[med-svn] [python-pysam] 01/02: package builds but I dont understand whats happening in the rule dh_auto_test
Jorge Soares
jssoares-guest at moszumanska.debian.org
Thu Nov 27 17:06:10 UTC 2014
This is an automated email from the git hooks/post-receive script.
jssoares-guest pushed a commit to branch master
in repository python-pysam.
commit 1f2a97521a766e649c5721c2a21f1895c2de61af
Author: Jorge Soares <j.s.soares at gmail.com>
Date: Thu Nov 27 16:54:29 2014 +0000
package builds but I dont understand whats happening in the rule dh_auto_test
---
debian/control | 8 +-
debian/patches/adding-include-hts-dirs | 11 +
.../change-htslib-statement-to-link-to-debian | 25 +
...e-htslib-statement-in-setuppy-to-link-to-debian | 12 +
debian/patches/do_not_use_distribute_setup.patch | 17 -
..._use_distribute_setup_python2_and_python3.patch | 12 -
debian/patches/fix_cleanup_tests.patch | 19 -
.../import-setuptools-at-the-beginning.patch | 19 -
debian/patches/offline-tests.patch | 1824 --
debian/patches/series | 3 +-
debian/patches/use_external_htslib.patch | 23 -
debian/rules | 36 +-
pysam.egg-info/PKG-INFO | 16 -
pysam.egg-info/SOURCES.txt | 204 -
pysam.egg-info/dependency_links.txt | 1 -
pysam.egg-info/not-zip-safe | 1 -
pysam.egg-info/top_level.txt | 1 -
pysam/TabProxies.c | 14076 ---------
pysam/cfaidx.c | 8717 ------
pysam/chtslib.c | 3162 --
pysam/csamfile.c | 2876 --
pysam/csamtools.c | 6962 -----
pysam/ctabix.c | 15462 ----------
pysam/cvcf.c | 30127 -------------------
24 files changed, 73 insertions(+), 83541 deletions(-)
diff --git a/debian/control b/debian/control
index c06da2e..a8cadb6 100644
--- a/debian/control
+++ b/debian/control
@@ -6,15 +6,15 @@ Section: python
XS-Testsuite: autopkgtest
Priority: optional
Build-Depends: debhelper (>= 9),
+ samtools (>= 0.1.19),
+ libhts-dev,
+ zlib1g-dev,
python-all-dev,
python-setuptools,
cython,
python3-all-dev,
python3-setuptools,
- cython3,
- zlib1g-dev,
- samtools (>= 0.1.19),
- libhts-dev
+ cython3
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/python-pysam.git
Vcs-Git: git://anonscm.debian.org/debian-med/python-pysam.git
diff --git a/debian/patches/adding-include-hts-dirs b/debian/patches/adding-include-hts-dirs
new file mode 100644
index 0000000..ff5dd49
--- /dev/null
+++ b/debian/patches/adding-include-hts-dirs
@@ -0,0 +1,11 @@
+Description: Added the include dirs
+--- a/setup.py
++++ b/setup.py
+@@ -92,6 +92,7 @@
+ chtslib_sources = []
+ shared_htslib_sources = htslib_sources
+ htslib_library_dirs = HTSLIB_LIBRARY_DIR
++ htslib_include_dirs = [HTSLIB_INCLUDE_DIR]
+ htslib_libraries = ['hts']
+ else:
+ raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
diff --git a/debian/patches/change-htslib-statement-to-link-to-debian b/debian/patches/change-htslib-statement-to-link-to-debian
new file mode 100644
index 0000000..bd77a16
--- /dev/null
+++ b/debian/patches/change-htslib-statement-to-link-to-debian
@@ -0,0 +1,25 @@
+Description: Trying to bind to debian htslib
+--- a/setup.py
++++ b/setup.py
+@@ -30,7 +30,7 @@
+ # pysam.
+ # external: use shared libhts.so compiled outside of
+ # pysam
+-HTSLIB_MODE = "separate"
++HTSLIB_MODE = "external"
+ HTSLIB_LIBRARY_DIR = os.environ.get('HTSLIB_LIBRARY_DIR', None)
+ HTSLIB_INCLUDE_DIR = os.environ.get('HTSLIB_INCLUDE_DIR', None)
+
+@@ -87,6 +87,12 @@
+ htslib_library_dirs = ['pysam']
+ htslib_include_dirs = ['htslib']
+ htslib_libraries = ['chtslib']
++elif HTSLIB_MODE == 'external':
++ htslib_sources = []
++ chtslib_sources = []
++ shared_htslib_sources = htslib_sources
++ htslib_library_dirs = HTSLIB_LIBRARY_DIR
++ htslib_libraries = ['hts']
+ else:
+ raise ValueError("unknown HTSLIB value '%s'" % HTSLIB_MODE)
+
diff --git a/debian/patches/chenge-htslib-statement-in-setuppy-to-link-to-debian b/debian/patches/chenge-htslib-statement-in-setuppy-to-link-to-debian
new file mode 100644
index 0000000..491924b
--- /dev/null
+++ b/debian/patches/chenge-htslib-statement-in-setuppy-to-link-to-debian
@@ -0,0 +1,12 @@
+Description: Tries to link against debian htslib
+--- a/setup.py
++++ b/setup.py
+@@ -30,7 +30,7 @@
+ # pysam.
+ # external: use shared libhts.so compiled outside of
+ # pysam
+-HTSLIB_MODE = "separate"
++HTSLIB_MODE = "shared"
+ HTSLIB_LIBRARY_DIR = os.environ.get('HTSLIB_LIBRARY_DIR', None)
+ HTSLIB_INCLUDE_DIR = os.environ.get('HTSLIB_INCLUDE_DIR', None)
+
diff --git a/debian/patches/do_not_use_distribute_setup.patch b/debian/patches/do_not_use_distribute_setup.patch
deleted file mode 100644
index 7506fe2..0000000
--- a/debian/patches/do_not_use_distribute_setup.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Author: Olivier Sallou <olivier.sallou at irisa.fr>
-Last-Updated: Fri, 07 Feb 2014 18:29:40 +0100
-Description: Prevent downloading distribute_setup
-
---- a/setup.py
-+++ b/setup.py
-@@ -205,8 +205,8 @@ if len(sys.argv) == 2 and sys.argv[1] ==
- try:
- from setuptools import Extension, setup
- except ImportError:
-- from ez_setup import use_setuptools
-- use_setuptools()
-+ #from ez_setup import use_setuptools
-+ #use_setuptools()
- from setuptools import Extension, setup
-
- #######################################################
diff --git a/debian/patches/do_not_use_distribute_setup_python2_and_python3.patch b/debian/patches/do_not_use_distribute_setup_python2_and_python3.patch
deleted file mode 100644
index 5bc456b..0000000
--- a/debian/patches/do_not_use_distribute_setup_python2_and_python3.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Description: Removing the call to setuptools
---- a/setup.py
-+++ b/setup.py
-@@ -214,7 +214,7 @@
- # cp samtools/*.h pysam/*.h pysam/include
- # cp samtools/win32/*.h pysam/include/win32
-
--from setuptools import Extension, setup
-+#from setuptools import Extension, setup
-
- #######################################################
- #######################################################
diff --git a/debian/patches/fix_cleanup_tests.patch b/debian/patches/fix_cleanup_tests.patch
deleted file mode 100644
index 852dd09..0000000
--- a/debian/patches/fix_cleanup_tests.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Mon, 10 Feb 2014 11:29:40 +0100
-Description: Prevent tests makefile from deleting files which
- are contained inside the upstream source
-
---- a/tests/Makefile
-+++ b/tests/Makefile
-@@ -47,6 +47,11 @@
- samtools view -bS $< > $@
-
- clean:
-+ mkdir keep_bam_files
-+ mv ex9_fail.bam ex9_nofail.bam example_btag.bam example_empty_header.bam issue100.bam tag_bug.bam test_unaligned.bam keep_bam_files
- rm -fr *.bam *.bai *.fai *.pileup* \
- *~ calDepth *.dSYM pysam_*.sam \
- ex2.sam ex2.sam.gz ex1.sam
-+ mv keep_bam_files/* .
-+ rmdir keep_bam_files
-+ rm -rf pysam_test_work/
diff --git a/debian/patches/import-setuptools-at-the-beginning.patch b/debian/patches/import-setuptools-at-the-beginning.patch
deleted file mode 100644
index 3f285ea..0000000
--- a/debian/patches/import-setuptools-at-the-beginning.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-Description: CHanged location of setuptools import--- a/setup.py
-+++ b/setup.py
-@@ -14,6 +14,7 @@
- import re
- import fnmatch
- import platform
-+from setuptools import Extension, setup
-
- name = "pysam"
-
-@@ -214,7 +215,7 @@
- # cp samtools/*.h pysam/*.h pysam/include
- # cp samtools/win32/*.h pysam/include/win32
-
--from setuptools import Extension, setup
-+
-
- #######################################################
- #######################################################
diff --git a/debian/patches/offline-tests.patch b/debian/patches/offline-tests.patch
deleted file mode 100644
index 022dd10..0000000
--- a/debian/patches/offline-tests.patch
+++ /dev/null
@@ -1,1824 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Changed: Mon, 10 Feb 2014 11:29:40 +0100
-Description: Create a copy of the test suite script and remove those
- tests that try to fetch files from network
-
---- /dev/null
-+++ b/tests/pysam_test_offline.py
-@@ -0,0 +1,1816 @@
-+#!/usr/bin/env python
-+'''unit testing code for pysam.
-+
-+Execute in the :file:`tests` directory as it requires the Makefile
-+and data files located there.
-+'''
-+
-+import pysam
-+import unittest
-+import os, re, sys
-+import itertools
-+import collections
-+import subprocess
-+import shutil
-+import logging
-+
-+IS_PYTHON3 = sys.version_info[0] >= 3
-+
-+if IS_PYTHON3:
-+ from itertools import zip_longest
-+else:
-+ from itertools import izip as zip_longest
-+
-+
-+SAMTOOLS="samtools"
-+WORKDIR="pysam_test_work"
-+
-+def checkBinaryEqual( filename1, filename2 ):
-+ '''return true if the two files are binary equal.'''
-+ if os.path.getsize( filename1 ) != os.path.getsize( filename2 ):
-+ return False
-+
-+ infile1 = open(filename1, "rb")
-+ infile2 = open(filename2, "rb")
-+
-+ def chariter( infile ):
-+ while 1:
-+ c = infile.read(1)
-+ if c == b"": break
-+ yield c
-+
-+ found = False
-+ for c1,c2 in zip_longest( chariter( infile1), chariter( infile2) ):
-+ if c1 != c2: break
-+ else:
-+ found = True
-+
-+ infile1.close()
-+ infile2.close()
-+ return found
-+
-+def runSamtools( cmd ):
-+ '''run a samtools command'''
-+
-+ try:
-+ retcode = subprocess.call(cmd, shell=True,
-+ stderr = subprocess.PIPE)
-+ if retcode < 0:
-+ print("Child was terminated by signal", -retcode)
-+ except OSError as e:
-+ print("Execution failed:", e)
-+
-+def getSamtoolsVersion():
-+ '''return samtools version'''
-+
-+ with subprocess.Popen(SAMTOOLS, shell=True, stderr=subprocess.PIPE).stderr as pipe:
-+ lines = b"".join(pipe.readlines())
-+
-+ if IS_PYTHON3:
-+ lines = lines.decode('ascii')
-+ return re.search( "Version:\s+(\S+)", lines).groups()[0]
-+
-+class BinaryTest(unittest.TestCase):
-+ '''test samtools command line commands and compare
-+ against pysam commands.
-+
-+ Tests fail, if the output is not binary identical.
-+ '''
-+
-+ first_time = True
-+
-+ # a dictionary of commands to test
-+ # first entry: (samtools output file, samtools command)
-+ # second entry: (pysam output file, (pysam function, pysam options) )
-+ commands = \
-+ {
-+ "view" :
-+ (
-+ ("ex1.view", "view ex1.bam > ex1.view"),
-+ ("pysam_ex1.view", (pysam.view, "ex1.bam" ) ),
-+ ),
-+ "view2" :
-+ (
-+ ("ex1.view", "view -bT ex1.fa -o ex1.view2 ex1.sam"),
-+ # note that -o ex1.view2 throws exception.
-+ ("pysam_ex1.view", (pysam.view, "-bT ex1.fa -oex1.view2 ex1.sam" ) ),
-+ ),
-+ "sort" :
-+ (
-+ ( "ex1.sort.bam", "sort ex1.bam ex1.sort" ),
-+ ( "pysam_ex1.sort.bam", (pysam.sort, "ex1.bam pysam_ex1.sort" ) ),
-+ ),
-+ "mpileup" :
-+ (
-+ ("ex1.pileup", "mpileup ex1.bam > ex1.pileup" ),
-+ ("pysam_ex1.mpileup", (pysam.mpileup, "ex1.bam" ) ),
-+ ),
-+ "depth" :
-+ (
-+ ("ex1.depth", "depth ex1.bam > ex1.depth" ),
-+ ("pysam_ex1.depth", (pysam.depth, "ex1.bam" ) ),
-+ ),
-+ "faidx" :
-+ (
-+ ("ex1.fa.fai", "faidx ex1.fa"),
-+ ("pysam_ex1.fa.fai", (pysam.faidx, "ex1.fa") ),
-+ ),
-+ "index":
-+ (
-+ ("ex1.bam.bai", "index ex1.bam" ),
-+ ("pysam_ex1.bam.bai", (pysam.index, "pysam_ex1.bam" ) ),
-+ ),
-+ "idxstats" :
-+ (
-+ ("ex1.idxstats", "idxstats ex1.bam > ex1.idxstats" ),
-+ ("pysam_ex1.idxstats", (pysam.idxstats, "pysam_ex1.bam" ) ),
-+ ),
-+ "fixmate" :
-+ (
-+ ("ex1.fixmate", "fixmate ex1.bam ex1.fixmate" ),
-+ ("pysam_ex1.fixmate", (pysam.fixmate, "pysam_ex1.bam pysam_ex1.fixmate") ),
-+ ),
-+ "flagstat" :
-+ (
-+ ("ex1.flagstat", "flagstat ex1.bam > ex1.flagstat" ),
-+ ("pysam_ex1.flagstat", (pysam.flagstat, "pysam_ex1.bam") ),
-+ ),
-+ "calmd" :
-+ (
-+ ("ex1.calmd", "calmd ex1.bam ex1.fa > ex1.calmd" ),
-+ ("pysam_ex1.calmd", (pysam.calmd, "pysam_ex1.bam ex1.fa") ),
-+ ),
-+ "merge" :
-+ (
-+ ("ex1.merge", "merge -f ex1.merge ex1.bam ex1.bam" ),
-+ # -f option does not work - following command will cause the subsequent
-+ # command to fail
-+ ("pysam_ex1.merge", (pysam.merge, "pysam_ex1.merge pysam_ex1.bam pysam_ex1.bam") ),
-+ ),
-+ "rmdup" :
-+ (
-+ ("ex1.rmdup", "rmdup ex1.bam ex1.rmdup" ),
-+ ("pysam_ex1.rmdup", (pysam.rmdup, "pysam_ex1.bam pysam_ex1.rmdup" )),
-+ ),
-+ "reheader" :
-+ (
-+ ( "ex1.reheader", "reheader ex1.bam ex1.bam > ex1.reheader"),
-+ ( "pysam_ex1.reheader", (pysam.reheader, "ex1.bam ex1.bam" ) ),
-+ ),
-+ "cat":
-+ (
-+ ( "ex1.cat", "cat ex1.bam ex1.bam > ex1.cat"),
-+ ( "pysam_ex1.cat", (pysam.cat, "ex1.bam ex1.bam" ) ),
-+ ),
-+ "targetcut":
-+ (
-+ ("ex1.targetcut", "targetcut ex1.bam > ex1.targetcut" ),
-+ ("pysam_ex1.targetcut", (pysam.targetcut, "pysam_ex1.bam") ),
-+ ),
-+ "phase":
-+ (
-+ ("ex1.phase", "phase ex1.bam > ex1.phase" ),
-+ ("pysam_ex1.phase", (pysam.phase, "pysam_ex1.bam") ),
-+ ),
-+ "import" :
-+ (
-+ ("ex1.bam", "import ex1.fa.fai ex1.sam.gz ex1.bam" ),
-+ ("pysam_ex1.bam", (pysam.samimport, "ex1.fa.fai ex1.sam.gz pysam_ex1.bam") ),
-+ ),
-+ "bam2fq":
-+ (
-+ ("ex1.bam2fq", "bam2fq ex1.bam > ex1.bam2fq" ),
-+ ("pysam_ex1.bam2fq", (pysam.bam2fq, "pysam_ex1.bam") ),
-+ ),
-+ "pad2unpad":
-+ (
-+ ("ex2.unpad", "pad2unpad -T ex1.fa ex2.bam > ex2.unpad" ),
-+ ("pysam_ex2.unpad", (pysam.pad2unpad, "-T ex1.fa ex2.bam") ),
-+ ),
-+ "bamshuf":
-+ (
-+ ("ex1.bamshuf.bam", "bamshuf ex1.bam ex1.bamshuf" ),
-+ ("pysam_ex1.bamshuf.bam", (pysam.bamshuf, "ex1.bam pysam_ex1.bamshuf") ),
-+ ),
-+ "bedcov":
-+ (
-+ ("ex1.bedcov", "bedcov ex1.bed ex1.bam > ex1.bedcov" ),
-+ ("pysam_ex1.bedcov", (pysam.bedcov, "ex1.bed ex1.bam") ),
-+ ),
-+ }
-+
-+ # some tests depend on others. The order specifies in which order
-+ # the samtools commands are executed.
-+ # The first three (faidx, import, index) need to be in that order,
-+ # the rest is arbitrary.
-+ order = ('faidx', 'import', 'index',
-+ # 'pileup1', 'pileup2', deprecated
-+ # 'glfview', deprecated
-+ 'view', 'view2',
-+ 'sort',
-+ 'mpileup',
-+ 'depth',
-+ 'idxstats',
-+ 'fixmate',
-+ 'flagstat',
-+ ## 'calmd',
-+ 'merge',
-+ 'rmdup',
-+ 'reheader',
-+ 'cat',
-+ 'bedcov',
-+ 'targetcut',
-+ 'phase',
-+ 'bamshuf',
-+ 'bam2fq',
-+ 'pad2unpad',
-+ )
-+
-+ def setUp( self ):
-+ '''setup tests.
-+
-+ For setup, all commands will be run before the first test is
-+ executed. Individual tests will then just compare the output
-+ files.
-+ '''
-+ if BinaryTest.first_time:
-+
-+ # remove previous files
-+ if os.path.exists( WORKDIR ):
-+ shutil.rmtree( WORKDIR )
-+ pass
-+
-+ # copy the source files to WORKDIR
-+ os.makedirs( WORKDIR )
-+
-+ shutil.copy( "ex1.fa", os.path.join( WORKDIR, "pysam_ex1.fa" ) )
-+ shutil.copy( "ex1.fa", os.path.join( WORKDIR, "ex1.fa" ) )
-+ shutil.copy( "ex1.sam.gz", os.path.join( WORKDIR, "ex1.sam.gz" ) )
-+ shutil.copy( "ex1.sam", os.path.join( WORKDIR, "ex1.sam" ) )
-+ shutil.copy( "ex2.bam", os.path.join( WORKDIR, "ex2.bam" ) )
-+
-+ # cd to workdir
-+ savedir = os.getcwd()
-+ os.chdir( WORKDIR )
-+
-+ for label in self.order:
-+ # print ("command=", label)
-+ command = self.commands[label]
-+ # build samtools command and target and run
-+ samtools_target, samtools_command = command[0]
-+ runSamtools( " ".join( (SAMTOOLS, samtools_command )))
-+
-+ # get pysam command and run
-+ try:
-+ pysam_target, pysam_command = command[1]
-+ except ValueError as msg:
-+ raise ValueError( "error while setting up %s=%s: %s" %\
-+ (label, command, msg) )
-+
-+ pysam_method, pysam_options = pysam_command
-+ try:
-+ output = pysam_method( *pysam_options.split(" "), raw=True)
-+ except pysam.SamtoolsError as msg:
-+ raise pysam.SamtoolsError( "error while executing %s: options=%s: msg=%s" %\
-+ (label, pysam_options, msg) )
-+
-+
-+ if ">" in samtools_command:
-+ with open( pysam_target, "wb" ) as outfile:
-+ if type(output) == list:
-+ if IS_PYTHON3:
-+ for line in output:
-+ outfile.write( line.encode('ascii') )
-+ else:
-+ for line in output: outfile.write( line )
-+ else:
-+ outfile.write(output)
-+
-+ os.chdir( savedir )
-+ BinaryTest.first_time = False
-+
-+ samtools_version = getSamtoolsVersion()
-+
-+
-+ def _r( s ):
-+ # patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a -> 0.1.12
-+ if s.count('-') > 0: s = s[0:s.find('-')]
-+ return re.sub( "[^0-9.]", "", s )
-+
-+ if _r(samtools_version) != _r( pysam.__samtools_version__):
-+ raise ValueError("versions of pysam/samtools and samtools differ: %s != %s" % \
-+ (pysam.__samtools_version__,
-+ samtools_version ))
-+
-+ def checkCommand( self, command ):
-+ if command:
-+ samtools_target, pysam_target = self.commands[command][0][0], self.commands[command][1][0]
-+ samtools_target = os.path.join( WORKDIR, samtools_target )
-+ pysam_target = os.path.join( WORKDIR, pysam_target )
-+ self.assertTrue( checkBinaryEqual( samtools_target, pysam_target ),
-+ "%s failed: files %s and %s are not the same" % (command, samtools_target, pysam_target) )
-+
-+ def testImport( self ):
-+ self.checkCommand( "import" )
-+
-+ def testIndex( self ):
-+ self.checkCommand( "index" )
-+
-+ def testSort( self ):
-+ self.checkCommand( "sort" )
-+
-+ def testMpileup( self ):
-+ self.checkCommand( "mpileup" )
-+
-+ def testDepth( self ):
-+ self.checkCommand( "depth" )
-+
-+ def testIdxstats( self ):
-+ self.checkCommand( "idxstats" )
-+
-+ def testFixmate( self ):
-+ self.checkCommand( "fixmate" )
-+
-+ def testFlagstat( self ):
-+ self.checkCommand( "flagstat" )
-+
-+ def testMerge( self ):
-+ self.checkCommand( "merge" )
-+
-+ def testRmdup( self ):
-+ self.checkCommand( "rmdup" )
-+
-+ def testReheader( self ):
-+ self.checkCommand( "reheader" )
-+
-+ def testCat( self ):
-+ self.checkCommand( "cat" )
-+
-+ def testTargetcut( self ):
-+ self.checkCommand( "targetcut" )
-+
-+ def testPhase( self ):
-+ self.checkCommand( "phase" )
-+
-+ def testBam2fq( self ):
-+ self.checkCommand( "bam2fq" )
-+
-+ def testBedcov( self ):
-+ self.checkCommand( "bedcov" )
-+
-+ def testBamshuf( self ):
-+ self.checkCommand( "bamshuf" )
-+
-+ def testPad2Unpad( self ):
-+ self.checkCommand( "pad2unpad" )
-+
-+ # def testPileup1( self ):
-+ # self.checkCommand( "pileup1" )
-+
-+ # def testPileup2( self ):
-+ # self.checkCommand( "pileup2" )
-+
-+ # deprecated
-+ # def testGLFView( self ):
-+ # self.checkCommand( "glfview" )
-+
-+ def testView( self ):
-+ self.checkCommand( "view" )
-+
-+ def testEmptyIndex( self ):
-+ self.assertRaises( IOError, pysam.index, "exdoesntexist.bam" )
-+
-+ def __del__(self):
-+ if os.path.exists( WORKDIR ):
-+ pass
-+ # shutil.rmtree( WORKDIR )
-+
-+class IOTest(unittest.TestCase):
-+ '''check if reading samfile and writing a samfile are consistent.'''
