx_k_158[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
+static char __pyx_k_159[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
+static char __pyx_k_160[] = "MISSING_REF:Reference allele missing";
+static char __pyx_k_161[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
+static char __pyx_k_162[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
+static char __pyx_k_163[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
+static char __pyx_k_164[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
+static char __pyx_k_165[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
+static char __pyx_k_166[] = "WRONG_REF:Wrong reference %s";
+static char __pyx_k_167[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
+static char __pyx_k_168[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
+static char __pyx_k_169[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
+static char __pyx_k_170[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
+static char __pyx_k_171[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'";
+static char __pyx_k_172[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s";
+static char __pyx_k_173[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value";
static char __pyx_k__DP[] = "DP";
static char __pyx_k__EC[] = "EC";
static char __pyx_k__FT[] = "FT";
@@ -1556,7 +1607,6 @@ static char __pyx_k__alt1[] = "alt1";
static char __pyx_k__alt2[] = "alt2";
static char __pyx_k__cols[] = "cols";
static char __pyx_k__copy[] = "copy";
-static char __pyx_k__cvcf[] = "cvcf";
static char __pyx_k__data[] = "data";
static char __pyx_k__dict[] = "dict";
static char __pyx_k__elts[] = "elts";
@@ -1783,8 +1833,8 @@ static PyObject *__pyx_kp_s_126;
static PyObject *__pyx_kp_s_128;
static PyObject *__pyx_kp_s_130;
static PyObject *__pyx_kp_s_134;
-static PyObject *__pyx_kp_s_137;
-static PyObject *__pyx_kp_s_139;
+static PyObject *__pyx_n_s_135;
+static PyObject *__pyx_kp_s_138;
static PyObject *__pyx_kp_s_14;
static PyObject *__pyx_kp_s_140;
static PyObject *__pyx_kp_s_141;
@@ -1819,6 +1869,7 @@ static PyObject *__pyx_kp_s_169;
static PyObject *__pyx_kp_s_170;
static PyObject *__pyx_kp_s_171;
static PyObject *__pyx_kp_s_172;
+static PyObject *__pyx_kp_s_173;
static PyObject *__pyx_n_s_18;
static PyObject *__pyx_kp_s_19;
static PyObject *__pyx_kp_s_2;
@@ -2000,7 +2051,6 @@ static PyObject *__pyx_n_s__connect;
static PyObject *__pyx_n_s__convertGT;
static PyObject *__pyx_n_s__convertGTback;
static PyObject *__pyx_n_s__copy;
-static PyObject *__pyx_n_s__cvcf;
static PyObject *__pyx_n_s__d;
static PyObject *__pyx_n_s__data;
static PyObject *__pyx_n_s__datagenerator;
@@ -2253,111 +2303,110 @@ static PyObject *__pyx_k_tuple_127;
static PyObject *__pyx_k_tuple_129;
static PyObject *__pyx_k_tuple_131;
static PyObject *__pyx_k_tuple_132;
-static PyObject *__pyx_k_tuple_135;
-static PyObject *__pyx_k_tuple_138;
-static PyObject *__pyx_k_tuple_173;
-static PyObject *__pyx_k_tuple_175;
-static PyObject *__pyx_k_tuple_177;
+static PyObject *__pyx_k_tuple_136;
+static PyObject *__pyx_k_tuple_139;
+static PyObject *__pyx_k_tuple_174;
+static PyObject *__pyx_k_tuple_176;
static PyObject *__pyx_k_tuple_178;
-static PyObject *__pyx_k_tuple_180;
-static PyObject *__pyx_k_tuple_182;
-static PyObject *__pyx_k_tuple_184;
-static PyObject *__pyx_k_tuple_186;
-static PyObject *__pyx_k_tuple_188;
-static PyObject *__pyx_k_tuple_190;
-static PyObject *__pyx_k_tuple_192;
-static PyObject *__pyx_k_tuple_194;
-static PyObject *__pyx_k_tuple_196;
-static PyObject *__pyx_k_tuple_198;
-static PyObject *__pyx_k_tuple_200;
-static PyObject *__pyx_k_tuple_202;
-static PyObject *__pyx_k_tuple_204;
-static PyObject *__pyx_k_tuple_206;
-static PyObject *__pyx_k_tuple_208;
-static PyObject *__pyx_k_tuple_210;
-static PyObject *__pyx_k_tuple_212;
-static PyObject *__pyx_k_tuple_214;
-static PyObject *__pyx_k_tuple_216;
-static PyObject *__pyx_k_tuple_218;
-static PyObject *__pyx_k_tuple_220;
-static PyObject *__pyx_k_tuple_222;
-static PyObject *__pyx_k_tuple_224;
-static PyObject *__pyx_k_tuple_226;
-static PyObject *__pyx_k_tuple_228;
-static PyObject *__pyx_k_tuple_230;
-static PyObject *__pyx_k_tuple_232;
-static PyObject *__pyx_k_tuple_234;
-static PyObject *__pyx_k_tuple_236;
-static PyObject *__pyx_k_tuple_238;
-static PyObject *__pyx_k_tuple_240;
-static PyObject *__pyx_k_tuple_242;
-static PyObject *__pyx_k_tuple_244;
-static PyObject *__pyx_k_tuple_246;
-static PyObject *__pyx_k_tuple_248;
-static PyObject *__pyx_k_tuple_250;
-static PyObject *__pyx_k_tuple_252;
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__Pyx_RefNannySetupContext("get_sequence (wrapper)", 0);
- __pyx_self = __pyx_self;
{
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Py_ssize_t kw_args;
@@ -2373,24 +2422,20 @@ static PyObject *__pyx_pw_4cvcf_1get_sequence(PyObject *__pyx_self, PyObject *__
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switch (pos_args) {
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- values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__chrom);
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__Pyx_RaiseArgtupleInvalid("get_sequence", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L3_error;}
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__pyx_t_5 = 0;
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PyObject* sequence = __pyx_t_3;
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__Pyx_INCREF(__pyx_t_4);
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* format += ">" # <<<<<<<<<<<<<<
@@ -6475,7 +6531,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L5:;
- /* "cvcf.pyx":352
+ /* "pysam/cvcf.pyx":352
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format += ">"
* format = format[1:-1] # <<<<<<<<<<<<<<
@@ -6491,7 +6547,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L3:;
- /* "cvcf.pyx":353
+ /* "pysam/cvcf.pyx":353
* format += ">"
* format = format[1:-1]
* data = {'id':None,'number':None,'type':None,'descr':None} # <<<<<<<<<<<<<<
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__pyx_v_data = __pyx_t_2;
__pyx_t_2 = 0;
- /* "cvcf.pyx":354
+ /* "pysam/cvcf.pyx":354
* format = format[1:-1]
* data = {'id':None,'number':None,'type':None,'descr':None}
* idx = 0 # <<<<<<<<<<<<<<
@@ -6517,7 +6573,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
__Pyx_INCREF(__pyx_int_0);
__pyx_v_idx = __pyx_int_0;
- /* "cvcf.pyx":355
+ /* "pysam/cvcf.pyx":355
* data = {'id':None,'number':None,'type':None,'descr':None}
* idx = 0
* while len(format.strip())>0: # <<<<<<<<<<<<<<
@@ -6535,7 +6591,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
__pyx_t_3 = (__pyx_t_6 > 0);
if (!__pyx_t_3) break;
- /* "cvcf.pyx":356
+ /* "pysam/cvcf.pyx":356
* idx = 0
* while len(format.strip())>0:
* elts = format.strip().split(',') # <<<<<<<<<<<<<<
@@ -6557,7 +6613,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
__pyx_v_elts = __pyx_t_2;
__pyx_t_2 = 0;
- /* "cvcf.pyx":357
+ /* "pysam/cvcf.pyx":357
* while len(format.strip())>0:
* elts = format.strip().split(',')
* first, rest = elts[0], ','.join(elts[1:]) # <<<<<<<<<<<<<<
@@ -6586,7 +6642,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
__pyx_v_rest = __pyx_t_5;
__pyx_t_5 = 0;
- /* "cvcf.pyx":358
+ /* "pysam/cvcf.pyx":358
* elts = format.strip().split(',')
* first, rest = elts[0], ','.join(elts[1:])
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
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- __Pyx_GOTREF(__pyx_t_5);
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
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__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -6609,8 +6664,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_int_0, Py_GE); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
@@ -6625,8 +6679,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
__pyx_t_7 = PyObject_Call(__pyx_t_5, ((PyObject *)__pyx_k_tuple_35), NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_7);
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
- __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_t_2, __pyx_t_7, Py_GT); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
__pyx_t_8 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_8 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 358; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
@@ -6641,7 +6694,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
}
if (__pyx_t_4) {
- /* "cvcf.pyx":359
+ /* "pysam/cvcf.pyx":359
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
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@@ -6650,8 +6703,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
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__Pyx_GOTREF(__pyx_t_5);
- __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_7);
+ __pyx_t_7 = PyObject_RichCompare(__pyx_t_5, __pyx_int_40, Py_EQ); __Pyx_XGOTREF(__pyx_t_7); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_7); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_7); __pyx_t_7 = 0;
@@ -6677,15 +6729,14 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L9:;
- /* "cvcf.pyx":360
+ /* "pysam/cvcf.pyx":360
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')):
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING) # <<<<<<<<<<<<<<
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
*/
- __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_GOTREF(__pyx_t_5);
+ __pyx_t_5 = PyObject_RichCompare(__pyx_v_idx, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__pyx_t_4 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_4 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 360; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0;
if (__pyx_t_4) {
@@ -6710,7 +6761,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L10:;
- /* "cvcf.pyx":361
+ /* "pysam/cvcf.pyx":361
* if self._version == 40: self.error(line,self.V40_FORMAT_MUST_HAVE_NAMED_FIELDS)
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first # <<<<<<<<<<<<<<
@@ -6744,7 +6795,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
}
__pyx_L8:;
- /* "cvcf.pyx":362
+ /* "pysam/cvcf.pyx":362
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<<
@@ -6772,7 +6823,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
goto __pyx_L11;
}
- /* "cvcf.pyx":363
+ /* "pysam/cvcf.pyx":363
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<<
@@ -6800,7 +6851,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_4parse_format(CYTHON_UNUSED PyObject *__pyx
goto __pyx_L11;
}
- /* "cvcf.pyx":364
+ /* "pysam/cvcf.pyx":364
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<<
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goto __pyx_L11;
}
- /* "cvcf.pyx":365
+ /* "pysam/cvcf.pyx":365
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='): # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
if (__pyx_t_4) {
- /* "cvcf.pyx":366
+ /* "pysam/cvcf.pyx":366
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='):
* elts = format.split('"') # <<<<<<<<<<<<<<
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__pyx_v_elts = __pyx_t_7;
__pyx_t_7 = 0;
- /* "cvcf.pyx":367
+ /* "pysam/cvcf.pyx":367
* elif first.startswith('Description='):
* elts = format.split('"')
* if len(elts)<3: # <<<<<<<<<<<<<<
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__pyx_t_4 = (__pyx_t_6 < 3);
if (__pyx_t_4) {
- /* "cvcf.pyx":368
+ /* "pysam/cvcf.pyx":368
* elts = format.split('"')
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES) # <<<<<<<<<<<<<<
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "cvcf.pyx":369
+ /* "pysam/cvcf.pyx":369
* if len(elts)<3:
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}
__pyx_L12:;
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+ /* "pysam/cvcf.pyx":370
* self.error(line,self.FORMAT_MISSING_QUOTES)
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* elts = first.split('=') + [rest]
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__pyx_v_rest = __pyx_t_2;
__pyx_t_2 = 0;
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}
/*else*/ {
- /* "cvcf.pyx":374
+ /* "pysam/cvcf.pyx":374
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__pyx_v_format = __pyx_v_rest;
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__pyx_t_2 = 0;
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if (__pyx_t_4) {
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__pyx_L14:;
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* idx += 1
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}
__pyx_L15:;
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if (__pyx_t_4) {
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@@ -8105,7 +8176,7 @@ static PyObject *__pyx_pf_4cvcf_3VCF_6format_format(CYTHON_UNUSED PyObject *__py
}
/*else*/ {
- /* "cvcf.pyx":426
+ /* "pysam/cvcf.pyx":426
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}
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- /* "cvcf.pyx":427
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* raise ValueError("Unknown number type encountered: %s" % fmt.numbertype)
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}
__pyx_L3:;
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* values.append( ('Number',nmb) )
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- /* "cvcf.pyx":430
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* values.append( ('Type', fmt.type) )
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- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_6, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++;
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+ __pyx_t_9 = PySequence_ITEM(__pyx_t_6, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
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+ Py_ssize_t size = Py_SIZE(sequence);
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+ {__pyx_filename = __pyx_f[0]; __pyx_lineno = 431; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__pyx_t_11 = PyList_GET_ITEM(sequence, 1);
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__Pyx_INCREF(__pyx_t_11);
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__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
goto __pyx_L9_unpacking_done;
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__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
- if (PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_StopIteration)) PyErr_Clear();
- if (!PyErr_Occurred()) __Pyx_RaiseNeedMoreValuesError(index);
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}
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- __pyx_t_9 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_9); __pyx_t_8++;
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+ __pyx_t_9 = PySequence_ITEM(__pyx_t_2, __pyx_t_8); __pyx_t_8++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 433; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if ((likely(PyTuple_CheckExact(__pyx_t_9))) || (PyList_CheckExact(__pyx_t_9))) {
PyObject* sequence = __pyx_t_9;
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__pyx_t_10 = PyList_GET_ITEM(sequence, 1);
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__Pyx_INCREF(__pyx_t_10);
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__Pyx_DECREF(__pyx_t_12); __pyx_t_12 = 0;
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- __Pyx_GOTREF(__pyx_t_1);
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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__pyx_t_1 = 0;
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- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
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} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
+ #if CYTHON_COMPILING_IN_CPYTHON
+ __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 468; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ #endif
} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
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- __pyx_t_2 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
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} else if (!__pyx_t_5 && PyTuple_CheckExact(__pyx_t_1)) {
if (__pyx_t_4 >= PyTuple_GET_SIZE(__pyx_t_1)) break;
- __pyx_t_2 = PyTuple_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_2); __pyx_t_4++;
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} else {
__pyx_t_2 = __pyx_t_5(__pyx_t_1);
if (unlikely(!__pyx_t_2)) {
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__pyx_t_2 = 0;
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__Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0;
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- __pyx_t_7 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_8); __Pyx_INCREF(__pyx_t_7); __pyx_t_8++;
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- __pyx_t_6 = PyList_GET_ITEM(__pyx_t_1, __pyx_t_4); __Pyx_INCREF(__pyx_t_6); __pyx_t_4++;
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__pyx_t_5 = (__pyx_t_4 == 8);
if (__pyx_t_5) {
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}
/*else*/ {
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__Pyx_GOTREF(__pyx_t_2);
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}
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__Pyx_XDECREF(__pyx_t_10); __pyx_t_10 = 0;
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*
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if (__Pyx_GetException(&__pyx_t_10, &__pyx_t_9, &__pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 663; __pyx_clineno = __LINE__; goto __pyx_L7_except_error;}
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__pyx_L12_try_end:;
}
- /* "cvcf.pyx":664
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__Pyx_DECREF(__pyx_t_10); __pyx_t_10 = 0;
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/*else*/ {
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- __pyx_t_8 = PyList_GET_ITEM(__pyx_t_2, __pyx_t_4); __Pyx_INCREF(__pyx_t_8); __pyx_t_4++;
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Py_XDECREF(tmp);
return 0;
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PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
@@ -22933,62 +23238,62 @@ static PyObject *__pyx_sq_item_4cvcf_VCFRecord(PyObject *o, Py_ssize_t i) {
return r;
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_contig(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_6contig_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_contig(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_6contig_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_pos(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_3pos_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_pos(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_3pos_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_id(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_2id_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_id(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_2id_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_ref(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_3ref_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_ref(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_3ref_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_alt(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_3alt_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_alt(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_3alt_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_qual(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_4qual_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_qual(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_4qual_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_filter(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_6filter_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_filter(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_6filter_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_info(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_4info_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_4info_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_format(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_6format_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_format(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_6format_1__get__(o);
}
-static PyObject *__pyx_getprop_4cvcf_9VCFRecord_samples(PyObject *o, void *x) {
- return __pyx_pw_4cvcf_9VCFRecord_7samples_1__get__(o);
+static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_samples(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_pw_5pysam_4cvcf_9VCFRecord_7samples_1__get__(o);
}
-static PyMethodDef __pyx_methods_4cvcf_VCFRecord[] = {
- {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_4cvcf_9VCFRecord_5error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_4cvcf_9VCFRecord_4error)},
+static PyMethodDef __pyx_methods_5pysam_4cvcf_VCFRecord[] = {
+ {__Pyx_NAMESTR("error"), (PyCFunction)__pyx_pw_5pysam_4cvcf_9VCFRecord_5error, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_4cvcf_9VCFRecord_4error)},
{0, 0, 0, 0}
};
-static struct PyGetSetDef __pyx_getsets_4cvcf_VCFRecord[] = {
- {(char *)"contig", __pyx_getprop_4cvcf_9VCFRecord_contig, 0, 0, 0},
- {(char *)"pos", __pyx_getprop_4cvcf_9VCFRecord_pos, 0, 0, 0},
- {(char *)"id", __pyx_getprop_4cvcf_9VCFRecord_id, 0, 0, 0},
- {(char *)"ref", __pyx_getprop_4cvcf_9VCFRecord_ref, 0, 0, 0},
- {(char *)"alt", __pyx_getprop_4cvcf_9VCFRecord_alt, 0, 0, 0},
- {(char *)"qual", __pyx_getprop_4cvcf_9VCFRecord_qual, 0, 0, 0},
- {(char *)"filter", __pyx_getprop_4cvcf_9VCFRecord_filter, 0, 0, 0},
- {(char *)"info", __pyx_getprop_4cvcf_9VCFRecord_info, 0, 0, 0},
- {(char *)"format", __pyx_getprop_4cvcf_9VCFRecord_format, 0, 0, 0},
- {(char *)"samples", __pyx_getprop_4cvcf_9VCFRecord_samples, 0, 0, 0},
+static struct PyGetSetDef __pyx_getsets_5pysam_4cvcf_VCFRecord[] = {
+ {(char *)"contig", __pyx_getprop_5pysam_4cvcf_9VCFRecord_contig, 0, 0, 0},
+ {(char *)"pos", __pyx_getprop_5pysam_4cvcf_9VCFRecord_pos, 0, 0, 0},
+ {(char *)"id", __pyx_getprop_5pysam_4cvcf_9VCFRecord_id, 0, 0, 0},
+ {(char *)"ref", __pyx_getprop_5pysam_4cvcf_9VCFRecord_ref, 0, 0, 0},
+ {(char *)"alt", __pyx_getprop_5pysam_4cvcf_9VCFRecord_alt, 0, 0, 0},
+ {(char *)"qual", __pyx_getprop_5pysam_4cvcf_9VCFRecord_qual, 0, 0, 0},
+ {(char *)"filter", __pyx_getprop_5pysam_4cvcf_9VCFRecord_filter, 0, 0, 0},
+ {(char *)"info", __pyx_getprop_5pysam_4cvcf_9VCFRecord_info, 0, 0, 0},
+ {(char *)"format", __pyx_getprop_5pysam_4cvcf_9VCFRecord_format, 0, 0, 0},
+ {(char *)"samples", __pyx_getprop_5pysam_4cvcf_9VCFRecord_samples, 0, 0, 0},
{0, 0, 0, 0, 0}
};
@@ -23051,10 +23356,10 @@ static PyNumberMethods __pyx_tp_as_number_VCFRecord = {
};
static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = {
- __pyx_pw_4cvcf_9VCFRecord_7__len__, /*sq_length*/
+ __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*sq_length*/
0, /*sq_concat*/
0, /*sq_repeat*/
- __pyx_sq_item_4cvcf_VCFRecord, /*sq_item*/
+ __pyx_sq_item_5pysam_4cvcf_VCFRecord, /*sq_item*/
0, /*sq_slice*/
0, /*sq_ass_item*/
0, /*sq_ass_slice*/
@@ -23064,8 +23369,8 @@ static PySequenceMethods __pyx_tp_as_sequence_VCFRecord = {
};
static PyMappingMethods __pyx_tp_as_mapping_VCFRecord = {
- __pyx_pw_4cvcf_9VCFRecord_7__len__, /*mp_length*/
- __pyx_pw_4cvcf_9VCFRecord_9__getitem__, /*mp_subscript*/
+ __pyx_pw_5pysam_4cvcf_9VCFRecord_7__len__, /*mp_length*/
+ __pyx_pw_5pysam_4cvcf_9VCFRecord_9__getitem__, /*mp_subscript*/
0, /*mp_ass_subscript*/
};
@@ -23090,12 +23395,12 @@ static PyBufferProcs __pyx_tp_as_buffer_VCFRecord = {
#endif
};
-static PyTypeObject __pyx_type_4cvcf_VCFRecord = {
+static PyTypeObject __pyx_type_5pysam_4cvcf_VCFRecord = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cvcf.VCFRecord"), /*tp_name*/
- sizeof(struct __pyx_obj_4cvcf_VCFRecord), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.cvcf.VCFRecord"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_4cvcf_VCFRecord), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_4cvcf_VCFRecord, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_4cvcf_VCFRecord, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -23116,23 +23421,23 @@ static PyTypeObject __pyx_type_4cvcf_VCFRecord = {
&__pyx_tp_as_buffer_VCFRecord, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("vcf record.\n\n initialized from data and vcf meta \n "), /*tp_doc*/
- __pyx_tp_traverse_4cvcf_VCFRecord, /*tp_traverse*/
- __pyx_tp_clear_4cvcf_VCFRecord, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_4cvcf_VCFRecord, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_4cvcf_VCFRecord, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_4cvcf_VCFRecord, /*tp_methods*/