-+
-+ def checkEcho( self, input_filename,
-+ reference_filename,
-+ output_filename,
-+ input_mode, output_mode, use_template = True ):
-+ '''iterate through *input_filename* writing to *output_filename* and
-+ comparing the output to *reference_filename*.
-+
-+ The files are opened according to the *input_mode* and *output_mode*.
-+
-+ If *use_template* is set, the header is copied from infile using the
-+ template mechanism, otherwise target names and lengths are passed
-+ explicitely.
-+
-+ '''
-+
-+ infile = pysam.Samfile( input_filename, input_mode )
-+ if use_template:
-+ outfile = pysam.Samfile( output_filename, output_mode, template = infile )
-+ else:
-+ outfile = pysam.Samfile( output_filename, output_mode,
-+ referencenames = infile.references,
-+ referencelengths = infile.lengths,
-+ add_sq_text = False )
-+
-+ iter = infile.fetch()
-+
-+ for x in iter: outfile.write( x )
-+ infile.close()
-+ outfile.close()
-+
-+ self.assertTrue( checkBinaryEqual( reference_filename, output_filename),
-+ "files %s and %s are not the same" % (reference_filename, output_filename) )
-+
-+
-+ def testReadWriteBam( self ):
-+
-+ input_filename = "ex1.bam"
-+ output_filename = "pysam_ex1.bam"
-+ reference_filename = "ex1.bam"
-+
-+ self.checkEcho( input_filename, reference_filename, output_filename,
-+ "rb", "wb" )
-+
-+ def testReadWriteBamWithTargetNames( self ):
-+
-+ input_filename = "ex1.bam"
-+ output_filename = "pysam_ex1.bam"
-+ reference_filename = "ex1.bam"
-+
-+ self.checkEcho( input_filename, reference_filename, output_filename,
-+ "rb", "wb", use_template = False )
-+
-+ def testReadWriteSamWithHeader( self ):
-+
-+ input_filename = "ex2.sam"
-+ output_filename = "pysam_ex2.sam"
-+ reference_filename = "ex2.sam"
-+
-+ self.checkEcho( input_filename, reference_filename, output_filename,
-+ "r", "wh" )
-+
-+ def testReadWriteSamWithoutHeader( self ):
-+
-+ input_filename = "ex2.sam"
-+ output_filename = "pysam_ex2.sam"
-+ reference_filename = "ex1.sam"
-+
-+ self.checkEcho( input_filename, reference_filename, output_filename,
-+ "r", "w" )
-+
-+ def testReadSamWithoutTargetNames( self ):
-+ '''see issue 104.'''
-+ input_filename = "example_unmapped_reads_no_sq.sam"
-+
-+ # raise exception in default mode
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" )
-+
-+ # raise exception if no SQ files
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r",
-+ check_header = True)
-+
-+ infile = pysam.Samfile( input_filename, check_header = False, check_sq = False )
-+ result = list(infile.fetch())
-+
-+ def testReadBamWithoutTargetNames( self ):
-+ '''see issue 104.'''
-+ input_filename = "example_unmapped_reads_no_sq.bam"
-+
-+ # raise exception in default mode
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" )
-+
-+ # raise exception if no SQ files
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r",
-+ check_header = True)
-+
-+
-+ infile = pysam.Samfile( input_filename, check_header = False, check_sq = False )
-+ result = list(infile.fetch( until_eof = True))
-+
-+ def testReadSamWithoutHeader( self ):
-+ input_filename = "ex1.sam"
-+ output_filename = "pysam_ex1.sam"
-+ reference_filename = "ex1.sam"
-+
-+ # reading from a samfile without header is not implemented.
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" )
-+
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r",
-+ check_header = False )
-+
-+ def testReadUnformattedFile( self ):
-+ '''test reading from a file that is not bam/sam formatted'''
-+ input_filename = "example.vcf40"
-+
-+ # bam - file raise error
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "rb" )
-+
-+ # sam - file error, but can't fetch
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r" )
-+
-+ self.assertRaises( ValueError, pysam.Samfile, input_filename, "r",
-+ check_header = False)
-+
-+ def testBAMWithoutAlignedReads( self ):
-+ '''see issue 117'''
-+ input_filename = "test_unaligned.bam"
-+ samfile = pysam.Samfile( input_filename, "rb", check_sq = False )
-+ samfile.fetch( until_eof = True )
-+
-+ def testBAMWithShortBAI( self ):
-+ '''see issue 116'''
-+ input_filename = "example_bai.bam"
-+ samfile = pysam.Samfile( input_filename, "rb", check_sq = False )
-+ samfile.fetch( 'chr2' )
-+
-+ def testFetchFromClosedFile( self ):
-+
-+ samfile = pysam.Samfile( "ex1.bam", "rb" )
-+ samfile.close()
-+ self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120)
-+
-+ def testClosedFile( self ):
-+ '''test that access to a closed samfile raises ValueError.'''
-+
-+ samfile = pysam.Samfile( "ex1.bam", "rb" )
-+ samfile.close()
-+ self.assertRaises( ValueError, samfile.fetch, 'chr1', 100, 120)
-+ self.assertRaises( ValueError, samfile.pileup, 'chr1', 100, 120)
-+ self.assertRaises( ValueError, samfile.getrname, 0 )
-+ self.assertRaises( ValueError, samfile.tell )
-+ self.assertRaises( ValueError, samfile.seek, 0 )
-+ self.assertRaises( ValueError, getattr, samfile, "nreferences" )
-+ self.assertRaises( ValueError, getattr, samfile, "references" )
-+ self.assertRaises( ValueError, getattr, samfile, "lengths" )
-+ self.assertRaises( ValueError, getattr, samfile, "text" )
-+ self.assertRaises( ValueError, getattr, samfile, "header" )
-+
-+ # write on closed file
-+ self.assertEqual( 0, samfile.write(None) )
-+
-+ def testAutoDetection( self ):
-+ '''test if autodetection works.'''
-+
-+ samfile = pysam.Samfile( "ex3.sam" )
-+ self.assertRaises( ValueError, samfile.fetch, 'chr1' )
-+ samfile.close()
-+
-+ samfile = pysam.Samfile( "ex3.bam" )
-+ samfile.fetch('chr1')
-+ samfile.close()
-+
-+ def testReadingFromSamFileWithoutHeader( self ):
-+ '''read from samfile without header.
-+ '''
-+ samfile = pysam.Samfile( "ex7.sam", check_header = False, check_sq = False )
-+ self.assertRaises( NotImplementedError, samfile.__iter__ )
-+
-+ def testReadingFromFileWithoutIndex( self ):
-+ '''read from bam file without index.'''
-+
-+ assert not os.path.exists( "ex2.bam.bai" )
-+ samfile = pysam.Samfile( "ex2.bam", "rb" )
-+ self.assertRaises( ValueError, samfile.fetch )
-+ self.assertEqual( len(list( samfile.fetch(until_eof = True) )), 3270 )
-+
-+ def testReadingUniversalFileMode( self ):
-+ '''read from samfile without header.
-+ '''
-+
-+ input_filename = "ex2.sam"
-+ output_filename = "pysam_ex2.sam"
-+ reference_filename = "ex1.sam"
-+
-+ self.checkEcho( input_filename, reference_filename, output_filename,
-+ "rU", "w" )
-+
-+class TestFloatTagBug( unittest.TestCase ):
-+ '''see issue 71'''
-+
-+ def testFloatTagBug( self ):
-+ '''a float tag before another exposed a parsing bug in bam_aux_get.
-+
-+ Fixed in 0.1.19
-+ '''
-+ samfile = pysam.Samfile("tag_bug.bam")
-+ read = next(samfile.fetch(until_eof=True))
-+ self.assertTrue( ('XC',1) in read.tags )
-+ self.assertEqual(read.opt('XC'), 1)
-+
-+class TestLargeFieldBug( unittest.TestCase ):
-+ '''see issue 100'''
-+
-+ def testLargeFileBug( self ):
-+ '''when creating a read with a large entry in the tag field
-+ causes an errror:
-+ NotImplementedError: tags field too large
-+ '''
-+ samfile = pysam.Samfile("issue100.bam")
-+ read = next(samfile.fetch(until_eof=True))
-+ new_read = pysam.AlignedRead()
-+ new_read.tags = read.tags
-+ self.assertEqual( new_read.tags, read.tags )
-+
-+class TestTagParsing( unittest.TestCase ):
-+ '''tests checking the accuracy of tag setting and retrieval.'''
-+
-+ def makeRead( self ):
-+ a = pysam.AlignedRead()
-+ a.qname = "read_12345"
-+ a.tid = 0
-+ a.seq="ACGT" * 3
-+ a.flag = 0
-+ a.rname = 0
-+ a.pos = 1
-+ a.mapq = 20
-+ a.cigar = ( (0,10), (2,1), (0,25) )
-+ a.mrnm = 0
-+ a.mpos=200
-+ a.isize = 0
-+ a.qual ="1234" * 3
-+ # todo: create tags
-+ return a
-+
-+ def testNegativeIntegers( self ):
-+ x = -2
-+ aligned_read = self.makeRead()
-+ aligned_read.tags = [("XD", int(x) ) ]
-+ # print (aligned_read.tags)
-+
-+ def testNegativeIntegers2( self ):
-+ x = -2
-+ r = self.makeRead()
-+ r.tags = [("XD", int(x) ) ]
-+ outfile = pysam.Samfile( "test.bam",
-+ "wb",
-+ referencenames = ("chr1",),
-+ referencelengths = (1000,) )
-+ outfile.write (r )
-+ outfile.close()
-+
-+ def testCigarString( self ):
-+ r = self.makeRead()
-+ self.assertEqual( r.cigarstring, "10M1D25M" )
-+ r.cigarstring = "20M10D20M"
-+ self.assertEqual( r.cigar, [(0,20), (2,10), (0,20)])
-+
-+ def testLongTags( self ):
-+ '''see issue 115'''
-+
-+ r = self.makeRead()
-+ rg = 'HS2000-899_199.L3'
-+ tags = [('XC', 85), ('XT', 'M'), ('NM', 5), ('SM', 29), ('AM', 29), ('XM', 1), ('XO', 1), ('XG', 4), ('MD', '37^ACCC29T18'), ('XA','5,+11707,36M1I48M,2;21,-48119779,46M1I38M,2;hs37d5,-10060835,40M1D45M,3;5,+11508,36M1I48M,3;hs37d5,+6743812,36M1I48M,3;19,-59118894,46M1I38M,3;4,-191044002,6M1I78M,3;')]
-+
-+ r.tags = tags
-+ r.tags += [("RG",rg)] * 100
-+ tags += [("RG",rg)] * 100
-+
-+ self.assertEqual( tags, r.tags )
-+
-+class TestIteratorRow(unittest.TestCase):
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex1.bam","rb" )
-+
-+ def checkRange( self, rnge ):
-+ '''compare results from iterator with those from samtools.'''
-+ ps = list(self.samfile.fetch(region=rnge))
-+ sa = list(pysam.view( "ex1.bam", rnge, raw = True) )
-+ self.assertEqual( len(ps), len(sa), "unequal number of results for range %s: %i != %i" % (rnge, len(ps), len(sa) ))
-+ # check if the same reads are returned and in the same order
-+ for line, (a, b) in enumerate( list(zip( ps, sa )) ):
-+ d = b.split("\t")
-+ self.assertEqual( a.qname, d[0], "line %i: read id mismatch: %s != %s" % (line, a.rname, d[0]) )
-+ self.assertEqual( a.pos, int(d[3])-1, "line %i: read position mismatch: %s != %s, \n%s\n%s\n" % \
-+ (line, a.pos, int(d[3])-1,
-+ str(a), str(d) ) )
-+ if sys.version_info[0] < 3:
-+ qual = d[10]
-+ else:
-+ qual = d[10].encode('ascii')
-+ self.assertEqual( a.qual, qual, "line %i: quality mismatch: %s != %s, \n%s\n%s\n" % \
-+ (line, a.qual, qual,
-+ str(a), str(d) ) )
-+
-+ def testIteratePerContig(self):
-+ '''check random access per contig'''
-+ for contig in self.samfile.references:
-+ self.checkRange( contig )
-+
-+ def testIterateRanges(self):
-+ '''check random access per range'''
-+ for contig, length in zip(self.samfile.references, self.samfile.lengths):
-+ for start in range( 1, length, 90):
-+ self.checkRange( "%s:%i-%i" % (contig, start, start + 90) ) # this includes empty ranges
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+
-+class TestIteratorRowAll(unittest.TestCase):
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex1.bam","rb" )
-+
-+ def testIterate(self):
-+ '''compare results from iterator with those from samtools.'''
-+ ps = list(self.samfile.fetch())
-+ sa = list(pysam.view( "ex1.bam", raw = True) )
-+ self.assertEqual( len(ps), len(sa), "unequal number of results: %i != %i" % (len(ps), len(sa) ))
-+ # check if the same reads are returned
-+ for line, pair in enumerate( list(zip( ps, sa )) ):
-+ data = pair[1].split("\t")
-+ self.assertEqual( pair[0].qname, data[0], "read id mismatch in line %i: %s != %s" % (line, pair[0].rname, data[0]) )
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+class TestIteratorColumn(unittest.TestCase):
-+ '''test iterator column against contents of ex4.bam.'''
-+
-+ # note that samfile contains 1-based coordinates
-+ # 1D means deletion with respect to reference sequence
-+ #
-+ mCoverages = { 'chr1' : [ 0 ] * 20 + [1] * 36 + [0] * (100 - 20 -35 ),
-+ 'chr2' : [ 0 ] * 20 + [1] * 35 + [0] * (100 - 20 -35 ),
-+ }
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex4.bam","rb" )
-+
-+ def checkRange( self, contig, start = None, end = None, truncate = False ):
-+ '''compare results from iterator with those from samtools.'''
-+ # check if the same reads are returned and in the same order
-+ for column in self.samfile.pileup(contig, start, end, truncate = truncate):
-+ if truncate:
-+ self.assertGreaterEqual( column.pos, start )
-+ self.assertLess( column.pos, end )
-+ thiscov = len(column.pileups)
-+ refcov = self.mCoverages[self.samfile.getrname(column.tid)][column.pos]
-+ self.assertEqual( thiscov, refcov, "wrong coverage at pos %s:%i %i should be %i" % (self.samfile.getrname(column.tid), column.pos, thiscov, refcov))
-+
-+ def testIterateAll(self):
-+ '''check random access per contig'''
-+ self.checkRange( None )
-+
-+ def testIteratePerContig(self):
-+ '''check random access per contig'''
-+ for contig in self.samfile.references:
-+ self.checkRange( contig )
-+
-+ def testIterateRanges(self):
-+ '''check random access per range'''
-+ for contig, length in zip(self.samfile.references, self.samfile.lengths):
-+ for start in range( 1, length, 90):
-+ self.checkRange( contig, start, start + 90 ) # this includes empty ranges
-+
-+ def testInverse( self ):
-+ '''test the inverse, is point-wise pileup accurate.'''
-+ for contig, refseq in list(self.mCoverages.items()):
-+ refcolumns = sum(refseq)
-+ for pos, refcov in enumerate( refseq ):
-+ columns = list(self.samfile.pileup( contig, pos, pos+1) )
-+ if refcov == 0:
-+ # if no read, no coverage
-+ self.assertEqual( len(columns), refcov, "wrong number of pileup columns returned for position %s:%i, %i should be %i" %(contig,pos,len(columns), refcov) )
-+ elif refcov == 1:
-+ # one read, all columns of the read are returned
-+ self.assertEqual( len(columns), refcolumns, "pileup incomplete at position %i: got %i, expected %i " %\
-+ (pos, len(columns), refcolumns))
-+
-+ def testIterateTruncate( self ):
-+ '''check random access per range'''
-+ for contig, length in zip(self.samfile.references, self.samfile.lengths):
-+ for start in range( 1, length, 90):
-+ self.checkRange( contig, start, start + 90, truncate = True ) # this includes empty ranges
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+class TestIteratorColumn2(unittest.TestCase):
-+ '''test iterator column against contents of ex1.bam.'''
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex1.bam","rb" )
-+
-+ def testStart( self ):
-+ #print self.samfile.fetch().next().pos
-+ #print self.samfile.pileup().next().pos
-+ pass
-+
-+ def testTruncate( self ):
-+ '''see issue 107.'''