+ __pyx_methods_5pysam_4cvcf_VCFRecord, /*tp_methods*/
0, /*tp_members*/
- __pyx_getsets_4cvcf_VCFRecord, /*tp_getset*/
+ __pyx_getsets_5pysam_4cvcf_VCFRecord, /*tp_getset*/
0, /*tp_base*/
0, /*tp_dict*/
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_4cvcf_9VCFRecord_1__init__, /*tp_init*/
+ __pyx_pw_5pysam_4cvcf_9VCFRecord_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_4cvcf_VCFRecord, /*tp_new*/
+ __pyx_tp_new_5pysam_4cvcf_VCFRecord, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -23146,46 +23451,44 @@ static PyTypeObject __pyx_type_4cvcf_VCFRecord = {
#endif
};
-static PyObject *__pyx_tp_new_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_4cvcf_asVCFRecord *p;
- PyObject *o = __pyx_ptype_6ctabix_Parser->tp_new(t, a, k);
+static PyObject *__pyx_tp_new_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p;
+ PyObject *o = __pyx_ptype_5pysam_6ctabix_Parser->tp_new(t, a, k);
if (!o) return 0;
- p = ((struct __pyx_obj_4cvcf_asVCFRecord *)o);
+ p = ((struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o);
p->vcffile = Py_None; Py_INCREF(Py_None);
return o;
}
-static void __pyx_tp_dealloc_4cvcf_asVCFRecord(PyObject *o) {
- struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o;
- Py_XDECREF(p->vcffile);
- __pyx_ptype_6ctabix_Parser->tp_dealloc(o);
+static void __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->vcffile);
+ PyObject_GC_Track(o);
+ if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) __pyx_ptype_5pysam_6ctabix_Parser->tp_dealloc(o); else __Pyx_call_next_tp_dealloc(o, __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord);
}
-static int __pyx_tp_traverse_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o;
- if (__pyx_ptype_6ctabix_Parser->tp_traverse) {
- e = __pyx_ptype_6ctabix_Parser->tp_traverse(o, v, a); if (e) return e;
- }
+ struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
+ e = ((likely(__pyx_ptype_5pysam_6ctabix_Parser)) ? ((__pyx_ptype_5pysam_6ctabix_Parser->tp_traverse) ? __pyx_ptype_5pysam_6ctabix_Parser->tp_traverse(o, v, a) : 0) : __Pyx_call_next_tp_traverse(o, v, a, __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord)); if (e) return e;
if (p->vcffile) {
e = (*v)(p->vcffile, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_4cvcf_asVCFRecord(PyObject *o) {
- struct __pyx_obj_4cvcf_asVCFRecord *p = (struct __pyx_obj_4cvcf_asVCFRecord *)o;
+static int __pyx_tp_clear_5pysam_4cvcf_asVCFRecord(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf_asVCFRecord *p = (struct __pyx_obj_5pysam_4cvcf_asVCFRecord *)o;
PyObject* tmp;
- if (__pyx_ptype_6ctabix_Parser->tp_clear) {
- __pyx_ptype_6ctabix_Parser->tp_clear(o);
- }
+ if (likely(__pyx_ptype_5pysam_6ctabix_Parser)) { if (__pyx_ptype_5pysam_6ctabix_Parser->tp_clear) __pyx_ptype_5pysam_6ctabix_Parser->tp_clear(o); } else __Pyx_call_next_tp_clear(o, __pyx_tp_clear_5pysam_4cvcf_asVCFRecord);
tmp = ((PyObject*)p->vcffile);
p->vcffile = Py_None; Py_INCREF(Py_None);
Py_XDECREF(tmp);
return 0;
}
-static PyMethodDef __pyx_methods_4cvcf_asVCFRecord[] = {
+static PyMethodDef __pyx_methods_5pysam_4cvcf_asVCFRecord[] = {
{0, 0, 0, 0}
};
@@ -23287,12 +23590,12 @@ static PyBufferProcs __pyx_tp_as_buffer_asVCFRecord = {
#endif
};
-static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
+static PyTypeObject __pyx_type_5pysam_4cvcf_asVCFRecord = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cvcf.asVCFRecord"), /*tp_name*/
- sizeof(struct __pyx_obj_4cvcf_asVCFRecord), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.cvcf.asVCFRecord"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_4cvcf_asVCFRecord), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_4cvcf_asVCFRecord, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_4cvcf_asVCFRecord, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -23306,20 +23609,20 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
&__pyx_tp_as_sequence_asVCFRecord, /*tp_as_sequence*/
&__pyx_tp_as_mapping_asVCFRecord, /*tp_as_mapping*/
0, /*tp_hash*/
- __pyx_pw_4cvcf_11asVCFRecord_3__call__, /*tp_call*/
+ __pyx_pw_5pysam_4cvcf_11asVCFRecord_3__call__, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
&__pyx_tp_as_buffer_asVCFRecord, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
__Pyx_DOCSTR("converts a :term:`tabix row` into a VCF record."), /*tp_doc*/
- __pyx_tp_traverse_4cvcf_asVCFRecord, /*tp_traverse*/
- __pyx_tp_clear_4cvcf_asVCFRecord, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_4cvcf_asVCFRecord, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_4cvcf_asVCFRecord, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_4cvcf_asVCFRecord, /*tp_methods*/
+ __pyx_methods_5pysam_4cvcf_asVCFRecord, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -23327,9 +23630,9 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
0, /*tp_descr_get*/
0, /*tp_descr_set*/
0, /*tp_dictoffset*/
- __pyx_pw_4cvcf_11asVCFRecord_1__init__, /*tp_init*/
+ __pyx_pw_5pysam_4cvcf_11asVCFRecord_1__init__, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_4cvcf_asVCFRecord, /*tp_new*/
+ __pyx_tp_new_5pysam_4cvcf_asVCFRecord, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -23343,32 +23646,34 @@ static PyTypeObject __pyx_type_4cvcf_asVCFRecord = {
#endif
};
-static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p;
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o);
+ p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o);
p->__pyx_v_alt = 0;
return o;
}
-static void __pyx_tp_dealloc_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
- struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o;
- Py_XDECREF(p->__pyx_v_alt);
+static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_alt);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_4cvcf___pyx_scope_struct__parse_data(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o;
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o;
if (p->__pyx_v_alt) {
e = (*v)(p->__pyx_v_alt, a); if (e) return e;
}
return 0;
}
-static int __pyx_tp_clear_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
- struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)o;
+static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)o;
PyObject* tmp;
tmp = ((PyObject*)p->__pyx_v_alt);
p->__pyx_v_alt = Py_None; Py_INCREF(Py_None);
@@ -23376,7 +23681,7 @@ static int __pyx_tp_clear_4cvcf___pyx_scope_struct__parse_data(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_4cvcf___pyx_scope_struct__parse_data[] = {
+static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data[] = {
{0, 0, 0, 0}
};
@@ -23478,12 +23783,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct__parse_data = {
#endif
};
-static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = {
+static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cvcf.__pyx_scope_struct__parse_data"), /*tp_name*/
- sizeof(struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct__parse_data"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_4cvcf___pyx_scope_struct__parse_data, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -23504,13 +23809,13 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = {
&__pyx_tp_as_buffer___pyx_scope_struct__parse_data, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_4cvcf___pyx_scope_struct__parse_data, /*tp_traverse*/
- __pyx_tp_clear_4cvcf___pyx_scope_struct__parse_data, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_4cvcf___pyx_scope_struct__parse_data, /*tp_methods*/
+ __pyx_methods_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -23520,7 +23825,7 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_4cvcf___pyx_scope_struct__parse_data, /*tp_new*/
+ __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct__parse_data, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -23534,28 +23839,30 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct__parse_data = {
#endif
};
-static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p;
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o);
+ p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o);
p->__pyx_outer_scope = 0;
p->__pyx_v_allele = 0;
p->__pyx_t_0 = 0;
return o;
}
-static void __pyx_tp_dealloc_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o;
- Py_XDECREF(((PyObject *)p->__pyx_outer_scope));
- Py_XDECREF(p->__pyx_v_allele);
- Py_XDECREF(p->__pyx_t_0);
+static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_outer_scope);
+ Py_CLEAR(p->__pyx_v_allele);
+ Py_CLEAR(p->__pyx_t_0);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o;
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o;
if (p->__pyx_outer_scope) {
e = (*v)(((PyObject*)p->__pyx_outer_scope), a); if (e) return e;
}
@@ -23568,11 +23875,11 @@ static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o, vis
return 0;
}
-static int __pyx_tp_clear_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
- struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr *)o;
+static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr *)o;
PyObject* tmp;
tmp = ((PyObject*)p->__pyx_outer_scope);
- p->__pyx_outer_scope = ((struct __pyx_obj_4cvcf___pyx_scope_struct__parse_data *)Py_None); Py_INCREF(Py_None);
+ p->__pyx_outer_scope = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct__parse_data *)Py_None); Py_INCREF(Py_None);
Py_XDECREF(tmp);
tmp = ((PyObject*)p->__pyx_v_allele);
p->__pyx_v_allele = Py_None; Py_INCREF(Py_None);
@@ -23583,7 +23890,7 @@ static int __pyx_tp_clear_4cvcf___pyx_scope_struct_1_genexpr(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_4cvcf___pyx_scope_struct_1_genexpr[] = {
+static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct_1_genexpr[] = {
{0, 0, 0, 0}
};
@@ -23685,12 +23992,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = {
+static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cvcf.__pyx_scope_struct_1_genexpr"), /*tp_name*/
- sizeof(struct __pyx_obj_4cvcf___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct_1_genexpr"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_1_genexpr), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_4cvcf___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -23711,13 +24018,13 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = {
&__pyx_tp_as_buffer___pyx_scope_struct_1_genexpr, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_4cvcf___pyx_scope_struct_1_genexpr, /*tp_traverse*/
- __pyx_tp_clear_4cvcf___pyx_scope_struct_1_genexpr, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_4cvcf___pyx_scope_struct_1_genexpr, /*tp_methods*/
+ __pyx_methods_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -23727,7 +24034,7 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_4cvcf___pyx_scope_struct_1_genexpr, /*tp_new*/
+ __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_1_genexpr, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -23741,11 +24048,11 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_1_genexpr = {
#endif
};
-static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p;
+static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p;
PyObject *o = (*t->tp_alloc)(t, 0);
if (!o) return 0;
- p = ((struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o);
+ p = ((struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o);
p->__pyx_v_d = 0;
p->__pyx_v_line = 0;
p->__pyx_v_self = 0;
@@ -23754,19 +24061,21 @@ static PyObject *__pyx_tp_new_4cvcf___pyx_scope_struct_2__parse(PyTypeObject *t,
return o;
}
-static void __pyx_tp_dealloc_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
- struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o;
- Py_XDECREF(p->__pyx_v_d);
- Py_XDECREF(p->__pyx_v_line);
- Py_XDECREF(p->__pyx_v_self);
- Py_XDECREF(p->__pyx_v_stream);
- Py_XDECREF(p->__pyx_t_1);
+static void __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o;
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->__pyx_v_d);
+ Py_CLEAR(p->__pyx_v_line);
+ Py_CLEAR(p->__pyx_v_self);
+ Py_CLEAR(p->__pyx_v_stream);
+ Py_CLEAR(p->__pyx_t_1);
+ PyObject_GC_Track(o);
(*Py_TYPE(o)->tp_free)(o);
}
-static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visitproc v, void *a) {
+static int __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visitproc v, void *a) {
int e;
- struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o;
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o;
if (p->__pyx_v_d) {
e = (*v)(p->__pyx_v_d, a); if (e) return e;
}
@@ -23785,8 +24094,8 @@ static int __pyx_tp_traverse_4cvcf___pyx_scope_struct_2__parse(PyObject *o, visi
return 0;
}
-static int __pyx_tp_clear_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
- struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse *)o;
+static int __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
+ struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *p = (struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse *)o;
PyObject* tmp;
tmp = ((PyObject*)p->__pyx_v_d);
p->__pyx_v_d = Py_None; Py_INCREF(Py_None);
@@ -23806,7 +24115,7 @@ static int __pyx_tp_clear_4cvcf___pyx_scope_struct_2__parse(PyObject *o) {
return 0;
}
-static PyMethodDef __pyx_methods_4cvcf___pyx_scope_struct_2__parse[] = {
+static PyMethodDef __pyx_methods_5pysam_4cvcf___pyx_scope_struct_2__parse[] = {
{0, 0, 0, 0}
};
@@ -23908,12 +24217,12 @@ static PyBufferProcs __pyx_tp_as_buffer___pyx_scope_struct_2__parse = {
#endif
};
-static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_2__parse = {
+static PyTypeObject __pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse = {
PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cvcf.__pyx_scope_struct_2__parse"), /*tp_name*/
- sizeof(struct __pyx_obj_4cvcf___pyx_scope_struct_2__parse), /*tp_basicsize*/
+ __Pyx_NAMESTR("pysam.cvcf.__pyx_scope_struct_2__parse"), /*tp_name*/
+ sizeof(struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct_2__parse), /*tp_basicsize*/
0, /*tp_itemsize*/
- __pyx_tp_dealloc_4cvcf___pyx_scope_struct_2__parse, /*tp_dealloc*/
+ __pyx_tp_dealloc_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_dealloc*/
0, /*tp_print*/
0, /*tp_getattr*/
0, /*tp_setattr*/
@@ -23934,13 +24243,13 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_2__parse = {
&__pyx_tp_as_buffer___pyx_scope_struct_2__parse, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
0, /*tp_doc*/
- __pyx_tp_traverse_4cvcf___pyx_scope_struct_2__parse, /*tp_traverse*/
- __pyx_tp_clear_4cvcf___pyx_scope_struct_2__parse, /*tp_clear*/
+ __pyx_tp_traverse_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_traverse*/
+ __pyx_tp_clear_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_clear*/
0, /*tp_richcompare*/
0, /*tp_weaklistoffset*/
0, /*tp_iter*/
0, /*tp_iternext*/
- __pyx_methods_4cvcf___pyx_scope_struct_2__parse, /*tp_methods*/
+ __pyx_methods_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_methods*/
0, /*tp_members*/
0, /*tp_getset*/
0, /*tp_base*/
@@ -23950,7 +24259,7 @@ static PyTypeObject __pyx_type_4cvcf___pyx_scope_struct_2__parse = {
0, /*tp_dictoffset*/
0, /*tp_init*/
0, /*tp_alloc*/
- __pyx_tp_new_4cvcf___pyx_scope_struct_2__parse, /*tp_new*/
+ __pyx_tp_new_5pysam_4cvcf___pyx_scope_struct_2__parse, /*tp_new*/
0, /*tp_free*/
0, /*tp_is_gc*/
0, /*tp_bases*/
@@ -24002,8 +24311,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_128, __pyx_k_128, sizeof(__pyx_k_128), 0, 0, 1, 0},
{&__pyx_kp_s_130, __pyx_k_130, sizeof(__pyx_k_130), 0, 0, 1, 0},
{&__pyx_kp_s_134, __pyx_k_134, sizeof(__pyx_k_134), 0, 0, 1, 0},
- {&__pyx_kp_s_137, __pyx_k_137, sizeof(__pyx_k_137), 0, 0, 1, 0},
- {&__pyx_kp_s_139, __pyx_k_139, sizeof(__pyx_k_139), 0, 0, 1, 0},
+ {&__pyx_n_s_135, __pyx_k_135, sizeof(__pyx_k_135), 0, 0, 1, 1},
+ {&__pyx_kp_s_138, __pyx_k_138, sizeof(__pyx_k_138), 0, 0, 1, 0},
{&__pyx_kp_s_14, __pyx_k_14, sizeof(__pyx_k_14), 0, 0, 1, 0},
{&__pyx_kp_s_140, __pyx_k_140, sizeof(__pyx_k_140), 0, 0, 1, 0},
{&__pyx_kp_s_141, __pyx_k_141, sizeof(__pyx_k_141), 0, 0, 1, 0},
@@ -24038,6 +24347,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_kp_s_170, __pyx_k_170, sizeof(__pyx_k_170), 0, 0, 1, 0},
{&__pyx_kp_s_171, __pyx_k_171, sizeof(__pyx_k_171), 0, 0, 1, 0},
{&__pyx_kp_s_172, __pyx_k_172, sizeof(__pyx_k_172), 0, 0, 1, 0},
+ {&__pyx_kp_s_173, __pyx_k_173, sizeof(__pyx_k_173), 0, 0, 1, 0},
{&__pyx_n_s_18, __pyx_k_18, sizeof(__pyx_k_18), 0, 0, 1, 1},
{&__pyx_kp_s_19, __pyx_k_19, sizeof(__pyx_k_19), 0, 0, 1, 0},
{&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0},
@@ -24219,7 +24529,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = {
{&__pyx_n_s__convertGT, __pyx_k__convertGT, sizeof(__pyx_k__convertGT), 0, 0, 1, 1},
{&__pyx_n_s__convertGTback, __pyx_k__convertGTback, sizeof(__pyx_k__convertGTback), 0, 0, 1, 1},
{&__pyx_n_s__copy, __pyx_k__copy, sizeof(__pyx_k__copy), 0, 0, 1, 1},
- {&__pyx_n_s__cvcf, __pyx_k__cvcf, sizeof(__pyx_k__cvcf), 0, 0, 1, 1},
{&__pyx_n_s__d, __pyx_k__d, sizeof(__pyx_k__d), 0, 0, 1, 1},
{&__pyx_n_s__data, __pyx_k__data, sizeof(__pyx_k__data), 0, 0, 1, 1},
{&__pyx_n_s__datagenerator, __pyx_k__datagenerator, sizeof(__pyx_k__datagenerator), 0, 0, 1, 1},
@@ -24401,7 +24710,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_RefNannyDeclarations
__Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0);
- /* "cvcf.pyx":70
+ /* "pysam/cvcf.pyx":70
* def parse_regions( string ):
* result = []
* for r in string.split(','): # <<<<<<<<<<<<<<
@@ -24415,7 +24724,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_3));
- /* "cvcf.pyx":71
+ /* "pysam/cvcf.pyx":71
* result = []
* for r in string.split(','):
* elts = r.split(':') # <<<<<<<<<<<<<<
@@ -24429,7 +24738,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_5));
- /* "cvcf.pyx":76
+ /* "pysam/cvcf.pyx":76
* elif len(elts)==2:
* if len(elts[1])>0:
* ielts = elts[1].split('-') # <<<<<<<<<<<<<<
@@ -24443,7 +24752,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_6));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_7));
- /* "cvcf.pyx":157
+ /* "pysam/cvcf.pyx":157
* alt = self.fields[4]
* if alt == ".": alt = []
* else: alt = alt.upper().split(',') # <<<<<<<<<<<<<<
@@ -24457,7 +24766,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_10));
- /* "cvcf.pyx":173
+ /* "pysam/cvcf.pyx":173
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
* if f == b"." or f == b"PASS" or f == b"0": return []
* else: return f.split(';') # <<<<<<<<<<<<<<
@@ -24471,7 +24780,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_12));
- /* "cvcf.pyx":181
+ /* "pysam/cvcf.pyx":181
* info = {}
* if col != b".":
* for blurp in col.split(';'): # <<<<<<<<<<<<<<
@@ -24485,7 +24794,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_13));
- /* "cvcf.pyx":182
+ /* "pysam/cvcf.pyx":182
* if col != b".":
* for blurp in col.split(';'):
* elts = blurp.split('=') # <<<<<<<<<<<<<<
@@ -24499,7 +24808,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_15));
- /* "cvcf.pyx":191
+ /* "pysam/cvcf.pyx":191
* property format:
* def __get__(self):
* return self.fields[8].split(':') # <<<<<<<<<<<<<<
@@ -24513,7 +24822,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_16));
- /* "cvcf.pyx":200
+ /* "pysam/cvcf.pyx":200
*
* # parse sample columns
* values = self.fields[self.vcf._sample2column[key]].split(':') # <<<<<<<<<<<<<<
@@ -24527,7 +24836,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_17));
- /* "cvcf.pyx":316
+ /* "pysam/cvcf.pyx":316
* def __init__(self, _copy=None, reference=None, regions=None, lines=None, leftalign=False):
* # make error identifiers accessible by name
* for id in self._errors.keys(): self.__dict__[self._errors[id].split(':')[0]] = id # <<<<<<<<<<<<<<
@@ -24541,7 +24850,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_22));
- /* "cvcf.pyx":337
+ /* "pysam/cvcf.pyx":337
* def error(self,line,error,opt=None):
* if error in self._ignored_errors: return
* errorlabel, errorstring = self._errors[error].split(':') # <<<<<<<<<<<<<<
@@ -24555,7 +24864,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_23));
- /* "cvcf.pyx":346
+ /* "pysam/cvcf.pyx":346
* def parse_format(self,line,format,filter=False):
* if self._version == 40:
* if not format.startswith('<'): # <<<<<<<<<<<<<<
@@ -24569,7 +24878,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_25));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_26));
- /* "cvcf.pyx":349
+ /* "pysam/cvcf.pyx":349
* self.error(line,self.V40_MISSING_ANGLE_BRACKETS)
* format = "<"+format
* if not format.endswith('>'): # <<<<<<<<<<<<<<
@@ -24583,7 +24892,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_28));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_29));
- /* "cvcf.pyx":356
+ /* "pysam/cvcf.pyx":356
* idx = 0
* while len(format.strip())>0:
* elts = format.strip().split(',') # <<<<<<<<<<<<<<
@@ -24597,7 +24906,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_30));
- /* "cvcf.pyx":358
+ /* "pysam/cvcf.pyx":358
* elts = format.strip().split(',')
* first, rest = elts[0], ','.join(elts[1:])
* if first.find('=') == -1 or (first.find('"')>=0 and first.find('=') > first.find('"')): # <<<<<<<<<<<<<<
@@ -24629,7 +24938,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_35));
- /* "cvcf.pyx":362
+ /* "pysam/cvcf.pyx":362
* if idx == 4: self.error(line,self.BADLY_FORMATTED_FORMAT_STRING)
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1] # <<<<<<<<<<<<<<
@@ -24649,7 +24958,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_43));
- /* "cvcf.pyx":363
+ /* "pysam/cvcf.pyx":363
* first = ["ID=","Number=","Type=","Description="][idx] + first
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1] # <<<<<<<<<<<<<<
@@ -24669,7 +24978,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_45));
- /* "cvcf.pyx":364
+ /* "pysam/cvcf.pyx":364
* if first.startswith('ID='): data['id'] = first.split('=')[1]
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1] # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_47));
- /* "cvcf.pyx":365
+ /* "pysam/cvcf.pyx":365
* elif first.startswith('Number='): data['number'] = first.split('=')[1]
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='): # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_41));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_48));
- /* "cvcf.pyx":366
+ /* "pysam/cvcf.pyx":366
* elif first.startswith('Type='): data['type'] = first.split('=')[1]
* elif first.startswith('Description='):
* elts = format.split('"') # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_32));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_49));
- /* "cvcf.pyx":369
+ /* "pysam/cvcf.pyx":369
* if len(elts)<3:
* self.error(line,self.FORMAT_MISSING_QUOTES)
* elts = first.split('=') + [rest] # <<<<<<<<<<<<<<
@@ -24731,7 +25040,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_51));
- /* "cvcf.pyx":372
+ /* "pysam/cvcf.pyx":372
* data['descr'] = elts[1]
* rest = '"'.join(elts[2:])
* if rest.startswith(','): rest = rest[1:] # <<<<<<<<<<<<<<
@@ -24745,7 +25054,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_52));
- /* "cvcf.pyx":492
+ /* "pysam/cvcf.pyx":492
* # snip off trailing missing data
* while len(output) > 1:
* last = output[-1].replace(',','').replace('.','') # <<<<<<<<<<<<<<
@@ -24771,7 +25080,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_1));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_63));
- /* "cvcf.pyx":518
+ /* "pysam/cvcf.pyx":518
*
* def parse_header( self, line ):
* assert line.startswith('##') # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_77));
- /* "cvcf.pyx":519
+ /* "pysam/cvcf.pyx":519
* def parse_header( self, line ):
* assert line.startswith('##')
* elts = line[2:].split('=') # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_78));
- /* "cvcf.pyx":554
+ /* "pysam/cvcf.pyx":554
*
* def parse_heading( self, line ):
* assert line.startswith('#') # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_86));
- /* "cvcf.pyx":555
+ /* "pysam/cvcf.pyx":555
* def parse_heading( self, line ):
* assert line.startswith('#')
* assert not line.startswith('##') # <<<<<<<<<<<<<<
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_87));
- /* "cvcf.pyx":556
+ /* "pysam/cvcf.pyx":556
* assert line.startswith('#')
* assert not line.startswith('##')
* headings = line[1:].split('\t') # <<<<<<<<<<<<<<
@@ -24841,7 +25150,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_88));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_89));
- /* "cvcf.pyx":608
+ /* "pysam/cvcf.pyx":608
* if value is not None: self.error(line,self.ERROR_FLAG_HAS_VALUE)
* return []
* values = value.split(',') # <<<<<<<<<<<<<<
@@ -24855,7 +25164,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_97));
- /* "cvcf.pyx":610
+ /* "pysam/cvcf.pyx":610
* values = value.split(',')