-+ # note that ranges in regions start from 1
-+ p = self.samfile.pileup(region='chr1:170:172', truncate=True)
-+ columns = [ x.pos for x in p ]
-+ self.assertEqual( len(columns), 3)
-+ self.assertEqual( columns, [169,170,171] )
-+
-+ p = self.samfile.pileup( 'chr1', 169, 172, truncate=True)
-+ columns = [ x.pos for x in p ]
-+
-+ self.assertEqual( len(columns), 3)
-+ self.assertEqual( columns, [169,170,171] )
-+
-+class TestAlignedReadFromBam(unittest.TestCase):
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex3.bam","rb" )
-+ self.reads=list(self.samfile.fetch())
-+
-+ def testARqname(self):
-+ self.assertEqual( self.reads[0].qname, "read_28833_29006_6945", "read name mismatch in read 1: %s != %s" % (self.reads[0].qname, "read_28833_29006_6945") )
-+ self.assertEqual( self.reads[1].qname, "read_28701_28881_323b", "read name mismatch in read 2: %s != %s" % (self.reads[1].qname, "read_28701_28881_323b") )
-+
-+ def testARflag(self):
-+ self.assertEqual( self.reads[0].flag, 99, "flag mismatch in read 1: %s != %s" % (self.reads[0].flag, 99) )
-+ self.assertEqual( self.reads[1].flag, 147, "flag mismatch in read 2: %s != %s" % (self.reads[1].flag, 147) )
-+
-+ def testARrname(self):
-+ self.assertEqual( self.reads[0].rname, 0, "chromosome/target id mismatch in read 1: %s != %s" % (self.reads[0].rname, 0) )
-+ self.assertEqual( self.reads[1].rname, 1, "chromosome/target id mismatch in read 2: %s != %s" % (self.reads[1].rname, 1) )
-+
-+ def testARpos(self):
-+ self.assertEqual( self.reads[0].pos, 33-1, "mapping position mismatch in read 1: %s != %s" % (self.reads[0].pos, 33-1) )
-+ self.assertEqual( self.reads[1].pos, 88-1, "mapping position mismatch in read 2: %s != %s" % (self.reads[1].pos, 88-1) )
-+
-+ def testARmapq(self):
-+ self.assertEqual( self.reads[0].mapq, 20, "mapping quality mismatch in read 1: %s != %s" % (self.reads[0].mapq, 20) )
-+ self.assertEqual( self.reads[1].mapq, 30, "mapping quality mismatch in read 2: %s != %s" % (self.reads[1].mapq, 30) )
-+
-+ def testARcigar(self):
-+ self.assertEqual( self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)], "read name length mismatch in read 1: %s != %s" % (self.reads[0].cigar, [(0, 10), (2, 1), (0, 25)]) )
-+ self.assertEqual( self.reads[1].cigar, [(0, 35)], "read name length mismatch in read 2: %s != %s" % (self.reads[1].cigar, [(0, 35)]) )
-+
-+ def testARcigarstring(self):
-+ self.assertEqual( self.reads[0].cigarstring, '10M1D25M' )
-+ self.assertEqual( self.reads[1].cigarstring, '35M' )
-+
-+ def testARmrnm(self):
-+ self.assertEqual( self.reads[0].mrnm, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].mrnm, 0) )
-+ self.assertEqual( self.reads[1].mrnm, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].mrnm, 1) )
-+ self.assertEqual( self.reads[0].rnext, 0, "mate reference sequence name mismatch in read 1: %s != %s" % (self.reads[0].rnext, 0) )
-+ self.assertEqual( self.reads[1].rnext, 1, "mate reference sequence name mismatch in read 2: %s != %s" % (self.reads[1].rnext, 1) )
-+
-+ def testARmpos(self):
-+ self.assertEqual( self.reads[0].mpos, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].mpos, 200-1) )
-+ self.assertEqual( self.reads[1].mpos, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].mpos, 500-1) )
-+ self.assertEqual( self.reads[0].pnext, 200-1, "mate mapping position mismatch in read 1: %s != %s" % (self.reads[0].pnext, 200-1) )
-+ self.assertEqual( self.reads[1].pnext, 500-1, "mate mapping position mismatch in read 2: %s != %s" % (self.reads[1].pnext, 500-1) )
-+
-+ def testARisize(self):
-+ self.assertEqual( self.reads[0].isize, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].isize, 167) )
-+ self.assertEqual( self.reads[1].isize, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].isize, 412) )
-+ self.assertEqual( self.reads[0].tlen, 167, "insert size mismatch in read 1: %s != %s" % (self.reads[0].tlen, 167) )
-+ self.assertEqual( self.reads[1].tlen, 412, "insert size mismatch in read 2: %s != %s" % (self.reads[1].tlen, 412) )
-+
-+ def testARseq(self):
-+ self.assertEqual( self.reads[0].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 1: %s != %s" % (self.reads[0].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") )
-+ self.assertEqual( self.reads[1].seq, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "sequence size mismatch in read 2: %s != %s" % (self.reads[1].seq, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") )
-+ self.assertEqual( self.reads[3].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "sequence mismatch in read 4: %s != %s" % (self.reads[3].seq, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") )
-+
-+ def testARqual(self):
-+ self.assertEqual( self.reads[0].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "quality string mismatch in read 1: %s != %s" % (self.reads[0].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") )
-+ self.assertEqual( self.reads[1].qual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "quality string mismatch in read 2: %s != %s" % (self.reads[1].qual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") )
-+ self.assertEqual( self.reads[3].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "quality string mismatch in read 3: %s != %s" % (self.reads[3].qual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") )
-+
-+ def testARquery(self):
-+ self.assertEqual( self.reads[0].query, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG", "query mismatch in read 1: %s != %s" % (self.reads[0].query, b"AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG") )
-+ self.assertEqual( self.reads[1].query, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA", "query size mismatch in read 2: %s != %s" % (self.reads[1].query, b"ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA") )
-+ self.assertEqual( self.reads[3].query, b"TAGCTAGCTACCTATATCTTGGTCTT", "query mismatch in read 4: %s != %s" % (self.reads[3].query, b"TAGCTAGCTACCTATATCTTGGTCTT") )
-+
-+ def testARqqual(self):
-+ self.assertEqual( self.reads[0].qqual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<", "qquality string mismatch in read 1: %s != %s" % (self.reads[0].qqual, b"<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<") )
-+ self.assertEqual( self.reads[1].qqual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<", "qquality string mismatch in read 2: %s != %s" % (self.reads[1].qqual, b"<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<") )
-+ self.assertEqual( self.reads[3].qqual, b"<<<<<<<<<<<<<<<<<:<9/,&,22", "qquality string mismatch in read 3: %s != %s" % (self.reads[3].qqual, b"<<<<<<<<<<<<<<<<<:<9/,&,22") )
-+
-+ def testPresentOptionalFields(self):
-+ self.assertEqual( self.reads[0].opt('NM'), 1, "optional field mismatch in read 1, NM: %s != %s" % (self.reads[0].opt('NM'), 1) )
-+ self.assertEqual( self.reads[0].opt('RG'), 'L1', "optional field mismatch in read 1, RG: %s != %s" % (self.reads[0].opt('RG'), 'L1') )
-+ self.assertEqual( self.reads[1].opt('RG'), 'L2', "optional field mismatch in read 2, RG: %s != %s" % (self.reads[1].opt('RG'), 'L2') )
-+ self.assertEqual( self.reads[1].opt('MF'), 18, "optional field mismatch in read 2, MF: %s != %s" % (self.reads[1].opt('MF'), 18) )
-+
-+ def testPairedBools(self):
-+ self.assertEqual( self.reads[0].is_paired, True, "is paired mismatch in read 1: %s != %s" % (self.reads[0].is_paired, True) )
-+ self.assertEqual( self.reads[1].is_paired, True, "is paired mismatch in read 2: %s != %s" % (self.reads[1].is_paired, True) )
-+ self.assertEqual( self.reads[0].is_proper_pair, True, "is proper pair mismatch in read 1: %s != %s" % (self.reads[0].is_proper_pair, True) )
-+ self.assertEqual( self.reads[1].is_proper_pair, True, "is proper pair mismatch in read 2: %s != %s" % (self.reads[1].is_proper_pair, True) )
-+
-+ def testTags( self ):
-+ self.assertEqual( self.reads[0].tags,
-+ [('NM', 1), ('RG', 'L1'),
-+ ('PG', 'P1'), ('XT', 'U')] )
-+ self.assertEqual( self.reads[1].tags,
-+ [('MF', 18), ('RG', 'L2'),
-+ ('PG', 'P2'),('XT', 'R') ] )
-+
-+ def testOpt( self ):
-+ self.assertEqual( self.reads[0].opt("XT"), "U" )
-+ self.assertEqual( self.reads[1].opt("XT"), "R" )
-+
-+ def testMissingOpt( self ):
-+ self.assertRaises( KeyError, self.reads[0].opt, "XP" )
-+
-+ def testEmptyOpt( self ):
-+ self.assertRaises( KeyError, self.reads[2].opt, "XT" )
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+class TestAlignedReadFromSam(TestAlignedReadFromBam):
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex3.sam","r" )
-+ self.reads=list(self.samfile.fetch())
-+
-+# needs to be implemented
-+# class TestAlignedReadFromSamWithoutHeader(TestAlignedReadFromBam):
-+#
-+# def setUp(self):
-+# self.samfile=pysam.Samfile( "ex7.sam","r" )
-+# self.reads=list(self.samfile.fetch())
-+
-+class TestHeaderSam(unittest.TestCase):
-+
-+ header = {'SQ': [{'LN': 1575, 'SN': 'chr1'},
-+ {'LN': 1584, 'SN': 'chr2'}],
-+ 'RG': [{'LB': 'SC_1', 'ID': 'L1', 'SM': 'NA12891', 'PU': 'SC_1_10', "CN":"name:with:colon"},
-+ {'LB': 'SC_2', 'ID': 'L2', 'SM': 'NA12891', 'PU': 'SC_2_12', "CN":"name:with:colon"}],
-+ 'PG': [{'ID': 'P1', 'VN': '1.0'}, {'ID': 'P2', 'VN': '1.1'}],
-+ 'HD': {'VN': '1.0'},
-+ 'CO' : [ 'this is a comment', 'this is another comment'],
-+ }
-+
-+ def compareHeaders( self, a, b ):
-+ '''compare two headers a and b.'''
-+ for ak,av in a.items():
-+ self.assertTrue( ak in b, "key '%s' not in '%s' " % (ak,b) )
-+ self.assertEqual( av, b[ak] )
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex3.sam","r" )
-+
-+ def testHeaders(self):
-+ self.compareHeaders( self.header, self.samfile.header )
-+ self.compareHeaders( self.samfile.header, self.header )
-+
-+ def testNameMapping( self ):
-+ for x, y in enumerate( ("chr1", "chr2")):
-+ tid = self.samfile.gettid( y )
-+ ref = self.samfile.getrname( x )
-+ self.assertEqual( tid, x )
-+ self.assertEqual( ref, y )
-+
-+ self.assertEqual( self.samfile.gettid("chr?"), -1 )
-+ self.assertRaises( ValueError, self.samfile.getrname, 2 )
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+class TestHeaderBam(TestHeaderSam):
-+
-+ def setUp(self):
-+ 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"
-+ bamfile = "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/phase3_EX_or_LC_only_alignment/data/HG00104/alignment/HG00104.chrom11.ILLUMINA.bwa.GBR.low_coverage.20130415.bam"
-+
-+ def testRead( self ):
-+
-+ # Skip fetching files from web when building the package
-+ #f = pysam.Samfile( self.bamfile, "rb" )
-+ #data = f.header.copy()
-+ #self.assertTrue( data )
-+ self.assertTrue( True )
-+
-+class TestUnmappedReads(unittest.TestCase):
-+
-+ def testSAM(self):
-+ samfile=pysam.Samfile( "ex5.sam","r" )
-+ self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 )
-+ samfile.close()
-+
-+ def testBAM(self):
-+ samfile=pysam.Samfile( "ex5.bam","rb" )
-+ self.assertEqual( len(list(samfile.fetch( until_eof = True))), 2 )
-+ samfile.close()
-+
-+class TestPileupObjects(unittest.TestCase):
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex1.bam","rb" )
-+
-+ def testPileupColumn(self):
-+ for pcolumn1 in self.samfile.pileup( region="chr1:105" ):
-+ if pcolumn1.pos == 104:
-+ self.assertEqual( pcolumn1.tid, 0, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn1.tid, 0) )
-+ self.assertEqual( pcolumn1.pos, 105-1, "position mismatch in position 1: %s != %s" % (pcolumn1.pos, 105-1) )
-+ self.assertEqual( pcolumn1.n, 2, "# reads mismatch in position 1: %s != %s" % (pcolumn1.n, 2) )
-+ for pcolumn2 in self.samfile.pileup( region="chr2:1480" ):
-+ if pcolumn2.pos == 1479:
-+ self.assertEqual( pcolumn2.tid, 1, "chromosome/target id mismatch in position 1: %s != %s" % (pcolumn2.tid, 1) )
-+ self.assertEqual( pcolumn2.pos, 1480-1, "position mismatch in position 1: %s != %s" % (pcolumn2.pos, 1480-1) )
-+ self.assertEqual( pcolumn2.n, 12, "# reads mismatch in position 1: %s != %s" % (pcolumn2.n, 12) )
-+
-+ def testPileupRead(self):
-+ for pcolumn1 in self.samfile.pileup( region="chr1:105" ):
-+ if pcolumn1.pos == 104:
-+ self.assertEqual( len(pcolumn1.pileups), 2, "# reads aligned to column mismatch in position 1: %s != %s" % (len(pcolumn1.pileups), 2) )
-+# self.assertEqual( pcolumn1.pileups[0] # need to test additional properties here
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+ def testIteratorOutOfScope( self ):
-+ '''test if exception is raised if pileup col is accessed after iterator is exhausted.'''
-+
-+ for pileupcol in self.samfile.pileup():
-+ pass
-+
-+ self.assertRaises( ValueError, getattr, pileupcol, "pileups" )
-+
-+class TestContextManager(unittest.TestCase):
-+
-+ def testManager( self ):
-+ with pysam.Samfile('ex1.bam', 'rb') as samfile:
-+ samfile.fetch()
-+ self.assertEqual( samfile._isOpen(), False )
-+
-+class TestExceptions(unittest.TestCase):
-+
-+ def setUp(self):
-+ self.samfile=pysam.Samfile( "ex1.bam","rb" )
-+
-+ def testMissingFile(self):
-+
-+ self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.bam", "rb" )
-+ self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.sam", "r" )
-+ self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.bam", "r" )
-+ self.assertRaises( IOError, pysam.Samfile, "exdoesntexist.sam", "rb" )
-+
-+ def testBadContig(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr88" )
-+
-+ def testMeaninglessCrap(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, "skljf" )
-+
-+ def testBackwardsOrderNewFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, 'chr1', 100, 10 )
-+
-+ def testBackwardsOrderOldFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, region="chr1:100-10")
-+
-+ def testOutOfRangeNegativeNewFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, -10 )
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", 5, 0 )
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", -5, -10 )
-+
-+ self.assertRaises( ValueError, self.samfile.count, "chr1", 5, -10 )
-+ self.assertRaises( ValueError, self.samfile.count, "chr1", 5, 0 )
-+ self.assertRaises( ValueError, self.samfile.count, "chr1", -5, -10 )
-+
-+ def testOutOfRangeNegativeOldFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5-10" )
-+ self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5-0" )
-+ self.assertRaises( ValueError, self.samfile.fetch, region="chr1:-5--10" )
-+
-+ self.assertRaises( ValueError, self.samfile.count, region="chr1:-5-10" )
-+ self.assertRaises( ValueError, self.samfile.count, region="chr1:-5-0" )
-+ self.assertRaises( ValueError, self.samfile.count, region="chr1:-5--10" )
-+
-+ def testOutOfRangNewFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999, 99999999999 )
-+ self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999, 99999999999 )
-+
-+ def testOutOfRangeLargeNewFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 )
-+ self.assertRaises( ValueError, self.samfile.count, "chr1", 9999999999999999999999999999999, 9999999999999999999999999999999999999999 )
-+
-+ def testOutOfRangeLargeOldFormat(self):
-+ self.assertRaises( ValueError, self.samfile.fetch, "chr1:99999999999999999-999999999999999999" )
-+ self.assertRaises( ValueError, self.samfile.count, "chr1:99999999999999999-999999999999999999" )
-+
-+ def testZeroToZero(self):
-+ '''see issue 44'''
-+ self.assertEqual( len(list(self.samfile.fetch('chr1', 0, 0))), 0)
-+
-+ def tearDown(self):
-+ self.samfile.close()
-+
-+class TestWrongFormat(unittest.TestCase):
-+ '''test cases for opening files not in bam/sam format.'''
-+
-+ def testOpenSamAsBam( self ):
-+ self.assertRaises( ValueError, pysam.Samfile, 'ex1.sam', 'rb' )
-+
-+ def testOpenBamAsSam( self ):
-+ # test fails, needs to be implemented.
-+ # sam.fetch() fails on reading, not on opening
-+ # self.assertRaises( ValueError, pysam.Samfile, 'ex1.bam', 'r' )
-+ pass
-+
-+ def testOpenFastaAsSam( self ):
-+ # test fails, needs to be implemented.
-+ # sam.fetch() fails on reading, not on opening
-+ # self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'r' )
-+ pass
-+
-+ def testOpenFastaAsBam( self ):
-+ self.assertRaises( ValueError, pysam.Samfile, 'ex1.fa', 'rb' )
-+
-+class TestFastaFile(unittest.TestCase):
-+
-+ mSequences = { 'chr1' :
-+ b"CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCGTCCATGGCCCAGCATTAGGGAGCTGTGGACCCTGCAGCCTGGCTGTGGGGGCCGCAGTGGCTGAGGGGTGCAGAGCCGAGTCACGGGGTTGCCAGCACAGGGGCTTAACCTCTGGTGACTGCCAGAGCTGCTGGCAAGCTAGAGTCCCATTTGGAGCCCCTCTAAGCCGTTCTATTTGTAATGAAAACTATATTTATGCTATTCAGTTCTAAATATAGAAATTGAAACAGCTGTGTTTAGTGCCTTTGTTCAACCCCCTTGCAACAACCTTGAGAACCCCAGGGAATTTGTCAATGTCAGGGAAGGAGCATTTTGTCAGTTACCAAATGTGTTTATTACCAGAGGGATGGAGGGAAGAGGGACGCTGAAGAACTTTGATGCCCTCTTCTTCCAAAGATGAAACGCGTAACTGCGCTCTCATTCACTCCAG [...]
-+ 'chr2' :
-+ b"TTCAAATGAACTTCTGTAATTGAAAAATTCATTTAAGAAATTACAAAATATAGTTGAAAGCTCTAACAATAGACTAAACCAAGCAGAAGAAAGAGGTTCAGAACTTGAAGACAAGTCTCTTATGAATTAACCCAGTCAGACAAAAATAAAGAAAAAAATTTTAAAAATGAACAGAGCTTTCAAGAAGTATGAGATTATGTAAAGTAACTGAACCTATGAGTCACAGGTATTCCTGAGGAAAAAGAAAAAGTGAGAAGTTTGGAAAAACTATTTGAGGAAGTAATTGGGGAAAACCTCTTTAGTCTTGCTAGAGATTTAGACATCTAAATGAAAGAGGCTCAAAGAATGCCAGGAAGATACATTGCAAGACAGACTTCATCAAGATATGTAGTCATCAGACTATCTAAAGTCAACATGAAGGAAAAAAATTCTAAAATCAGCAAGAGAAAAGCATACAGTCATCTAT [...]
-+ }
-+
-+ def setUp(self):
-+ self.file=pysam.Fastafile( "ex1.fa" )
-+
-+ def testFetch(self):
-+ for id, seq in list(self.mSequences.items()):
-+ self.assertEqual( seq, self.file.fetch( id ) )
-+ for x in range( 0, len(seq), 10):
-+ self.assertEqual( seq[x:x+10], self.file.fetch( id, x, x+10) )
-+ # test x:end
-+ self.assertEqual( seq[x:], self.file.fetch( id, x) )
-+ # test 0:x
-+ self.assertEqual( seq[:x], self.file.fetch( id, None, x) )
-+
-+
-+ # unknown sequence returns ""
-+ self.assertEqual( b"", self.file.fetch("chr12") )
-+
-+ def testOutOfRangeAccess( self ):
-+ '''test out of range access.'''
-+ # out of range access returns an empty string
-+ for contig, s in self.mSequences.items():
-+ self.assertEqual( self.file.fetch( contig, len(s), len(s)+1), b"" )
-+
-+ self.assertEqual( self.file.fetch( "chr3", 0 , 100), b"" )
-+
-+ def testFetchErrors( self ):
-+ self.assertRaises( ValueError, self.file.fetch )
-+ self.assertRaises( IndexError, self.file.fetch, "chr1", -1, 10 )
-+ self.assertRaises( ValueError, self.file.fetch, "chr1", 20, 10 )
-+
-+ def testLength( self ):
-+ self.assertEqual( len(self.file), 2 )
-+
-+ def tearDown(self):
-+ self.file.close()
-+
-+class TestAlignedRead(unittest.TestCase):
-+ '''tests to check if aligned read can be constructed
-+ and manipulated.
-+ '''
-+
-+ def checkFieldEqual( self, read1, read2, exclude = []):
-+ '''check if two reads are equal by comparing each field.'''
-+
-+ for x in ("qname", "seq", "flag",
-+ "rname", "pos", "mapq", "cigar",
-+ "mrnm", "mpos", "isize", "qual",
-+ "is_paired", "is_proper_pair",
-+ "is_unmapped", "mate_is_unmapped",
-+ "is_reverse", "mate_is_reverse",
-+ "is_read1", "is_read2",
-+ "is_secondary", "is_qcfail",
-+ "is_duplicate", "bin"):
-+ if x in exclude: continue
-+ self.assertEqual( getattr(read1, x), getattr(read2,x), "attribute mismatch for %s: %s != %s" %
-+ (x, getattr(read1, x), getattr(read2,x)))
-+
-+ def testEmpty( self ):
-+ a = pysam.AlignedRead()
-+ self.assertEqual( a.qname, None )
-+ self.assertEqual( a.seq, None )
-+ self.assertEqual( a.qual, None )
-+ self.assertEqual( a.flag, 0 )
-+ self.assertEqual( a.rname, 0 )
-+ self.assertEqual( a.mapq, 0 )
-+ self.assertEqual( a.cigar, None )
-+ self.assertEqual( a.tags, [] )
-+ self.assertEqual( a.mrnm, 0 )
-+ self.assertEqual( a.mpos, 0 )
-+ self.assertEqual( a.isize, 0 )
-+
-+ def buildRead( self ):
-+ '''build an example read.'''
-+
-+ a = pysam.AlignedRead()
-+ a.qname = "read_12345"
-+ a.seq="ACGT" * 10
-+ a.flag = 0
-+ a.rname = 0
-+ a.pos = 20
-+ a.mapq = 20
-+ a.cigar = ( (0,10), (2,1), (0,9), (1,1), (0,20) )
-+ a.mrnm = 0
-+ a.mpos=200
-+ a.isize=167
-+ a.qual="1234" * 10
-+ # todo: create tags
-+ return a
-+
-+ def testUpdate( self ):
-+ '''check if updating fields affects other variable length data
-+ '''
-+ a = self.buildRead()
-+ b = self.buildRead()
-+
-+ # check qname
-+ b.qname = "read_123"
-+ self.checkFieldEqual( a, b, "qname" )
-+ b.qname = "read_12345678"
-+ self.checkFieldEqual( a, b, "qname" )
-+ b.qname = "read_12345"
-+ self.checkFieldEqual( a, b)
-+
-+ # check cigar
-+ b.cigar = ( (0,10), )
-+ self.checkFieldEqual( a, b, "cigar" )
-+ b.cigar = ( (0,10), (2,1), (0,10) )
-+ self.checkFieldEqual( a, b, "cigar" )
-+ b.cigar = ( (0,10), (2,1), (0,9), (1,1), (0,20) )
-+ self.checkFieldEqual( a, b)
-+
-+ # check seq
-+ b.seq = "ACGT"
-+ self.checkFieldEqual( a, b, ("seq", "qual") )
-+ b.seq = "ACGT" * 3
-+ self.checkFieldEqual( a, b, ("seq", "qual") )
-+ b.seq = "ACGT" * 10
-+ self.checkFieldEqual( a, b, ("qual",))
-+
-+ # reset qual
-+ b = self.buildRead()
-+
-+ # check flags:
-+ for x in (
-+ "is_paired", "is_proper_pair",
-+ "is_unmapped", "mate_is_unmapped",
-+ "is_reverse", "mate_is_reverse",
-+ "is_read1", "is_read2",
-+ "is_secondary", "is_qcfail",
-+ "is_duplicate"):
-+ setattr( b, x, True )
-+ self.assertEqual( getattr(b, x), True )
-+ self.checkFieldEqual( a, b, ("flag", x,) )
-+ setattr( b, x, False )
-+ self.assertEqual( getattr(b, x), False )
-+ self.checkFieldEqual( a, b )
-+
-+ def testLargeRead( self ):
-+ '''build an example read.'''