* # deal with trailing data in some early VCF files
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1: # <<<<<<<<<<<<<<
@@ -24869,7 +25178,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_98));
- /* "cvcf.pyx":612
+ /* "pysam/cvcf.pyx":612
* if f.type in ["Float","Integer"] and len(values)>0 and values[-1].find(';') > -1:
* self.error(line,self.ERROR_TRAILING_DATA,values[-1])
* values[-1] = values[-1].split(';')[0] # <<<<<<<<<<<<<<
@@ -24883,7 +25192,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_99));
- /* "cvcf.pyx":648
+ /* "pysam/cvcf.pyx":648
*
* def parse_data( self, line, lineparse=False ):
* cols = line.split('\t') # <<<<<<<<<<<<<<
@@ -24897,7 +25206,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_88));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_103));
- /* "cvcf.pyx":694
+ /* "pysam/cvcf.pyx":694
* # convert v3.3 to v4.0 alleles below
* if cols[4] == ".": alt = []
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@@ -24911,7 +25220,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_2));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_107));
- /* "cvcf.pyx":703
+ /* "pysam/cvcf.pyx":703
* # postpone checking that filters exist. Encode missing filter or no filtering as empty list
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_108));
- /* "cvcf.pyx":708
+ /* "pysam/cvcf.pyx":708
* info = {}
* if cols[7] != ".":
* for blurp in cols[7].split(';'): # <<<<<<<<<<<<<<
@@ -24939,7 +25248,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_11));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_109));
- /* "cvcf.pyx":709
+ /* "pysam/cvcf.pyx":709
* if cols[7] != ".":
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@@ -24953,7 +25262,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_14));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_110));
- /* "cvcf.pyx":720
+ /* "pysam/cvcf.pyx":720
* # Gracefully deal with absent FORMAT column
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_111));
- /* "cvcf.pyx":738
+ /* "pysam/cvcf.pyx":738
* for a in alt:
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@@ -24981,7 +25290,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__I));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_112));
- /* "cvcf.pyx":739
+ /* "pysam/cvcf.pyx":739
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@@ -24995,7 +25304,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_n_s__D));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_113));
- /* "cvcf.pyx":820
+ /* "pysam/cvcf.pyx":820
* for sample in cols[9:]:
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@@ -25009,7 +25318,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_4));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_117));
- /* "cvcf.pyx":890
+ /* "pysam/cvcf.pyx":890
* for line in stream:
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@@ -25023,7 +25332,7 @@ static int __Pyx_InitCachedConstants(void) {
__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_119));
- /* "cvcf.pyx":892
+ /* "pysam/cvcf.pyx":892
* if line.startswith('##'):
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_85));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_120));
- /* "cvcf.pyx":901
+ /* "pysam/cvcf.pyx":901
* def _parse(self, line, stream):
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_76));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_122));
- /* "cvcf.pyx":958
+ /* "pysam/cvcf.pyx":958
*
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_123));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_124));
- /* "cvcf.pyx":1036
+ /* "pysam/cvcf.pyx":1036
* '''
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_126));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_127));
- /* "cvcf.pyx":54
+ /* "pysam/cvcf.pyx":54
* import pysam
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_128));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_129));
- /* "cvcf.pyx":55
+ /* "pysam/cvcf.pyx":55
*
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__Pyx_GIVEREF(((PyObject *)__pyx_kp_s_130));
__Pyx_GIVEREF(((PyObject *)__pyx_k_tuple_131));
- /* "cvcf.pyx":58
+ /* "pysam/cvcf.pyx":58
*
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- /* "cvcf.pyx":86
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+ Py_INCREF(__pyx_b);
#endif
- __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME));
- if (!__pyx_b) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
/*--- Initialize various global constants etc. ---*/
if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__pyx_module_is_main_cvcf) {
+ if (__pyx_module_is_main_pysam__cvcf) {
if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s____main__) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;};
}
/*--- Builtin init code ---*/
@@ -26463,53 +26779,53 @@ PyMODINIT_FUNC PyInit_cvcf(void)
/*--- Variable export code ---*/
/*--- Function export code ---*/
/*--- Type init code ---*/
- __pyx_ptype_10TabProxies_TupleProxy = __Pyx_ImportType("TabProxies", "TupleProxy", sizeof(struct __pyx_obj_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_4cvcf_VCFRecord = &__pyx_vtable_4cvcf_VCFRecord;
- __pyx_vtable_4cvcf_VCFRecord.__pyx_base = *__pyx_vtabptr_10TabProxies_TupleProxy;
- __pyx_vtable_4cvcf_VCFRecord.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_4cvcf_9VCFRecord_update;
- __pyx_type_4cvcf_VCFRecord.tp_base = __pyx_ptype_10TabProxies_TupleProxy;
- if (PyType_Ready(&__pyx_type_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetVtable(__pyx_type_4cvcf_VCFRecord.tp_dict, __pyx_vtabptr_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_4cvcf_VCFRecord = &__pyx_type_4cvcf_VCFRecord;
- __pyx_ptype_6ctabix_Parser = __Pyx_ImportType("ctabix", "Parser", sizeof(struct __pyx_obj_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_type_4cvcf_asVCFRecord.tp_base = __pyx_ptype_6ctabix_Parser;
- if (PyType_Ready(&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_4cvcf_asVCFRecord = &__pyx_type_4cvcf_asVCFRecord;
- if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_4cvcf___pyx_scope_struct__parse_data = &__pyx_type_4cvcf___pyx_scope_struct__parse_data;
- if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_4cvcf___pyx_scope_struct_1_genexpr = &__pyx_type_4cvcf___pyx_scope_struct_1_genexpr;
- if (PyType_Ready(&__pyx_type_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_4cvcf___pyx_scope_struct_2__parse;
+ __pyx_ptype_5pysam_10TabProxies_TupleProxy = __Pyx_ImportType("pysam.TabProxies", "TupleProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_10TabProxies_TupleProxy = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__Pyx_GetVtable(__pyx_ptype_5pysam_10TabProxies_TupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_10TabProxies_TupleProxy)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_4cvcf_VCFRecord = &__pyx_vtable_5pysam_4cvcf_VCFRecord;
+ __pyx_vtable_5pysam_4cvcf_VCFRecord.__pyx_base = *__pyx_vtabptr_5pysam_10TabProxies_TupleProxy;
+ __pyx_vtable_5pysam_4cvcf_VCFRecord.__pyx_base.update = (PyObject *(*)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t))__pyx_f_5pysam_4cvcf_9VCFRecord_update;
+ __pyx_type_5pysam_4cvcf_VCFRecord.tp_base = __pyx_ptype_5pysam_10TabProxies_TupleProxy;
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetVtable(__pyx_type_5pysam_4cvcf_VCFRecord.tp_dict, __pyx_vtabptr_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "VCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_VCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 94; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_4cvcf_VCFRecord = &__pyx_type_5pysam_4cvcf_VCFRecord;
+ __pyx_ptype_5pysam_6ctabix_Parser = __Pyx_ImportType("pysam.ctabix", "Parser", sizeof(struct __pyx_obj_5pysam_6ctabix_Parser), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Parser)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_type_5pysam_4cvcf_asVCFRecord.tp_base = __pyx_ptype_5pysam_6ctabix_Parser;
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ if (__Pyx_SetAttrString(__pyx_m, "asVCFRecord", (PyObject *)&__pyx_type_5pysam_4cvcf_asVCFRecord) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 226; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_4cvcf_asVCFRecord = &__pyx_type_5pysam_4cvcf_asVCFRecord;
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 647; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_4cvcf___pyx_scope_struct__parse_data = &__pyx_type_5pysam_4cvcf___pyx_scope_struct__parse_data;
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_4cvcf___pyx_scope_struct_1_genexpr = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_1_genexpr;
+ if (PyType_Ready(&__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 899; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_4cvcf___pyx_scope_struct_2__parse = &__pyx_type_5pysam_4cvcf___pyx_scope_struct_2__parse;
/*--- Type import code ---*/
- __pyx_ptype_6ctabix_Tabixfile = __Pyx_ImportType("ctabix", "Tabixfile", sizeof(struct __pyx_obj_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_TabixIterator = __Pyx_ImportType("ctabix", "TabixIterator", sizeof(struct __pyx_obj_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_TabixHeaderIterator = __Pyx_ImportType("ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_asTuple = __Pyx_ImportType("ctabix", "asTuple", sizeof(struct __pyx_obj_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_asGTF = __Pyx_ImportType("ctabix", "asGTF", sizeof(struct __pyx_obj_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_asBed = __Pyx_ImportType("ctabix", "asBed", sizeof(struct __pyx_obj_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_asVCF = __Pyx_ImportType("ctabix", "asVCF", sizeof(struct __pyx_obj_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_TabixIteratorParsed = __Pyx_ImportType("ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_tabix_inplace_iterator = __Pyx_ImportType("ctabix", "tabix_inplace_iterator", sizeof(struct __pyx_obj_6ctabix_tabix_inplace_iterator), 1); if (unlikely(!__pyx_ptype_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_6ctabix_tabix_inplace_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_inplace_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_inplace_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_6ctabix_tabix_copy_iterator = __Pyx_ImportType("ctabix", "tabix_copy_iterator", sizeof(struct __pyx_obj_6ctabix_tabix_copy_iterator), 1); if (unlikely(!__pyx_ptype_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_GTFProxy = __Pyx_ImportType("TabProxies", "GTFProxy", sizeof(struct __pyx_obj_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_GTFProxy = (struct __pyx_vtabstruct_10TabProxies_GTFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_GTFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_NamedTupleProxy = __Pyx_ImportType("TabProxies", "NamedTupleProxy", sizeof(struct __pyx_obj_10TabProxies_NamedTupleProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_NamedTupleProxy = (struct __pyx_vtabstruct_10TabProxies_NamedTupleProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_NamedTupleProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_NamedTupleProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_BedProxy = __Pyx_ImportType("TabProxies", "BedProxy", sizeof(struct __pyx_obj_10TabProxies_BedProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_BedProxy = (struct __pyx_vtabstruct_10TabProxies_BedProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_BedProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_BedProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_ptype_10TabProxies_VCFProxy = __Pyx_ImportType("TabProxies", "VCFProxy", sizeof(struct __pyx_obj_10TabProxies_VCFProxy), 1); if (unlikely(!__pyx_ptype_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __pyx_vtabptr_10TabProxies_VCFProxy = (struct __pyx_vtabstruct_10TabProxies_VCFProxy*)__Pyx_GetVtable(__pyx_ptype_10TabProxies_VCFProxy->tp_dict); if (unlikely(!__pyx_vtabptr_10TabProxies_VCFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_Tabixfile = __Pyx_ImportType("pysam.ctabix", "Tabixfile", sizeof(struct __pyx_obj_5pysam_6ctabix_Tabixfile), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_Tabixfile)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixIterator = __Pyx_ImportType("pysam.ctabix", "TabixIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 182; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixHeaderIterator = __Pyx_ImportType("pysam.ctabix", "TabixHeaderIterator", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixHeaderIterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixHeaderIterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asTuple = __Pyx_ImportType("pysam.ctabix", "asTuple", sizeof(struct __pyx_obj_5pysam_6ctabix_asTuple), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asTuple)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asGTF = __Pyx_ImportType("pysam.ctabix", "asGTF", sizeof(struct __pyx_obj_5pysam_6ctabix_asGTF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asGTF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 196; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asBed = __Pyx_ImportType("pysam.ctabix", "asBed", sizeof(struct __pyx_obj_5pysam_6ctabix_asBed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asBed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 199; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_asVCF = __Pyx_ImportType("pysam.ctabix", "asVCF", sizeof(struct __pyx_obj_5pysam_6ctabix_asVCF), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_asVCF)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 202; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = __Pyx_ImportType("pysam.ctabix", "TabixIteratorParsed", sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 205; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_inplace_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_inplace_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_inplace_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_inplace_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_inplace_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 210; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_6ctabix_tabix_copy_iterator = __Pyx_ImportType("pysam.ctabix", "tabix_copy_iterator", sizeof(struct __pyx_obj_5pysam_6ctabix_tabix_copy_iterator), 1); if (unlikely(!__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator = (struct __pyx_vtabstruct_5pysam_6ctabix_tabix_copy_iterator*)__Pyx_GetVtable(__pyx_ptype_5pysam_6ctabix_tabix_copy_iterator->tp_dict); if (unlikely(!__pyx_vtabptr_5pysam_6ctabix_tabix_copy_iterator)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_ptype_5pysam_10TabProxies_GTFProxy = __Pyx_ImportType("pysam.TabProxies", "GTFProxy", sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), 1); if (unlikely(!__pyx_ptype_5pysam_10TabProxies_GTFProxy)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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/*--- Variable import code ---*/
/*--- Function import code ---*/
/*--- Execution code ---*/
- /* "cvcf.pyx":46
+ /* "pysam/cvcf.pyx":46
* #
*
* from collections import namedtuple, defaultdict # <<<<<<<<<<<<<<
@@ -26545,7 +26861,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "cvcf.pyx":47
+ /* "pysam/cvcf.pyx":47
*
* from collections import namedtuple, defaultdict
* from operator import itemgetter # <<<<<<<<<<<<<<
@@ -26570,12 +26886,12 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":48
+ /* "pysam/cvcf.pyx":48
* from collections import namedtuple, defaultdict
* from operator import itemgetter
* import sys, re, copy, bisect # <<<<<<<<<<<<<<
*
- * cimport ctabix
+ * from pysam cimport ctabix
*/
__pyx_t_1 = __Pyx_Import(((PyObject *)__pyx_n_s__sys), 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
@@ -26594,9 +26910,9 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":52
- * cimport ctabix
- * cimport TabProxies
+ /* "pysam/cvcf.pyx":52
+ * from pysam cimport ctabix
+ * from pysam cimport TabProxies
* import pysam # <<<<<<<<<<<<<<
*
* gtsRegEx = re.compile("[|/\\\\]")
@@ -26606,7 +26922,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__pysam, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 52; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":54
+ /* "pysam/cvcf.pyx":54
* import pysam
*
* gtsRegEx = re.compile("[|/\\\\]") # <<<<<<<<<<<<<<
@@ -26624,7 +26940,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__gtsRegEx, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 54; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/cvcf.pyx":55
*
* gtsRegEx = re.compile("[|/\\\\]")
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@@ -26642,31 +26958,31 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/cvcf.pyx":58
*
* # Utility function. Uses 0-based coordinates
* def get_sequence(chrom, start, end, fa): # <<<<<<<<<<<<<<
* # obtain sequence from .fa file, without truncation
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/cvcf.pyx":68
*
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* result = []
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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*
*
* FORMAT = namedtuple('FORMAT','id numbertype number type description missingvalue') # <<<<<<<<<<<<<<
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__Pyx_GOTREF(__pyx_t_2);
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__FORMAT, __pyx_t_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0;
- /* "cvcf.pyx":237
+ /* "pysam/cvcf.pyx":237
* return r
*
* class VCF(object): # <<<<<<<<<<<<<<
@@ -26691,7 +27007,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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__Pyx_GOTREF(((PyObject *)__pyx_t_2));
- /* "cvcf.pyx":240
+ /* "pysam/cvcf.pyx":240
*
* # types
* NT_UNKNOWN = 0 # <<<<<<<<<<<<<<
@@ -26700,7 +27016,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_UNKNOWN, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 240; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "cvcf.pyx":241
+ /* "pysam/cvcf.pyx":241
* # types
* NT_UNKNOWN = 0
* NT_NUMBER = 1 # <<<<<<<<<<<<<<
@@ -26709,7 +27025,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
*/
if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NUMBER, __pyx_int_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 241; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "cvcf.pyx":242
+ /* "pysam/cvcf.pyx":242
* NT_UNKNOWN = 0
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@@ -26718,7 +27034,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_ALLELES, __pyx_int_2) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 242; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "cvcf.pyx":243
+ /* "pysam/cvcf.pyx":243
* NT_NUMBER = 1
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@@ -26727,7 +27043,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_NR_ALLELES, __pyx_int_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 243; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "cvcf.pyx":244
+ /* "pysam/cvcf.pyx":244
* NT_ALLELES = 2
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@@ -26736,7 +27052,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_GENOTYPES, __pyx_int_4) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 244; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "cvcf.pyx":245
+ /* "pysam/cvcf.pyx":245
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@@ -26745,7 +27061,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__NT_PHASED_GENOTYPES, __pyx_int_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 245; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- /* "cvcf.pyx":247
+ /* "pysam/cvcf.pyx":247
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@@ -26754,44 +27070,44 @@ PyMODINIT_FUNC PyInit_cvcf(void)
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__pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 247; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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* self._reference = ref
*
* def ignoreerror(self, errorstring): # <<<<<<<<<<<<<<
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* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*/
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":972
+ /* "pysam/cvcf.pyx":972
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def warnerror(self, errorstring): # <<<<<<<<<<<<<<
* try: self._warn_errors.add(self.__dict__[errorstring])
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*/
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+ /* "pysam/cvcf.pyx":976
* except KeyError: raise ValueError("Invalid error string: %s" % errorstring)
*
* def parse(self, stream): # <<<<<<<<<<<<<<
* """ Parse a stream of VCF-formatted lines. Initializes class instance and return generator """
* last_line = self._parse_header(stream)
*/
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+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_72parse, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_246)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__parse, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 976; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":983
+ /* "pysam/cvcf.pyx":983
* return self._parse(last_line, stream)
*
* def write(self, stream, datagenerator): # <<<<<<<<<<<<<<
* """ Writes a VCF file to a stream, using a data generator (or list) """
* self.write_header(stream)
*/
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+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_74write, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_248)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__write, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 983; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":989
+ /* "pysam/cvcf.pyx":989
* for data in datagenerator: self.write_data(stream,data)
*
* def writeheader(self, stream): # <<<<<<<<<<<<<<
* """ Writes a VCF header """
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*/
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+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_76writeheader, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_250)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 989; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":994
+ /* "pysam/cvcf.pyx":994
* self.write_heading(stream)
*
* def compare_calls(self, pos1, ref1, alt1, pos2, ref2, alt2): # <<<<<<<<<<<<<<
* """ Utility function: compares two calls for equality """
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*/
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+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_78compare_calls, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_252)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__compare_calls, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 994; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":1016
+ /* "pysam/cvcf.pyx":1016
* ###########################################################################################################
*
* def connect( self, filename ): # <<<<<<<<<<<<<<
* '''connect to tabix file.'''
* self.tabixfile = pysam.Tabixfile( filename )
*/
- __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_4cvcf_3VCF_80connect, 0, NULL, __pyx_n_s__cvcf, ((PyObject *)__pyx_k_codeobj_253)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_80connect, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_254)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__connect, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1016; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/cvcf.pyx":1021
* self._parse_header(self.tabixfile.header)
*
* def fetch(self, # <<<<<<<<<<<<<<
* reference = None,
* start = None,
*/
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+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_82fetch, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_256)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
- __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_256));
+ __Pyx_CyFunction_SetDefaultsTuple(__pyx_t_1, ((PyObject *)__pyx_k_tuple_257));
if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__fetch, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1021; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
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+ /* "pysam/cvcf.pyx":1030
* return self.tabixfile.fetch( reference, start, end, region, parser = asVCFRecord( self ) )
*
* def validate( self, record ): # <<<<<<<<<<<<<<
* '''validate vcf record.
*
*/
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+ __pyx_t_1 = __Pyx_CyFunction_NewEx(&__pyx_mdef_5pysam_4cvcf_3VCF_84validate, 0, NULL, __pyx_n_s_135, ((PyObject *)__pyx_k_codeobj_259)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_1);
if (PyObject_SetItem(__pyx_t_2, __pyx_n_s__validate, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1030; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- /* "cvcf.pyx":237
+ /* "pysam/cvcf.pyx":237
* return r
*
* class VCF(object): # <<<<<<<<<<<<<<
@@ -27540,14 +27856,14 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__Pyx_INCREF(__pyx_builtin_object);
PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_builtin_object);
__Pyx_GIVEREF(__pyx_builtin_object);
- __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s__cvcf); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_t_3 = __Pyx_CreateClass(((PyObject *)__pyx_t_1), ((PyObject *)__pyx_t_2), __pyx_n_s__VCF, __pyx_n_s_135); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_GOTREF(__pyx_t_3);
__Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0;
if (PyObject_SetAttr(__pyx_m, __pyx_n_s__VCF, __pyx_t_3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 237; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0;
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "cvcf.pyx":1155
+ /* "pysam/cvcf.pyx":1155
* pos -= 1
*
* __all__ = [ # <<<<<<<<<<<<<<
@@ -27565,7 +27881,7 @@ PyMODINIT_FUNC PyInit_cvcf(void)
if (PyObject_SetAttr(__pyx_m, __pyx_n_s____all__, ((PyObject *)__pyx_t_2)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1155; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
__Pyx_DECREF(((PyObject *)__pyx_t_2)); __pyx_t_2 = 0;
- /* "cvcf.pyx":1
+ /* "pysam/cvcf.pyx":1
* # # <<<<<<<<<<<<<<
* # Code to read, write and edit VCF files
* #
@@ -27580,10 +27896,10 @@ PyMODINIT_FUNC PyInit_cvcf(void)
__Pyx_XDECREF(__pyx_t_2);
__Pyx_XDECREF(__pyx_t_3);
if (__pyx_m) {
- __Pyx_AddTraceback("init cvcf", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ __Pyx_AddTraceback("init pysam.cvcf", __pyx_clineno, __pyx_lineno, __pyx_filename);
Py_DECREF(__pyx_m); __pyx_m = 0;
} else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_ImportError, "init cvcf");
+ PyErr_SetString(PyExc_ImportError, "init pysam.cvcf");
}
__pyx_L0:;
__Pyx_RefNannyFinishContext();
@@ -27646,7 +27962,7 @@ static void __Pyx_RaiseArgtupleInvalid(
more_or_less = "exactly";
}
PyErr_Format(PyExc_TypeError,
- "%s() takes %s %"PY_FORMAT_SIZE_T"d positional argument%s (%"PY_FORMAT_SIZE_T"d given)",
+ "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" CYTHON_FORMAT_SSIZE_T "d given)",
func_name, more_or_less, num_expected,
(num_expected == 1) ? "" : "s", num_found);
}
@@ -27660,7 +27976,7 @@ static void __Pyx_RaiseDoubleKeywordsError(
"%s() got multiple values for keyword argument '%U'", func_name, kw_name);
#else
"%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AS_STRING(kw_name));
+ PyString_AsString(kw_name));
#endif
}
@@ -27681,48 +27997,72 @@ static int __Pyx_ParseOptionalKeywords(
while (*name && (**name != key)) name++;
if (*name) {
values[name-argnames] = value;
- } else {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key))) {
- #else
- if (unlikely(!PyUnicode_Check(key))) {
- #endif
- goto invalid_keyword_type;
- } else {
- for (name = first_kw_arg; *name; name++) {
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) break;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) break;
- #endif
- }
- if (*name) {
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
values[name-argnames] = value;
- } else {
- for (name=argnames; name != first_kw_arg; name++) {
- if (**name == key) goto arg_passed_twice;
- #if PY_MAJOR_VERSION >= 3
- if (PyUnicode_GET_SIZE(**name) == PyUnicode_GET_SIZE(key) &&
- PyUnicode_Compare(**name, key) == 0) goto arg_passed_twice;
- #else
- if (PyString_GET_SIZE(**name) == PyString_GET_SIZE(key) &&
- _PyString_Eq(**name, key)) goto arg_passed_twice;
- #endif
- }
- if (kwds2) {
- if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
- } else {
- goto invalid_keyword;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
}
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
}
}
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
}
}
return 0;
arg_passed_twice:
- __Pyx_RaiseDoubleKeywordsError(function_name, **name);
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
goto bad;
invalid_keyword_type:
PyErr_Format(PyExc_TypeError,
@@ -27741,10 +28081,9 @@ bad:
return -1;
}
-
-
static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
local_type = tstate->curexc_type;
@@ -27753,19 +28092,27 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->curexc_type = 0;
tstate->curexc_value = 0;
tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
goto bad;
#if PY_MAJOR_VERSION >= 3
if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
goto bad;
#endif
- *type = local_type;
- *value = local_value;
- *tb = local_tb;
Py_INCREF(local_type);
Py_INCREF(local_value);
Py_INCREF(local_tb);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
tmp_tb = tstate->exc_traceback;
@@ -27773,10 +28120,13 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb)
tstate->exc_value = local_value;
tstate->exc_traceback = local_tb;
/* Make sure tstate is in a consistent state when we XDECREF
- these objects (XDECREF may run arbitrary code). */
+ these objects (DECREF may run arbitrary code). */
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
return 0;
bad:
*type = 0;
@@ -27823,33 +28173,38 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
CYTHON_UNUSED PyObject *cause) {
Py_XINCREF(type);
- Py_XINCREF(value);
- Py_XINCREF(tb);
- if (tb == Py_None) {
- Py_DECREF(tb);
- tb = 0;
- }
- else if (tb != NULL && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto raise_error;
- }
- if (value == NULL) {
- value = Py_None;
+ if (!value || value == Py_None)
+ value = NULL;
+ else
Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
}
#if PY_VERSION_HEX < 0x02050000
- if (!PyClass_Check(type))
+ if (PyClass_Check(type)) {
#else
- if (!PyType_Check(type))
+ if (PyType_Check(type)) {
#endif
- {
- if (value != Py_None) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
PyErr_SetString(PyExc_TypeError,
"instance exception may not have a separate value");
goto raise_error;
}
- Py_DECREF(value);
value = type;
#if PY_VERSION_HEX < 0x02050000
if (PyInstance_Check(type)) {
@@ -27882,6 +28237,7 @@ raise_error:
}
#else /* Python 3+ */
static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
if (tb == Py_None) {
tb = 0;
} else if (tb && !PyTraceBack_Check(tb)) {
@@ -27899,12 +28255,36 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
value = type;
type = (PyObject*) Py_TYPE(value);
- } else if (!PyExceptionClass_Check(type)) {
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ }
+ else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyEval_CallObject(type, args);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ } else {
PyErr_SetString(PyExc_TypeError,
"raise: exception class must be a subclass of BaseException");
goto bad;
}
- if (cause) {
+ if (cause && cause != Py_None) {
PyObject *fixed_cause;
if (PyExceptionClass_Check(cause)) {
fixed_cause = PyObject_CallObject(cause, NULL);
@@ -27921,9 +28301,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
"BaseException");
goto bad;
}
- if (!value) {
- value = PyObject_CallObject(type, NULL);
- }
PyException_SetCause(value, fixed_cause);
}
PyErr_SetObject(type, value);
@@ -27937,12 +28314,16 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject
}
}
bad:
+ Py_XDECREF(owned_instance);
return;
}
#endif
static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyObject* float_value;
+#if CYTHON_COMPILING_IN_PYPY
+ float_value = PyNumber_Float(obj);
+#else
if (Py_TYPE(obj)->tp_as_number && Py_TYPE(obj)->tp_as_number->nb_float) {
return PyFloat_AsDouble(obj);
} else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
@@ -27959,6 +28340,7 @@ static double __Pyx__PyObject_AsDouble(PyObject* obj) {
PyTuple_SET_ITEM(args, 0, 0);
Py_DECREF(args);
}
+#endif
if (likely(float_value)) {
double value = PyFloat_AS_DOUBLE(float_value);
Py_DECREF(float_value);
@@ -27972,19 +28354,49 @@ static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
}
-static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) {
- PyErr_SetString(PyExc_TypeError, "'NoneType' object is unsubscriptable");
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
}
static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
PyErr_Format(PyExc_ValueError,
- "need more than %"PY_FORMAT_SIZE_T"d value%s to unpack",
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%s to unpack",
index, (index == 1) ? "" : "s");
}
-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
- PyErr_Format(PyExc_ValueError,
- "too many values to unpack (expected %"PY_FORMAT_SIZE_T"d)", expected);
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
}
static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
@@ -27992,13 +28404,8 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
Py_DECREF(retval);
__Pyx_RaiseTooManyValuesError(expected);
return -1;
- } else if (PyErr_Occurred()) {
- if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
- PyErr_Clear();
- return 0;
- } else {
- return -1;
- }
+ } else {
+ return __Pyx_IterFinish();
}
return 0;
}
@@ -28010,13 +28417,197 @@ static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b)
return q;
}
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
+}
+
+static void __Pyx_UnpackTupleError(PyObject *t, Py_ssize_t index) {
+ if (t == Py_None) {
+ __Pyx_RaiseNoneNotIterableError();
+ } else if (PyTuple_GET_SIZE(t) < index) {
+ __Pyx_RaiseNeedMoreValuesError(PyTuple_GET_SIZE(t));
+ } else {
+ __Pyx_RaiseTooManyValuesError(index);
+ }
+}
+
+static CYTHON_INLINE int __Pyx_unpack_tuple2(PyObject* tuple, PyObject** pvalue1, PyObject** pvalue2,
+ int is_tuple, int has_known_size, int decref_tuple) {
+ Py_ssize_t index;
+ PyObject *value1 = NULL, *value2 = NULL, *iter = NULL;
+ if (!is_tuple && unlikely(!PyTuple_Check(tuple))) {
+ iternextfunc iternext;
+ iter = PyObject_GetIter(tuple);
+ if (unlikely(!iter)) goto bad;
+ if (decref_tuple) { Py_DECREF(tuple); tuple = NULL; }
+ iternext = Py_TYPE(iter)->tp_iternext;
+ value1 = iternext(iter); if (unlikely(!value1)) { index = 0; goto unpacking_failed; }
+ value2 = iternext(iter); if (unlikely(!value2)) { index = 1; goto unpacking_failed; }
+ if (!has_known_size && unlikely(__Pyx_IternextUnpackEndCheck(iternext(iter), 2))) goto bad;
+ Py_DECREF(iter);
+ } else {
+ if (!has_known_size && unlikely(PyTuple_GET_SIZE(tuple) != 2)) {
+ __Pyx_UnpackTupleError(tuple, 2);
+ goto bad;
+ }
+#if CYTHON_COMPILING_IN_PYPY
+ value1 = PySequence_ITEM(tuple, 0);
+ if (unlikely(!value1)) goto bad;
+ value2 = PySequence_ITEM(tuple, 1);
+ if (unlikely(!value2)) goto bad;
+#else
+ value1 = PyTuple_GET_ITEM(tuple, 0);
+ value2 = PyTuple_GET_ITEM(tuple, 1);
+ Py_INCREF(value1);
+ Py_INCREF(value2);
+#endif
+ if (decref_tuple) { Py_DECREF(tuple); }
+ }
+ *pvalue1 = value1;
+ *pvalue2 = value2;
+ return 0;
+unpacking_failed:
+ if (!has_known_size && __Pyx_IterFinish() == 0)
+ __Pyx_RaiseNeedMoreValuesError(index);
+bad:
+ Py_XDECREF(iter);
+ Py_XDECREF(value1);
+ Py_XDECREF(value2);
+ if (decref_tuple) { Py_XDECREF(tuple); }
+ return -1;
+}
+static CYTHON_INLINE PyObject* __Pyx_dict_iterator(PyObject* iterable, int is_dict, PyObject* method_name,
+ Py_ssize_t* p_orig_length, int* p_source_is_dict) {
+ is_dict = is_dict || likely(PyDict_CheckExact(iterable));
+ *p_source_is_dict = is_dict;
+#if !CYTHON_COMPILING_IN_PYPY
+ if (is_dict) {
+ *p_orig_length = PyDict_Size(iterable);
+ Py_INCREF(iterable);
+ return iterable;
+ }
+#endif
+ *p_orig_length = 0;
+ if (method_name) {
+ PyObject* iter;
+ iterable = PyObject_CallMethodObjArgs(iterable, method_name, NULL);
+ if (!iterable)
+ return NULL;
+#if !CYTHON_COMPILING_IN_PYPY
+ if (PyTuple_CheckExact(iterable) || PyList_CheckExact(iterable))
+ return iterable;
+#endif
+ iter = PyObject_GetIter(iterable);
+ Py_DECREF(iterable);
+ return iter;
+ }
+ return PyObject_GetIter(iterable);
+}
+static CYTHON_INLINE int __Pyx_dict_iter_next(PyObject* iter_obj, Py_ssize_t orig_length, Py_ssize_t* ppos,
+ PyObject** pkey, PyObject** pvalue, PyObject** pitem, int source_is_dict) {
+ PyObject* next_item;
+#if !CYTHON_COMPILING_IN_PYPY
+ if (source_is_dict) {
+ PyObject *key, *value;
+ if (unlikely(orig_length != PyDict_Size(iter_obj))) {
+ PyErr_SetString(PyExc_RuntimeError, "dictionary changed size during iteration");
+ return -1;
+ }
+ if (unlikely(!PyDict_Next(iter_obj, ppos, &key, &value))) {
+ return 0;
+ }
+ if (pitem) {
+ PyObject* tuple = PyTuple_New(2);
+ if (unlikely(!tuple)) {
+ return -1;
+ }
+ Py_INCREF(key);
+ Py_INCREF(value);
+ PyTuple_SET_ITEM(tuple, 0, key);
+ PyTuple_SET_ITEM(tuple, 1, value);
+ *pitem = tuple;
+ } else {
+ if (pkey) {
+ Py_INCREF(key);
+ *pkey = key;
+ }
+ if (pvalue) {
+ Py_INCREF(value);
+ *pvalue = value;
+ }
+ }
+ return 1;
+ } else if (PyTuple_CheckExact(iter_obj)) {
+ Py_ssize_t pos = *ppos;
+ if (unlikely(pos >= PyTuple_GET_SIZE(iter_obj))) return 0;
+ *ppos = pos + 1;
+ next_item = PyTuple_GET_ITEM(iter_obj, pos);
+ Py_INCREF(next_item);
+ } else if (PyList_CheckExact(iter_obj)) {
+ Py_ssize_t pos = *ppos;
+ if (unlikely(pos >= PyList_GET_SIZE(iter_obj))) return 0;
+ *ppos = pos + 1;
+ next_item = PyList_GET_ITEM(iter_obj, pos);
+ Py_INCREF(next_item);
+ } else
+#endif
+ {
+ next_item = PyIter_Next(iter_obj);
+ if (unlikely(!next_item)) {
+ return __Pyx_IterFinish();
+ }
+ }
+ if (pitem) {
+ *pitem = next_item;
+ } else if (pkey && pvalue) {
+ if (__Pyx_unpack_tuple2(next_item, pkey, pvalue, source_is_dict, source_is_dict, 1))
+ return -1;
+ } else if (pkey) {
+ *pkey = next_item;
+ } else {
+ *pvalue = next_item;
+ }
+ return 1;
+}
static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
}
+static void __Pyx_call_next_tp_dealloc(PyObject* obj, destructor current_tp_dealloc) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_dealloc != current_tp_dealloc)
+ type = type->tp_base;
+ while (type && type->tp_dealloc == current_tp_dealloc)
+ type = type->tp_base;
+ if (type)
+ type->tp_dealloc(obj);
+}
+
+static int __Pyx_call_next_tp_traverse(PyObject* obj, visitproc v, void *a, traverseproc current_tp_traverse) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_traverse != current_tp_traverse)
+ type = type->tp_base;
+ while (type && type->tp_traverse == current_tp_traverse)
+ type = type->tp_base;
+ if (type && type->tp_traverse)
+ return type->tp_traverse(obj, v, a);
+ return 0;
+}
+
+static void __Pyx_call_next_tp_clear(PyObject* obj, inquiry current_tp_clear) {
+ PyTypeObject* type = Py_TYPE(obj);
+ while (type && type->tp_clear != current_tp_clear)
+ type = type->tp_base;
+ while (type && type->tp_clear == current_tp_clear)
+ type = type->tp_base;
+ if (type && type->tp_clear)
+ type->tp_clear(obj);
+}
+
static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
*type = tstate->exc_type;
*value = tstate->exc_value;
@@ -28024,8 +28615,12 @@ static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value,
Py_XINCREF(*type);
Py_XINCREF(*value);
Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
}
static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
PyObject *tmp_type, *tmp_value, *tmp_tb;
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
@@ -28037,6 +28632,9 @@ static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb)
Py_XDECREF(tmp_type);
Py_XDECREF(tmp_value);
Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
}
static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) {
@@ -28119,7 +28717,6 @@ static CYTHON_INLINE void __Pyx_RaiseImportError(PyObject *name) {
static PyObject *__Pyx_FindPy2Metaclass(PyObject *bases) {
PyObject *metaclass;
- /* Default metaclass */
#if PY_MAJOR_VERSION < 3
if (PyTuple_Check(bases) && PyTuple_GET_SIZE(bases) > 0) {
PyObject *base = PyTuple_GET_ITEM(bases, 0);
@@ -28149,7 +28746,6 @@ static PyObject *__Pyx_CreateClass(PyObject *bases, PyObject *dict, PyObject *na
PyObject *metaclass;
if (PyDict_SetItemString(dict, "__module__", modname) < 0)
return NULL;
- /* Python2 __metaclass__ */
metaclass = PyDict_GetItemString(dict, "__metaclass__");
if (metaclass) {
Py_INCREF(metaclass);
@@ -28441,6 +29037,56 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
PyString_AsString(func_name), (void *)op);
#endif
}
+#if CYTHON_COMPILING_IN_PYPY
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ PyCFunctionObject* f = (PyCFunctionObject*)func;
+ PyCFunction meth = PyCFunction_GET_FUNCTION(func);
+ PyObject *self = PyCFunction_GET_SELF(func);
+ Py_ssize_t size;
+ switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
+ case METH_VARARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0)
+ return (*meth)(self, arg);
+ break;
+ case METH_VARARGS | METH_KEYWORDS:
+ return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
+ case METH_NOARGS:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 0)
+ return (*meth)(self, NULL);
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes no arguments (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ case METH_O:
+ if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
+ size = PyTuple_GET_SIZE(arg);
+ if (size == 1)
+ return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() takes exactly one argument (%zd given)",
+ f->m_ml->ml_name, size);
+ return NULL;
+ }
+ break;
+ default:
+ PyErr_SetString(PyExc_SystemError, "Bad call flags in "
+ "__Pyx_CyFunction_Call. METH_OLDARGS is no "
+ "longer supported!");
+ return NULL;
+ }
+ PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
+ f->m_ml->ml_name);
+ return NULL;
+}
+#else
+static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
+ return PyCFunction_Call(func, arg, kw);
+}
+#endif
static PyTypeObject __pyx_CyFunctionType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
@@ -28460,7 +29106,7 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_as_sequence*/
0, /*tp_as_mapping*/
0, /*tp_hash*/
- __Pyx_PyCFunction_Call, /*tp_call*/
+ __Pyx_CyFunction_Call, /*tp_call*/
0, /*tp_str*/
0, /*tp_getattro*/
0, /*tp_setattro*/
@@ -28496,15 +29142,16 @@ static PyTypeObject __pyx_CyFunctionType_type = {
0, /*tp_version_tag*/
#endif
};
-static int __Pyx_CyFunction_init(void)
-{
+static int __Pyx_CyFunction_init(void) {
+#if !CYTHON_COMPILING_IN_PYPY
+ __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
+#endif
if (PyType_Ready(&__pyx_CyFunctionType_type) < 0)
return -1;
__pyx_CyFunctionType = &__pyx_CyFunctionType_type;
return 0;
}
-void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
-{
+static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults = PyMem_Malloc(size);
if (!m->defaults)
@@ -28513,8 +29160,7 @@ void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects)
m->defaults_pyobjects = pyobjects;
return m->defaults;
}
-static void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple)
-{
+static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
__pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
m->defaults_tuple = tuple;
Py_INCREF(tuple);
@@ -28545,78 +29191,6 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_uint32_t(uint32_t val) {
}
}
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- if (PyBytes_GET_SIZE(s1) != PyBytes_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyBytes_GET_SIZE(s1) == 1) {
- if (equals == Py_EQ)
- return (PyBytes_AS_STRING(s1)[0] == PyBytes_AS_STRING(s2)[0]);
- else
- return (PyBytes_AS_STRING(s1)[0] != PyBytes_AS_STRING(s2)[0]);
- } else {
- int result = memcmp(PyBytes_AS_STRING(s1), PyBytes_AS_STRING(s2), (size_t)PyBytes_GET_SIZE(s1));
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) {
- #if CYTHON_PEP393_ENABLED
- if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0))
- return -1;
- if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_LENGTH(s1) == 1) {
- Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0);
- Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0);
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #else
- if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) {
- return (equals == Py_NE);
- } else if (PyUnicode_GET_SIZE(s1) == 1) {
- Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0];
- Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0];
- return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2);
- #endif
- } else {
- int result = PyUnicode_Compare(s1, s2);
- if ((result == -1) && unlikely(PyErr_Occurred()))
- return -1;
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) {
- return (equals == Py_NE);
- } else if ((s2 == Py_None) & PyUnicode_CheckExact(s1)) {
- return (equals == Py_NE);
- } else {
- int result;
- PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
- if (!py_result)
- return -1;
- result = __Pyx_PyObject_IsTrue(py_result);
- Py_DECREF(py_result);
- return result;
- }
-}
-
static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) {
const unsigned char neg_one = (unsigned char)-1, const_zero = 0;
const int is_unsigned = neg_one > const_zero;
@@ -29019,6 +29593,7 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject*
static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
PyObject *tmp_type, *tmp_value, *tmp_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
PyThreadState *tstate = PyThreadState_GET();
tmp_type = tstate->exc_type;
tmp_value = tstate->exc_value;
@@ -29026,6 +29601,10 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value,
tstate->exc_type = *type;
tstate->exc_value = *value;
tstate->exc_traceback = *tb;
+#else
+ PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
+ PyErr_SetExcInfo(*type, *value, *tb);
+#endif
*type = tmp_type;
*value = tmp_value;
*tb = tmp_tb;
@@ -29035,9 +29614,70 @@ static PyObject *__Pyx_Generator_Next(PyObject *self);
static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value);
static PyObject *__Pyx_Generator_Close(PyObject *self);
static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args);
+static PyTypeObject *__pyx_GeneratorType = 0;
+#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType)
+#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom)
+#if 1 || PY_VERSION_HEX < 0x030300B0
+static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) {
+ PyObject *et, *ev, *tb;
+ PyObject *value = NULL;
+ __Pyx_ErrFetch(&et, &ev, &tb);
+ if (!et) {
+ Py_XDECREF(tb);
+ Py_XDECREF(ev);
+ Py_INCREF(Py_None);
+ *pvalue = Py_None;
+ return 0;
+ }
+ if (unlikely(et != PyExc_StopIteration) &&
+ unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ if (likely(et == PyExc_StopIteration)) {
+ if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) {
+ if (!ev) {
+ Py_INCREF(Py_None);
+ ev = Py_None;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+ *pvalue = ev;
+ return 0;
+ }
+ }
+ PyErr_NormalizeException(&et, &ev, &tb);
+ if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) {
+ __Pyx_ErrRestore(et, ev, tb);
+ return -1;
+ }
+ Py_XDECREF(tb);
+ Py_DECREF(et);
+#if PY_VERSION_HEX >= 0x030300A0
+ value = ((PyStopIterationObject *)ev)->value;
+ Py_INCREF(value);
+ Py_DECREF(ev);
+#else
+ {
+ PyObject* args = PyObject_GetAttrString(ev, "args");
+ Py_DECREF(ev);
+ if (likely(args)) {
+ value = PyObject_GetItem(args, 0);
+ Py_DECREF(args);
+ }
+ if (unlikely(!value)) {
+ __Pyx_ErrRestore(NULL, NULL, NULL);
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+ }
+#endif
+ *pvalue = value;
+ return 0;
+}
+#endif
static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
-{
+void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
PyObject *exc_type = self->exc_type;
PyObject *exc_value = self->exc_value;
PyObject *exc_traceback = self->exc_traceback;
@@ -29049,14 +29689,18 @@ void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self)
Py_XDECREF(exc_traceback);
}
static CYTHON_INLINE
-PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
-{
- PyObject *retval;
- if (unlikely(self->is_running)) {
+int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
+ if (unlikely(gen->is_running)) {
PyErr_SetString(PyExc_ValueError,
"generator already executing");
- return NULL;
+ return 1;
}
+ return 0;
+}
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) {
+ PyObject *retval;
+ assert(!self->is_running);
if (unlikely(self->resume_label == 0)) {
if (unlikely(value && value != Py_None)) {
PyErr_SetString(PyExc_TypeError,
@@ -29069,81 +29713,240 @@ PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value)
PyErr_SetNone(PyExc_StopIteration);
return NULL;
}
- if (value)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (value) {
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Generators always return to their most recent caller, not
+ * necessarily their creator. */
+ if (self->exc_traceback) {
+ PyThreadState *tstate = PyThreadState_GET();
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_XINCREF(tstate->frame);
+ assert(f->f_back == NULL);
+ f->f_back = tstate->frame;
+ }
+#endif
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+ } else {
__Pyx_Generator_ExceptionClear(self);
+ }
self->is_running = 1;
retval = self->body((PyObject *) self, value);
self->is_running = 0;
- if (retval)
- __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback);
- else
+ if (retval) {
+ __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value,
+ &self->exc_traceback);
+#if CYTHON_COMPILING_IN_PYPY
+#else
+ /* Don't keep the reference to f_back any longer than necessary. It
+ * may keep a chain of frames alive or it could create a reference
+ * cycle. */
+ if (self->exc_traceback) {
+ PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback;
+ PyFrameObject *f = tb->tb_frame;
+ Py_CLEAR(f->f_back);
+ }
+#endif
+ } else {
__Pyx_Generator_ExceptionClear(self);
+ }
return retval;
}
-static PyObject *__Pyx_Generator_Next(PyObject *self)
-{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, Py_None);
+static CYTHON_INLINE
+PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) {
+ PyObject *ret;
+ PyObject *val = NULL;
+ __Pyx_Generator_Undelegate(gen);
+ __Pyx_PyGen_FetchStopIterationValue(&val);
+ ret = __Pyx_Generator_SendEx(gen, val);
+ Py_XDECREF(val);
+ return ret;
+}
+static PyObject *__Pyx_Generator_Next(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ ret = Py_TYPE(yf)->tp_iternext(yf);
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, Py_None);
}
-static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value)
-{
- return __Pyx_Generator_SendEx((__pyx_GeneratorObject *) self, value);
+static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self;
+ PyObject *yf = gen->yieldfrom;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Send(yf, value);
+ } else {
+ if (value == Py_None)
+ ret = PyIter_Next(yf);
+ else
+ ret = PyObject_CallMethod(yf, (char*)"send", (char*)"O", value);
+ }
+ gen->is_running = 0;
+ if (likely(ret)) {
+ return ret;
+ }
+ return __Pyx_Generator_FinishDelegation(gen);
+ }
+ return __Pyx_Generator_SendEx(gen, value);
}
-static PyObject *__Pyx_Generator_Close(PyObject *self)
-{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
- PyObject *retval;
+static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) {
+ PyObject *retval = NULL;
+ int err = 0;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ retval = __Pyx_Generator_Close(yf);
+ if (!retval)
+ return -1;
+ } else {
+ PyObject *meth;
+ gen->is_running = 1;
+ meth = PyObject_GetAttrString(yf, "close");
+ if (unlikely(!meth)) {
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_WriteUnraisable(yf);
+ }
+ PyErr_Clear();
+ } else {
+ retval = PyObject_CallFunction(meth, NULL);
+ Py_DECREF(meth);
+ if (!retval)
+ err = -1;
+ }
+ gen->is_running = 0;
+ }
+ Py_XDECREF(retval);
+ return err;
+}
+static PyObject *__Pyx_Generator_Close(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ PyObject *retval, *raised_exception;
+ PyObject *yf = gen->yieldfrom;
+ int err = 0;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ Py_INCREF(yf);
+ err = __Pyx_Generator_CloseIter(gen, yf);
+ __Pyx_Generator_Undelegate(gen);
+ Py_DECREF(yf);
+ }
+ if (err == 0)
#if PY_VERSION_HEX < 0x02050000
- PyErr_SetNone(PyExc_StopIteration);
+ PyErr_SetNone(PyExc_StopIteration);
#else
- PyErr_SetNone(PyExc_GeneratorExit);
+ PyErr_SetNone(PyExc_GeneratorExit);
#endif
- retval = __Pyx_Generator_SendEx(generator, NULL);
+ retval = __Pyx_Generator_SendEx(gen, NULL);
if (retval) {
Py_DECREF(retval);
PyErr_SetString(PyExc_RuntimeError,
"generator ignored GeneratorExit");
return NULL;
}
-#if PY_VERSION_HEX < 0x02050000
- if (PyErr_ExceptionMatches(PyExc_StopIteration))
-#else
- if (PyErr_ExceptionMatches(PyExc_StopIteration)
- || PyErr_ExceptionMatches(PyExc_GeneratorExit))
+ raised_exception = PyErr_Occurred();
+ if (!raised_exception
+ || raised_exception == PyExc_StopIteration
+#if PY_VERSION_HEX >= 0x02050000
+ || raised_exception == PyExc_GeneratorExit
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_GeneratorExit)
#endif
+ || PyErr_GivenExceptionMatches(raised_exception, PyExc_StopIteration))
{
- PyErr_Clear(); /* ignore these errors */
+ if (raised_exception) PyErr_Clear(); /* ignore these errors */
Py_INCREF(Py_None);
return Py_None;
}
return NULL;
}
-static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args)
-{
- __pyx_GeneratorObject *generator = (__pyx_GeneratorObject *) self;
+static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject *typ;
PyObject *tb = NULL;
PyObject *val = NULL;
+ PyObject *yf = gen->yieldfrom;
if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb))
return NULL;
+ if (unlikely(__Pyx_Generator_CheckRunning(gen)))
+ return NULL;
+ if (yf) {
+ PyObject *ret;
+ Py_INCREF(yf);
+#if PY_VERSION_HEX >= 0x02050000
+ if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) {
+ int err = __Pyx_Generator_CloseIter(gen, yf);
+ Py_DECREF(yf);
+ __Pyx_Generator_Undelegate(gen);
+ if (err < 0)
+ return __Pyx_Generator_SendEx(gen, NULL);
+ goto throw_here;
+ }
+#endif
+ gen->is_running = 1;
+ if (__Pyx_Generator_CheckExact(yf)) {
+ ret = __Pyx_Generator_Throw(yf, args);
+ } else {
+ PyObject *meth = PyObject_GetAttrString(yf, "throw");
+ if (unlikely(!meth)) {
+ Py_DECREF(yf);
+ if (!PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ gen->is_running = 0;
+ return NULL;
+ }
+ PyErr_Clear();
+ __Pyx_Generator_Undelegate(gen);
+ gen->is_running = 0;
+ goto throw_here;
+ }
+ ret = PyObject_CallObject(meth, args);
+ Py_DECREF(meth);
+ }
+ gen->is_running = 0;
+ Py_DECREF(yf);
+ if (!ret) {
+ ret = __Pyx_Generator_FinishDelegation(gen);
+ }
+ return ret;
+ }
+throw_here:
__Pyx_Raise(typ, val, tb, NULL);
- return __Pyx_Generator_SendEx(generator, NULL);
+ return __Pyx_Generator_SendEx(gen, NULL);
}
-static int
-__Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg)
-{
+static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
Py_VISIT(gen->closure);
Py_VISIT(gen->classobj);
+ Py_VISIT(gen->yieldfrom);
Py_VISIT(gen->exc_type);
Py_VISIT(gen->exc_value);
Py_VISIT(gen->exc_traceback);
return 0;
}
-static void
-__Pyx_Generator_dealloc(PyObject *self)
-{
+static int __Pyx_Generator_clear(PyObject *self) {
+ __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
+ Py_CLEAR(gen->closure);
+ Py_CLEAR(gen->classobj);
+ Py_CLEAR(gen->yieldfrom);
+ Py_CLEAR(gen->exc_type);
+ Py_CLEAR(gen->exc_value);
+ Py_CLEAR(gen->exc_traceback);
+ return 0;
+}
+static void __Pyx_Generator_dealloc(PyObject *self) {
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
PyObject_GC_UnTrack(gen);
if (gen->gi_weakreflist != NULL)
@@ -29155,16 +29958,10 @@ __Pyx_Generator_dealloc(PyObject *self)
return; /* resurrected. :( */
}
PyObject_GC_UnTrack(self);
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
+ __Pyx_Generator_clear(self);
PyObject_GC_Del(gen);
}
-static void
-__Pyx_Generator_del(PyObject *self)
-{
+static void __Pyx_Generator_del(PyObject *self) {
PyObject *res;
PyObject *error_type, *error_value, *error_traceback;
__pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
@@ -29193,11 +29990,13 @@ __Pyx_Generator_del(PyObject *self)
_Py_NewReference(self);
self->ob_refcnt = refcnt;
}
+#if CYTHON_COMPILING_FOR_CPYTHON
assert(PyType_IS_GC(self->ob_type) &&
_Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
/* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
* we need to undo that. */
_Py_DEC_REFTOTAL;
+#endif
/* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
* chain, so no more to do there.