-+
-+ a = pysam.AlignedRead()
-+ a.qname = "read_12345"
-+ a.seq="ACGT" * 200
-+ a.flag = 0
-+ a.rname = 0
-+ a.pos = 20
-+ a.mapq = 20
-+ a.cigar = ( (0, 4 * 200), )
-+ a.mrnm = 0
-+ a.mpos=200
-+ a.isize=167
-+ a.qual="1234" * 200
-+
-+ return a
-+
-+ def testTagParsing( self ):
-+ '''test for tag parsing
-+
-+ see http://groups.google.com/group/pysam-user-group/browse_thread/thread/67ca204059ea465a
-+ '''
-+ samfile=pysam.Samfile( "ex8.bam","rb" )
-+
-+ for entry in samfile:
-+ before = entry.tags
-+ entry.tags = entry.tags
-+ after = entry.tags
-+ self.assertEqual( after, before )
-+
-+ def testUpdateTlen( self ):
-+ '''check if updating tlen works'''
-+ a = self.buildRead()
-+ oldlen = a.tlen
-+ oldlen *= 2
-+ a.tlen = oldlen
-+ self.assertEqual( a.tlen, oldlen )
-+
-+ def testPositions( self ):
-+ a = self.buildRead()
-+ self.assertEqual( a.positions,
-+ [20, 21, 22, 23, 24, 25, 26, 27, 28, 29,
-+ 31, 32, 33, 34, 35, 36, 37, 38, 39,
-+ 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
-+ 50, 51, 52, 53, 54, 55, 56, 57, 58, 59] )
-+
-+ self.assertEqual( a.aligned_pairs,
-+ [(0, 20), (1, 21), (2, 22), (3, 23), (4, 24),
-+ (5, 25), (6, 26), (7, 27), (8, 28), (9, 29),
-+ (None, 30),
-+ (10, 31), (11, 32), (12, 33), (13, 34), (14, 35),
-+ (15, 36), (16, 37), (17, 38), (18, 39), (19, None),
-+ (20, 40), (21, 41), (22, 42), (23, 43), (24, 44),
-+ (25, 45), (26, 46), (27, 47), (28, 48), (29, 49),
-+ (30, 50), (31, 51), (32, 52), (33, 53), (34, 54),
-+ (35, 55), (36, 56), (37, 57), (38, 58), (39, 59)] )
-+
-+ self.assertEqual( a.positions, [x[1] for x in a.aligned_pairs if x[0] != None and x[1] != None] )
-+ # alen is the length of the aligned read in genome
-+ self.assertEqual( a.alen, a.aligned_pairs[-1][0] + 1 )
-+ # aend points to one beyond last aligned base in ref
-+ self.assertEqual( a.positions[-1], a.aend - 1 )
-+
-+class TestDeNovoConstruction(unittest.TestCase):
-+ '''check BAM/SAM file construction using ex6.sam
-+
-+ (note these are +1 coordinates):
-+
-+ read_28833_29006_6945 99 chr1 33 20 10M1D25M = 200 167 AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG <<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<< NM:i:1 RG:Z:L1
-+ read_28701_28881_323b 147 chr2 88 30 35M = 500 412 ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA <<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<< MF:i:18 RG:Z:L2
-+ '''
-+
-+ header = { 'HD': {'VN': '1.0'},
-+ 'SQ': [{'LN': 1575, 'SN': 'chr1'},
-+ {'LN': 1584, 'SN': 'chr2'}], }
-+
-+ bamfile = "ex6.bam"
-+ samfile = "ex6.sam"
-+
-+ def checkFieldEqual( self, read1, read2, exclude = []):
-+ '''check if two reads are equal by comparing each field.'''
-+
-+ for x in ("qname", "seq", "flag",
-+ "rname", "pos", "mapq", "cigar",
-+ "mrnm", "mpos", "isize", "qual",
-+ "bin",
-+ "is_paired", "is_proper_pair",
-+ "is_unmapped", "mate_is_unmapped",
-+ "is_reverse", "mate_is_reverse",
-+ "is_read1", "is_read2",
-+ "is_secondary", "is_qcfail",
-+ "is_duplicate"):
-+ if x in exclude: continue
-+ self.assertEqual( getattr(read1, x), getattr(read2,x), "attribute mismatch for %s: %s != %s" %
-+ (x, getattr(read1, x), getattr(read2,x)))
-+
-+ def setUp( self ):
-+
-+ a = pysam.AlignedRead()
-+ a.qname = "read_28833_29006_6945"
-+ a.seq="AGCTTAGCTAGCTACCTATATCTTGGTCTTGGCCG"
-+ a.flag = 99
-+ a.rname = 0
-+ a.pos = 32
-+ a.mapq = 20
-+ a.cigar = ( (0,10), (2,1), (0,25) )
-+ a.mrnm = 0
-+ a.mpos=199
-+ a.isize=167
-+ a.qual="<<<<<<<<<<<<<<<<<<<<<:<9/,&,22;;<<<"
-+ a.tags = ( ("NM", 1),
-+ ("RG", "L1") )
-+
-+ b = pysam.AlignedRead()
-+ b.qname = "read_28701_28881_323b"
-+ b.seq="ACCTATATCTTGGCCTTGGCCGATGCGGCCTTGCA"
-+ b.flag = 147
-+ b.rname = 1
-+ b.pos = 87
-+ b.mapq = 30
-+ b.cigar = ( (0,35), )
-+ b.mrnm = 1
-+ b.mpos=499
-+ b.isize=412
-+ b.qual="<<<<<;<<<<7;:<<<6;<<<<<<<<<<<<7<<<<"
-+ b.tags = ( ("MF", 18),
-+ ("RG", "L2") )
-+
-+ self.reads = (a,b)
-+
-+ def testSAMWholeFile( self ):
-+
-+ tmpfilename = "tmp_%i.sam" % id(self)
-+
-+ outfile = pysam.Samfile( tmpfilename, "wh", header = self.header )
-+
-+ for x in self.reads: outfile.write( x )
-+ outfile.close()
-+ self.assertTrue( checkBinaryEqual( tmpfilename, self.samfile ),
-+ "mismatch when construction SAM file, see %s %s" % (tmpfilename, self.samfile))
-+
-+ os.unlink( tmpfilename )
-+
-+ def testBAMPerRead( self ):
-+ '''check if individual reads are binary equal.'''
-+ infile = pysam.Samfile( self.bamfile, "rb")
-+
-+ others = list(infile)
-+ for denovo, other in zip( others, self.reads):
-+ self.checkFieldEqual( other, denovo )
-+ self.assertEqual( other.compare( denovo ), 0 )
-+
-+ def testSAMPerRead( self ):
-+ '''check if individual reads are binary equal.'''
-+ infile = pysam.Samfile( self.samfile, "r")
-+
-+ others = list(infile)
-+ for denovo, other in zip( others, self.reads):
-+ self.checkFieldEqual( other, denovo )
-+ self.assertEqual( other.compare( denovo), 0 )
-+
-+ def testBAMWholeFile( self ):
-+
-+ tmpfilename = "tmp_%i.bam" % id(self)
-+
-+ outfile = pysam.Samfile( tmpfilename, "wb", header = self.header )
-+
-+ for x in self.reads: outfile.write( x )
-+ outfile.close()
-+
-+ self.assertTrue( checkBinaryEqual( tmpfilename, self.bamfile ),
-+ "mismatch when construction BAM file, see %s %s" % (tmpfilename, self.bamfile))
-+
-+ os.unlink( tmpfilename )
-+
-+class TestDeNovoConstructionUserTags(TestDeNovoConstruction):
-+ '''test de novo construction with a header that contains lower-case tags.'''
-+
-+ header = { 'HD': {'VN': '1.0'},
-+ 'SQ': [{'LN': 1575, 'SN': 'chr1'},
-+ {'LN': 1584, 'SN': 'chr2'}],
-+ 'x1': {'A': 2, 'B': 5 },
-+ 'x3': {'A': 6, 'B': 5 },
-+ 'x2': {'A': 4, 'B': 5 } }
-+
-+ bamfile = "example_user_header.bam"
-+ samfile = "example_user_header.sam"
-+
-+class TestEmptyHeader( unittest.TestCase ):
-+ '''see issue 84.'''
-+
-+ def testEmptyHeader( self ):
-+
-+ s = pysam.Samfile('example_empty_header.bam')
-+ self.assertEqual( s.header, {'SQ': [{'LN': 1000, 'SN': 'chr1'}]} )
-+
-+class TestBTagSam( unittest.TestCase ):
-+ '''see issue 81.'''
-+
-+ compare = [ [100, 1, 91, 0, 7, 101, 0, 201, 96, 204, 0, 0, 87, 109, 0, 7, 97, 112, 1, 12, 78, 197, 0, 7, 100, 95, 101, 202, 0, 6, 0, 1, 186, 0, 84, 0, 244, 0, 0, 324, 0, 107, 195, 101, 113, 0, 102, 0, 104, 3, 0, 101, 1, 0, 212, 6, 0, 0, 1, 0, 74, 1, 11, 0, 196, 2, 197, 103, 0, 108, 98, 2, 7, 0, 1, 2, 194, 0, 180, 0, 108, 0, 203, 104, 16, 5, 205, 0, 0, 0, 1, 1, 100, 98, 0, 0, 204, 6, 0, 79, 0, 0, 101, 7, 109, 90, 265, 1, 27, 10, 109, 102, 9, 0, 292, 0, 110, 0, 0, 102, 112, 0, 0, 84, [...]
-+ [-100,200,-300,-400],
-+ [-100,12],
-+ [12,15],
-+ [-1.0,5.0,2.5] ]
-+
-+ filename = 'example_btag.sam'
-+
-+ def testRead( self ):
-+
-+ s = pysam.Samfile(self.filename)
-+ for x, read in enumerate(s):
-+ if x == 0:
-+ self.assertEqual( read.tags, [('RG', 'QW85I'), ('PG', 'tmap'), ('MD', '140'), ('NM', 0), ('AS', 140), ('FZ', [100, 1, 91, 0, 7, 101, 0, 201, 96, 204, 0, 0, 87, 109, 0, 7, 97, 112, 1, 12, 78, 197, 0, 7, 100, 95, 101, 202, 0, 6, 0, 1, 186, 0, 84, 0, 244, 0, 0, 324, 0, 107, 195, 101, 113, 0, 102, 0, 104, 3, 0, 101, 1, 0, 212, 6, 0, 0, 1, 0, 74, 1, 11, 0, 196, 2, 197, 103, 0, 108, 98, 2, 7, 0, 1, 2, 194, 0, 180, 0, 108, 0, 203, 104, 16, 5, 205, 0, 0, 0, 1, 1, 100, 98, 0, 0, [...]
-+ )
-+
-+ fz = dict(read.tags)["FZ"]
-+ self.assertEqual( fz, self.compare[x] )
-+ self.assertEqual( read.opt("FZ"), self.compare[x])
-+
-+ def testWrite( self ):
-+
-+ s = pysam.Samfile(self.filename)
-+ for read in s:
-+ before = read.tags
-+ read.tags = read.tags
-+ after = read.tags
-+ self.assertEqual( after, before )
-+
-+class TestBTagBam( TestBTagSam ):
-+ filename = 'example_btag.bam'
-+
-+class TestDoubleFetch(unittest.TestCase):
-+ '''check if two iterators on the same bamfile are independent.'''
-+
-+ def testDoubleFetch( self ):
-+
-+ samfile1 = pysam.Samfile('ex1.bam', 'rb')
-+
-+ for a,b in zip(samfile1.fetch(), samfile1.fetch()):
-+ self.assertEqual( a.compare( b ), 0 )
-+
-+ def testDoubleFetchWithRegion( self ):
-+
-+ samfile1 = pysam.Samfile('ex1.bam', 'rb')
-+ chr, start, stop = 'chr1', 200, 3000000
-+ self.assertTrue(len(list(samfile1.fetch ( chr, start, stop))) > 0) #just making sure the test has something to catch
-+
-+ for a,b in zip(samfile1.fetch( chr, start, stop), samfile1.fetch( chr, start, stop)):
-+ self.assertEqual( a.compare( b ), 0 )
-+
-+ def testDoubleFetchUntilEOF( self ):
-+
-+ samfile1 = pysam.Samfile('ex1.bam', 'rb')
-+
-+ for a,b in zip(samfile1.fetch( until_eof = True),
-+ samfile1.fetch( until_eof = True )):
-+ self.assertEqual( a.compare( b), 0 )
-+
-+class TestRemoteFileFTP(unittest.TestCase):
-+ '''test remote access.
-+
-+ '''
-+
-+ # Need to find an ftp server without password on standard
-+ # port.
-+
-+ url = "ftp://ftp.sanger.ac.uk/pub/rd/humanSequences/CV.bam"
-+ region = "1:1-1000"
-+
-+ def testFTPView( self ):
-+ return
-+ result = pysam.view( self.url, self.region )
-+ self.assertEqual( len(result), 36 )
-+
-+ def testFTPFetch( self ):
-+ return
-+ samfile = pysam.Samfile(self.url, "rb")
-+ result = list(samfile.fetch( region = self.region ))
-+ self.assertEqual( len(result), 36 )
-+
-+class TestLargeOptValues( unittest.TestCase ):
-+
-+ ints = ( 65536, 214748, 2147484, 2147483647 )
-+ floats = ( 65536.0, 214748.0, 2147484.0 )
-+
-+ def check( self, samfile ):
-+
-+ i = samfile.fetch()
-+ for exp in self.ints:
-+ rr = next(i)
-+ obs = rr.opt("ZP")
-+ self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr)))
-+
-+ for exp in [ -x for x in self.ints ]:
-+ rr = next(i)
-+ obs = rr.opt("ZP")
-+ self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr)))
-+
-+ for exp in self.floats:
-+ rr = next(i)
-+ obs = rr.opt("ZP")
-+ self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr)))
-+
-+ for exp in [ -x for x in self.floats ]:
-+ rr = next(i)
-+ obs = rr.opt("ZP")
-+ self.assertEqual( exp, obs, "expected %s, got %s\n%s" % (str(exp), str(obs), str(rr)))
-+
-+ def testSAM( self ):
-+ samfile = pysam.Samfile("ex10.sam", "r")
-+ self.check( samfile )
-+
-+ def testBAM( self ):
-+ samfile = pysam.Samfile("ex10.bam", "rb")
-+ self.check( samfile )
-+
-+# class TestSNPCalls( unittest.TestCase ):
-+# '''test pysam SNP calling ability.'''
-+
-+# def checkEqual( self, a, b ):
-+# for x in ("reference_base",
-+# "pos",
-+# "genotype",
-+# "consensus_quality",
-+# "snp_quality",
-+# "mapping_quality",
-+# "coverage" ):
-+# self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" %
-+# (x, getattr(a, x), getattr(b,x), str(a), str(b)))
-+
-+# def testAllPositionsViaIterator( self ):
-+# samfile = pysam.Samfile( "ex1.bam", "rb")
-+# fastafile = pysam.Fastafile( "ex1.fa" )
-+# try:
-+# refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base != "*"]
-+# except pysam.SamtoolsError:
-+# pass
-+
-+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
-+# calls = list(pysam.IteratorSNPCalls(i))
-+# for x,y in zip( refs, calls ):
-+# self.checkEqual( x, y )
-+
-+# def testPerPositionViaIterator( self ):
-+# # test pileup for each position. This is a slow operation
-+# # so this test is disabled
-+# return
-+# samfile = pysam.Samfile( "ex1.bam", "rb")
-+# fastafile = pysam.Fastafile( "ex1.fa" )
-+# for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
-+# if x.reference_base == "*": continue
-+# i = samfile.pileup( x.chromosome, x.pos, x.pos+1,
-+# fastafile = fastafile,
-+# stepper = "samtools" )
-+# z = [ zz for zz in pysam.IteratorSamtools(i) if zz.pos == x.pos ]
-+# self.assertEqual( len(z), 1 )
-+# self.checkEqual( x, z[0] )
-+
-+# def testPerPositionViaCaller( self ):
-+# # test pileup for each position. This is a fast operation
-+# samfile = pysam.Samfile( "ex1.bam", "rb")
-+# fastafile = pysam.Fastafile( "ex1.fa" )
-+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
-+# caller = pysam.SNPCaller( i )
-+
-+# for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
-+# if x.reference_base == "*": continue
-+# call = caller.call( x.chromosome, x.pos )
-+# self.checkEqual( x, call )
-+
-+# class TestIndelCalls( unittest.TestCase ):
-+# '''test pysam indel calling.'''
-+
-+# def checkEqual( self, a, b ):
-+
-+# for x in ("pos",
-+# "genotype",
-+# "consensus_quality",
-+# "snp_quality",
-+# "mapping_quality",
-+# "coverage",
-+# "first_allele",
-+# "second_allele",
-+# "reads_first",
-+# "reads_second",
-+# "reads_diff"):
-+# if b.genotype == "*/*" and x == "second_allele":
-+# # ignore test for second allele (positions chr2:439 and chr2:1512)
-+# continue
-+# self.assertEqual( getattr(a, x), getattr(b,x), "%s mismatch: %s != %s\n%s\n%s" %
-+# (x, getattr(a, x), getattr(b,x), str(a), str(b)))
-+
-+# def testAllPositionsViaIterator( self ):
-+
-+# samfile = pysam.Samfile( "ex1.bam", "rb")
-+# fastafile = pysam.Fastafile( "ex1.fa" )
-+# try:
-+# refs = [ x for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ) if x.reference_base == "*"]
-+# except pysam.SamtoolsError:
-+# pass
-+
-+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
-+# calls = [ x for x in list(pysam.IteratorIndelCalls(i)) if x != None ]
-+# for x,y in zip( refs, calls ):
-+# self.checkEqual( x, y )
-+
-+# def testPerPositionViaCaller( self ):
-+# # test pileup for each position. This is a fast operation
-+# samfile = pysam.Samfile( "ex1.bam", "rb")
-+# fastafile = pysam.Fastafile( "ex1.fa" )
-+# i = samfile.pileup( stepper = "samtools", fastafile = fastafile )
-+# caller = pysam.IndelCaller( i )
-+
-+# for x in pysam.pileup( "-c", "-f", "ex1.fa", "ex1.bam" ):
-+# if x.reference_base != "*": continue
-+# call = caller.call( x.chromosome, x.pos )
-+# self.checkEqual( x, call )
-+
-+class TestLogging( unittest.TestCase ):
-+ '''test around bug issue 42,
-+
-+ failed in versions < 0.4
-+ '''
-+
-+ def check( self, bamfile, log ):
-+
-+ if log:
-+ logger = logging.getLogger('franklin')
-+ logger.setLevel(logging.INFO)
-+ formatter = logging.Formatter('%(asctime)s %(levelname)s %(message)s')
-+ log_hand = logging.FileHandler('log.txt')
-+ log_hand.setFormatter(formatter)
-+ logger.addHandler(log_hand)
-+
-+ bam = pysam.Samfile(bamfile, 'rb')
-+ cols = bam.pileup()
-+ self.assertTrue( True )
-+
-+ def testFail1( self ):
-+ self.check( "ex9_fail.bam", False )
-+ self.check( "ex9_fail.bam", True )
-+
-+ def testNoFail1( self ):
-+ self.check( "ex9_nofail.bam", False )
-+ self.check( "ex9_nofail.bam", True )
-+
-+ def testNoFail2( self ):
-+ self.check( "ex9_nofail.bam", True )
-+ self.check( "ex9_nofail.bam", True )
-+
-+# TODOS
-+# 1. finish testing all properties within pileup objects
-+# 2. check exceptions and bad input problems (missing files, optional fields that aren't present, etc...)
-+# 3. check: presence of sequence
-+
-+class TestSamfileUtilityFunctions( unittest.TestCase ):
-+
-+ def testCount( self ):
-+
-+ samfile = pysam.Samfile( "ex1.bam", "rb" )
-+
-+ for contig in ("chr1", "chr2" ):
-+ for start in range( 0, 2000, 100 ):
-+ end = start + 1
-+ self.assertEqual( len( list( samfile.fetch( contig, start, end ) ) ),
-+ samfile.count( contig, start, end ) )
-+
-+ # test empty intervals
-+ self.assertEqual( len( list( samfile.fetch( contig, start, start ) ) ),
-+ samfile.count( contig, start, start ) )
-+
-+ # test half empty intervals
-+ self.assertEqual( len( list( samfile.fetch( contig, start ) ) ),
-+ samfile.count( contig, start ) )
-+
-+ def testMate( self ):
-+ '''test mate access.'''
-+
-+ with open( "ex1.sam", "rb" ) as inf:
-+ readnames = [ x.split(b"\t")[0] for x in inf.readlines() ]
-+ if sys.version_info[0] >= 3:
-+ readnames = [ name.decode('ascii') for name in readnames ]
-+
-+ counts = collections.defaultdict( int )
-+ for x in readnames: counts[x] += 1
-+
-+ samfile = pysam.Samfile( "ex1.bam", "rb" )
-+ for read in samfile.fetch():
-+ if not read.is_paired:
-+ self.assertRaises( ValueError, samfile.mate, read )
-+ elif read.mate_is_unmapped:
-+ self.assertRaises( ValueError, samfile.mate, read )
-+ else:
-+ if counts[read.qname] == 1:
-+ self.assertRaises( ValueError, samfile.mate, read )
-+ else:
-+ mate = samfile.mate( read )
-+ self.assertEqual( read.qname, mate.qname )
-+ self.assertEqual( read.is_read1, mate.is_read2 )
-+ self.assertEqual( read.is_read2, mate.is_read1 )
-+ self.assertEqual( read.pos, mate.mpos )
-+ self.assertEqual( read.mpos, mate.pos )
-+
-+ def testIndexStats( self ):
-+ '''test if total number of mapped/unmapped reads is correct.'''
-+
-+ samfile = pysam.Samfile( "ex1.bam", "rb" )
-+ self.assertEqual( samfile.mapped, 3235 )
-+ self.assertEqual( samfile.unmapped, 35 )
-+
-+class TestSamtoolsProxy( unittest.TestCase ):
-+ '''tests for sanity checking access to samtools functions.'''