* If COUNT_ALLOCS, the original decref bumped tp_frees, and
@@ -29205,13 +30004,17 @@ __Pyx_Generator_del(PyObject *self)
* undone.
*/
#ifdef COUNT_ALLOCS
- --self->ob_type->tp_frees;
- --self->ob_type->tp_allocs;
+ --Py_TYPE(self)->tp_frees;
+ --Py_TYPE(self)->tp_allocs;
#endif
}
static PyMemberDef __pyx_Generator_memberlist[] = {
{(char *) "gi_running",
- T_INT,
+#if PY_VERSION_HEX >= 0x02060000
+ T_BOOL,
+#else
+ T_BYTE,
+#endif
offsetof(__pyx_GeneratorObject, is_running),
READONLY,
NULL},
@@ -29223,7 +30026,7 @@ static PyMethodDef __pyx_Generator_methods[] = {
{__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
{0, 0, 0, 0}
};
-static PyTypeObject __pyx_GeneratorType = {
+static PyTypeObject __pyx_GeneratorType_type = {
PyVarObject_HEAD_INIT(0, 0)
__Pyx_NAMESTR("generator"), /*tp_name*/
sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
@@ -29244,7 +30047,7 @@ static PyTypeObject __pyx_GeneratorType = {
0, /*tp_hash*/
0, /*tp_call*/
0, /*tp_str*/
- PyObject_GenericGetAttr, /*tp_getattro*/
+ 0, /*tp_getattro*/
0, /*tp_setattro*/
0, /*tp_as_buffer*/
Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
@@ -29253,7 +30056,7 @@ static PyTypeObject __pyx_GeneratorType = {
0, /*tp_clear*/
0, /*tp_richcompare*/
offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- PyObject_SelfIter, /*tp_iter*/
+ 0, /*tp_iter*/
(iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
__pyx_Generator_methods, /*tp_methods*/
__pyx_Generator_memberlist, /*tp_members*/
@@ -29278,12 +30081,10 @@ static PyTypeObject __pyx_GeneratorType = {
0, /*tp_version_tag*/
#endif
};
-static
-__pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure)
-{
+static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
+ PyObject *closure) {
__pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType);
+ PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
if (gen == NULL)
return NULL;
gen->body = body;
@@ -29292,6 +30093,7 @@ __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
gen->is_running = 0;
gen->resume_label = 0;
gen->classobj = NULL;
+ gen->yieldfrom = NULL;
gen->exc_type = NULL;
gen->exc_value = NULL;
gen->exc_traceback = NULL;
@@ -29299,9 +30101,14 @@ __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
PyObject_GC_Track(gen);
return gen;
}
-static int __pyx_Generator_init(void)
-{
- return PyType_Ready(&__pyx_GeneratorType);
+static int __pyx_Generator_init(void) {
+ __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
+ __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
+ if (PyType_Ready(&__pyx_GeneratorType_type)) {
+ return -1;
+ }
+ __pyx_GeneratorType = &__pyx_GeneratorType_type;
+ return 0;
}
static int __Pyx_check_binary_version(void) {
@@ -29323,6 +30130,23 @@ static int __Pyx_check_binary_version(void) {
return 0;
}
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
#ifndef __PYX_HAVE_RT_ImportType
#define __PYX_HAVE_RT_ImportType
static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
@@ -29375,23 +30199,6 @@ bad:
}
#endif
-#ifndef __PYX_HAVE_RT_ImportModule
-#define __PYX_HAVE_RT_ImportModule
-static PyObject *__Pyx_ImportModule(const char *name) {
- PyObject *py_name = 0;
- PyObject *py_module = 0;
- py_name = __Pyx_PyIdentifier_FromString(name);
- if (!py_name)
- goto bad;
- py_module = PyImport_Import(py_name);
- Py_DECREF(py_name);
- return py_module;
-bad:
- Py_XDECREF(py_name);
- return 0;
-}
-#endif
-
static void* __Pyx_GetVtable(PyObject *dict) {
void* ptr;
PyObject *ob = PyMapping_GetItemString(dict, (char *)"__pyx_vtable__");
diff --git a/pysam/cvcf.pyx b/pysam/cvcf.pyx
index 86ff882..edde706 100644
--- a/pysam/cvcf.pyx
+++ b/pysam/cvcf.pyx
@@ -47,8 +47,8 @@ from collections import namedtuple, defaultdict
from operator import itemgetter
import sys, re, copy, bisect
-cimport ctabix
-cimport TabProxies
+from pysam cimport ctabix
+from pysam cimport TabProxies
import pysam
gtsRegEx = re.compile("[|/\\\\]")
diff --git a/pysam/version.py b/pysam/version.py
index 48345d8..eb98027 100644
--- a/pysam/version.py
+++ b/pysam/version.py
@@ -1,6 +1,6 @@
# pysam versioning information
-__version__ = "0.7.2"
+__version__ = "0.7.3"
__samtools_version__ = "0.1.18"
diff --git a/setup.py b/setup.py
index 7dfc9e0..182c30f 100644
--- a/setup.py
+++ b/setup.py
@@ -4,8 +4,6 @@
pysam
*****
-For more information, see http://code.google.com/p/pysam.
-
'''
import os, sys, glob, shutil, hashlib, re, fnmatch
@@ -116,10 +114,19 @@ if len(sys.argv) >= 2 and sys.argv[1] == "refresh":
sys.exit(0)
+
+###################
+# populate headers
+# mkdir pysam/include pysam/include/win32
+# touch pysam/include/__init__.py pysam/include/win32/__init__.py
+# 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
+from setuptools import Extension, setup, find_packages
#######################################################
#######################################################
@@ -129,8 +136,8 @@ except ImportError:
# no Cython available - use existing C code
cmdclass = { }
csamtools_sources = [ "pysam/csamtools.c" ]
- tabix_sources = [ "pysam/tabix.c" ]
- tabproxies_sources = ["pysam/TabProxies.c" ]
+ tabix_sources = [ "pysam/ctabix.c" ]
+ tabproxies_sourcess = ["pysam/TabProxies.c" ]
cvcf_sources = ["pysam/cvcf.c" ]
else:
cmdclass = { 'build_ext' : build_ext }
@@ -221,27 +228,16 @@ metadata = {
'license': "MIT",
'platforms': "ALL",
'url': "http://code.google.com/p/pysam/",
- 'py_modules': [
- "pysam/__init__",
- "pysam/Pileup",
- "pysam/version" ],
- # cython larger that 0.16 for yield support
- 'requires' : ['cython (>=0.16)'],
+ 'packages' : find_packages(),
+ 'requires' : ['cython (>=0.17)'],
'ext_modules': [samtools, tabix, tabproxies, cvcf ],
'cmdclass' : cmdclass,
- 'install_requires' : ['cython>=0.16',],
- 'data_files' : [('pysam', glob.glob('pysam/*.pxd')),
- ('include/pysam', glob.glob('pysam/*.h')),
- ('include/samtools', glob.glob('samtools/*.h')),
- ('include/samtools/win32', glob.glob('samtools/win32/*.h'))],
+ 'install_requires' : ['cython>=0.17',],
+ 'package_data' : { '' : ['*.pxd', '*.h'], },
# do not pack in order to permit linking to csamtools.so
'zip_safe' :False,
'use_2to3': True,
}
-if sys.version_info[0] < 3:
- metadata['py_modules'].append("pysam/namedtuple")
-
if __name__=='__main__':
dist = setup(**metadata)
-
diff --git a/tabix/bedidx.c b/tabix/bedidx.c
new file mode 100644
index 0000000..722877d
--- /dev/null
+++ b/tabix/bedidx.c
@@ -0,0 +1,156 @@
+#include <stdlib.h>
+#include <stdint.h>
+#include <string.h>
+#include <stdio.h>
+#include <zlib.h>
+
+#include "ksort.h"
+KSORT_INIT_GENERIC(uint64_t)
+
+#include "kseq.h"
+KSTREAM_INIT(gzFile, gzread, 8192)
+
+typedef struct {
+ int n, m;
+ uint64_t *a;
+ int *idx;
+} bed_reglist_t;
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(reg, bed_reglist_t)
+
+#define LIDX_SHIFT 13
+
+typedef kh_reg_t reghash_t;
+
+int *bed_index_core(int n, uint64_t *a, int *n_idx)
+{
+ int i, j, m, *idx;
+ m = *n_idx = 0; idx = 0;
+ for (i = 0; i < n; ++i) {
+ int beg, end;
+ beg = a[i]>>32 >> LIDX_SHIFT; end = ((uint32_t)a[i]) >> LIDX_SHIFT;
+ if (m < end + 1) {
+ int oldm = m;
+ m = end + 1;
+ kroundup32(m);
+ idx = realloc(idx, m * sizeof(int));
+ for (j = oldm; j < m; ++j) idx[j] = -1;
+ }
+ if (beg == end) {
+ if (idx[beg] < 0) idx[beg] = i;
+ } else {
+ for (j = beg; j <= end; ++j)
+ if (idx[j] < 0) idx[j] = i;
+ }
+ *n_idx = end + 1;
+ }
+ return idx;
+}
+
+void bed_index(void *_h)
+{
+ reghash_t *h = (reghash_t*)_h;
+ khint_t k;
+ for (k = 0; k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ bed_reglist_t *p = &kh_val(h, k);
+ if (p->idx) free(p->idx);
+ ks_introsort(uint64_t, p->n, p->a);
+ p->idx = bed_index_core(p->n, p->a, &p->m);
+ }
+ }
+}
+
+int bed_overlap_core(const bed_reglist_t *p, int beg, int end)
+{
+ int i, min_off;
+ if (p->n == 0) return 0;
+ min_off = (beg>>LIDX_SHIFT >= p->n)? p->idx[p->n-1] : p->idx[beg>>LIDX_SHIFT];
+ if (min_off < 0) { // TODO: this block can be improved, but speed should not matter too much here
+ int n = beg>>LIDX_SHIFT;
+ if (n > p->n) n = p->n;
+ for (i = n - 1; i >= 0; --i)
+ if (p->idx[i] >= 0) break;
+ min_off = i >= 0? p->idx[i] : 0;
+ }
+ for (i = min_off; i < p->n; ++i) {
+ if ((int)(p->a[i]>>32) >= end) break; // out of range; no need to proceed
+ if ((int32_t)p->a[i] > beg && (int32_t)(p->a[i]>>32) < end)
+ return 1; // find the overlap; return
+ }
+ return 0;
+}
+
+int bed_overlap(const void *_h, const char *chr, int beg, int end)
+{
+ const reghash_t *h = (const reghash_t*)_h;
+ khint_t k;
+ if (!h) return 0;
+ k = kh_get(reg, h, chr);
+ if (k == kh_end(h)) return 0;
+ return bed_overlap_core(&kh_val(h, k), beg, end);
+}
+
+void *bed_read(const char *fn)
+{
+ reghash_t *h = kh_init(reg);
+ gzFile fp;
+ kstream_t *ks;
+ int dret;
+ kstring_t *str;
+ // read the list
+ fp = strcmp(fn, "-")? gzopen(fn, "r") : gzdopen(fileno(stdin), "r");
+ if (fp == 0) return 0;
+ str = calloc(1, sizeof(kstring_t));
+ ks = ks_init(fp);
+ while (ks_getuntil(ks, 0, str, &dret) >= 0) { // read the chr name
+ int beg = -1, end = -1;
+ bed_reglist_t *p;
+ khint_t k = kh_get(reg, h, str->s);
+ if (k == kh_end(h)) { // absent from the hash table
+ int ret;
+ char *s = strdup(str->s);
+ k = kh_put(reg, h, s, &ret);
+ memset(&kh_val(h, k), 0, sizeof(bed_reglist_t));
+ }
+ p = &kh_val(h, k);
+ if (dret != '\n') { // if the lines has other characters
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0])) {
+ beg = atoi(str->s); // begin
+ if (dret != '\n') {
+ if (ks_getuntil(ks, 0, str, &dret) > 0 && isdigit(str->s[0]))
+ end = atoi(str->s); // end
+ }
+ }
+ }
+ if (dret != '\n') while ((dret = ks_getc(ks)) > 0 && dret != '\n'); // skip the rest of the line
+ if (end < 0 && beg > 0) end = beg, beg = beg - 1; // if there is only one column
+ if (beg >= 0 && end > beg) {
+ if (p->n == p->m) {
+ p->m = p->m? p->m<<1 : 4;
+ p->a = realloc(p->a, p->m * 8);
+ }
+ p->a[p->n++] = (uint64_t)beg<<32 | end;
+ }
+ }
+ ks_destroy(ks);
+ gzclose(fp);
+ free(str->s); free(str);
+ bed_index(h);
+ return h;
+}
+
+void bed_destroy(void *_h)
+{
+ reghash_t *h = (reghash_t*)_h;
+ khint_t k;
+ for (k = 0; k < kh_end(h); ++k) {
+ if (kh_exist(h, k)) {
+ free(kh_val(h, k).a);
+ free(kh_val(h, k).idx);
+ free((char*)kh_key(h, k));
+ }
+ }
+ kh_destroy(reg, h);
+}
diff --git a/tabix/bgzf.c b/tabix/bgzf.c
new file mode 100644
index 0000000..3bea718
--- /dev/null
+++ b/tabix/bgzf.c
@@ -0,0 +1,555 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+ 2011 Attractive Chaos <attractor at live.co.uk>
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <assert.h>
+#include <sys/types.h>
+#include "bgzf.h"
+
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+typedef knetFile *_bgzf_file_t;
+#define _bgzf_open(fn, mode) knet_open(fn, mode)
+#define _bgzf_dopen(fp, mode) knet_dopen(fp, mode)
+#define _bgzf_close(fp) knet_close(fp)
+#define _bgzf_fileno(fp) ((fp)->fd)
+#define _bgzf_tell(fp) knet_tell(fp)
+#define _bgzf_seek(fp, offset, whence) knet_seek(fp, offset, whence)
+#define _bgzf_read(fp, buf, len) knet_read(fp, buf, len)
+#define _bgzf_write(fp, buf, len) knet_write(fp, buf, len)
+#else // ~defined(_USE_KNETFILE)
+#if defined(_WIN32) || defined(_MSC_VER)
+#define ftello(fp) ftell(fp)
+#define fseeko(fp, offset, whence) fseek(fp, offset, whence)
+#else // ~defined(_WIN32)
+extern off_t ftello(FILE *stream);
+extern int fseeko(FILE *stream, off_t offset, int whence);
+#endif // ~defined(_WIN32)
+typedef FILE *_bgzf_file_t;
+#define _bgzf_open(fn, mode) fopen(fn, mode)
+#define _bgzf_dopen(fp, mode) fdopen(fp, mode)
+#define _bgzf_close(fp) fclose(fp)
+#define _bgzf_fileno(fp) fileno(fp)
+#define _bgzf_tell(fp) ftello(fp)
+#define _bgzf_seek(fp, offset, whence) fseeko(fp, offset, whence)
+#define _bgzf_read(fp, buf, len) fread(buf, 1, len, fp)
+#define _bgzf_write(fp, buf, len) fwrite(buf, 1, len, fp)
+#endif // ~define(_USE_KNETFILE)
+
+#define BLOCK_HEADER_LENGTH 18
+#define BLOCK_FOOTER_LENGTH 8
+
+/* BGZF/GZIP header (speciallized from RFC 1952; little endian):
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+ | 31|139| 8| 4| 0| 0|255| 6| 66| 67| 2|BLK_LEN|
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+*/
+static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0";
+
+#ifdef BGZF_CACHE
+typedef struct {
+ int size;
+ uint8_t *block;
+ int64_t end_offset;
+} cache_t;
+#include "khash.h"
+KHASH_MAP_INIT_INT64(cache, cache_t)
+#endif
+
+static inline void packInt16(uint8_t *buffer, uint16_t value)
+{
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+}
+
+static inline int unpackInt16(const uint8_t *buffer)
+{
+ return buffer[0] | buffer[1] << 8;
+}
+
+static inline void packInt32(uint8_t *buffer, uint32_t value)
+{
+ buffer[0] = value;
+ buffer[1] = value >> 8;
+ buffer[2] = value >> 16;
+ buffer[3] = value >> 24;
+}
+
+static BGZF *bgzf_read_init()
+{
+ BGZF *fp;
+ fp = calloc(1, sizeof(BGZF));
+ fp->open_mode = 'r';
+ fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE);
+ fp->compressed_block = malloc(BGZF_BLOCK_SIZE);
+#ifdef BGZF_CACHE
+ fp->cache = kh_init(cache);
+#endif
+ return fp;
+}
+
+static BGZF *bgzf_write_init(int compress_level) // compress_level==-1 for the default level
+{
+ BGZF *fp;
+ fp = calloc(1, sizeof(BGZF));
+ fp->open_mode = 'w';
+ fp->uncompressed_block = malloc(BGZF_BLOCK_SIZE);
+ fp->compressed_block = malloc(BGZF_BLOCK_SIZE);
+ fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
+ if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
+ return fp;
+}
+// get the compress level from the mode string
+static int mode2level(const char *__restrict mode)
+{
+ int i, compress_level = -1;
+ for (i = 0; mode[i]; ++i)
+ if (mode[i] >= '0' && mode[i] <= '9') break;
+ if (mode[i]) compress_level = (int)mode[i] - '0';
+ if (strchr(mode, 'u')) compress_level = 0;
+ return compress_level;
+}
+
+BGZF *bgzf_open(const char *path, const char *mode)
+{
+ BGZF *fp = 0;
+ if (strchr(mode, 'r') || strchr(mode, 'R')) {
+ _bgzf_file_t fpr;
+ if ((fpr = _bgzf_open(path, "r")) == 0) return 0;
+ fp = bgzf_read_init();
+ fp->fp = fpr;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ FILE *fpw;
+ if ((fpw = fopen(path, "w")) == 0) return 0;
+ fp = bgzf_write_init(mode2level(mode));
+ fp->fp = fpw;
+ }
+ return fp;
+}
+
+BGZF *bgzf_dopen(int fd, const char *mode)
+{
+ BGZF *fp = 0;
+ if (strchr(mode, 'r') || strchr(mode, 'R')) {
+ _bgzf_file_t fpr;
+ if ((fpr = _bgzf_dopen(fd, "r")) == 0) return 0;
+ fp = bgzf_read_init();
+ fp->fp = fpr;
+ } else if (strchr(mode, 'w') || strchr(mode, 'W')) {
+ FILE *fpw;
+ if ((fpw = fdopen(fd, "w")) == 0) return 0;
+ fp = bgzf_write_init(mode2level(mode));
+ fp->fp = fpw;
+ }
+ return fp;
+}
+
+// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.
+static int deflate_block(BGZF *fp, int block_length)
+{
+ uint8_t *buffer = fp->compressed_block;
+ int buffer_size = BGZF_BLOCK_SIZE;
+ int input_length = block_length;
+ int compressed_length = 0;
+ int remaining;
+ uint32_t crc;
+
+ assert(block_length <= BGZF_BLOCK_SIZE); // guaranteed by the caller
+ memcpy(buffer, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block
+ while (1) { // loop to retry for blocks that do not compress enough
+ int status;
+ z_stream zs;
+ zs.zalloc = NULL;
+ zs.zfree = NULL;
+ zs.next_in = fp->uncompressed_block;
+ zs.avail_in = input_length;
+ zs.next_out = (void*)&buffer[BLOCK_HEADER_LENGTH];
+ zs.avail_out = buffer_size - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+ status = deflateInit2(&zs, fp->compress_level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer
+ if (status != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ status = deflate(&zs, Z_FINISH);
+ if (status != Z_STREAM_END) { // not compressed enough
+ deflateEnd(&zs); // reset the stream
+ if (status == Z_OK) { // reduce the size and recompress
+ input_length -= 1024;
+ assert(input_length > 0); // logically, this should not happen
+ continue;
+ }
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (deflateEnd(&zs) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ compressed_length = zs.total_out;
+ compressed_length += BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
+ assert(compressed_length <= BGZF_BLOCK_SIZE);
+ break;
+ }
+
+ assert(compressed_length > 0);
+ packInt16((uint8_t*)&buffer[16], compressed_length - 1); // write the compressed_length; -1 to fit 2 bytes
+ crc = crc32(0L, NULL, 0L);
+ crc = crc32(crc, fp->uncompressed_block, input_length);
+ packInt32((uint8_t*)&buffer[compressed_length-8], crc);
+ packInt32((uint8_t*)&buffer[compressed_length-4], input_length);
+
+ remaining = block_length - input_length;
+ if (remaining > 0) {
+ assert(remaining <= input_length);
+ memcpy(fp->uncompressed_block, fp->uncompressed_block + input_length, remaining);
+ }
+ fp->block_offset = remaining;
+ return compressed_length;
+}
+
+// Inflate the block in fp->compressed_block into fp->uncompressed_block
+static int inflate_block(BGZF* fp, int block_length)
+{
+ z_stream zs;
+ zs.zalloc = NULL;
+ zs.zfree = NULL;
+ zs.next_in = fp->compressed_block + 18;
+ zs.avail_in = block_length - 16;
+ zs.next_out = fp->uncompressed_block;
+ zs.avail_out = BGZF_BLOCK_SIZE;
+
+ if (inflateInit2(&zs, -15) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (inflate(&zs, Z_FINISH) != Z_STREAM_END) {
+ inflateEnd(&zs);
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ if (inflateEnd(&zs) != Z_OK) {
+ fp->errcode |= BGZF_ERR_ZLIB;
+ return -1;
+ }
+ return zs.total_out;
+}
+
+static int check_header(const uint8_t *header)
+{
+ return (header[0] == 31 && header[1] == 139 && header[2] == 8 && (header[3] & 4) != 0
+ && unpackInt16((uint8_t*)&header[10]) == 6
+ && header[12] == 'B' && header[13] == 'C'
+ && unpackInt16((uint8_t*)&header[14]) == 2);
+}
+
+#ifdef BGZF_CACHE
+static void free_cache(BGZF *fp)
+{
+ khint_t k;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ if (fp->open_mode != 'r') return;
+ for (k = kh_begin(h); k < kh_end(h); ++k)
+ if (kh_exist(h, k)) free(kh_val(h, k).block);
+ kh_destroy(cache, h);
+}
+
+static int load_block_from_cache(BGZF *fp, int64_t block_address)
+{
+ khint_t k;
+ cache_t *p;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ k = kh_get(cache, h, block_address);
+ if (k == kh_end(h)) return 0;
+ p = &kh_val(h, k);
+ if (fp->block_length != 0) fp->block_offset = 0;
+ fp->block_address = block_address;
+ fp->block_length = p->size;
+ memcpy(fp->uncompressed_block, p->block, BGZF_BLOCK_SIZE);
+ _bgzf_seek((_bgzf_file_t)fp->fp, p->end_offset, SEEK_SET);
+ return p->size;
+}
+
+static void cache_block(BGZF *fp, int size)
+{
+ int ret;
+ khint_t k;
+ cache_t *p;
+ khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+ if (BGZF_BLOCK_SIZE >= fp->cache_size) return;
+ if ((kh_size(h) + 1) * BGZF_BLOCK_SIZE > fp->cache_size) {
+ /* A better way would be to remove the oldest block in the
+ * cache, but here we remove a random one for simplicity. This
+ * should not have a big impact on performance. */
+ for (k = kh_begin(h); k < kh_end(h); ++k)
+ if (kh_exist(h, k)) break;
+ if (k < kh_end(h)) {
+ free(kh_val(h, k).block);
+ kh_del(cache, h, k);
+ }
+ }
+ k = kh_put(cache, h, fp->block_address, &ret);
+ if (ret == 0) return; // if this happens, a bug!