-+
-+ def testIndex( self ):
-+ self.assertRaises( IOError, pysam.index, "missing_file" )
-+
-+ def testView( self ):
-+ # note that view still echos "open: No such file or directory"
-+ self.assertRaises( pysam.SamtoolsError, pysam.view, "missing_file" )
-+
-+ def testSort( self ):
-+ self.assertRaises( pysam.SamtoolsError, pysam.sort, "missing_file" )
-+
-+class TestSamfileIndex( unittest.TestCase):
-+
-+ def testIndex( self ):
-+ samfile = pysam.Samfile( "ex1.bam", "rb" )
-+ index = pysam.IndexedReads( samfile )
-+ index.build()
-+
-+ reads = collections.defaultdict( int )
-+
-+ for read in samfile: reads[read.qname] += 1
-+
-+ for qname, counts in reads.items():
-+ found = list(index.find( qname ))
-+ self.assertEqual( len(found), counts )
-+ for x in found: self.assertEqual( x.qname, qname )
-+
-+
-+if __name__ == "__main__":
-+ # build data files
-+ print ("building data files")
-+ subprocess.call( "make", shell=True)
-+ print ("starting tests")
-+ unittest.main()
-+ print ("completed tests")
diff --git a/debian/patches/series b/debian/patches/series
index 54addc7..7de87be 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
-import-setuptools-at-the-beginning.patch
+change-htslib-statement-to-link-to-debian
+adding-include-hts-dirs
diff --git a/debian/patches/use_external_htslib.patch b/debian/patches/use_external_htslib.patch
deleted file mode 100644
index 31bd62f..0000000
--- a/debian/patches/use_external_htslib.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Tue, 19 Aug 2014 21:26:37 +0200
-Description: setup.py allows to use external htslib which we do hereby
-
---- a/setup.py
-+++ b/setup.py
-@@ -32,7 +32,7 @@ IS_PYTHON3 = sys.version_info[0] >= 3
- # pysam.
- # external: use shared libhts.so compiled outside of
- # pysam
--HTSLIB = "separate"
-+HTSLIB = "external"
- HTSLIB_DIR = []
-
- # collect pysam version
-@@ -55,6 +55,7 @@ tabix_dest = os.path.abspath("tabix")
- if HTSLIB == 'external':
- htslib_sources = []
- chtslib_sources = []
-+ shared_htslib_sources = htslib_sources
- htslib_library_dirs = HTSLIB_DIR
- htslib_libraries = ['hts']
- elif HTSLIB == 'separate':
diff --git a/debian/rules b/debian/rules
index 423cfce..90b3ebe 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,6 +6,8 @@ DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
TESTPKG := $(DEBPKGNAME)-tests
HTSLIBDIR := /usr/lib/$(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
+export HTSLIB_INCLUDE_DIR=/usr/include
# DEB_BUILD_OPTIONS := nocheck
@@ -29,21 +31,21 @@ override_dh_clean:
fi
override_dh_auto_build: debian/savefiles
- HTSLIB_LIBRARY_DIR=$(HTSLIBDIR) HTSLIB_INCLUDE_DIR=/usr/include dh_auto_build
-
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
- LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
- --test-args='set -e; \
- cp -a $(CURDIR)/tests {build_dir}/tests ; \
- cd {build_dir}/tests && HTSLIB_LIBRARY_DIR=$(HTSLIBDIR) HTSLIB_INCLUDE_DIR=/usr/include PYTHONPATH={build_dir} {interpreter} ./pysam_test.py \
- && HTSLIB_LIBRARY_DIR=$(HTSLIBDIR) HTSLIB_INCLUDE_DIR=/usr/include PYTHONPATH={build_dir} {interpreter} ./tabix_test.py '
-endif
-
-override_dh_install-indep:
- dh_install -p $(TESTPKG)
- cd debian/$(TESTPKG)/usr/share/doc/python-pysam/tests; \
- make clean; \
- rm -f log.txt ; \
- chmod a+x tabix_test.py
+ dh_auto_build
+
+# override_dh_auto_test:
+# ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+# LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
+# --test-args='set -e; \
+# cp -a $(CURDIR)/tests ${build_dir}/tests ; \
+# cd {build_dir}/tests PYTHONPATH=${build_dir} ${interpreter} ./pysam_test.py \
+# && HTSLIB_LIBRARY_DIR=$(HTSLIBDIR) HTSLIB_INCLUDE_DIR=/usr/include PYTHONPATH=${build_dir} ${interpreter} ./tabix_test.py '
+# endif
+
+# override_dh_install-indep:
+# dh_install -p $(TESTPKG)
+# cd debian/$(TESTPKG)/usr/share/doc/python-pysam/tests; \
+# make clean; \
+# rm -f log.txt ; \
+# chmod a+x tabix_test.py
diff --git a/pysam.egg-info/PKG-INFO b/pysam.egg-info/PKG-INFO
deleted file mode 100644
index 354479b..0000000
--- a/pysam.egg-info/PKG-INFO
+++ /dev/null
@@ -1,16 +0,0 @@
-Metadata-Version: 1.1
-Name: pysam
-Version: 0.8.1
-Summary: pysam
-Home-page: https://github.com/pysam-developers/pysam
-Author: Andreas Heger
-Author-email: andreas.heger at gmail.com
-License: MIT
-Description:
-
- pysam
- *****
-
-
-Platform: ALL
-Requires: cython (>=0.20.1)
diff --git a/pysam.egg-info/SOURCES.txt b/pysam.egg-info/SOURCES.txt
deleted file mode 100644
index ee169f1..0000000
--- a/pysam.egg-info/SOURCES.txt
+++ /dev/null
@@ -1,204 +0,0 @@
-COPYING
-INSTALL
-KNOWN_BUGS
-MANIFEST.in
-README.rst
-THANKS
-pysam.py
-setup.cfg
-setup.py
-doc/Makefile
-doc/api.rst
-doc/conf.py
-doc/developer.rst
-doc/faq.rst
-doc/glossary.rst
-doc/index.rst
-doc/make.bat
-doc/out
-doc/release.rst
-doc/usage.rst
-htslib/bgzf.c
-htslib/bgzip.c
-htslib/config.h
-htslib/faidx.c
-htslib/hfile.c
-htslib/hfile_internal.h
-htslib/hfile_net.c
-htslib/hts.c
-htslib/kfunc.c
-htslib/knetfile.c
-htslib/kstring.c
-htslib/sam.c
-htslib/synced_bcf_reader.c
-htslib/tabix.c
-htslib/tbx.c
-htslib/vcf.c
-htslib/vcf_sweep.c
-htslib/vcfutils.c
-htslib/version.h
-htslib/cram/cram.h
-htslib/cram/cram_codecs.c
-htslib/cram/cram_codecs.h
-htslib/cram/cram_decode.c
-htslib/cram/cram_decode.h
-htslib/cram/cram_encode.c
-htslib/cram/cram_encode.h
-htslib/cram/cram_index.c
-htslib/cram/cram_index.h
-htslib/cram/cram_io.c
-htslib/cram/cram_io.h
-htslib/cram/cram_samtools.c
-htslib/cram/cram_samtools.h
-htslib/cram/cram_stats.c
-htslib/cram/cram_stats.h
-htslib/cram/cram_structs.h
-htslib/cram/files.c
-htslib/cram/mFILE.c
-htslib/cram/mFILE.h
-htslib/cram/md5.c
-htslib/cram/md5.h
-htslib/cram/misc.h
-htslib/cram/open_trace_file.c
-htslib/cram/open_trace_file.h
-htslib/cram/os.h
-htslib/cram/pooled_alloc.c
-htslib/cram/pooled_alloc.h
-htslib/cram/sam_header.c
-htslib/cram/sam_header.h
-htslib/cram/string_alloc.c
-htslib/cram/string_alloc.h
-htslib/cram/thread_pool.c
-htslib/cram/thread_pool.h
-htslib/cram/vlen.c
-htslib/cram/vlen.h
-htslib/cram/zfio.c
-htslib/cram/zfio.h
-htslib/htslib/bgzf.h
-htslib/htslib/faidx.h
-htslib/htslib/hfile.h
-htslib/htslib/hts.h
-htslib/htslib/hts_defs.h
-htslib/htslib/kfunc.h
-htslib/htslib/khash.h
-htslib/htslib/khash_str2int.h
-htslib/htslib/klist.h
-htslib/htslib/knetfile.h
-htslib/htslib/kseq.h
-htslib/htslib/ksort.h
-htslib/htslib/kstring.h
-htslib/htslib/sam.h
-htslib/htslib/synced_bcf_reader.h
-htslib/htslib/tbx.h
-htslib/htslib/vcf.h
-htslib/htslib/vcf_sweep.h
-htslib/htslib/vcfutils.h
-pysam/Pileup.py
-pysam/TabProxies.c
-pysam/TabProxies.pxd
-pysam/TabProxies.pyx
-pysam/__init__.py
-pysam/calignmentfile.c
-pysam/calignmentfile.pxd
-pysam/calignmentfile.pyx
-pysam/cfaidx.c
-pysam/cfaidx.pxd
-pysam/cfaidx.pyx
-pysam/chtslib.c
-pysam/chtslib.pxd
-pysam/chtslib.pyx
-pysam/csamfile.c
-pysam/csamfile.pxd
-pysam/csamfile.pyx
-pysam/csamtools.c
-pysam/csamtools.pxd
-pysam/csamtools.pyx
-pysam/ctabix.c
-pysam/ctabix.pxd
-pysam/ctabix.pyx
-pysam/cvcf.c
-pysam/cvcf.pxd
-pysam/cvcf.pyx
-pysam/htslib_util.c
-pysam/htslib_util.h
-pysam/namedtuple.py
-pysam/pysam_stream.h
-pysam/pysam_util.c
-pysam/pysam_util.h
-pysam/samfile_util.c
-pysam/samfile_util.h
-pysam/tabix_util.c
-pysam/tabix_util.h
-pysam/version.py
-pysam.egg-info/PKG-INFO
-pysam.egg-info/SOURCES.txt
-pysam.egg-info/dependency_links.txt
-pysam.egg-info/not-zip-safe
-pysam.egg-info/top_level.txt
-pysam/include/__init__.py
-samtools/bam.c.pysam.c
-samtools/bam.h
-samtools/bam2bcf.c.pysam.c
-samtools/bam2bcf.h
-samtools/bam2bcf_indel.c.pysam.c
-samtools/bam2depth.c.pysam.c
-samtools/bam_aux.c.pysam.c
-samtools/bam_cat.c.pysam.c
-samtools/bam_color.c.pysam.c
-samtools/bam_endian.h
-samtools/bam_flags.c.pysam.c
-samtools/bam_import.c.pysam.c
-samtools/bam_index.c.pysam.c
-samtools/bam_lpileup.c.pysam.c
-samtools/bam_lpileup.h
-samtools/bam_mate.c.pysam.c
-samtools/bam_md.c.pysam.c
-samtools/bam_plbuf.c.pysam.c
-samtools/bam_plbuf.h
-samtools/bam_plcmd.c.pysam.c
-samtools/bam_reheader.c.pysam.c
-samtools/bam_rmdup.c.pysam.c
-samtools/bam_rmdupse.c.pysam.c
-samtools/bam_sort.c.pysam.c
-samtools/bam_split.c.pysam.c
-samtools/bam_stat.c.pysam.c
-samtools/bam_tview.c.pysam.c
-samtools/bam_tview.h
-samtools/bam_tview_curses.c.pysam.c
-samtools/bam_tview_html.c.pysam.c
-samtools/bamshuf.c.pysam.c
-samtools/bedcov.c.pysam.c
-samtools/bedidx.c.pysam.c
-samtools/cut_target.c.pysam.c
-samtools/errmod.c.pysam.c
-samtools/errmod.h
-samtools/faidx.c.pysam.c
-samtools/kaln.c.pysam.c
-samtools/kaln.h
-samtools/kprobaln.c
-samtools/kprobaln.c.pysam.c
-samtools/kprobaln.h
-samtools/padding.c.pysam.c
-samtools/phase.c.pysam.c
-samtools/pysam.h
-samtools/sam.c.pysam.c
-samtools/sam.h
-samtools/sam_header.c.pysam.c
-samtools/sam_header.h
-samtools/sam_view.c.pysam.c
-samtools/sample.c.pysam.c
-samtools/sample.h
-samtools/samtools.h
-samtools/stats.c.pysam.c
-samtools/stats_isize.c.pysam.c
-samtools/stats_isize.h
-samtools/version.h
-samtools/misc/ace2sam.c.pysam.c
-samtools/misc/md5.c.pysam.c
-samtools/misc/md5.h
-samtools/test/test.c.pysam.c
-samtools/test/test.h
-samtools/win32/xcurses.h
-samtools/win32/zconf.h
-samtools/win32/zlib.h
-tests/00README.txt
\ No newline at end of file
diff --git a/pysam.egg-info/dependency_links.txt b/pysam.egg-info/dependency_links.txt
deleted file mode 100644
index 8b13789..0000000
--- a/pysam.egg-info/dependency_links.txt
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/pysam.egg-info/not-zip-safe b/pysam.egg-info/not-zip-safe
deleted file mode 100644
index 8b13789..0000000
--- a/pysam.egg-info/not-zip-safe
+++ /dev/null
@@ -1 +0,0 @@
-
diff --git a/pysam.egg-info/top_level.txt b/pysam.egg-info/top_level.txt
deleted file mode 100644
index 23f03da..0000000
--- a/pysam.egg-info/top_level.txt
+++ /dev/null
@@ -1 +0,0 @@
-pysam
diff --git a/pysam/TabProxies.c b/pysam/TabProxies.c
deleted file mode 100644
index 06ef6b0..0000000
--- a/pysam/TabProxies.c
+++ /dev/null
@@ -1,14076 +0,0 @@
-/* Generated by Cython 0.20.1 on Fri Nov 21 19:49:04 2014 */
-
-#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#define CYTHON_ABI "0_20_1"
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #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
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if CYTHON_COMPILING_IN_PYPY
-#define Py_OptimizeFlag 0
-#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_As_int(o)
- #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \
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- "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"
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- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #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)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (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))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #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))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
-#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
-#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
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- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
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-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
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- #define __PYX_EXTERN_C extern
- #endif
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-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__pysam__TabProxies
-#define __PYX_HAVE_API__pysam__TabProxies
-#include "stdlib.h"
-#include "string.h"
-#include "stdint.h"
-#include "stdio.h"
-#include "pythread.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
-#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
-#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((char*)s)
-#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
-#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return u_end - u - 1;
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#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))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
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- int c;
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- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
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- PyExc_ValueError,
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- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
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-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
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- #endif /* __GNUC__ > 2 ... */
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-#endif /* __GNUC__ */
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-static const char *__pyx_filename;
-
-
-static const char *__pyx_f[] = {
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-struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_BedProxy;
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
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-struct __pyx_opt_args_5pysam_10TabProxies__charptr_to_str;
-struct __pyx_opt_args_5pysam_10TabProxies__force_str;
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- * u"""convert string or unicode object to bytes, assuming ascii encoding.
- * """
- */
-struct __pyx_opt_args_5pysam_10TabProxies__force_bytes {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "pysam/TabProxies.pyx":43
- * return _force_bytes(s)
- *
- * cdef _charptr_to_str(char* s, encoding="ascii"): # <<<<<<<<<<<<<<
- * if PY_MAJOR_VERSION < 3:
- * return s
- */
-struct __pyx_opt_args_5pysam_10TabProxies__charptr_to_str {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "pysam/TabProxies.pyx":49
- * return s.decode(encoding)
- *
- * cdef inline _force_str(object s, encoding="ascii"): # <<<<<<<<<<<<<<
- * """Return s converted to str type of current Python "
- * "(bytes in Py2, unicode in Py3)"""
- */
-struct __pyx_opt_args_5pysam_10TabProxies__force_str {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "pysam/TabProxies.pxd":41
- * ctypedef int uint64_t
- *
- * cdef class TupleProxy: # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
- char *data;
- char **fields;
- int nfields;
- int index;
- int nbytes;
- int offset;
- int is_modified;
- PyObject *encoding;
-};
-
-
-/* "pysam/TabProxies.pxd":63
- * cdef update(self, char * buffer, size_t nbytes)
- *
- * cdef class GTFProxy(TupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
-};
-
-
-/* "pysam/TabProxies.pxd":73
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- *
- * cdef class NamedTupleProxy(TupleProxy) : # <<<<<<<<<<<<<<
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- */
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- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
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-
-/* "pysam/TabProxies.pxd":76
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- * cdef:
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- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
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-
-/* "pysam/TabProxies.pxd":88
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- * cdef:
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-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
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-
-
-
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-struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy {
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- PyObject *(*present)(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *, char *, size_t);
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-
-
-/* "pysam/TabProxies.pyx":630
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-struct __pyx_vtabstruct_5pysam_10TabProxies_NamedTupleProxy {
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- */
-
-struct __pyx_vtabstruct_5pysam_10TabProxies_BedProxy {
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-
-/* "pysam/TabProxies.pyx":724
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-struct __pyx_vtabstruct_5pysam_10TabProxies_VCFProxy {
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- #define __Pyx_GIVEREF(r)
- #define __Pyx_XINCREF(r) Py_XINCREF(r)
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- #define __Pyx_XGOTREF(r)
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-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
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-static PyObject *__Pyx_GetBuiltinName(PyObject *name); /*proto*/
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-#include <string.h>
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-static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
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-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
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-static void __Pyx_WriteUnraisable(const char *name, int clineno,
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-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
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-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
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-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
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-static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
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-static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) {
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-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); /*proto*/
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-static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) {
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-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed); /*proto*/
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-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/
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-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
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- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
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- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
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-static double __Pyx__PyObject_AsDouble(PyObject* obj); /* proto */
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-#define __Pyx_PyObject_AsDouble(obj) \
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- PyFloat_AsDouble(obj) : __Pyx__PyObject_AsDouble(obj))
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-#define __Pyx_PyObject_AsDouble(obj) \
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- PyFloat_AS_DOUBLE(obj) : __Pyx__PyObject_AsDouble(obj))
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-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
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- PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
- int has_cstart, int has_cstop, int wraparound);
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_ListComp_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);
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- return 0;
- }
- return PyList_Append(list, x);
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-#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
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-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
-static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
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-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL)
-static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_setattro))
- return tp->tp_setattro(obj, attr_name, value);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_setattr))
- return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
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-#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
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-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
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-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
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-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
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-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
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-static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *);
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-static int __Pyx_check_binary_version(void);
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-#if !defined(__Pyx_PyIdentifier_FromString)
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- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
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-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
-typedef struct {
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-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
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-
-/* Module declarations from 'cpython.version' */
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-/* Module declarations from 'cpython.ref' */
-
-/* Module declarations from 'cpython.exc' */
-
-/* Module declarations from 'cpython.module' */
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-/* Module declarations from 'cpython.mem' */
-
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-
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-/* Module declarations from 'libc.string' */
-
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-/* Module declarations from 'cpython.object' */
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-
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-
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-
-/* Module declarations from 'cpython.function' */
-
-/* Module declarations from 'cpython.method' */
-
-/* Module declarations from 'cpython.weakref' */
-
-/* Module declarations from 'cpython.getargs' */
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-/* Module declarations from 'cpython.pythread' */
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-static char *__pyx_f_5pysam_10TabProxies_StrOrEmpty(char *); /*proto*/
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-/* Implementation of 'pysam.TabProxies' */
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-static PyObject *__pyx_builtin_xrange;
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-static PyObject *__pyx_pf_5pysam_10TabProxies_10TupleProxy_14__iter__(struct __pyx_obj_5pysam_10TabProxies_TupleProxy *__pyx_v_self); /* proto */
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-static PyObject *__pyx_pf_5pysam_10TabProxies_2quote(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_v); /* proto */
-static int __pyx_pf_5pysam_10TabProxies_8GTFProxy___cinit__(struct __pyx_obj_5pysam_10TabProxies_GTFProxy *__pyx_v_self); /* proto */
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-static int __pyx_mp_ass_subscript_5pysam_10TabProxies_TupleProxy(PyObject *o, PyObject *i, PyObject *v) {
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-static PyMethodDef __pyx_methods_5pysam_10TabProxies_TupleProxy[] = {
- {__Pyx_NAMESTR("_getindex"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_10TupleProxy_5_getindex, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_10TupleProxy_4_getindex)},
- {__Pyx_NAMESTR("_setindex"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_10TupleProxy_9_setindex, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_10TupleProxy_8_setindex)},
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_10TupleProxy_16__next__)},
- {0, 0, 0, 0}
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-static PySequenceMethods __pyx_tp_as_sequence_TupleProxy = {
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- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- __pyx_sq_item_5pysam_10TabProxies_TupleProxy, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
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- 0, /*sq_inplace_concat*/
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-
-static PyMappingMethods __pyx_tp_as_mapping_TupleProxy = {
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_7__getitem__, /*mp_subscript*/
- __pyx_mp_ass_subscript_5pysam_10TabProxies_TupleProxy, /*mp_ass_subscript*/
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-
-static PyTypeObject __pyx_type_5pysam_10TabProxies_TupleProxy = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.TabProxies.TupleProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_10TabProxies_TupleProxy), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- &__pyx_tp_as_sequence_TupleProxy, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_TupleProxy, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_19__str__, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("Proxy class for access to parsed row as a tuple.\n\n This class represents a table row for fast read-access.\n\n Access to individual fields is via the [] operator.\n \n Only read-only access is implemented.\n\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_10TabProxies_TupleProxy, /*tp_traverse*/
- __pyx_tp_clear_5pysam_10TabProxies_TupleProxy, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
- __pyx_methods_5pysam_10TabProxies_TupleProxy, /*tp_methods*/
- 0, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
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- __pyx_tp_new_5pysam_10TabProxies_TupleProxy, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
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-
-static PyObject *__pyx_tp_new_5pysam_10TabProxies_GTFProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_10TabProxies_GTFProxy *p;
- PyObject *o = __pyx_tp_new_5pysam_10TabProxies_TupleProxy(t, a, k);
- if (unlikely(!o)) return 0;
- p = ((struct __pyx_obj_5pysam_10TabProxies_GTFProxy *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy*)__pyx_vtabptr_5pysam_10TabProxies_GTFProxy;
- if (unlikely(__pyx_pw_5pysam_10TabProxies_8GTFProxy_1__cinit__(o, __pyx_empty_tuple, NULL) < 0)) {
- Py_DECREF(o); o = 0;
- }
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-static void __pyx_tp_dealloc_5pysam_10TabProxies_GTFProxy(PyObject *o) {
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
- PyObject_GC_UnTrack(o);
- {
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- ++Py_REFCNT(o);
- __pyx_pw_5pysam_10TabProxies_8GTFProxy_3__dealloc__(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- PyObject_GC_Track(o);
- __pyx_tp_dealloc_5pysam_10TabProxies_TupleProxy(o);
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-static PyObject *__pyx_sq_item_5pysam_10TabProxies_GTFProxy(PyObject *o, Py_ssize_t i) {
- PyObject *r;
- PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
- r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
- Py_DECREF(x);
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-static PyObject *__pyx_tp_getattro_5pysam_10TabProxies_GTFProxy(PyObject *o, PyObject *n) {
- PyObject *v = PyObject_GenericGetAttr(o, n);
- if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Clear();
- v = __pyx_pw_5pysam_10TabProxies_8GTFProxy_17__getattr__(o, n);
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_contig(PyObject *o, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_contig(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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- }
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_source(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_10TabProxies_8GTFProxy_6source_1__get__(o);
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_source(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_feature(PyObject *o, CYTHON_UNUSED void *x) {
- return __pyx_pw_5pysam_10TabProxies_8GTFProxy_7feature_1__get__(o);
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_feature(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
- if (v) {
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- PyErr_SetString(PyExc_NotImplementedError, "__del__");
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_start(PyObject *o, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_start(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_end(PyObject *o, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_end(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_score(PyObject *o, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_score(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_strand(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_frame(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static PyObject *__pyx_getprop_5pysam_10TabProxies_8GTFProxy_attributes(PyObject *o, CYTHON_UNUSED void *x) {
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-static int __pyx_setprop_5pysam_10TabProxies_8GTFProxy_attributes(PyObject *o, PyObject *v, CYTHON_UNUSED void *x) {
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-static PyMethodDef __pyx_methods_5pysam_10TabProxies_GTFProxy[] = {
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- {__Pyx_NAMESTR("fromDict"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_7fromDict, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_6fromDict)},
- {__Pyx_NAMESTR("invert"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_11invert, METH_O, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_10invert)},
- {__Pyx_NAMESTR("keys"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_13keys, METH_NOARGS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_12keys)},
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- {__Pyx_NAMESTR("setAttribute"), (PyCFunction)__pyx_pw_5pysam_10TabProxies_8GTFProxy_19setAttribute, METH_VARARGS|METH_KEYWORDS, __Pyx_DOCSTR(__pyx_doc_5pysam_10TabProxies_8GTFProxy_18setAttribute)},
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-static struct PyGetSetDef __pyx_getsets_5pysam_10TabProxies_GTFProxy[] = {
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- {(char *)"source", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_source, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_source, __Pyx_DOCSTR(__pyx_k_feature_source), 0},
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- {(char *)"start", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_start, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_start, __Pyx_DOCSTR(__pyx_k_feature_start_in_0_based_open_cl), 0},
- {(char *)"end", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_end, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_end, __Pyx_DOCSTR(__pyx_k_feature_end_in_0_based_open_clos), 0},
- {(char *)"score", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_score, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_score, __Pyx_DOCSTR(__pyx_k_feature_score), 0},
- {(char *)"strand", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_strand, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_strand, __Pyx_DOCSTR(__pyx_k_feature_strand), 0},
- {(char *)"frame", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_frame, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_frame, __Pyx_DOCSTR(__pyx_k_feature_frame), 0},
- {(char *)"attributes", __pyx_getprop_5pysam_10TabProxies_8GTFProxy_attributes, __pyx_setprop_5pysam_10TabProxies_8GTFProxy_attributes, __Pyx_DOCSTR(__pyx_k_feature_attributes_as_a_string), 0},
- {0, 0, 0, 0, 0}
-};
-
-static PySequenceMethods __pyx_tp_as_sequence_GTFProxy = {
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*sq_length*/
- #else
- 0, /*sq_length*/
- #endif
- 0, /*sq_concat*/
- 0, /*sq_repeat*/
- __pyx_sq_item_5pysam_10TabProxies_GTFProxy, /*sq_item*/
- 0, /*sq_slice*/
- 0, /*sq_ass_item*/
- 0, /*sq_ass_slice*/
- 0, /*sq_contains*/
- 0, /*sq_inplace_concat*/
- 0, /*sq_inplace_repeat*/
-};
-
-static PyMappingMethods __pyx_tp_as_mapping_GTFProxy = {
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_13__len__, /*mp_length*/
- #else
- 0, /*mp_length*/
- #endif
- __pyx_pw_5pysam_10TabProxies_8GTFProxy_15__getitem__, /*mp_subscript*/
- 0, /*mp_ass_subscript*/
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-static PyTypeObject __pyx_type_5pysam_10TabProxies_GTFProxy = {
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- __Pyx_NAMESTR("pysam.TabProxies.GTFProxy"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_10TabProxies_GTFProxy), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_10TabProxies_GTFProxy, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- &__pyx_tp_as_sequence_GTFProxy, /*tp_as_sequence*/
- &__pyx_tp_as_mapping_GTFProxy, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- __pyx_pw_5pysam_10TabProxies_8GTFProxy_9__str__, /*tp_str*/
- __pyx_tp_getattro_5pysam_10TabProxies_GTFProxy, /*tp_getattro*/
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- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("Proxy class for access to GTF fields.\n\n This class represents a GTF entry for fast read-access.\n Write-access has been added as well, though some care must\n be taken. If any of the string fields (contig, source, ...)\n are set, the new value is tied to the lifetime of the\n argument that was supplied.\n\n The only exception is the attributes field when set from\n a dictionary - this field will manage its own memory.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_10TabProxies_TupleProxy, /*tp_traverse*/
- __pyx_tp_clear_5pysam_10TabProxies_TupleProxy, /*tp_clear*/
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- 0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_15__iter__, /*tp_iter*/
- #else
- 0, /*tp_iter*/
- #endif
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_10TabProxies_10TupleProxy_17__next__, /*tp_iternext*/
- #else
- 0, /*tp_iternext*/
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- __pyx_methods_5pysam_10TabProxies_GTFProxy, /*tp_methods*/
- 0, /*tp_members*/
- __pyx_getsets_5pysam_10TabProxies_GTFProxy, /*tp_getset*/
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- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
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- 0, /*tp_init*/
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- __pyx_tp_new_5pysam_10TabProxies_GTFProxy, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
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- 0, /*tp_subclasses*/
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-
-static PyObject *__pyx_tp_new_5pysam_10TabProxies_NamedTupleProxy(PyTypeObject *t, PyObject *a, PyObject *k) {
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-
-static PyObject *__pyx_tp_getattro_5pysam_10TabProxies_NamedTupleProxy(PyObject *o, PyObject *n) {
- PyObject *v = PyObject_GenericGetAttr(o, n);
- if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Clear();
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- return v;
-}
-
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- * import sys
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- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L0;
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- if (__pyx_m) {
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-#if CYTHON_REFNANNY
-static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
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- p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
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-#if PY_MAJOR_VERSION >= 3
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- 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))) {
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- return PyUnicode_FromUnicode(NULL, 0);
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-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
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-#if PY_VERSION_HEX >= 0x02060000
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
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-#endif
- result = (*call)(func, arg, kw);
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- Py_LeaveRecursiveCall();
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- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
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-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
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-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
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- Py_INCREF(tb);
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- PyErr_SetString(PyExc_TypeError,
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- goto raise_error;
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- #if PY_VERSION_HEX < 0x02050000
- if (PyClass_Check(type)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
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- value = Py_None;
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-#endif
- PyErr_NormalizeException(&type, &value, &tb);
- } else {
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- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- } else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
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- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
- }
- if (!instance_class) {
- 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 = PyObject_Call(type, args, NULL);
- 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 PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
- int full_traceback) {
- PyObject *old_exc, *old_val, *old_tb;
- PyObject *ctx;
- __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
- if (full_traceback) {
- Py_XINCREF(old_exc);
- Py_XINCREF(old_val);
- Py_XINCREF(old_tb);
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- PyErr_PrintEx(1);
- }
- #if PY_MAJOR_VERSION < 3
- ctx = PyString_FromString(name);
- #else
- ctx = PyUnicode_FromString(name);
- #endif
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- if (!ctx) {
- PyErr_WriteUnraisable(Py_None);
- } else {
- PyErr_WriteUnraisable(ctx);
- Py_DECREF(ctx);
- }
-}
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- 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;
- 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, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" 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 %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-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) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
- if (likely(PyList_CheckExact(L))) {
- if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
- } else {
- PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
- if (unlikely(!retval))
- return -1;
- Py_DECREF(retval);
- }
- return 0;
-}
-
-#if !CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
- return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL)
-}
-#endif
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (result) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
- PyObject *kwdict,
- const char* function_name,
- int kw_allowed)
-{
- PyObject* key = 0;
- Py_ssize_t pos = 0;
-#if CPYTHON_COMPILING_IN_PYPY
- if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
- goto invalid_keyword;
- return 1;
-#else
- while (PyDict_Next(kwdict, &pos, &key, 0)) {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
- #endif
- if (unlikely(!PyUnicode_Check(key)))
- goto invalid_keyword_type;
- }
- if ((!kw_allowed) && unlikely(key))
- goto invalid_keyword;
- return 1;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- return 0;
-#endif
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- const char *ps1, *ps2;
- Py_ssize_t length = PyBytes_GET_SIZE(s1);
- if (length != PyBytes_GET_SIZE(s2))
- return (equals == Py_NE);
- ps1 = PyBytes_AS_STRING(s1);
- ps2 = PyBytes_AS_STRING(s2);
- if (ps1[0] != ps2[0]) {
- return (equals == Py_NE);
- } else if (length == 1) {
- return (equals == Py_EQ);
- } else {
- int result = memcmp(ps1, ps2, (size_t)length);
- 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;
- }
-#endif
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
-#if PY_MAJOR_VERSION < 3
- PyObject* owned_ref = NULL;
-#endif
- int s1_is_unicode, s2_is_unicode;
- if (s1 == s2) {
- goto return_eq;
- }
- s1_is_unicode = PyUnicode_CheckExact(s1);
- s2_is_unicode = PyUnicode_CheckExact(s2);
-#if PY_MAJOR_VERSION < 3
- if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
- owned_ref = PyUnicode_FromObject(s2);
- if (unlikely(!owned_ref))
- return -1;
- s2 = owned_ref;
- s2_is_unicode = 1;
- } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
- owned_ref = PyUnicode_FromObject(s1);
- if (unlikely(!owned_ref))
- return -1;
- s1 = owned_ref;
- s1_is_unicode = 1;
- } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
- return __Pyx_PyBytes_Equals(s1, s2, equals);
- }
-#endif
- if (s1_is_unicode & s2_is_unicode) {
- Py_ssize_t length;
- int kind;
- void *data1, *data2;
- #if CYTHON_PEP393_ENABLED
- if (unlikely(PyUnicode_READY(s1) < 0) || unlikely(PyUnicode_READY(s2) < 0))
- return -1;
- #endif
- length = __Pyx_PyUnicode_GET_LENGTH(s1);
- if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
- goto return_ne;
- }
- kind = __Pyx_PyUnicode_KIND(s1);
- if (kind != __Pyx_PyUnicode_KIND(s2)) {
- goto return_ne;
- }
- data1 = __Pyx_PyUnicode_DATA(s1);
- data2 = __Pyx_PyUnicode_DATA(s2);
- if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
- goto return_ne;
- } else if (length == 1) {
- goto return_eq;
- } else {
- int result = memcmp(data1, data2, length * kind);
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & s2_is_unicode) {
- goto return_ne;
- } else if ((s2 == Py_None) & s1_is_unicode) {
- goto return_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;
- }
-return_eq:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ);
-return_ne:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_NE);
-#endif
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-static double __Pyx__PyObject_AsDouble(PyObject* obj) {
- PyObject* float_value;
-#if CYTHON_COMPILING_IN_PYPY
- float_value = PyNumber_Float(obj);
-#else
- PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number;
- if (likely(nb) && likely(nb->nb_float)) {
- float_value = nb->nb_float(obj);
- if (likely(float_value) && unlikely(!PyFloat_Check(float_value))) {
- PyErr_Format(PyExc_TypeError,
- "__float__ returned non-float (type %.200s)",
- Py_TYPE(float_value)->tp_name);
- Py_DECREF(float_value);
- goto bad;
- }
- } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
-#if PY_MAJOR_VERSION >= 3
- float_value = PyFloat_FromString(obj);
-#else
- float_value = PyFloat_FromString(obj, 0);
-#endif
- } else {
- PyObject* args = PyTuple_New(1);
- if (unlikely(!args)) goto bad;
- PyTuple_SET_ITEM(args, 0, obj);
- float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
- 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);
- return value;
- }
-bad:
- return (double)-1;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
- int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyMappingMethods* mp;
-#if PY_MAJOR_VERSION < 3
- PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
- if (likely(ms && ms->sq_slice)) {
- if (!has_cstart) {
- if (_py_start && (*_py_start != Py_None)) {
- cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
- if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstart = 0;
- }
- if (!has_cstop) {
- if (_py_stop && (*_py_stop != Py_None)) {
- cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
- if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstop = PY_SSIZE_T_MAX;
- }
- if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
- Py_ssize_t l = ms->sq_length(obj);
- if (likely(l >= 0)) {
- if (cstop < 0) {
- cstop += l;
- if (cstop < 0) cstop = 0;
- }
- if (cstart < 0) {
- cstart += l;
- if (cstart < 0) cstart = 0;
- }
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- goto bad;
- }
- }
- return ms->sq_slice(obj, cstart, cstop);
- }
-#endif
- mp = Py_TYPE(obj)->tp_as_mapping;
- if (likely(mp && mp->mp_subscript))
-#endif
- {
- PyObject* result;
- PyObject *py_slice, *py_start, *py_stop;
- if (_py_slice) {
- py_slice = *_py_slice;
- } else {
- PyObject* owned_start = NULL;
- PyObject* owned_stop = NULL;
- if (_py_start) {
- py_start = *_py_start;
- } else {
- if (has_cstart) {
- owned_start = py_start = PyInt_FromSsize_t(cstart);
- if (unlikely(!py_start)) goto bad;
- } else
- py_start = Py_None;
- }
- if (_py_stop) {
- py_stop = *_py_stop;
- } else {
- if (has_cstop) {
- owned_stop = py_stop = PyInt_FromSsize_t(cstop);
- if (unlikely(!py_stop)) {
- Py_XDECREF(owned_start);
- goto bad;
- }
- } else
- py_stop = Py_None;
- }
- py_slice = PySlice_New(py_start, py_stop, Py_None);
- Py_XDECREF(owned_start);
- Py_XDECREF(owned_stop);
- if (unlikely(!py_slice)) goto bad;
- }
-#if CYTHON_COMPILING_IN_CPYTHON
- result = mp->mp_subscript(obj, py_slice);
-#else
- result = PyObject_GetItem(obj, py_slice);
-#endif
- if (!_py_slice) {
- Py_DECREF(py_slice);
- }
- return result;
- }
- PyErr_Format(PyExc_TypeError,
- "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
-bad:
- return NULL;
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE void __Pyx_crop_slice(Py_ssize_t* _start, Py_ssize_t* _stop, Py_ssize_t* _length) {
- Py_ssize_t start = *_start, stop = *_stop, length = *_length;
- if (start < 0) {
- start += length;
- if (start < 0)
- start = 0;
- }
- if (stop < 0)
- stop += length;
- else if (stop > length)
- stop = length;
- *_length = stop - start;
- *_start = start;
- *_stop = stop;
-}
-static CYTHON_INLINE void __Pyx_copy_object_array(PyObject** CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) {
- PyObject *v;
- Py_ssize_t i;
- for (i = 0; i < length; i++) {
- v = dest[i] = src[i];
- Py_INCREF(v);
- }
-}
-static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(
- PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
- PyObject* dest;
- Py_ssize_t length = PyList_GET_SIZE(src);
- __Pyx_crop_slice(&start, &stop, &length);
- if (unlikely(length <= 0))
- return PyList_New(0);
- dest = PyList_New(length);
- if (unlikely(!dest))
- return NULL;
- __Pyx_copy_object_array(
- ((PyListObject*)src)->ob_item + start,
- ((PyListObject*)dest)->ob_item,
- length);
- return dest;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(
- PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
- PyObject* dest;
- Py_ssize_t length = PyTuple_GET_SIZE(src);
- __Pyx_crop_slice(&start, &stop, &length);
- if (unlikely(length <= 0))
- return PyTuple_New(0);
- dest = PyTuple_New(length);
- if (unlikely(!dest))
- return NULL;
- __Pyx_copy_object_array(
- ((PyTupleObject*)src)->ob_item + start,
- ((PyTupleObject*)dest)->ob_item,
- length);
- return dest;
-}
-#endif
-
-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;
- *tb = tstate->exc_traceback;
- 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;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *x) {
- const uint32_t neg_one = (uint32_t) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(uint32_t) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(uint32_t, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to uint32_t");
- return (uint32_t) -1;
- }
- return (uint32_t) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(uint32_t)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (uint32_t) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to uint32_t");
- return (uint32_t) -1;
- }
- if (sizeof(uint32_t) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(uint32_t) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(uint32_t, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(uint32_t)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(uint32_t) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(uint32_t) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(uint32_t) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(uint32_t, long, PyLong_AsLong)
- } else if (sizeof(uint32_t) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(uint32_t, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- uint32_t val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (uint32_t) -1;
- }
- } else {
- uint32_t val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (uint32_t) -1;
- val = __Pyx_PyInt_As_uint32_t(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
- const uint32_t neg_one = (uint32_t) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(uint32_t) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(uint32_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(uint32_t) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(uint32_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
- little, !is_unsigned);
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
-#if !CYTHON_COMPILING_IN_PYPY
-#if PY_VERSION_HEX >= 0x02060000
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
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diff --git a/pysam/cfaidx.c b/pysam/cfaidx.c
deleted file mode 100644
index 80a55a2..0000000
--- a/pysam/cfaidx.c
+++ /dev/null
@@ -1,8717 +0,0 @@
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-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
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- } else {
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- int c;
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- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
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-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
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- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
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-
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- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
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-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_d;
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-static const char *__pyx_filename;
-
-
-static const char *__pyx_f[] = {
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- "bool.pxd",
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-
-/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_6cfaidx_FastaFile;
-struct __pyx_obj_5pysam_6cfaidx_FastqProxy;
-struct __pyx_obj_5pysam_6cfaidx_FastqFile;
-struct __pyx_obj_5pysam_6cfaidx_Fastafile;
-struct __pyx_obj_5pysam_6cfaidx_Fastqfile;
-struct __pyx_obj_5pysam_6cfaidx___pyx_scope_struct___open;
-struct __pyx_obj_5pysam_6cfaidx___pyx_scope_struct_1_genexpr;
-struct __pyx_obj_5pysam_6cfaidx___pyx_scope_struct_2_genexpr;
-
-/* "pysam/cfaidx.pxd":14
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- *
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- * cdef faidx_t* fastafile
- */
-struct __pyx_obj_5pysam_6cfaidx_FastaFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6cfaidx_FastaFile *__pyx_vtab;
- PyObject *_filename;
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- PyObject *_lengths;
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-
-
-/* "pysam/cfaidx.pxd":21
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-
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-
-
-/* "pysam/cfaidx.pxd":38
- * pass
- *
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-
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-struct __pyx_vtabstruct_5pysam_6cfaidx_FastaFile {
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-
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-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE int __Pyx_ListComp_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_ListComp_Append(L,x) PyList_Append(L,x)
-#endif
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-static void __Pyx_WriteUnraisable(const char *name, int clineno,
- int lineno, const char *filename,
- int full_traceback); /*proto*/
-
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name); /*proto*/
-
-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-
-static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-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));
-}
-
-#include <string.h>
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
-
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
-
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
-
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
-
-static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) {
- PyObject *method, *result = NULL;
- if (unlikely(!args)) return NULL;
- method = __Pyx_PyObject_GetAttrStr(obj, method_name);
- if (unlikely(!method)) goto bad;
- result = __Pyx_PyObject_Call(method, args, NULL);
- Py_DECREF(method);
-bad:
- Py_DECREF(args);
- return result;
-}
-#define __Pyx_PyObject_CallMethod3(obj, name, arg1, arg2, arg3) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(3, arg1, arg2, arg3))
-#define __Pyx_PyObject_CallMethod2(obj, name, arg1, arg2) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(2, arg1, arg2))
-#define __Pyx_PyObject_CallMethod1(obj, name, arg1) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(1, arg1))
-#define __Pyx_PyObject_CallMethod0(obj, name) \
- __Pyx_PyObject_CallMethodTuple(obj, name, (Py_INCREF(__pyx_empty_tuple), __pyx_empty_tuple))
-
-#define __Pyx_Generator_USED
-#include <structmember.h>
-#include <frameobject.h>
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-typedef struct {
- PyObject_HEAD
- __pyx_generator_body_t body;
- PyObject *closure;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
- PyObject *gi_weakreflist;
- PyObject *classobj;
- PyObject *yieldfrom;
- int resume_label;
- char is_running;
-} __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);
-
-#if !defined(__Pyx_PyIdentifier_FromString)
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
-#else
- #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
-#endif
-#endif
-
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-
-
-/* Module declarations from 'libc.stdint' */
-
-/* Module declarations from 'libc.string' */
-
-/* Module declarations from 'libc.stdlib' */
-
-/* Module declarations from 'libc.stdio' */
-
-/* Module declarations from 'pysam.chtslib' */
-
-/* Module declarations from 'cpython.version' */
-
-/* Module declarations from 'cpython.ref' */
-
-/* Module declarations from 'cpython.exc' */
-
-/* Module declarations from 'cpython.module' */
-
-/* Module declarations from 'cpython.mem' */
-
-/* Module declarations from 'cpython.tuple' */
-
-/* Module declarations from 'cpython.list' */
-
-/* Module declarations from 'cpython.object' */
-
-/* Module declarations from 'cpython.sequence' */
-
-/* Module declarations from 'cpython.mapping' */
-
-/* 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' */
-
-/* Module declarations from 'cpython.int' */
-
-/* Module declarations from '__builtin__' */
-
-/* Module declarations from 'cpython.bool' */
-static PyTypeObject *__pyx_ptype_7cpython_4bool_bool = 0;
-
-/* Module declarations from 'cpython.long' */
-
-/* Module declarations from 'cpython.float' */
-
-/* Module declarations from '__builtin__' */
-
-/* Module declarations from 'cpython.complex' */
-static PyTypeObject *__pyx_ptype_7cpython_7complex_complex = 0;
-
-/* Module declarations from 'cpython.string' */
-