+ p = &kh_val(h, k);
+ p->size = fp->block_length;
+ p->end_offset = fp->block_address + size;
+ p->block = malloc(BGZF_BLOCK_SIZE);
+ memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_BLOCK_SIZE);
+}
+#else
+static void free_cache(BGZF *fp) {}
+static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;}
+static void cache_block(BGZF *fp, int size) {}
+#endif
+
+int bgzf_read_block(BGZF *fp)
+{
+ uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
+ int count, size = 0, block_length, remaining;
+ int64_t block_address;
+ block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ if (load_block_from_cache(fp, block_address)) return 0;
+ count = _bgzf_read(fp->fp, header, sizeof(header));
+ if (count == 0) { // no data read
+ fp->block_length = 0;
+ return 0;
+ }
+ if (count != sizeof(header) || !check_header(header)) {
+ fp->errcode |= BGZF_ERR_HEADER;
+ return -1;
+ }
+ size = count;
+ block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
+ compressed_block = (uint8_t*)fp->compressed_block;
+ memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
+ remaining = block_length - BLOCK_HEADER_LENGTH;
+ count = _bgzf_read(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
+ if (count != remaining) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+ size += count;
+ if ((count = inflate_block(fp, block_length)) < 0) return -1;
+ if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek.
+ fp->block_address = block_address;
+ fp->block_length = count;
+ cache_block(fp, size);
+ return 0;
+}
+
+ssize_t bgzf_read(BGZF *fp, void *data, ssize_t length)
+{
+ ssize_t bytes_read = 0;
+ uint8_t *output = data;
+ if (length <= 0) return 0;
+ assert(fp->open_mode == 'r');
+ while (bytes_read < length) {
+ int copy_length, available = fp->block_length - fp->block_offset;
+ uint8_t *buffer;
+ if (available <= 0) {
+ if (bgzf_read_block(fp) != 0) return -1;
+ available = fp->block_length - fp->block_offset;
+ if (available <= 0) break;
+ }
+ copy_length = length - bytes_read < available? length - bytes_read : available;
+ buffer = fp->uncompressed_block;
+ memcpy(output, buffer + fp->block_offset, copy_length);
+ fp->block_offset += copy_length;
+ output += copy_length;
+ bytes_read += copy_length;
+ }
+ if (fp->block_offset == fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = fp->block_length = 0;
+ }
+ return bytes_read;
+}
+
+int bgzf_flush(BGZF *fp)
+{
+ assert(fp->open_mode == 'w');
+ while (fp->block_offset > 0) {
+ int block_length;
+ block_length = deflate_block(fp, fp->block_offset);
+ if (block_length < 0) return -1;
+ if (fwrite(fp->compressed_block, 1, block_length, fp->fp) != block_length) {
+ fp->errcode |= BGZF_ERR_IO; // possibly truncated file
+ return -1;
+ }
+ fp->block_address += block_length;
+ }
+ return 0;
+}
+
+int bgzf_flush_try(BGZF *fp, ssize_t size)
+{
+ if (fp->block_offset + size > BGZF_BLOCK_SIZE)
+ return bgzf_flush(fp);
+ return -1;
+}
+
+ssize_t bgzf_write(BGZF *fp, const void *data, ssize_t length)
+{
+ const uint8_t *input = data;
+ int block_length = BGZF_BLOCK_SIZE, bytes_written;
+ assert(fp->open_mode == 'w');
+ input = data;
+ bytes_written = 0;
+ while (bytes_written < length) {
+ uint8_t* buffer = fp->uncompressed_block;
+ int copy_length = block_length - fp->block_offset < length - bytes_written? block_length - fp->block_offset : length - bytes_written;
+ memcpy(buffer + fp->block_offset, input, copy_length);
+ fp->block_offset += copy_length;
+ input += copy_length;
+ bytes_written += copy_length;
+ if (fp->block_offset == block_length && bgzf_flush(fp)) break;
+ }
+ return bytes_written;
+}
+
+int bgzf_close(BGZF* fp)
+{
+ int ret, count, block_length;
+ if (fp == 0) return -1;
+ if (fp->open_mode == 'w') {
+ if (bgzf_flush(fp) != 0) return -1;
+ block_length = deflate_block(fp, 0); // write an empty block
+ count = fwrite(fp->compressed_block, 1, block_length, fp->fp);
+ if (fflush(fp->fp) != 0) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+ }
+ ret = fp->open_mode == 'w'? fclose(fp->fp) : _bgzf_close(fp->fp);
+ if (ret != 0) return -1;
+ free(fp->uncompressed_block);
+ free(fp->compressed_block);
+ free_cache(fp);
+ free(fp);
+ return 0;
+}
+
+void bgzf_set_cache_size(BGZF *fp, int cache_size)
+{
+ if (fp) fp->cache_size = cache_size;
+}
+
+int bgzf_check_EOF(BGZF *fp)
+{
+ static uint8_t magic[28] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0";
+ uint8_t buf[28];
+ off_t offset;
+ offset = _bgzf_tell((_bgzf_file_t)fp->fp);
+ if (_bgzf_seek(fp->fp, -28, SEEK_END) < 0) return 0;
+ _bgzf_read(fp->fp, buf, 28);
+ _bgzf_seek(fp->fp, offset, SEEK_SET);
+ return (memcmp(magic, buf, 28) == 0)? 1 : 0;
+}
+
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
+{
+ int block_offset;
+ int64_t block_address;
+
+ if (fp->open_mode != 'r' || where != SEEK_SET) {
+ fp->errcode |= BGZF_ERR_MISUSE;
+ return -1;
+ }
+ block_offset = pos & 0xFFFF;
+ block_address = pos >> 16;
+ if (_bgzf_seek(fp->fp, block_address, SEEK_SET) < 0) {
+ fp->errcode |= BGZF_ERR_IO;
+ return -1;
+ }
+ fp->block_length = 0; // indicates current block has not been loaded
+ fp->block_address = block_address;
+ fp->block_offset = block_offset;
+ return 0;
+}
+
+int bgzf_is_bgzf(const char *fn)
+{
+ uint8_t buf[16];
+ int n;
+ _bgzf_file_t fp;
+ if ((fp = _bgzf_open(fn, "r")) == 0) return 0;
+ n = _bgzf_read(fp, buf, 16);
+ _bgzf_close(fp);
+ if (n != 16) return 0;
+ return memcmp(g_magic, buf, 16) == 0? 1 : 0;
+}
+
+int bgzf_getc(BGZF *fp)
+{
+ int c;
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) return -2; /* error */
+ if (fp->block_length == 0) return -1; /* end-of-file */
+ }
+ c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+ if (fp->block_offset == fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ return c;
+}
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
+{
+ int l, state = 0;
+ unsigned char *buf = (unsigned char*)fp->uncompressed_block;
+ str->l = 0;
+ do {
+ if (fp->block_offset >= fp->block_length) {
+ if (bgzf_read_block(fp) != 0) { state = -2; break; }
+ if (fp->block_length == 0) { state = -1; break; }
+ }
+ for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l);
+ if (l < fp->block_length) state = 1;
+ l -= fp->block_offset;
+ if (str->l + l + 1 >= str->m) {
+ str->m = str->l + l + 2;
+ kroundup32(str->m);
+ str->s = (char*)realloc(str->s, str->m);
+ }
+ memcpy(str->s + str->l, buf + fp->block_offset, l);
+ str->l += l;
+ fp->block_offset += l + 1;
+ if (fp->block_offset >= fp->block_length) {
+ fp->block_address = _bgzf_tell((_bgzf_file_t)fp->fp);
+ fp->block_offset = 0;
+ fp->block_length = 0;
+ }
+ } while (state == 0);
+ if (str->l == 0 && state < 0) return state;
+ str->s[str->l] = 0;
+ return str->l;
+}
diff --git a/tabix/bgzip.c b/tabix/bgzip.c
new file mode 100644
index 0000000..5429a22
--- /dev/null
+++ b/tabix/bgzip.c
@@ -0,0 +1,206 @@
+/* The MIT License
+
+ Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+*/
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include <sys/select.h>
+#include <sys/stat.h>
+#include "bgzf.h"
+
+static const int WINDOW_SIZE = 64 * 1024;
+
+static int bgzip_main_usage()
+{
+ fprintf(stderr, "\n");
+ fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n");
+ fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n");
+ fprintf(stderr, " -d decompress\n");
+ fprintf(stderr, " -f overwrite files without asking\n");
+ fprintf(stderr, " -b INT decompress at virtual file pointer INT\n");
+ fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n");
+ fprintf(stderr, " -h give this help\n");
+ fprintf(stderr, "\n");
+ return 1;
+}
+
+static int write_open(const char *fn, int is_forced)
+{
+ int fd = -1;
+ char c;
+ if (!is_forced) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
+ fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
+ scanf("%c", &c);
+ if (c != 'Y' && c != 'y') {
+ fprintf(stderr, "[bgzip] not overwritten\n");
+ exit(1);
+ }
+ }
+ }
+ if (fd < 0) {
+ if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
+ fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
+ exit(1);
+ }
+ }
+ return fd;
+}
+
+static void fail(BGZF* fp)
+{
+ fprintf(stderr, "Error: %d\n", fp->errcode);
+ exit(1);
+}
+
+int main(int argc, char **argv)
+{
+ int c, compress, pstdout, is_forced;
+ BGZF *fp;
+ void *buffer;
+ long start, end, size;
+
+ compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
+ while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){
+ switch(c){
+ case 'h': return bgzip_main_usage();
+ case 'd': compress = 0; break;
+ case 'c': pstdout = 1; break;
+ case 'b': start = atol(optarg); break;
+ case 's': size = atol(optarg); break;
+ case 'f': is_forced = 1; break;
+ }
+ }
+ if (size >= 0) end = start + size;
+ if (end >= 0 && end < start) {
+ fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
+ return 1;
+ }
+ if (compress == 1) {
+ struct stat sbuf;
+ int f_src = fileno(stdin);
+ int f_dst = fileno(stdout);
+
+ if ( argc>optind )
+ {
+ if ( stat(argv[optind],&sbuf)<0 )
+ {
+ fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+ return 1;
+ }
+
+ if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
+ fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+ return 1;
+ }
+
+ if (pstdout)
+ f_dst = fileno(stdout);
+ else
+ {
+ char *name = malloc(strlen(argv[optind]) + 5);
+ strcpy(name, argv[optind]);
+ strcat(name, ".gz");
+ f_dst = write_open(name, is_forced);
+ if (f_dst < 0) return 1;
+ free(name);
+ }
+ }
+ else if (!pstdout && isatty(fileno((FILE *)stdout)) )
+ return bgzip_main_usage();
+
+ fp = bgzf_dopen(f_dst, "w");
+ buffer = malloc(WINDOW_SIZE);
+ while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
+ if (bgzf_write(fp, buffer, c) < 0) fail(fp);
+ // f_dst will be closed here
+ if (bgzf_close(fp) < 0) fail(fp);
+ if (argc > optind && !pstdout) unlink(argv[optind]);
+ free(buffer);
+ close(f_src);
+ return 0;
+ } else {
+ struct stat sbuf;
+ int f_dst;
+
+ if ( argc>optind )
+ {
+ if ( stat(argv[optind],&sbuf)<0 )
+ {
+ fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+ return 1;
+ }
+ char *name;
+ int len = strlen(argv[optind]);
+ if ( strcmp(argv[optind]+len-3,".gz") )
+ {
+ fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
+ return 1;
+ }
+ fp = bgzf_open(argv[optind], "r");
+ if (fp == NULL) {
+ fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
+ return 1;
+ }
+
+ if (pstdout) {
+ f_dst = fileno(stdout);
+ }
+ else {
+ name = strdup(argv[optind]);
+ name[strlen(name) - 3] = '\0';
+ f_dst = write_open(name, is_forced);
+ free(name);
+ }
+ }
+ else if (!pstdout && isatty(fileno((FILE *)stdin)) )
+ return bgzip_main_usage();
+ else
+ {
+ f_dst = fileno(stdout);
+ fp = bgzf_dopen(fileno(stdin), "r");
+ if (fp == NULL) {
+ fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
+ return 1;
+ }
+ }
+ buffer = malloc(WINDOW_SIZE);
+ if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
+ while (1) {
+ if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
+ else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+ if (c == 0) break;
+ if (c < 0) fail(fp);
+ start += c;
+ write(f_dst, buffer, c);
+ if (end >= 0 && start >= end) break;
+ }
+ free(buffer);
+ if (bgzf_close(fp) < 0) fail(fp);
+ if (!pstdout) unlink(argv[optind]);
+ return 0;
+ }
+}
diff --git a/tabix/index.c b/tabix/index.c
new file mode 100644
index 0000000..15cd65e
--- /dev/null
+++ b/tabix/index.c
@@ -0,0 +1,967 @@
+#include <ctype.h>
+#include <assert.h>
+#include <sys/stat.h>
+#include "khash.h"
+#include "ksort.h"
+#include "kstring.h"
+#include "bam_endian.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
+#include "tabix.h"
+
+#define TAD_MIN_CHUNK_GAP 32768
+// 1<<14 is the size of minimum bin.
+#define TAD_LIDX_SHIFT 14
+
+typedef struct {
+ uint64_t u, v;
+} pair64_t;
+
+#define pair64_lt(a,b) ((a).u < (b).u)
+KSORT_INIT(offt, pair64_t, pair64_lt)
+
+typedef struct {
+ uint32_t m, n;
+ pair64_t *list;
+} ti_binlist_t;
+
+typedef struct {
+ int32_t n, m;
+ uint64_t *offset;
+} ti_lidx_t;
+
+KHASH_MAP_INIT_INT(i, ti_binlist_t)
+KHASH_MAP_INIT_STR(s, int)
+
+struct __ti_index_t {
+ ti_conf_t conf;
+ int32_t n, max;
+ khash_t(s) *tname;
+ khash_t(i) **index;
+ ti_lidx_t *index2;
+};
+
+struct __ti_iter_t {
+ int from_first; // read from the first record; no random access
+ int tid, beg, end, n_off, i, finished;
+ uint64_t curr_off;
+ kstring_t str;
+ const ti_index_t *idx;
+ pair64_t *off;
+};
+
+typedef struct {
+ int tid, beg, end, bin;
+} ti_intv_t;
+
+ti_conf_t ti_conf_gff = { 0, 1, 4, 5, '#', 0 };
+ti_conf_t ti_conf_bed = { TI_FLAG_UCSC, 1, 2, 3, '#', 0 };
+ti_conf_t ti_conf_psltbl = { TI_FLAG_UCSC, 15, 17, 18, '#', 0 };
+ti_conf_t ti_conf_sam = { TI_PRESET_SAM, 3, 4, 0, '@', 0 };
+ti_conf_t ti_conf_vcf = { TI_PRESET_VCF, 1, 2, 0, '#', 0 };
+
+/***************
+ * read a line *
+ ***************/
+
+/*
+int ti_readline(BGZF *fp, kstring_t *str)
+{
+ int c, l = 0;
+ str->l = 0;
+ while ((c = bgzf_getc(fp)) >= 0 && c != '\n') {
+ ++l;
+ if (c != '\r') kputc(c, str);
+ }
+ if (c < 0 && l == 0) return -1; // end of file
+ return str->l;
+}
+*/
+
+/* Below is a faster implementation largely equivalent to the one
+ * commented out above. */
+int ti_readline(BGZF *fp, kstring_t *str)
+{
+ return bgzf_getline(fp, '\n', str);
+}
+
+/*************************************
+ * get the interval from a data line *
+ *************************************/
+
+static inline int ti_reg2bin(uint32_t beg, uint32_t end)
+{
+ --end;
+ if (beg>>14 == end>>14) return 4681 + (beg>>14);
+ if (beg>>17 == end>>17) return 585 + (beg>>17);
+ if (beg>>20 == end>>20) return 73 + (beg>>20);
+ if (beg>>23 == end>>23) return 9 + (beg>>23);
+ if (beg>>26 == end>>26) return 1 + (beg>>26);
+ return 0;
+}
+
+static int get_tid(ti_index_t *idx, const char *ss)
+{
+ khint_t k;
+ int tid;
+ k = kh_get(s, idx->tname, ss);
+ if (k == kh_end(idx->tname)) { // a new target sequence
+ int ret, size;
+ // update idx->n, ->max, ->index and ->index2
+ if (idx->n == idx->max) {
+ idx->max = idx->max? idx->max<<1 : 8;
+ idx->index = realloc(idx->index, idx->max * sizeof(void*));
+ idx->index2 = realloc(idx->index2, idx->max * sizeof(ti_lidx_t));
+ }
+ memset(&idx->index2[idx->n], 0, sizeof(ti_lidx_t));
+ idx->index[idx->n++] = kh_init(i);
+ // update ->tname
+ tid = size = kh_size(idx->tname);
+ k = kh_put(s, idx->tname, strdup(ss), &ret);
+ kh_value(idx->tname, k) = size;
+ assert(idx->n == kh_size(idx->tname));
+ } else tid = kh_value(idx->tname, k);
+ return tid;
+}
+
+int ti_get_intv(const ti_conf_t *conf, int len, char *line, ti_interval_t *intv)
+{
+ int i, b = 0, id = 1, ncols = 0;
+ char *s;
+ intv->ss = intv->se = 0; intv->beg = intv->end = -1;
+ for (i = 0; i <= len; ++i) {
+ if (line[i] == '\t' || line[i] == 0) {
+ ++ncols;
+ if (id == conf->sc) {
+ intv->ss = line + b; intv->se = line + i;
+ } else if (id == conf->bc) {
+ // here ->beg is 0-based.