-/* Module declarations from 'cpython.unicode' */
-
-/* Module declarations from 'cpython.dict' */
-
-/* Module declarations from 'cpython.instance' */
-
-/* Module declarations from 'cpython.function' */
-
-/* Module declarations from 'cpython.method' */
-
-/* Module declarations from 'cpython.weakref' */
-
-/* Module declarations from 'cpython.getargs' */
-
-/* Module declarations from 'cpython.pythread' */
-
-/* Module declarations from 'cpython.pystate' */
-
-/* Module declarations from 'cpython.cobject' */
-
-/* Module declarations from 'cpython.oldbuffer' */
-
-/* Module declarations from 'cpython.set' */
-
-/* Module declarations from 'cpython.buffer' */
-
-/* Module declarations from 'cpython.bytes' */
-
-/* Module declarations from 'cpython.pycapsule' */
-
-/* Module declarations from 'cpython' */
-
-/* Module declarations from 'pysam.cfaidx' */
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx_FastaFile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx_FastqProxy = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx_FastqFile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx_Fastafile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx_Fastqfile = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx___pyx_scope_struct___open = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx___pyx_scope_struct_1_genexpr = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6cfaidx___pyx_scope_struct_2_genexpr = 0;
-static PyObject *__pyx_v_5pysam_6cfaidx__FILENAME_ENCODING = 0;
-static int __pyx_v_5pysam_6cfaidx_max_pos;
-static PyObject *__pyx_f_5pysam_6cfaidx_makeFastqProxy(kseq_t *); /*proto*/
-static PyObject *__pyx_f_5pysam_6cfaidx__encodeFilename(PyObject *); /*proto*/
-#define __Pyx_MODULE_NAME "pysam.cfaidx"
-int __pyx_module_is_main_pysam__cfaidx = 0;
-
-/* Implementation of 'pysam.cfaidx' */
-static PyObject *__pyx_builtin_TypeError;
-static PyObject *__pyx_builtin_ValueError;
-static PyObject *__pyx_builtin_IOError;
-static PyObject *__pyx_builtin_open;
-static PyObject *__pyx_builtin_zip;
-static PyObject *__pyx_builtin_IndexError;
-static PyObject *__pyx_builtin_StopIteration;
-static int __pyx_pf_5pysam_6cfaidx_9FastaFile___cinit__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_2_isOpen(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static Py_ssize_t __pyx_pf_5pysam_6cfaidx_9FastaFile_4__len__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_5_open_genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_5_open_3genexpr(PyObject *__pyx_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_6_open(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_8close(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_6cfaidx_9FastaFile_10__dealloc__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_8filename___get__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_10references___get__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_11nreferences___get__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_7lengths___get__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_12fetch(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__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_6cfaidx_9FastaFile_14get_reference_length(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastaFile_16__getitem__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static int __pyx_pf_5pysam_6cfaidx_9FastaFile_18__contains__(struct __pyx_obj_5pysam_6cfaidx_FastaFile *__pyx_v_self, PyObject *__pyx_v_reference); /* proto */
-static int __pyx_pf_5pysam_6cfaidx_10FastqProxy___init__(CYTHON_UNUSED struct __pyx_obj_5pysam_6cfaidx_FastqProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_10FastqProxy_4name___get__(struct __pyx_obj_5pysam_6cfaidx_FastqProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_10FastqProxy_8sequence___get__(struct __pyx_obj_5pysam_6cfaidx_FastqProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_10FastqProxy_7comment___get__(struct __pyx_obj_5pysam_6cfaidx_FastqProxy *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_10FastqProxy_7quality___get__(struct __pyx_obj_5pysam_6cfaidx_FastqProxy *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_6cfaidx_9FastqFile___cinit__(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastqFile_2_isOpen(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastqFile_4_open(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastqFile_6close(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_6cfaidx_9FastqFile_8__dealloc__(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastqFile_8filename___get__(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastqFile_10__iter__(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6cfaidx_9FastqFile_12__next__(struct __pyx_obj_5pysam_6cfaidx_FastqFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_tp_new_5pysam_6cfaidx_FastaFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx_FastqProxy(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx_FastqFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx_Fastafile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx_Fastqfile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx___pyx_scope_struct___open(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx___pyx_scope_struct_1_genexpr(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6cfaidx___pyx_scope_struct_2_genexpr(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static char __pyx_k_r[] = "r";
-static char __pyx_k__3[] = "\t";
-static char __pyx_k__8[] = "";
-static char __pyx_k_os[] = "os";
-static char __pyx_k_all[] = "__all__";
-static char __pyx_k_end[] = "end";
-static char __pyx_k_fai[] = ".fai";
-static char __pyx_k_sys[] = "sys";
-static char __pyx_k_zip[] = "zip";
-static char __pyx_k_args[] = "args";
-static char __pyx_k_exit[] = "__exit__";
-static char __pyx_k_main[] = "__main__";
-static char __pyx_k_open[] = "open";
-static char __pyx_k_path[] = "path";
-static char __pyx_k_send[] = "send";
-static char __pyx_k_test[] = "__test__";
-static char __pyx_k_ascii[] = "ascii";
-static char __pyx_k_close[] = "close";
-static char __pyx_k_enter[] = "__enter__";
-static char __pyx_k_fetch[] = "fetch";
-static char __pyx_k_s_i_i[] = "%s:%i-%i";
-static char __pyx_k_split[] = "split";
-static char __pyx_k_start[] = "start";
-static char __pyx_k_throw[] = "throw";
-static char __pyx_k_encode[] = "encode";
-static char __pyx_k_exists[] = "exists";
-static char __pyx_k_import[] = "__import__";
-static char __pyx_k_isOpen[] = "_isOpen";
-static char __pyx_k_open_2[] = "_open";
-static char __pyx_k_region[] = "region";
-static char __pyx_k_IOError[] = "IOError";
-static char __pyx_k_FastaFile[] = "FastaFile";
-static char __pyx_k_Fastafile[] = "Fastafile";
-static char __pyx_k_FastqFile[] = "FastqFile";
-static char __pyx_k_Fastqfile[] = "Fastqfile";
-static char __pyx_k_TypeError[] = "TypeError";
-static char __pyx_k_reference[] = "reference";
-static char __pyx_k_IS_PYTHON3[] = "IS_PYTHON3";
-static char __pyx_k_IndexError[] = "IndexError";
-static char __pyx_k_ValueError[] = "ValueError";
-static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
-static char __pyx_k_references[] = "references";
-static char __pyx_k_StopIteration[] = "StopIteration";
-static char __pyx_k_end_out_of_range_i[] = "end out of range (%i)";
-static char __pyx_k_getdefaultencoding[] = "getdefaultencoding";
-static char __pyx_k_start_out_of_range_i[] = "start out of range (%i)";
-static char __pyx_k_could_not_open_file_s[] = "could not open file `%s`";
-static char __pyx_k_getfilesystemencoding[] = "getfilesystemencoding";
-static char __pyx_k_calling_len_on_closed_file[] = "calling len() on closed file";
-static char __pyx_k_No_such_file_or_directory_s[] = "No such file or directory: %s";
-static char __pyx_k_could_not_locate_index_file[] = "could not locate index file";
-static char __pyx_k_no_sequence_region_supplied[] = "no sequence/region supplied.";
-static char __pyx_k_I_O_operation_on_closed_file[] = "I/O operation on closed file";
-static char __pyx_k_invalid_region_start_i_end_i[] = "invalid region: start (%i) > end (%i)";
-static char __pyx_k_Argument_must_be_string_or_unico[] = "Argument must be string or unicode.";
-static char __pyx_k_number_of_term_filename_associat[] = "number of :term:`filename` associated with this object.";
-static char __pyx_k_number_of_term_reference_sequenc[] = "number of :term:`reference` sequences in the file.";
-static char __pyx_k_tuple_with_the_lengths_of_term_r[] = "tuple with the lengths of :term:`reference` sequences.";
-static char __pyx_k_tuple_with_the_names_of_term_ref[] = "tuple with the names of :term:`reference` sequences.";
-static PyObject *__pyx_kp_u_Argument_must_be_string_or_unico;
-static PyObject *__pyx_n_s_FastaFile;
-static PyObject *__pyx_n_s_Fastafile;
-static PyObject *__pyx_n_s_FastqFile;
-static PyObject *__pyx_n_s_Fastqfile;
-static PyObject *__pyx_n_s_IOError;
-static PyObject *__pyx_n_s_IS_PYTHON3;
-static PyObject *__pyx_kp_s_I_O_operation_on_closed_file;
-static PyObject *__pyx_n_s_IndexError;
-static PyObject *__pyx_kp_s_No_such_file_or_directory_s;
-static PyObject *__pyx_n_s_StopIteration;
-static PyObject *__pyx_n_s_TypeError;
-static PyObject *__pyx_n_s_ValueError;
-static PyObject *__pyx_kp_s__3;
-static PyObject *__pyx_kp_b__8;
-static PyObject *__pyx_n_s_all;
-static PyObject *__pyx_n_s_args;
-static PyObject *__pyx_n_s_ascii;
-static PyObject *__pyx_kp_s_calling_len_on_closed_file;
-static PyObject *__pyx_n_s_close;
-static PyObject *__pyx_kp_s_could_not_locate_index_file;
-static PyObject *__pyx_kp_s_could_not_open_file_s;
-static PyObject *__pyx_n_s_encode;
-static PyObject *__pyx_n_s_end;
-static PyObject *__pyx_kp_s_end_out_of_range_i;
-static PyObject *__pyx_n_s_enter;
-static PyObject *__pyx_n_s_exists;
-static PyObject *__pyx_n_s_exit;
-static PyObject *__pyx_kp_b_fai;
-static PyObject *__pyx_n_s_fetch;
-static PyObject *__pyx_n_s_getdefaultencoding;
-static PyObject *__pyx_n_s_getfilesystemencoding;
-static PyObject *__pyx_n_s_import;
-static PyObject *__pyx_kp_s_invalid_region_start_i_end_i;
-static PyObject *__pyx_n_s_isOpen;
-static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_kp_s_no_sequence_region_supplied;
-static PyObject *__pyx_n_s_open;
-static PyObject *__pyx_n_s_open_2;
-static PyObject *__pyx_n_s_os;
-static PyObject *__pyx_n_s_path;
-static PyObject *__pyx_n_s_pyx_vtable;
-static PyObject *__pyx_n_s_reference;
-static PyObject *__pyx_n_s_references;
-static PyObject *__pyx_n_s_region;
-static PyObject *__pyx_kp_s_s_i_i;
-static PyObject *__pyx_n_s_send;
-static PyObject *__pyx_n_s_split;
-static PyObject *__pyx_n_s_start;
-static PyObject *__pyx_kp_s_start_out_of_range_i;
-static PyObject *__pyx_n_s_sys;
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- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- } else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
- }
- if (!instance_class) {
- 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 = PyObject_Call(type, args, NULL);
- 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 PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE int __Pyx_CheckKeywordStrings(
- PyObject *kwdict,
- const char* function_name,
- int kw_allowed)
-{
- PyObject* key = 0;
- Py_ssize_t pos = 0;
-#if CPYTHON_COMPILING_IN_PYPY
- if (!kw_allowed && PyDict_Next(kwdict, &pos, &key, 0))
- goto invalid_keyword;
- return 1;
-#else
- while (PyDict_Next(kwdict, &pos, &key, 0)) {
- #if PY_MAJOR_VERSION < 3
- if (unlikely(!PyString_CheckExact(key)) && unlikely(!PyString_Check(key)))
- #endif
- if (unlikely(!PyUnicode_Check(key)))
- goto invalid_keyword_type;
- }
- if ((!kw_allowed) && unlikely(key))
- goto invalid_keyword;
- return 1;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- return 0;
-#endif
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
- return 0;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseClosureNameError(const char *varname) {
- PyErr_Format(PyExc_NameError, "free variable '%s' referenced before assignment in enclosing scope", varname);
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (result) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-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;
- *tb = tstate->exc_traceback;
- 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;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-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;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- 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 (local_tb) {
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- }
- #endif
- Py_XINCREF(local_tb);
- Py_XINCREF(local_type);
- Py_XINCREF(local_value);
- *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;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- 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;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
- CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
- int full_traceback) {
- PyObject *old_exc, *old_val, *old_tb;
- PyObject *ctx;
- __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
- if (full_traceback) {
- Py_XINCREF(old_exc);
- Py_XINCREF(old_val);
- Py_XINCREF(old_tb);
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- PyErr_PrintEx(1);
- }
- #if PY_MAJOR_VERSION < 3
- ctx = PyString_FromString(name);
- #else
- ctx = PyUnicode_FromString(name);
- #endif
- __Pyx_ErrRestore(old_exc, old_val, old_tb);
- if (!ctx) {
- PyErr_WriteUnraisable(Py_None);
- } else {
- PyErr_WriteUnraisable(ctx);
- Py_DECREF(ctx);
- }
-}
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- 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;
- 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, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = *type;
- tstate->exc_value = *value;
- tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
- *type = tmp_type;
- *value = tmp_value;
- *tb = tmp_tb;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
- }
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
- PyObject* fake_module;
- PyTypeObject* cached_type = NULL;
- fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI);
- if (!fake_module) return NULL;
- Py_INCREF(fake_module);
- cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name);
- if (cached_type) {
- if (!PyType_Check((PyObject*)cached_type)) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s is not a type object",
- type->tp_name);
- goto bad;
- }
- if (cached_type->tp_basicsize != type->tp_basicsize) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s has the wrong size, try recompiling",
- type->tp_name);
- goto bad;
- }
- } else {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
- PyErr_Clear();
- if (PyType_Ready(type) < 0) goto bad;
- if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0)
- goto bad;
- Py_INCREF(type);
- cached_type = type;
- }
-done:
- Py_DECREF(fake_module);
- return cached_type;
-bad:
- Py_XDECREF(cached_type);
- cached_type = NULL;
- goto done;
-}
-
-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_GetAttr(ev, __pyx_n_s_args);
- Py_DECREF(ev);
- if (likely(args)) {
- value = PyObject_GetItem(args, 0);
- Py_DECREF(args);
- }
- if (unlikely(!value)) {
- __Pyx_ErrRestore(NULL, NULL, NULL);
- Py_INCREF(Py_None);
- value = Py_None;
- }
- }
-#endif
- *pvalue = value;
- return 0;
-}
-#endif
-static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
- PyObject *exc_type = self->exc_type;
- PyObject *exc_value = self->exc_value;
- PyObject *exc_traceback = self->exc_traceback;
- self->exc_type = NULL;
- self->exc_value = NULL;
- self->exc_traceback = NULL;
- Py_XDECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_traceback);
-}
-static CYTHON_INLINE
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
- if (unlikely(gen->is_running)) {
- PyErr_SetString(PyExc_ValueError,
- "generator already executing");
- 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,
- "can't send non-None value to a "
- "just-started generator");
- return NULL;
- }
- }
- if (unlikely(self->resume_label == -1)) {
- PyErr_SetNone(PyExc_StopIteration);
- return NULL;
- }
- 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);
-#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 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) {
- __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 = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value);
- }
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, value);
-}
-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_GetAttr(yf, __pyx_n_s_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);
-#else
- PyErr_SetNone(PyExc_GeneratorExit);
-#endif
- retval = __Pyx_Generator_SendEx(gen, NULL);
- if (retval) {
- Py_DECREF(retval);
- PyErr_SetString(PyExc_RuntimeError,
- "generator ignored GeneratorExit");
- return NULL;
- }
- 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))
- {
- 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 *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_GetAttr(yf, __pyx_n_s_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(gen, NULL);
-}
-static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_VISIT(gen->closure);
- Py_VISIT(gen->classobj);
- Py_VISIT(gen->yieldfrom);
- Py_VISIT(gen->exc_type);
- Py_VISIT(gen->exc_value);
- Py_VISIT(gen->exc_traceback);
- return 0;
-}
-static int __Pyx_Generator_clear(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->yieldfrom);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject_GC_UnTrack(gen);
- if (gen->gi_weakreflist != NULL)
- PyObject_ClearWeakRefs(self);
- if (gen->resume_label > 0) {
- PyObject_GC_Track(self);
-#if PY_VERSION_HEX >= 0x030400a1
- if (PyObject_CallFinalizerFromDealloc(self))
-#else
- Py_TYPE(gen)->tp_del(self);
- if (self->ob_refcnt > 0)
-#endif
- return; /* resurrected. :( */
- PyObject_GC_UnTrack(self);
- }
- __Pyx_Generator_clear(self);
- PyObject_GC_Del(gen);
-}
-static void __Pyx_Generator_del(PyObject *self) {
- PyObject *res;
- PyObject *error_type, *error_value, *error_traceback;
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- if (gen->resume_label <= 0)
- return ;
-#if PY_VERSION_HEX < 0x030400a1
- assert(self->ob_refcnt == 0);
- self->ob_refcnt = 1;
-#endif
- __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
- res = __Pyx_Generator_Close(self);
- if (res == NULL)
- PyErr_WriteUnraisable(self);
- else
- Py_DECREF(res);
- __Pyx_ErrRestore(error_type, error_value, error_traceback);
-#if PY_VERSION_HEX < 0x030400a1
- /* Undo the temporary resurrection; can't use DECREF here, it would
- * cause a recursive call.
- */
- assert(self->ob_refcnt > 0);
- if (--self->ob_refcnt == 0)
- return; /* this is the normal path out */
- /* close() resurrected it! Make it look like the original Py_DECREF
- * never happened.
- */
- {
- Py_ssize_t refcnt = self->ob_refcnt;
- _Py_NewReference(self);
- self->ob_refcnt = refcnt;
- }
-#if CYTHON_COMPILING_IN_CPYTHON
- assert(PyType_IS_GC(self->ob_type) &&
- _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
- /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
- * we need to undo that. */
- _Py_DEC_REFTOTAL;
-#endif
- /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
- * chain, so no more to do there.
- * If COUNT_ALLOCS, the original decref bumped tp_frees, and
- * _Py_NewReference bumped tp_allocs: both of those need to be
- * undone.
- */
-#ifdef COUNT_ALLOCS
- --Py_TYPE(self)->tp_frees;
- --Py_TYPE(self)->tp_allocs;
-#endif
-#endif
-}
-static PyMemberDef __pyx_Generator_memberlist[] = {
- {(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
- T_BOOL,
-#else
- T_BYTE,
-#endif
- offsetof(__pyx_GeneratorObject, is_running),
- READONLY,
- NULL},
- {0, 0, 0, 0, 0}
-};
-static PyMethodDef __pyx_Generator_methods[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
- {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
- {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
- {0, 0, 0, 0}
-};
-static PyTypeObject __pyx_GeneratorType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("generator"), /*tp_name*/
- sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_Generator_methods, /*tp_methods*/
- __pyx_Generator_memberlist, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
-#if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_del*/
-#else
- __Pyx_Generator_del, /*tp_del*/
-#endif
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-#if PY_VERSION_HEX >= 0x030400a1
- __Pyx_Generator_del, /*tp_finalize*/
-#endif
-};
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure) {
- __pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
- if (gen == NULL)
- return NULL;
- gen->body = body;
- gen->closure = closure;
- Py_XINCREF(closure);
- gen->is_running = 0;
- gen->resume_label = 0;
- gen->classobj = NULL;
- gen->yieldfrom = NULL;
- gen->exc_type = NULL;
- gen->exc_value = NULL;
- gen->exc_traceback = NULL;
- gen->gi_weakreflist = NULL;
- PyObject_GC_Track(gen);
- return gen;
-}
-static int __pyx_Generator_init(void) {
- __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
- __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
- __pyx_GeneratorType = __Pyx_FetchCommonType(&__pyx_GeneratorType_type);
- if (__pyx_GeneratorType == NULL) {
- return -1;
- }
- return 0;
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
-#if !CYTHON_COMPILING_IN_PYPY
-#if PY_VERSION_HEX >= 0x02060000
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- #if PY_VERSION_HEX < 0x02060000
- return PyInt_AsSsize_t(b);
- #else
- return PyLong_AsSsize_t(b);
- #endif
- }
- x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/pysam/chtslib.c b/pysam/chtslib.c
deleted file mode 100644
index 0c05607..0000000
--- a/pysam/chtslib.c
+++ /dev/null
@@ -1,3162 +0,0 @@
-/* Generated by Cython 0.20.1 on Fri Nov 21 19:49:04 2014 */
-
-#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#define CYTHON_ABI "0_20_1"
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #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
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if CYTHON_COMPILING_IN_PYPY
-#define Py_OptimizeFlag 0
-#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_As_int(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)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyClass_Type
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyType_Type
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #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 < 0x02060000
- #define Py_TPFLAGS_HAVE_VERSION_TAG 0
-#endif
-#if PY_VERSION_HEX < 0x02060000 && !defined(Py_TPFLAGS_IS_ABSTRACT)
- #define Py_TPFLAGS_IS_ABSTRACT 0
-#endif
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
- #define Py_TPFLAGS_HAVE_FINALIZE 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
- #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
- #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
- #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
-#else
- #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
- PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
-#endif
-#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
-#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
-#else
- #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
- #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
-#else
- #define __Pyx_PyBaseString_Check(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
- PyString_Check(obj) || PyUnicode_Check(obj))
- #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#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
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
- #define PyNumber_Int PyNumber_Long
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x030200A4
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #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)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (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))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #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))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
-#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
-#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__pysam__libchtslib
-#define __PYX_HAVE_API__pysam__libchtslib
-#include "string.h"
-#include "stdio.h"
-#include "pythread.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
-#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
-#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((char*)s)
-#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
-#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return u_end - u - 1;
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#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))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
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- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
-#if !CYTHON_COMPILING_IN_PYPY
-#if PY_VERSION_HEX >= 0x02060000
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
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diff --git a/pysam/csamfile.c b/pysam/csamfile.c
deleted file mode 100644
index c3e3252..0000000
--- a/pysam/csamfile.c
+++ /dev/null
@@ -1,2876 +0,0 @@
-/* Generated by Cython 0.20.1 on Fri Nov 21 19:49:04 2014 */
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-#define PY_SSIZE_T_CLEAN
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-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#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))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_d;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-
-static const char *__pyx_f[] = {
- "csamfile.pyx",
- "cfaidx.pxd",
- "calignmentfile.pxd",
- "type.pxd",
- "bool.pxd",
- "complex.pxd",
-};
-
-/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_6cfaidx_FastaFile;
-struct __pyx_obj_5pysam_6cfaidx_FastqProxy;
-struct __pyx_obj_5pysam_6cfaidx_FastqFile;
-struct __pyx_obj_5pysam_6cfaidx_Fastafile;
-struct __pyx_obj_5pysam_6cfaidx_Fastqfile;
-struct __pyx_obj_5pysam_14calignmentfile_AlignedSegment;
-struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile;
-struct __pyx_obj_5pysam_14calignmentfile_PileupColumn;
-struct __pyx_obj_5pysam_14calignmentfile_PileupRead;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRow;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowRegion;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowHead;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowAll;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowAllRefs;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowSelection;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorColumn;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorColumnRegion;
-struct __pyx_obj_5pysam_14calignmentfile_IteratorColumnAllRefs;
-struct __pyx_obj_5pysam_14calignmentfile_IndexedReads;
-struct __pyx_obj_5pysam_8csamfile_AlignedRead;
-struct __pyx_obj_5pysam_8csamfile_Samfile;
-struct __pyx_t_5pysam_14calignmentfile___iterdata;
-typedef struct __pyx_t_5pysam_14calignmentfile___iterdata __pyx_t_5pysam_14calignmentfile___iterdata;
-struct __pyx_opt_args_5pysam_14calignmentfile_14AlignedSegment_setTag;
-struct __pyx_opt_args_5pysam_14calignmentfile_14IteratorColumn_setupIteratorData;
-
-/* "calignmentfile.pxd":53
- * # Utility types
- *
- * ctypedef struct __iterdata: # <<<<<<<<<<<<<<
- * htsFile * htsfile
- * bam_hdr_t * header
- */
-struct __pyx_t_5pysam_14calignmentfile___iterdata {
- htsFile *htsfile;
- bam_hdr_t *header;
- hts_itr_t *iter;
- faidx_t *fastafile;
- int tid;
- char *seq;
- int seq_len;
-};
-
-/* "calignmentfile.pxd":72
- * # add an alignment tag with value to the AlignedSegment
- * # an existing tag of the same name will be replaced.