+ intv->beg = intv->end = strtol(line + b, &s, 0);
+ if (!(conf->preset&TI_FLAG_UCSC)) --intv->beg;
+ else ++intv->end;
+ if (intv->beg < 0) intv->beg = 0;
+ if (intv->end < 1) intv->end = 1;
+ } else {
+ if ((conf->preset&0xffff) == TI_PRESET_GENERIC) {
+ if (id == conf->ec) intv->end = strtol(line + b, &s, 0);
+ } else if ((conf->preset&0xffff) == TI_PRESET_SAM) {
+ if (id == 6) { // CIGAR
+ int l = 0, op;
+ char *t;
+ for (s = line + b; s < line + i;) {
+ long x = strtol(s, &t, 10);
+ op = toupper(*t);
+ if (op == 'M' || op == 'D' || op == 'N') l += x;
+ s = t + 1;
+ }
+ if (l == 0) l = 1;
+ intv->end = intv->beg + l;
+ }
+ } else if ((conf->preset&0xffff) == TI_PRESET_VCF) {
+ // FIXME: the following is NOT tested and is likely to be buggy
+ if (id == 4) {
+ if (b < i) intv->end = intv->beg + (i - b);
+ } else if (id == 8) { // look for "END="
+ int c = line[i];
+ line[i] = 0;
+ s = strstr(line + b, "END=");
+ if (s == line + b) s += 4;
+ else if (s) {
+ s = strstr(line + b, ";END=");
+ if (s) s += 5;
+ }
+ if (s) intv->end = strtol(s, &s, 0);
+ line[i] = c;
+ }
+ }
+ }
+ b = i + 1;
+ ++id;
+ }
+ }
+/*
+ if (ncols < conf->sc || ncols < conf->bc || ncols < conf->ec) {
+ if (ncols == 1) fprintf(stderr,"[get_intv] Is the file tab-delimited? The line has %d field only: %s\n", ncols, line);
+ else fprintf(stderr,"[get_intv] The line has %d field(s) only: %s\n", ncols, line);
+ exit(1);
+ }
+*/
+ if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
+ return 0;
+}
+
+static int get_intv(ti_index_t *idx, kstring_t *str, ti_intv_t *intv)
+{
+ ti_interval_t x;
+ intv->tid = intv->beg = intv->end = intv->bin = -1;
+ if (ti_get_intv(&idx->conf, str->l, str->s, &x) == 0) {
+ int c = *x.se;
+ *x.se = '\0'; intv->tid = get_tid(idx, x.ss); *x.se = c;
+ intv->beg = x.beg; intv->end = x.end;
+ intv->bin = ti_reg2bin(intv->beg, intv->end);
+ return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
+ } else {
+ fprintf(stderr, "[%s] the following line cannot be parsed and skipped: %s\n", __func__, str->s);
+ return -1;
+ }
+}
+
+/************
+ * indexing *
+ ************/
+
+// requirement: len <= LEN_MASK
+static inline void insert_offset(khash_t(i) *h, int bin, uint64_t beg, uint64_t end)
+{
+ khint_t k;
+ ti_binlist_t *l;
+ int ret;
+ k = kh_put(i, h, bin, &ret);
+ l = &kh_value(h, k);
+ if (ret) { // not present
+ l->m = 1; l->n = 0;
+ l->list = (pair64_t*)calloc(l->m, 16);
+ }
+ if (l->n == l->m) {
+ l->m <<= 1;
+ l->list = (pair64_t*)realloc(l->list, l->m * 16);
+ }
+ l->list[l->n].u = beg; l->list[l->n++].v = end;
+}
+
+static inline uint64_t insert_offset2(ti_lidx_t *index2, int _beg, int _end, uint64_t offset)
+{
+ int i, beg, end;
+ beg = _beg >> TAD_LIDX_SHIFT;
+ end = (_end - 1) >> TAD_LIDX_SHIFT;
+ if (index2->m < end + 1) {
+ int old_m = index2->m;
+ index2->m = end + 1;
+ kroundup32(index2->m);
+ index2->offset = (uint64_t*)realloc(index2->offset, index2->m * 8);
+ memset(index2->offset + old_m, 0, 8 * (index2->m - old_m));
+ }
+ if (beg == end) {
+ if (index2->offset[beg] == 0) index2->offset[beg] = offset;
+ } else {
+ for (i = beg; i <= end; ++i)
+ if (index2->offset[i] == 0) index2->offset[i] = offset;
+ }
+ if (index2->n < end + 1) index2->n = end + 1;
+ return (uint64_t)beg<<32 | end;
+}
+
+static void merge_chunks(ti_index_t *idx)
+{
+ khash_t(i) *index;
+ int i, l, m;
+ khint_t k;
+ for (i = 0; i < idx->n; ++i) {
+ index = idx->index[i];
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ ti_binlist_t *p;
+ if (!kh_exist(index, k)) continue;
+ p = &kh_value(index, k);
+ m = 0;
+ for (l = 1; l < p->n; ++l) {
+ if (p->list[m].v>>16 == p->list[l].u>>16) p->list[m].v = p->list[l].v;
+ else p->list[++m] = p->list[l];
+ } // ~for(l)
+ p->n = m + 1;
+ } // ~for(k)
+ } // ~for(i)
+}
+
+static void fill_missing(ti_index_t *idx)
+{
+ int i, j;
+ for (i = 0; i < idx->n; ++i) {
+ ti_lidx_t *idx2 = &idx->index2[i];
+ for (j = 1; j < idx2->n; ++j)
+ if (idx2->offset[j] == 0)
+ idx2->offset[j] = idx2->offset[j-1];
+ }
+}
+
+ti_index_t *ti_index_core(BGZF *fp, const ti_conf_t *conf)
+{
+ int ret;
+ ti_index_t *idx;
+ uint32_t last_bin, save_bin;
+ int32_t last_coor, last_tid, save_tid;
+ uint64_t save_off, last_off, lineno = 0, offset0 = (uint64_t)-1, tmp;
+ kstring_t *str;
+
+ str = calloc(1, sizeof(kstring_t));
+
+ idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
+ idx->conf = *conf;
+ idx->n = idx->max = 0;
+ idx->tname = kh_init(s);
+ idx->index = 0;
+ idx->index2 = 0;
+
+ save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
+ save_off = last_off = bgzf_tell(fp); last_coor = 0xffffffffu;
+ while ((ret = ti_readline(fp, str)) >= 0) {
+ ti_intv_t intv;
+ ++lineno;
+ if (lineno <= idx->conf.line_skip || str->s[0] == idx->conf.meta_char) {
+ last_off = bgzf_tell(fp);
+ continue;
+ }
+ get_intv(idx, str, &intv);
+ if ( intv.beg<0 || intv.end<0 )
+ {
+ fprintf(stderr,"[ti_index_core] the indexes overlap or are out of bounds\n");
+ exit(1);
+ }
+ if (last_tid != intv.tid) { // change of chromosomes
+ if (last_tid>intv.tid )
+ {
+ fprintf(stderr,"[ti_index_core] the chromosome blocks not continuous at line %llu, is the file sorted? [pos %d]\n",(unsigned long long)lineno,intv.beg+1);
+ exit(1);
+ }
+ last_tid = intv.tid;
+ last_bin = 0xffffffffu;
+ } else if (last_coor > intv.beg) {
+ fprintf(stderr, "[ti_index_core] the file out of order at line %llu\n", (unsigned long long)lineno);
+ exit(1);
+ }
+ tmp = insert_offset2(&idx->index2[intv.tid], intv.beg, intv.end, last_off);
+ if (last_off == 0) offset0 = tmp;
+ if (intv.bin != last_bin) { // then possibly write the binning index
+ if (save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
+ insert_offset(idx->index[save_tid], save_bin, save_off, last_off);
+ save_off = last_off;
+ save_bin = last_bin = intv.bin;
+ save_tid = intv.tid;
+ if (save_tid < 0) break;
+ }
+ if (bgzf_tell(fp) <= last_off) {
+ fprintf(stderr, "[ti_index_core] bug in BGZF: %llx < %llx\n",
+ (unsigned long long)bgzf_tell(fp), (unsigned long long)last_off);
+ exit(1);
+ }
+ last_off = bgzf_tell(fp);
+ last_coor = intv.beg;
+ }
+ if (save_tid >= 0) insert_offset(idx->index[save_tid], save_bin, save_off, bgzf_tell(fp));
+ merge_chunks(idx);
+ fill_missing(idx);
+ if (offset0 != (uint64_t)-1 && idx->n && idx->index2[0].offset) {
+ int i, beg = offset0>>32, end = offset0&0xffffffffu;
+ for (i = beg; i <= end; ++i) idx->index2[0].offset[i] = 0;
+ }
+
+ free(str->s); free(str);
+ return idx;
+}
+
+void ti_index_destroy(ti_index_t *idx)
+{
+ khint_t k;
+ int i;
+ if (idx == 0) return;
+ // destroy the name hash table
+ for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k) {
+ if (kh_exist(idx->tname, k))
+ free((char*)kh_key(idx->tname, k));
+ }
+ kh_destroy(s, idx->tname);
+ // destroy the binning index
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ ti_lidx_t *index2 = idx->index2 + i;
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k))
+ free(kh_value(index, k).list);
+ }
+ kh_destroy(i, index);
+ free(index2->offset);
+ }
+ free(idx->index);
+ // destroy the linear index
+ free(idx->index2);
+ free(idx);
+}
+
+/******************
+ * index file I/O *
+ ******************/
+
+void ti_index_save(const ti_index_t *idx, BGZF *fp)
+{
+ int32_t i, size, ti_is_be;
+ khint_t k;
+ ti_is_be = bam_is_big_endian();
+ bgzf_write(fp, "TBI\1", 4);
+ if (ti_is_be) {
+ uint32_t x = idx->n;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &idx->n, 4);
+ assert(sizeof(ti_conf_t) == 24);
+ if (ti_is_be) { // write ti_conf_t;
+ uint32_t x[6];
+ memcpy(x, &idx->conf, 24);
+ for (i = 0; i < 6; ++i) bgzf_write(fp, bam_swap_endian_4p(&x[i]), 4);
+ } else bgzf_write(fp, &idx->conf, sizeof(ti_conf_t));
+ { // write target names
+ char **name;
+ int32_t l = 0;
+ name = calloc(kh_size(idx->tname), sizeof(void*));
+ for (k = kh_begin(idx->tname); k != kh_end(idx->tname); ++k)
+ if (kh_exist(idx->tname, k))
+ name[kh_value(idx->tname, k)] = (char*)kh_key(idx->tname, k);
+ for (i = 0; i < kh_size(idx->tname); ++i)
+ l += strlen(name[i]) + 1;
+ if (ti_is_be) bgzf_write(fp, bam_swap_endian_4p(&l), 4);
+ else bgzf_write(fp, &l, 4);
+ for (i = 0; i < kh_size(idx->tname); ++i)
+ bgzf_write(fp, name[i], strlen(name[i]) + 1);
+ free(name);
+ }
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index = idx->index[i];
+ ti_lidx_t *index2 = idx->index2 + i;
+ // write binning index
+ size = kh_size(index);
+ if (ti_is_be) { // big endian
+ uint32_t x = size;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &size, 4);
+ for (k = kh_begin(index); k != kh_end(index); ++k) {
+ if (kh_exist(index, k)) {
+ ti_binlist_t *p = &kh_value(index, k);
+ if (ti_is_be) { // big endian
+ uint32_t x;
+ x = kh_key(index, k); bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ x = p->n; bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ bgzf_write(fp, p->list, 16 * p->n);
+ for (x = 0; (int)x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ } else {
+ bgzf_write(fp, &kh_key(index, k), 4);
+ bgzf_write(fp, &p->n, 4);
+ bgzf_write(fp, p->list, 16 * p->n);
+ }
+ }
+ }
+ // write linear index (index2)
+ if (ti_is_be) {
+ int x = index2->n;
+ bgzf_write(fp, bam_swap_endian_4p(&x), 4);
+ } else bgzf_write(fp, &index2->n, 4);
+ if (ti_is_be) { // big endian
+ int x;
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ bgzf_write(fp, index2->offset, 8 * index2->n);
+ for (x = 0; (int)x < index2->n; ++x)
+ bam_swap_endian_8p(&index2->offset[x]);
+ } else bgzf_write(fp, index2->offset, 8 * index2->n);
+ }
+}
+
+static ti_index_t *ti_index_load_core(BGZF *fp)
+{
+ int i, ti_is_be;
+ char magic[4];
+ ti_index_t *idx;
+ ti_is_be = bam_is_big_endian();
+ if (fp == 0) {
+ fprintf(stderr, "[ti_index_load_core] fail to load index.\n");
+ return 0;
+ }
+ bgzf_read(fp, magic, 4);
+ if (strncmp(magic, "TBI\1", 4)) {
+ fprintf(stderr, "[ti_index_load] wrong magic number.\n");
+ return 0;
+ }
+ idx = (ti_index_t*)calloc(1, sizeof(ti_index_t));
+ bgzf_read(fp, &idx->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&idx->n);
+ idx->tname = kh_init(s);
+ idx->index = (khash_t(i)**)calloc(idx->n, sizeof(void*));
+ idx->index2 = (ti_lidx_t*)calloc(idx->n, sizeof(ti_lidx_t));
+ // read idx->conf
+ bgzf_read(fp, &idx->conf, sizeof(ti_conf_t));
+ if (ti_is_be) {
+ bam_swap_endian_4p(&idx->conf.preset);
+ bam_swap_endian_4p(&idx->conf.sc);
+ bam_swap_endian_4p(&idx->conf.bc);
+ bam_swap_endian_4p(&idx->conf.ec);
+ bam_swap_endian_4p(&idx->conf.meta_char);
+ bam_swap_endian_4p(&idx->conf.line_skip);
+ }
+ { // read target names
+ int j, ret;
+ kstring_t *str;
+ int32_t l;
+ uint8_t *buf;
+ bgzf_read(fp, &l, 4);
+ if (ti_is_be) bam_swap_endian_4p(&l);
+ buf = calloc(l, 1);
+ bgzf_read(fp, buf, l);
+ str = calloc(1, sizeof(kstring_t));
+ for (i = j = 0; i < l; ++i) {
+ if (buf[i] == 0) {
+ khint_t k = kh_put(s, idx->tname, strdup(str->s), &ret);
+ kh_value(idx->tname, k) = j++;
+ str->l = 0;
+ } else kputc(buf[i], str);
+ }
+ free(str->s); free(str); free(buf);
+ }
+ for (i = 0; i < idx->n; ++i) {
+ khash_t(i) *index;
+ ti_lidx_t *index2 = idx->index2 + i;
+ uint32_t key, size;
+ khint_t k;
+ int j, ret;
+ ti_binlist_t *p;
+ index = idx->index[i] = kh_init(i);
+ // load binning index
+ bgzf_read(fp, &size, 4);
+ if (ti_is_be) bam_swap_endian_4p(&size);
+ for (j = 0; j < (int)size; ++j) {
+ bgzf_read(fp, &key, 4);
+ if (ti_is_be) bam_swap_endian_4p(&key);
+ k = kh_put(i, index, key, &ret);
+ p = &kh_value(index, k);
+ bgzf_read(fp, &p->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&p->n);
+ p->m = p->n;
+ p->list = (pair64_t*)malloc(p->m * 16);
+ bgzf_read(fp, p->list, 16 * p->n);
+ if (ti_is_be) {
+ int x;
+ for (x = 0; x < p->n; ++x) {
+ bam_swap_endian_8p(&p->list[x].u);
+ bam_swap_endian_8p(&p->list[x].v);
+ }
+ }
+ }
+ // load linear index
+ bgzf_read(fp, &index2->n, 4);
+ if (ti_is_be) bam_swap_endian_4p(&index2->n);
+ index2->m = index2->n;
+ index2->offset = (uint64_t*)calloc(index2->m, 8);
+ bgzf_read(fp, index2->offset, index2->n * 8);
+ if (ti_is_be)
+ for (j = 0; j < index2->n; ++j) bam_swap_endian_8p(&index2->offset[j]);
+ }
+ return idx;
+}
+
+ti_index_t *ti_index_load_local(const char *fnidx)
+{
+ BGZF *fp;
+ fp = bgzf_open(fnidx, "r");
+ if (fp) {
+ ti_index_t *idx = ti_index_load_core(fp);
+ bgzf_close(fp);
+ return idx;
+ } else return 0;
+}
+
+#ifdef _USE_KNETFILE
+static void download_from_remote(const char *url)
+{
+ const int buf_size = 1 * 1024 * 1024;
+ char *fn;
+ FILE *fp;
+ uint8_t *buf;
+ knetFile *fp_remote;
+ int l;
+ if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
+ l = strlen(url);
+ for (fn = (char*)url + l - 1; fn >= url; --fn)
+ if (*fn == '/') break;
+ ++fn; // fn now points to the file name
+ fp_remote = knet_open(url, "r");
+ if (fp_remote == 0) {
+ fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
+ return;
+ }
+ if ((fp = fopen(fn, "w")) == 0) {
+ fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
+ knet_close(fp_remote);
+ return;
+ }
+ buf = (uint8_t*)calloc(buf_size, 1);
+ while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+ fwrite(buf, 1, l, fp);
+ free(buf);
+ fclose(fp);
+ knet_close(fp_remote);
+}
+#else
+static void download_from_remote(const char *url)
+{
+ return;
+}
+#endif
+
+static char *get_local_version(const char *fn)
+{
+ struct stat sbuf;
+ char *fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcat(strcpy(fnidx, fn), ".tbi");
+ if ((strstr(fnidx, "ftp://") == fnidx || strstr(fnidx, "http://") == fnidx)) {
+ char *p, *url;
+ int l = strlen(fnidx);
+ for (p = fnidx + l - 1; p >= fnidx; --p)
+ if (*p == '/') break;
+ url = fnidx; fnidx = strdup(p + 1);
+ if (stat(fnidx, &sbuf) == 0) {
+ free(url);
+ return fnidx;
+ }
+ fprintf(stderr, "[%s] downloading the index file...\n", __func__);
+ download_from_remote(url);
+ free(url);
+ }
+ if (stat(fnidx, &sbuf) == 0) return fnidx;
+ free(fnidx); return 0;
+}
+
+const char **ti_seqname(const ti_index_t *idx, int *n)
+{
+ const char **names;
+ khint_t k;
+ *n = idx->n;
+ names = calloc(idx->n, sizeof(void*));
+ for (k = kh_begin(idx->tname); k < kh_end(idx->tname); ++k)
+ if (kh_exist(idx->tname, k))
+ names[kh_val(idx->tname, k)] = kh_key(idx->tname, k);
+ return names;
+}
+
+ti_index_t *ti_index_load(const char *fn)
+{
+ ti_index_t *idx;
+ char *fname = get_local_version(fn);
+ if (fname == 0) return 0;
+ idx = ti_index_load_local(fname);
+ if (idx == 0) fprintf(stderr, "[ti_index_load] fail to load the index: %s\n", fname);
+ free(fname);
+ return idx;
+}
+
+int ti_index_build2(const char *fn, const ti_conf_t *conf, const char *_fnidx)
+{
+ char *fnidx;
+ BGZF *fp, *fpidx;
+ ti_index_t *idx;
+ if ((fp = bgzf_open(fn, "r")) == 0) {
+ fprintf(stderr, "[ti_index_build2] fail to open the file: %s\n", fn);
+ return -1;
+ }
+ idx = ti_index_core(fp, conf);
+ bgzf_close(fp);
+ if (_fnidx == 0) {
+ fnidx = (char*)calloc(strlen(fn) + 5, 1);
+ strcpy(fnidx, fn); strcat(fnidx, ".tbi");
+ } else fnidx = strdup(_fnidx);
+ fpidx = bgzf_open(fnidx, "w");
+ if (fpidx == 0) {
+ fprintf(stderr, "[ti_index_build2] fail to create the index file.\n");
+ free(fnidx);
+ return -1;
+ }
+ ti_index_save(idx, fpidx);
+ ti_index_destroy(idx);
+ bgzf_close(fpidx);
+ free(fnidx);
+ return 0;
+}
+
+int ti_index_build(const char *fn, const ti_conf_t *conf)
+{
+ return ti_index_build2(fn, conf, 0);
+}
+
+/********************************************
+ * parse a region in the format chr:beg-end *
+ ********************************************/
+
+int ti_get_tid(const ti_index_t *idx, const char *name)
+{
+ khiter_t iter;
+ const khash_t(s) *h = idx->tname;
+ iter = kh_get(s, h, name); /* get the tid */
+ if (iter == kh_end(h)) return -1;
+ return kh_value(h, iter);
+}
+
+int ti_parse_region(const ti_index_t *idx, const char *str, int *tid, int *begin, int *end)
+{
+ char *s, *p;
+ int i, l, k;
+ l = strlen(str);
+ p = s = (char*)malloc(l+1);
+ /* squeeze out "," */
+ for (i = k = 0; i != l; ++i)
+ if (str[i] != ',' && !isspace(str[i])) s[k++] = str[i];
+ s[k] = 0;
+ for (i = 0; i != k; ++i) if (s[i] == ':') break;
+ s[i] = 0;
+ if ((*tid = ti_get_tid(idx, s)) < 0) {
+ free(s);
+ return -1;
+ }
+ if (i == k) { /* dump the whole sequence */
+ *begin = 0; *end = 1<<29; free(s);
+ return 0;
+ }
+ for (p = s + i + 1; i != k; ++i) if (s[i] == '-') break;
+ *begin = atoi(p);
+ if (i < k) {
+ p = s + i + 1;
+ *end = atoi(p);
+ } else *end = 1<<29;
+ if (*begin > 0) --*begin;
+ free(s);
+ if (*begin > *end) return -1;
+ return 0;
+}
+
+/*******************************
+ * retrieve a specified region *
+ *******************************/
+
+#define MAX_BIN 37450 // =(8^6-1)/7+1
+
+static inline int reg2bins(uint32_t beg, uint32_t end, uint16_t list[MAX_BIN])
+{
+ int i = 0, k;
+ if (beg >= end) return 0;
+ if (end >= 1u<<29) end = 1u<<29;
+ --end;
+ list[i++] = 0;
+ for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
+ for (k = 9 + (beg>>23); k <= 9 + (end>>23); ++k) list[i++] = k;
+ for (k = 73 + (beg>>20); k <= 73 + (end>>20); ++k) list[i++] = k;
+ for (k = 585 + (beg>>17); k <= 585 + (end>>17); ++k) list[i++] = k;
+ for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
+ return i;
+}
+
+ti_iter_t ti_iter_first()
+{
+ ti_iter_t iter;
+ iter = calloc(1, sizeof(struct __ti_iter_t));
+ iter->from_first = 1;
+ return iter;
+}
+
+ti_iter_t ti_iter_query(const ti_index_t *idx, int tid, int beg, int end)
+{
+ uint16_t *bins;
+ int i, n_bins, n_off;
+ pair64_t *off;
+ khint_t k;
+ khash_t(i) *index;
+ uint64_t min_off;
+ ti_iter_t iter = 0;
+
+ if (beg < 0) beg = 0;
+ if (end < beg) return 0;
+ // initialize the iterator
+ iter = calloc(1, sizeof(struct __ti_iter_t));
+ iter->idx = idx; iter->tid = tid; iter->beg = beg; iter->end = end; iter->i = -1;
+ // random access
+ bins = (uint16_t*)calloc(MAX_BIN, 2);
+ n_bins = reg2bins(beg, end, bins);
+ index = idx->index[tid];
+ if (idx->index2[tid].n > 0) {
+ min_off = (beg>>TAD_LIDX_SHIFT >= idx->index2[tid].n)? idx->index2[tid].offset[idx->index2[tid].n-1]
+ : idx->index2[tid].offset[beg>>TAD_LIDX_SHIFT];
+ if (min_off == 0) { // improvement for index files built by tabix prior to 0.1.4
+ int n = beg>>TAD_LIDX_SHIFT;
+ if (n > idx->index2[tid].n) n = idx->index2[tid].n;
+ for (i = n - 1; i >= 0; --i)
+ if (idx->index2[tid].offset[i] != 0) break;
+ if (i >= 0) min_off = idx->index2[tid].offset[i];
+ }
+ } else min_off = 0; // tabix 0.1.2 may produce such index files
+ for (i = n_off = 0; i < n_bins; ++i) {
+ if ((k = kh_get(i, index, bins[i])) != kh_end(index))
+ n_off += kh_value(index, k).n;
+ }
+ if (n_off == 0) {
+ free(bins); return iter;
+ }
+ off = (pair64_t*)calloc(n_off, 16);
+ for (i = n_off = 0; i < n_bins; ++i) {
+ if ((k = kh_get(i, index, bins[i])) != kh_end(index)) {
+ int j;
+ ti_binlist_t *p = &kh_value(index, k);
+ for (j = 0; j < p->n; ++j)
+ if (p->list[j].v > min_off) off[n_off++] = p->list[j];
+ }
+ }
+ if (n_off == 0) {
+ free(bins); free(off); return iter;
+ }
+ free(bins);
+ {
+ int l;
+ ks_introsort(offt, n_off, off);
+ // resolve completely contained adjacent blocks
+ for (i = 1, l = 0; i < n_off; ++i)
+ if (off[l].v < off[i].v)
+ off[++l] = off[i];
+ n_off = l + 1;
+ // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
+ for (i = 1; i < n_off; ++i)
+ if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
+ { // merge adjacent blocks
+ for (i = 1, l = 0; i < n_off; ++i) {
+ if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
+ else off[++l] = off[i];
+ }
+ n_off = l + 1;
+ }
+ }
+ iter->n_off = n_off; iter->off = off;
+ return iter;
+}
+
+const char *ti_iter_read(BGZF *fp, ti_iter_t iter, int *len)
+{
+ if (iter->finished) return 0;
+ if (iter->from_first) {
+ int ret;
+ if ((ret = ti_readline(fp, &iter->str)) < 0) {
+ iter->finished = 1;
+ return 0;
+ } else {
+ if (len) *len = iter->str.l;
+ return iter->str.s;
+ }
+ }
+ if (iter->n_off == 0) return 0;
+ while (1) {
+ int ret;
+ if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+ if (iter->i == iter->n_off - 1) break; // no more chunks
+ if (iter->i >= 0) assert(iter->curr_off == iter->off[iter->i].v); // otherwise bug
+ if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+ bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET);
+ iter->curr_off = bgzf_tell(fp);
+ }
+ ++iter->i;
+ }
+ if ((ret = ti_readline(fp, &iter->str)) >= 0) {
+ ti_intv_t intv;
+ iter->curr_off = bgzf_tell(fp);
+ if (iter->str.s[0] == iter->idx->conf.meta_char) continue;
+ get_intv((ti_index_t*)iter->idx, &iter->str, &intv);
+ if (intv.tid != iter->tid || intv.beg >= iter->end) break; // no need to proceed
+ else if (intv.end > iter->beg && iter->end > intv.beg) {
+ if (len) *len = iter->str.l;
+ return iter->str.s;
+ }
+ } else break; // end of file
+ }
+ iter->finished = 1;
+ return 0;
+}
+
+void ti_iter_destroy(ti_iter_t iter)
+{
+ if (iter) {
+ free(iter->str.s); free(iter->off);
+ free(iter);
+ }
+}
+
+int ti_fetch(BGZF *fp, const ti_index_t *idx, int tid, int beg, int end, void *data, ti_fetch_f func)
+{
+ ti_iter_t iter;
+ const char *s;
+ int len;
+ iter = ti_iter_query(idx, tid, beg, end);
+ while ((s = ti_iter_read(fp, iter, &len)) != 0)
+ func(len, s, data);
+ ti_iter_destroy(iter);
+ return 0;
+}
+
+const ti_conf_t *ti_get_conf(ti_index_t *idx) { return idx? &idx->conf : 0; }
+
+/*******************
+ * High-level APIs *
+ *******************/
+
+tabix_t *ti_open(const char *fn, const char *fnidx)
+{
+ tabix_t *t;
+ BGZF *fp;
+ if ((fp = bgzf_open(fn, "r")) == 0) return 0;
+ t = calloc(1, sizeof(tabix_t));
+ t->fn = strdup(fn);
+ if (fnidx) t->fnidx = strdup(fnidx);
+ t->fp = fp;
+ return t;
+}
+
+void ti_close(tabix_t *t)
+{
+ if (t) {
+ bgzf_close(t->fp);
+ if (t->idx) ti_index_destroy(t->idx);
+ free(t->fn); free(t->fnidx);
+ free(t);
+ }
+}
+
+int ti_lazy_index_load(tabix_t *t)
+{
+ if (t->idx == 0) { // load index
+ if (t->fnidx) t->idx = ti_index_load_local(t->fnidx);
+ else t->idx = ti_index_load(t->fn);
+ if (t->idx == 0) return -1; // fail to load index
+ }
+ return 0;
+}
+
+ti_iter_t ti_queryi(tabix_t *t, int tid, int beg, int end)
+{
+ if (tid < 0) return ti_iter_first();
+ if (ti_lazy_index_load(t) != 0) return 0;
+ return ti_iter_query(t->idx, tid, beg, end);
+}
+
+ti_iter_t ti_querys(tabix_t *t, const char *reg)
+{
+ int tid, beg, end;
+ if (reg == 0) return ti_iter_first();
+ if (ti_lazy_index_load(t) != 0) return 0;
+ if (ti_parse_region(t->idx, reg, &tid, &beg, &end) < 0) return 0;
+ return ti_iter_query(t->idx, tid, beg, end);
+}
+
+ti_iter_t ti_query(tabix_t *t, const char *name, int beg, int end)
+{
+ int tid;
+ if (name == 0) return ti_iter_first();
+ // then need to load the index
+ if (ti_lazy_index_load(t) != 0) return 0;
+ if ((tid = ti_get_tid(t->idx, name)) < 0) return 0;
+ return ti_iter_query(t->idx, tid, beg, end);
+}
+
+const char *ti_read(tabix_t *t, ti_iter_t iter, int *len)
+{
+ return ti_iter_read(t->fp, iter, len);
+}
diff --git a/tabix/knetfile.c b/tabix/knetfile.c
new file mode 100644
index 0000000..7c96a3e
--- /dev/null
+++ b/tabix/knetfile.c
@@ -0,0 +1,632 @@
+/* The MIT License
+
+ Copyright (c) 2008 Genome Research Ltd (GRL).
+
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3 at sanger.ac.uk> */
+
+/* Probably I will not do socket programming in the next few years and
+ therefore I decide to heavily annotate this file, for Linux and
+ Windows as well. -lh3 */
+
+#include <time.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <unistd.h>
+#include <sys/types.h>
+
+#ifdef _WIN32
+#include <winsock.h>
+#else
+#include <netdb.h>
+#include <arpa/inet.h>
+#include <sys/socket.h>
+#endif
+
+#include "knetfile.h"
+
+/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
+ * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
+ * integer -1. In knetfile.c, I use "int" for socket type
+ * throughout. This should be improved to avoid confusion.
+ *
+ * In Linux/Mac, recv() and read() do almost the same thing. You can see
+ * in the header file that netread() is simply an alias of read(). In
+ * Windows, however, they are different and using recv() is mandatory.
+ */
+
+/* This function tests if the file handler is ready for reading (or
+ * writing if is_read==0). */
+static int socket_wait(int fd, int is_read)
+{
+ fd_set fds, *fdr = 0, *fdw = 0;
+ struct timeval tv;
+ int ret;
+ tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
+ FD_ZERO(&fds);
+ FD_SET(fd, &fds);
+ if (is_read) fdr = &fds;
+ else fdw = &fds;
+ ret = select(fd+1, fdr, fdw, 0, &tv);
+#ifndef _WIN32
+ if (ret == -1) perror("select");
+#else
+ if (ret == 0)
+ fprintf(stderr, "select time-out\n");
+ else if (ret == SOCKET_ERROR)
+ fprintf(stderr, "select: %d\n", WSAGetLastError());
+#endif
+ return ret;
+}
+
+#ifndef _WIN32
+/* This function does not work with Windows due to the lack of
+ * getaddrinfo() in winsock. It is addapted from an example in "Beej's
+ * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
+static int socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
+
+ int on = 1, fd;
+ struct linger lng = { 0, 0 };
+ struct addrinfo hints, *res;
+ memset(&hints, 0, sizeof(struct addrinfo));
+ hints.ai_family = AF_UNSPEC;
+ hints.ai_socktype = SOCK_STREAM;
+ /* In Unix/Mac, getaddrinfo() is the most convenient way to get
+ * server information. */
+ if (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
+ if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
+ /* The following two setsockopt() are used by ftplib
+ * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
+ * necessary. */
+ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
+ if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+ if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
+ freeaddrinfo(res);
+ return fd;
+}
+#else
+/* MinGW's printf has problem with "%lld" */
+char *int64tostr(char *buf, int64_t x)
+{
+ int cnt;
+ int i = 0;
+ do {
+ buf[i++] = '0' + x % 10;
+ x /= 10;
+ } while (x);
+ buf[i] = 0;
+ for (cnt = i, i = 0; i < cnt/2; ++i) {
+ int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
+ }
+ return buf;
+}
+
+int64_t strtoint64(const char *buf)
+{
+ int64_t x;
+ for (x = 0; *buf != '\0'; ++buf)
+ x = x * 10 + ((int64_t) *buf - 48);
+ return x;
+}
+/* In windows, the first thing is to establish the TCP connection. */
+int knet_win32_init()
+{
+ WSADATA wsaData;
+ return WSAStartup(MAKEWORD(2, 2), &wsaData);
+}
+void knet_win32_destroy()
+{
+ WSACleanup();
+}
+/* A slightly modfied version of the following function also works on
+ * Mac (and presummably Linux). However, this function is not stable on
+ * my Mac. It sometimes works fine but sometimes does not. Therefore for
+ * non-Windows OS, I do not use this one. */
+static SOCKET socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func) \
+ do { \
+ fprintf(stderr, "%s: %d\n", func, WSAGetLastError()); \
+ return -1; \
+ } while (0)
+
+ int on = 1;
+ SOCKET fd;
+ struct linger lng = { 0, 0 };
+ struct sockaddr_in server;
+ struct hostent *hp = 0;
+ // open socket
+ if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
+ if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
+ if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+ // get host info
+ if (isalpha(host[0])) hp = gethostbyname(host);
+ else {
+ struct in_addr addr;
+ addr.s_addr = inet_addr(host);
+ hp = gethostbyaddr((char*)&addr, 4, AF_INET);
+ }
+ if (hp == 0) __err_connect("gethost");
+ // connect
+ server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
+ server.sin_family= AF_INET;
+ server.sin_port = htons(atoi(port));
+ if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
+ // freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
+ return fd;
+}
+#endif
+
+static off_t my_netread(int fd, void *buf, off_t len)
+{
+ off_t rest = len, curr, l = 0;
+ /* recv() and read() may not read the required length of data with
+ * one call. They have to be called repeatedly. */
+ while (rest) {
+ if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
+ curr = netread(fd, buf + l, rest);
+ /* According to the glibc manual, section 13.2, a zero returned
+ * value indicates end-of-file (EOF), which should mean that
+ * read() will not return zero if EOF has not been met but data
+ * are not immediately available. */
+ if (curr == 0) break;
+ l += curr; rest -= curr;
+ }
+ return l;
+}
+
+/*************************
+ * FTP specific routines *
+ *************************/
+
+static int kftp_get_response(knetFile *ftp)
+{
+#ifndef _WIN32
+ unsigned char c;
+#else
+ char c;
+#endif
+ int n = 0;
+ char *p;
+ if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
+ while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
+ //fputc(c, stderr);
+ if (n >= ftp->max_response) {
+ ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
+ ftp->response = realloc(ftp->response, ftp->max_response);
+ }
+ ftp->response[n++] = c;
+ if (c == '\n') {
+ if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
+ && ftp->response[3] != '-') break;
+ n = 0;
+ continue;
+ }
+ }
+ if (n < 2) return -1;
+ ftp->response[n-2] = 0;
+ return strtol(ftp->response, &p, 0);
+}
+
+static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
+{
+ if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
+ netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
+ return is_get? kftp_get_response(ftp) : 0;
+}
+
+static int kftp_pasv_prep(knetFile *ftp)
+{
+ char *p;
+ int v[6];
+ kftp_send_cmd(ftp, "PASV\r\n", 1);
+ for (p = ftp->response; *p && *p != '('; ++p);
+ if (*p != '(') return -1;
+ ++p;
+ sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
+ memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
+ ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
+ return 0;
+}
+
+
+static int kftp_pasv_connect(knetFile *ftp)
+{
+ char host[80], port[10];
+ if (ftp->pasv_port == 0) {
+ fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
+ return -1;
+ }
+ sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
+ sprintf(port, "%d", ftp->pasv_port);
+ ftp->fd = socket_connect(host, port);
+ if (ftp->fd == -1) return -1;
+ return 0;
+}
+
+int kftp_connect(knetFile *ftp)
+{
+ ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
+ if (ftp->ctrl_fd == -1) return -1;
+ kftp_get_response(ftp);
+ kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
+ kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
+ kftp_send_cmd(ftp, "TYPE I\r\n", 1);
+ return 0;
+}
+
+int kftp_reconnect(knetFile *ftp)
+{
+ if (ftp->ctrl_fd != -1) {
+ netclose(ftp->ctrl_fd);
+ ftp->ctrl_fd = -1;
+ }
+ netclose(ftp->fd);
+ ftp->fd = -1;
+ return kftp_connect(ftp);
+}
+
+// initialize ->type, ->host, ->retr and ->size
+knetFile *kftp_parse_url(const char *fn, const char *mode)
+{
+ knetFile *fp;
+ char *p;
+ int l;
+ if (strstr(fn, "ftp://") != fn) return 0;
+ for (p = (char*)fn + 6; *p && *p != '/'; ++p);
+ if (*p != '/') return 0;
+ l = p - fn - 6;
+ fp = calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_FTP;
+ fp->fd = -1;
+ /* the Linux/Mac version of socket_connect() also recognizes a port
+ * like "ftp", but the Windows version does not. */
+ fp->port = strdup("21");
+ fp->host = calloc(l + 1, 1);
+ if (strchr(mode, 'c')) fp->no_reconnect = 1;
+ strncpy(fp->host, fn + 6, l);
+ fp->retr = calloc(strlen(p) + 8, 1);
+ sprintf(fp->retr, "RETR %s\r\n", p);
+ fp->size_cmd = calloc(strlen(p) + 8, 1);
+ sprintf(fp->size_cmd, "SIZE %s\r\n", p);
+ fp->seek_offset = 0;
+ return fp;
+}
+// place ->fd at offset off
+int kftp_connect_file(knetFile *fp)
+{
+ int ret;
+ long long file_size;
+ if (fp->fd != -1) {
+ netclose(fp->fd);
+ if (fp->no_reconnect) kftp_get_response(fp);
+ }
+ kftp_pasv_prep(fp);
+ kftp_send_cmd(fp, fp->size_cmd, 1);
+#ifndef _WIN32
+ if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
+ {
+ fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
+ return -1;
+ }
+#else
+ const char *p = fp->response;
+ while (*p != ' ') ++p;
+ while (*p < '0' || *p > '9') ++p;
+ file_size = strtoint64(p);
+#endif
+ fp->file_size = file_size;
+ if (fp->offset>=0) {
+ char tmp[32];
+#ifndef _WIN32
+ sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
+#else
+ strcpy(tmp, "REST ");
+ int64tostr(tmp + 5, fp->offset);
+ strcat(tmp, "\r\n");
+#endif
+ kftp_send_cmd(fp, tmp, 1);
+ }
+ kftp_send_cmd(fp, fp->retr, 0);
+ kftp_pasv_connect(fp);
+ ret = kftp_get_response(fp);
+ if (ret != 150) {
+ fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
+ netclose(fp->fd);
+ fp->fd = -1;
+ return -1;
+ }
+ fp->is_ready = 1;
+ return 0;
+}
+
+
+/**************************
+ * HTTP specific routines *
+ **************************/
+
+knetFile *khttp_parse_url(const char *fn, const char *mode)
+{
+ knetFile *fp;
+ char *p, *proxy, *q;
+ int l;
+ if (strstr(fn, "http://") != fn) return 0;
+ // set ->http_host
+ for (p = (char*)fn + 7; *p && *p != '/'; ++p);
+ l = p - fn - 7;
+ fp = calloc(1, sizeof(knetFile));
+ fp->http_host = calloc(l + 1, 1);
+ strncpy(fp->http_host, fn + 7, l);
+ fp->http_host[l] = 0;
+ for (q = fp->http_host; *q && *q != ':'; ++q);
+ if (*q == ':') *q++ = 0;
+ // get http_proxy
+ proxy = getenv("http_proxy");
+ // set ->host, ->port and ->path
+ if (proxy == 0) {
+ fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
+ fp->port = strdup(*q? q : "80");
+ fp->path = strdup(*p? p : "/");
+ } else {
+ fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
+ for (q = fp->host; *q && *q != ':'; ++q);
+ if (*q == ':') *q++ = 0;
+ fp->port = strdup(*q? q : "80");
+ fp->path = strdup(fn);
+ }
+ fp->type = KNF_TYPE_HTTP;
+ fp->ctrl_fd = fp->fd = -1;
+ fp->seek_offset = 0;
+ return fp;
+}
+
+int khttp_connect_file(knetFile *fp)
+{
+ int ret, l = 0;
+ char *buf, *p;
+ if (fp->fd != -1) netclose(fp->fd);
+ fp->fd = socket_connect(fp->host, fp->port);
+ buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
+ l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
+ l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
+ l += sprintf(buf + l, "\r\n");
+ netwrite(fp->fd, buf, l);
+ l = 0;
+ while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
+ if (buf[l] == '\n' && l >= 3)
+ if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
+ ++l;
+ }
+ buf[l] = 0;
+ if (l < 14) { // prematured header
+ netclose(fp->fd);
+ fp->fd = -1;
+ return -1;
+ }
+ ret = strtol(buf + 8, &p, 0); // HTTP return code
+ if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
+ off_t rest = fp->offset;
+ while (rest) {
+ off_t l = rest < 0x10000? rest : 0x10000;
+ rest -= my_netread(fp->fd, buf, l);
+ }
+ } else if (ret != 206 && ret != 200) {
+ free(buf);
+ fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
+ netclose(fp->fd);
+ fp->fd = -1;
+ return -1;
+ }
+ free(buf);
+ fp->is_ready = 1;
+ return 0;
+}
+
+/********************
+ * Generic routines *
+ ********************/
+
+knetFile *knet_open(const char *fn, const char *mode)
+{
+ knetFile *fp = 0;
+ if (mode[0] != 'r') {
+ fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
+ return 0;
+ }
+ if (strstr(fn, "ftp://") == fn) {
+ fp = kftp_parse_url(fn, mode);
+ if (fp == 0) return 0;
+ if (kftp_connect(fp) == -1) {
+ knet_close(fp);
+ return 0;
+ }
+ kftp_connect_file(fp);
+ } else if (strstr(fn, "http://") == fn) {
+ fp = khttp_parse_url(fn, mode);
+ if (fp == 0) return 0;
+ khttp_connect_file(fp);
+ } else { // local file
+#ifdef _WIN32
+ /* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
+ * be undefined on some systems, although it is defined on my
+ * Mac and the Linux I have tested on. */
+ int fd = open(fn, O_RDONLY | O_BINARY);
+#else
+ int fd = open(fn, O_RDONLY);
+#endif
+ if (fd == -1) {
+ perror("open");
+ return 0;
+ }
+ fp = (knetFile*)calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_LOCAL;
+ fp->fd = fd;
+ fp->ctrl_fd = -1;
+ }
+ if (fp && fp->fd == -1) {
+ knet_close(fp);
+ return 0;
+ }
+ return fp;
+}
+
+knetFile *knet_dopen(int fd, const char *mode)
+{
+ knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
+ fp->type = KNF_TYPE_LOCAL;
+ fp->fd = fd;
+ return fp;
+}
+
+off_t knet_read(knetFile *fp, void *buf, off_t len)
+{
+ off_t l = 0;
+ if (fp->fd == -1) return 0;
+ if (fp->type == KNF_TYPE_FTP) {
+ if (fp->is_ready == 0) {
+ if (!fp->no_reconnect) kftp_reconnect(fp);
+ kftp_connect_file(fp);
+ }
+ } else if (fp->type == KNF_TYPE_HTTP) {
+ if (fp->is_ready == 0)
+ khttp_connect_file(fp);
+ }
+ if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
+ off_t rest = len, curr;
+ while (rest) {
+ curr = read(fp->fd, buf + l, rest);
+ if (curr == 0) break;
+ l += curr; rest -= curr;
+ }
+ } else l = my_netread(fp->fd, buf, len);
+ fp->offset += l;
+ return l;
+}
+
+off_t knet_seek(knetFile *fp, int64_t off, int whence)
+{
+ if (whence == SEEK_SET && off == fp->offset) return 0;
+ if (fp->type == KNF_TYPE_LOCAL) {
+ /* Be aware that lseek() returns the offset after seeking,
+ * while fseek() returns zero on success. */
+ off_t offset = lseek(fp->fd, off, whence);
+ if (offset == -1) {
+ // Be silent, it is OK for knet_seek to fail when the file is streamed
+ // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+ return -1;
+ }
+ fp->offset = offset;
+ return 0;
+ }
+ else if (fp->type == KNF_TYPE_FTP)
+ {
+ if (whence==SEEK_CUR)
+ fp->offset += off;
+ else if (whence==SEEK_SET)
+ fp->offset = off;
+ else if ( whence==SEEK_END)
+ fp->offset = fp->file_size+off;
+ fp->is_ready = 0;
+ return 0;
+ }
+ else if (fp->type == KNF_TYPE_HTTP)
+ {
+ if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
+ fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
+ errno = ESPIPE;
+ return -1;
+ }
+ if (whence==SEEK_CUR)
+ fp->offset += off;
+ else if (whence==SEEK_SET)
+ fp->offset = off;
+ fp->is_ready = 0;
+ return fp->offset;
+ }
+ errno = EINVAL;
+ fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+ return -1;
+}
+
+int knet_close(knetFile *fp)
+{
+ if (fp == 0) return 0;
+ if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
+ if (fp->fd != -1) {
+ /* On Linux/Mac, netclose() is an alias of close(), but on
+ * Windows, it is an alias of closesocket(). */
+ if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
+ else netclose(fp->fd);
+ }
+ free(fp->host); free(fp->port);
+ free(fp->response); free(fp->retr); free(fp->size_cmd); // FTP specific
+ free(fp->path); free(fp->http_host); // HTTP specific
+ free(fp);
+ return 0;
+}
+
+#ifdef KNETFILE_MAIN
+int main(void)
+{
+ char *buf;
+ knetFile *fp;
+ int type = 4, l;
+#ifdef _WIN32
+ knet_win32_init();
+#endif
+ buf = calloc(0x100000, 1);
+ if (type == 0) {
+ fp = knet_open("knetfile.c", "r");
+ knet_seek(fp, 1000, SEEK_SET);
+ } else if (type == 1) { // NCBI FTP, large file
+ fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
+ knet_seek(fp, 2500000000ll, SEEK_SET);
+ l = knet_read(fp, buf, 255);
+ } else if (type == 2) {
+ fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
+ knet_seek(fp, 1000, SEEK_SET);
+ } else if (type == 3) {
+ fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
+ knet_seek(fp, 1000, SEEK_SET);
+ } else if (type == 4) {
+ fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
+ knet_read(fp, buf, 10000);
+ knet_seek(fp, 20000, SEEK_SET);
+ knet_seek(fp, 10000, SEEK_SET);
+ l = knet_read(fp, buf+10000, 10000000) + 10000;
+ }
+ if (type != 4 && type != 1) {
+ knet_read(fp, buf, 255);
+ buf[255] = 0;
+ printf("%s\n", buf);
+ } else write(fileno(stdout), buf, l);
+ knet_close(fp);
+ free(buf);
+ return 0;
+}
+#endif
diff --git a/tabix/kstring.c b/tabix/kstring.c
new file mode 100644
index 0000000..e0203fa
--- /dev/null
+++ b/tabix/kstring.c
@@ -0,0 +1,165 @@
+#include <stdarg.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdint.h>
+#include "kstring.h"
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+ va_list ap;
+ int l;
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap); // This line does not work with glibc 2.0. See `man snprintf'.
+ va_end(ap);
+ if (l + 1 > s->m - s->l) {
+ s->m = s->l + l + 2;
+ kroundup32(s->m);
+ s->s = (char*)realloc(s->s, s->m);
+ va_start(ap, fmt);
+ l = vsnprintf(s->s + s->l, s->m - s->l, fmt, ap);
+ }
+ va_end(ap);
+ s->l += l;
+ return l;
+}
+
+// s MUST BE a null terminated string; l = strlen(s)
+int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
+{
+ int i, n, max, last_char, last_start, *offsets, l;
+ n = 0; max = *_max; offsets = *_offsets;
+ l = strlen(s);
+
+#define __ksplit_aux do { \
+ if (_offsets) { \
+ s[i] = 0; \
+ if (n == max) { \
+ max = max? max<<1 : 2; \
+ offsets = (int*)realloc(offsets, sizeof(int) * max); \
+ } \
+ offsets[n++] = last_start; \
+ } else ++n; \
+ } while (0)
+
+ for (i = 0, last_char = last_start = 0; i <= l; ++i) {
+ if (delimiter == 0) {
+ if (isspace(s[i]) || s[i] == 0) {
+ if (isgraph(last_char)) __ksplit_aux; // the end of a field
+ } else {
+ if (isspace(last_char) || last_char == 0) last_start = i;
+ }
+ } else {
+ if (s[i] == delimiter || s[i] == 0) {
+ if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
+ } else {
+ if (last_char == delimiter || last_char == 0) last_start = i;
+ }
+ }
+ last_char = s[i];
+ }
+ *_max = max; *_offsets = offsets;
+ return n;
+}
+
+/**********************
+ * Boyer-Moore search *
+ **********************/
+
+// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
+int *ksBM_prep(const uint8_t *pat, int m)
+{
+ int i, *suff, *prep, *bmGs, *bmBc;
+ prep = calloc(m + 256, 1);
+ bmGs = prep; bmBc = prep + m;
+ { // preBmBc()
+ for (i = 0; i < 256; ++i) bmBc[i] = m;
+ for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
+ }
+ suff = calloc(m, sizeof(int));
+ { // suffixes()
+ int f = 0, g;
+ suff[m - 1] = m;
+ g = m - 1;
+ for (i = m - 2; i >= 0; --i) {
+ if (i > g && suff[i + m - 1 - f] < i - g)
+ suff[i] = suff[i + m - 1 - f];
+ else {
+ if (i < g) g = i;
+ f = i;
+ while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
+ suff[i] = f - g;
+ }
+ }
+ }
+ { // preBmGs()
+ int j = 0;
+ for (i = 0; i < m; ++i) bmGs[i] = m;
+ for (i = m - 1; i >= 0; --i)
+ if (suff[i] == i + 1)
+ for (; j < m - 1 - i; ++j)
+ if (bmGs[j] == m)
+ bmGs[j] = m - 1 - i;
+ for (i = 0; i <= m - 2; ++i)
+ bmGs[m - 1 - suff[i]] = m - 1 - i;
+ }
+ free(suff);
+ return prep;
+}
+
+int *ksBM_search(const uint8_t *str, int n, const uint8_t *pat, int m, int *_prep, int *n_matches)
+{
+ int i, j, *prep, *bmGs, *bmBc;
+ int *matches = 0, mm = 0, nm = 0;
+ prep = _prep? _prep : ksBM_prep(pat, m);
+ bmGs = prep; bmBc = prep + m;
+ j = 0;
+ while (j <= n - m) {
+ for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
+ if (i < 0) {
+ if (nm == mm) {
+ mm = mm? mm<<1 : 1;
+ matches = realloc(matches, mm * sizeof(int));
+ }
+ matches[nm++] = j;
+ j += bmGs[0];
+ } else {
+ int max = bmBc[str[i+j]] - m + 1 + i;
+ if (max < bmGs[i]) max = bmGs[i];
+ j += max;
+ }
+ }
+ *n_matches = nm;
+ if (_prep == 0) free(prep);
+ return matches;
+}
+
+#ifdef KSTRING_MAIN
+#include <stdio.h>
+int main()
+{
+ kstring_t *s;
+ int *fields, n, i;
+ s = (kstring_t*)calloc(1, sizeof(kstring_t));
+ // test ksprintf()
+ ksprintf(s, " abcdefg: %d ", 100);
+ printf("'%s'\n", s->s);
+ // test ksplit()
+ fields = ksplit(s, 0, &n);
+ for (i = 0; i < n; ++i)
+ printf("field[%d] = '%s'\n", i, s->s + fields[i]);
+ free(s);
+
+ {
+ static char *str = "abcdefgcdg";
+ static char *pat = "cd";
+ int n, *matches;
+ matches = ksBM_search(str, strlen(str), pat, strlen(pat), 0, &n);
+ printf("%d: \n", n);
+ for (i = 0; i < n; ++i)
+ printf("- %d\n", matches[i]);
+ free(matches);
+ }
+ return 0;
+}
+#endif
diff --git a/tests/example_btag.bam b/tests/example_btag.bam
new file mode 100644
index 0000000..7cd5c0c
Binary files /dev/null and b/tests/example_btag.bam differ
diff --git a/tests/pysam_test.py b/tests/pysam_test.py
index 3407182..c8acf83 100755
--- a/tests/pysam_test.py
+++ b/tests/pysam_test.py
@@ -891,6 +891,16 @@ class TestHeaderBam(TestHeaderSam):
self.samfile=pysam.Samfile( "ex3.bam","rb" )
+class TestHeader1000Genomes( unittest.TestCase ):
+
+ bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase2b_alignment/data/NA07048/exome_alignment/NA07048.unmapped.ILLUMINA.bwa.CEU.exome.20120522_p2b.bam"
+
+ def testRead( self ):
+
+ f = pysam.Samfile( self.bamfile, "rb" )
+ data = f.header.copy()
+ self.assertTrue( data )
+
class TestUnmappedReads(unittest.TestCase):
def testSAM(self):
--
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