- * cpdef setTag( self, tag, value, value_type = ?, replace = ? ) # <<<<<<<<<<<<<<
- *
- * cdef class AlignmentFile:
- */
-struct __pyx_opt_args_5pysam_14calignmentfile_14AlignedSegment_setTag {
- int __pyx_n;
- PyObject *value_type;
- PyObject *replace;
-};
-
-/* "calignmentfile.pxd":179
- * cdef char * getSequence( self )
- * cdef setMask(self, mask)
- * cdef setupIteratorData(self, # <<<<<<<<<<<<<<
- * int tid,
- * int start,
- */
-struct __pyx_opt_args_5pysam_14calignmentfile_14IteratorColumn_setupIteratorData {
- int __pyx_n;
- int multiple_iterators;
-};
-
-/* "cfaidx.pxd":14
- * char *s
- *
- * cdef class FastaFile: # <<<<<<<<<<<<<<
- * cdef object _filename, _references, _lengths, reference2length
- * cdef faidx_t* fastafile
- */
-struct __pyx_obj_5pysam_6cfaidx_FastaFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6cfaidx_FastaFile *__pyx_vtab;
- PyObject *_filename;
- PyObject *_references;
- PyObject *_lengths;
- PyObject *reference2length;
- faidx_t *fastafile;
-};
-
-
-/* "cfaidx.pxd":21
- *
- *
- * cdef class FastqProxy: # <<<<<<<<<<<<<<
- * cdef kseq_t * _delegate
- *
- */
-struct __pyx_obj_5pysam_6cfaidx_FastqProxy {
- PyObject_HEAD
- kseq_t *_delegate;
-};
-
-
-/* "cfaidx.pxd":25
- *
- *
- * cdef class FastqFile: # <<<<<<<<<<<<<<
- * cdef object _filename
- * cdef gzFile fastqfile
- */
-struct __pyx_obj_5pysam_6cfaidx_FastqFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6cfaidx_FastqFile *__pyx_vtab;
- PyObject *_filename;
- gzFile fastqfile;
- kseq_t *entry;
-};
-
-
-/* "cfaidx.pxd":35
- *
- * # Compatibility Layer for pysam < 0.8
- * cdef class Fastafile(FastaFile): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6cfaidx_Fastafile {
- struct __pyx_obj_5pysam_6cfaidx_FastaFile __pyx_base;
-};
-
-
-/* "cfaidx.pxd":38
- * pass
- *
- * cdef class Fastqfile(FastqFile): # <<<<<<<<<<<<<<
- * pass
- */
-struct __pyx_obj_5pysam_6cfaidx_Fastqfile {
- struct __pyx_obj_5pysam_6cfaidx_FastqFile __pyx_base;
-};
-
-
-/* "calignmentfile.pxd":65
- * #
- * # Note: need to declare all C fields and methods here
- * cdef class AlignedSegment: # <<<<<<<<<<<<<<
- *
- * # object that this AlignedSegment represents
- */
-struct __pyx_obj_5pysam_14calignmentfile_AlignedSegment {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_14calignmentfile_AlignedSegment *__pyx_vtab;
- bam1_t *_delegate;
-};
-
-
-/* "calignmentfile.pxd":74
- * cpdef setTag( self, tag, value, value_type = ?, replace = ? )
- *
- * cdef class AlignmentFile: # <<<<<<<<<<<<<<
- *
- * cdef object _filename
- */
-struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_14calignmentfile_AlignmentFile *__pyx_vtab;
- PyObject *_filename;
- htsFile *htsfile;
- BGZF *fp;
- hts_idx_t *index;
- bam_hdr_t *header;
- int isbam;
- int isstream;
- int isremote;
- bam1_t *b;
- char *mode;
- int64_t start_offset;
-};
-
-
-/* "calignmentfile.pxd":111
- * cdef char * _getrname(self, int tid)
- *
- * cdef class PileupColumn: # <<<<<<<<<<<<<<
- * cdef bam_pileup1_t ** plp
- * cdef int tid
- */
-struct __pyx_obj_5pysam_14calignmentfile_PileupColumn {
- PyObject_HEAD
- bam_pileup1_t **plp;
- int tid;
- int pos;
- int n_pu;
-};
-
-
-/* "calignmentfile.pxd":117
- * cdef int n_pu
- *
- * cdef class PileupRead: # <<<<<<<<<<<<<<
- * cdef AlignedSegment _alignment
- * cdef int32_t _qpos
- */
-struct __pyx_obj_5pysam_14calignmentfile_PileupRead {
- PyObject_HEAD
- struct __pyx_obj_5pysam_14calignmentfile_AlignedSegment *_alignment;
- int32_t _qpos;
- int _indel;
- int _level;
- uint32_t _is_del;
- uint32_t _is_head;
- uint32_t _is_tail;
-};
-
-
-/* "calignmentfile.pxd":126
- * cdef uint32_t _is_tail
- *
- * cdef class IteratorRow: # <<<<<<<<<<<<<<
- * cdef int retval
- * cdef bam1_t * b
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRow {
- PyObject_HEAD
- int retval;
- bam1_t *b;
- struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *samfile;
- htsFile *htsfile;
- bam_hdr_t *header;
- int owns_samfile;
-};
-
-
-/* "calignmentfile.pxd":134
- * cdef int owns_samfile
- *
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef hts_itr_t * iter
- * cdef bam1_t * getCurrent( self )
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowRegion {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_14calignmentfile_IteratorRowRegion *__pyx_vtab;
- hts_itr_t *iter;
-};
-
-
-/* "calignmentfile.pxd":139
- * cdef int cnext(self)
- *
- * cdef class IteratorRowHead(IteratorRow): # <<<<<<<<<<<<<<
- * cdef int max_rows
- * cdef int current_row
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowHead {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_14calignmentfile_IteratorRowHead *__pyx_vtab;
- int max_rows;
- int current_row;
-};
-
-
-/* "calignmentfile.pxd":145
- * cdef int cnext(self)
- *
- * cdef class IteratorRowAll(IteratorRow): # <<<<<<<<<<<<<<
- * cdef bam1_t * getCurrent( self )
- * cdef int cnext(self)
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowAll {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_14calignmentfile_IteratorRowAll *__pyx_vtab;
-};
-
-
-/* "calignmentfile.pxd":149
- * cdef int cnext(self)
- *
- * cdef class IteratorRowAllRefs(IteratorRow): # <<<<<<<<<<<<<<
- * cdef int tid
- * cdef IteratorRowRegion rowiter
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowAllRefs {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRow __pyx_base;
- int tid;
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRowRegion *rowiter;
-};
-
-
-/* "calignmentfile.pxd":153
- * cdef IteratorRowRegion rowiter
- *
- * cdef class IteratorRowSelection(IteratorRow): # <<<<<<<<<<<<<<
- * cdef int current_pos
- * cdef positions
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorRowSelection {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRow __pyx_base;
- struct __pyx_vtabstruct_5pysam_14calignmentfile_IteratorRowSelection *__pyx_vtab;
- int current_pos;
- PyObject *positions;
- BGZF *fp;
-};
-
-
-/* "calignmentfile.pxd":160
- * cdef BGZF * fp
- *
- * cdef class IteratorColumn: # <<<<<<<<<<<<<<
- *
- * # result of the last plbuf_push
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorColumn {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_14calignmentfile_IteratorColumn *__pyx_vtab;
- struct __pyx_obj_5pysam_14calignmentfile_IteratorRowRegion *iter;
- int tid;
- int pos;
- int n_plp;
- int mask;
- bam_pileup1_t *plp;
- bam_plp_t pileup_iter;
- __pyx_t_5pysam_14calignmentfile___iterdata iterdata;
- struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *samfile;
- struct __pyx_obj_5pysam_6cfaidx_Fastafile *fastafile;
- PyObject *stepper;
- int max_depth;
-};
-
-
-/* "calignmentfile.pxd":188
- * cdef _free_pileup_iter(self)
- *
- * cdef class IteratorColumnRegion(IteratorColumn): # <<<<<<<<<<<<<<
- * cdef int start
- * cdef int end
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorColumnRegion {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorColumn __pyx_base;
- int start;
- int end;
- int truncate;
-};
-
-
-/* "calignmentfile.pxd":193
- * cdef int truncate
- *
- * cdef class IteratorColumnAllRefs(IteratorColumn): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_14calignmentfile_IteratorColumnAllRefs {
- struct __pyx_obj_5pysam_14calignmentfile_IteratorColumn __pyx_base;
-};
-
-
-/* "calignmentfile.pxd":196
- * pass
- *
- * cdef class IndexedReads: # <<<<<<<<<<<<<<
- * cdef AlignmentFile samfile
- * cdef htsFile * htsfile
- */
-struct __pyx_obj_5pysam_14calignmentfile_IndexedReads {
- PyObject_HEAD
- struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *samfile;
- htsFile *htsfile;
- PyObject *index;
- int owns_samfile;
- BGZF *fp;
- bam_hdr_t *header;
-};
-
-
-/* "pysam/csamfile.pxd":9
- * from chtslib cimport *
- *
- * cdef class AlignedRead(AlignedSegment): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_8csamfile_AlignedRead {
- struct __pyx_obj_5pysam_14calignmentfile_AlignedSegment __pyx_base;
-};
-
-
-/* "pysam/csamfile.pxd":12
- * pass
- *
- * cdef class Samfile(AlignmentFile): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_8csamfile_Samfile {
- struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile __pyx_base;
-};
-
-
-
-/* "cfaidx.pxd":14
- * char *s
- *
- * cdef class FastaFile: # <<<<<<<<<<<<<<
- * cdef object _filename, _references, _lengths, reference2length
- * cdef faidx_t* fastafile
- */
-
-struct __pyx_vtabstruct_5pysam_6cfaidx_FastaFile {
- char *(*_fetch)(struct __pyx_obj_5pysam_6cfaidx_FastaFile *, char *, int, int, int *);
-};
-static struct __pyx_vtabstruct_5pysam_6cfaidx_FastaFile *__pyx_vtabptr_5pysam_6cfaidx_FastaFile;
-
-
-/* "cfaidx.pxd":25
- *
- *
- * cdef class FastqFile: # <<<<<<<<<<<<<<
- * cdef object _filename
- * cdef gzFile fastqfile
- */
-
-struct __pyx_vtabstruct_5pysam_6cfaidx_FastqFile {
- kseq_t *(*getCurrent)(struct __pyx_obj_5pysam_6cfaidx_FastqFile *);
- int (*cnext)(struct __pyx_obj_5pysam_6cfaidx_FastqFile *);
-};
-static struct __pyx_vtabstruct_5pysam_6cfaidx_FastqFile *__pyx_vtabptr_5pysam_6cfaidx_FastqFile;
-
-
-/* "cfaidx.pxd":35
- *
- * # Compatibility Layer for pysam < 0.8
- * cdef class Fastafile(FastaFile): # <<<<<<<<<<<<<<
- * pass
- *
- */
-
-struct __pyx_vtabstruct_5pysam_6cfaidx_Fastafile {
- struct __pyx_vtabstruct_5pysam_6cfaidx_FastaFile __pyx_base;
-};
-static struct __pyx_vtabstruct_5pysam_6cfaidx_Fastafile *__pyx_vtabptr_5pysam_6cfaidx_Fastafile;
-
-
-/* "cfaidx.pxd":38
- * pass
- *
- * cdef class Fastqfile(FastqFile): # <<<<<<<<<<<<<<
- * pass
- */
-
-struct __pyx_vtabstruct_5pysam_6cfaidx_Fastqfile {
- struct __pyx_vtabstruct_5pysam_6cfaidx_FastqFile __pyx_base;
-};
-static struct __pyx_vtabstruct_5pysam_6cfaidx_Fastqfile *__pyx_vtabptr_5pysam_6cfaidx_Fastqfile;
-
-
-/* "calignmentfile.pxd":65
- * #
- * # Note: need to declare all C fields and methods here
- * cdef class AlignedSegment: # <<<<<<<<<<<<<<
- *
- * # object that this AlignedSegment represents
- */
-
-struct __pyx_vtabstruct_5pysam_14calignmentfile_AlignedSegment {
- PyObject *(*setTag)(struct __pyx_obj_5pysam_14calignmentfile_AlignedSegment *, PyObject *, PyObject *, int __pyx_skip_dispatch, struct __pyx_opt_args_5pysam_14calignmentfile_14AlignedSegment_setTag *__pyx_optional_args);
-};
-static struct __pyx_vtabstruct_5pysam_14calignmentfile_AlignedSegment *__pyx_vtabptr_5pysam_14calignmentfile_AlignedSegment;
-
-
-/* "calignmentfile.pxd":74
- * cpdef setTag( self, tag, value, value_type = ?, replace = ? )
- *
- * cdef class AlignmentFile: # <<<<<<<<<<<<<<
- *
- * cdef object _filename
- */
-
-struct __pyx_vtabstruct_5pysam_14calignmentfile_AlignmentFile {
- bam_hdr_t *(*_buildHeader)(struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *, PyObject *);
- bam1_t *(*getCurrent)(struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *);
- int (*cnext)(struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *);
- int (*write)(struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *, struct __pyx_obj_5pysam_14calignmentfile_AlignedSegment *, int __pyx_skip_dispatch);
- char *(*_getrname)(struct __pyx_obj_5pysam_14calignmentfile_AlignmentFile *, int);
-};
-static struct __pyx_vtabstruct_5pysam_14calignmentfile_AlignmentFile *__pyx_vtabptr_5pysam_14calignmentfile_AlignmentFile;
-
-
-/* "calignmentfile.pxd":134
- * cdef int owns_samfile
- *
- * cdef class IteratorRowRegion(IteratorRow): # <<<<<<<<<<<<<<
- * cdef hts_itr_t * iter
- * cdef bam1_t * getCurrent( self )
- */
-
-struct __pyx_vtabstruct_5pysam_14calignmentfile_IteratorRowRegion {
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- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
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diff --git a/pysam/csamtools.c b/pysam/csamtools.c
deleted file mode 100644
index 1c49dc0..0000000
--- a/pysam/csamtools.c
+++ /dev/null
@@ -1,6962 +0,0 @@
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-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
-#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
-#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((char*)s)
-#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
-#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return u_end - u - 1;
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-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#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))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
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-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_d;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-
-static const char *__pyx_f[] = {
- "csamtools.pyx",
- "type.pxd",
- "bool.pxd",
- "complex.pxd",
-};
-
-/*--- Type declarations ---*/
-#ifndef CYTHON_REFNANNY
- #define CYTHON_REFNANNY 0
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-#if CYTHON_REFNANNY
- typedef struct {
- void (*INCREF)(void*, PyObject*, int);
- void (*DECREF)(void*, PyObject*, int);
- void (*GOTREF)(void*, PyObject*, int);
- void (*GIVEREF)(void*, PyObject*, int);
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- void (*FinishContext)(void**);
- } __Pyx_RefNannyAPIStruct;
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- PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \
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- PyGILState_Release(__pyx_gilstate_save); \
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- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \
- }
-#else
- #define __Pyx_RefNannySetupContext(name, acquire_gil) \
- __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__)
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- #define __Pyx_XINCREF(r) do { if((r) != NULL) {__Pyx_INCREF(r); }} while(0)
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- #define __Pyx_XGOTREF(r) do { if((r) != NULL) {__Pyx_GOTREF(r); }} while(0)
- #define __Pyx_XGIVEREF(r) do { if((r) != NULL) {__Pyx_GIVEREF(r);}} while(0)
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- #define __Pyx_RefNannyDeclarations
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- #define __Pyx_INCREF(r) Py_INCREF(r)
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- #define __Pyx_GIVEREF(r)
- #define __Pyx_XINCREF(r) Py_XINCREF(r)
- #define __Pyx_XDECREF(r) Py_XDECREF(r)
- #define __Pyx_XGOTREF(r)
- #define __Pyx_XGIVEREF(r)
-#endif /* CYTHON_REFNANNY */
-#define __Pyx_XDECREF_SET(r, v) do { \
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-#define __Pyx_DECREF_SET(r, v) do { \
- PyObject *tmp = (PyObject *) r; \
- r = v; __Pyx_DECREF(tmp); \
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-#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
-#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_getattro))
- return tp->tp_getattro(obj, attr_name);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_getattr))
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-#endif
- return PyObject_GetAttr(obj, attr_name);
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-#else
-#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
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-
-static PyObject *__Pyx_GetBuiltinName(PyObject *name); /*proto*/
-
-#ifndef CYTHON_PROFILE
- #define CYTHON_PROFILE 1
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-#ifndef CYTHON_TRACE
- #define CYTHON_TRACE 0
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- #undef CYTHON_PROFILE_REUSE_FRAME
-#endif
-#ifndef CYTHON_PROFILE_REUSE_FRAME
- #define CYTHON_PROFILE_REUSE_FRAME 0
-#endif
-#if CYTHON_PROFILE || CYTHON_TRACE
- #include "compile.h"
- #include "frameobject.h"
- #include "traceback.h"
- #if CYTHON_PROFILE_REUSE_FRAME
- #define CYTHON_FRAME_MODIFIER static
- #define CYTHON_FRAME_DEL
- #else
- #define CYTHON_FRAME_MODIFIER
- #define CYTHON_FRAME_DEL Py_CLEAR(__pyx_frame)
- #endif
- #define __Pyx_TraceDeclarations \
- static PyCodeObject *__pyx_frame_code = NULL; \
- CYTHON_FRAME_MODIFIER PyFrameObject *__pyx_frame = NULL; \
- int __Pyx_use_tracing = 0;
- #define __Pyx_TraceCall(funcname, srcfile, firstlineno) \
- if (unlikely(PyThreadState_GET()->use_tracing && \
- (PyThreadState_GET()->c_profilefunc || (CYTHON_TRACE && PyThreadState_GET()->c_tracefunc)))) { \
- __Pyx_use_tracing = __Pyx_TraceSetupAndCall(&__pyx_frame_code, &__pyx_frame, funcname, srcfile, firstlineno); \
- }
- #define __Pyx_TraceException() \
- if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing && \
- (PyThreadState_GET()->c_profilefunc || (CYTHON_TRACE && PyThreadState_GET()->c_tracefunc))) { \
- PyThreadState* tstate = PyThreadState_GET(); \
- tstate->use_tracing = 0; \
- PyObject *exc_info = __Pyx_GetExceptionTuple(); \
- if (exc_info) { \
- if (CYTHON_TRACE && tstate->c_tracefunc) \
- tstate->c_tracefunc( \
- tstate->c_traceobj, __pyx_frame, PyTrace_EXCEPTION, exc_info); \
- tstate->c_profilefunc( \
- tstate->c_profileobj, __pyx_frame, PyTrace_EXCEPTION, exc_info); \
- Py_DECREF(exc_info); \
- } \
- tstate->use_tracing = 1; \
- }
- #define __Pyx_TraceReturn(result) \
- if (unlikely(__Pyx_use_tracing) && PyThreadState_GET()->use_tracing) { \
- PyThreadState* tstate = PyThreadState_GET(); \
- tstate->use_tracing = 0; \
- if (CYTHON_TRACE && tstate->c_tracefunc) \
- tstate->c_tracefunc( \
- tstate->c_traceobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
- if (tstate->c_profilefunc) \
- tstate->c_profilefunc( \
- tstate->c_profileobj, __pyx_frame, PyTrace_RETURN, (PyObject*)result); \
- CYTHON_FRAME_DEL; \
- tstate->use_tracing = 1; \
- }
- static PyCodeObject *__Pyx_createFrameCodeObject(const char *funcname, const char *srcfile, int firstlineno); /*proto*/
- static int __Pyx_TraceSetupAndCall(PyCodeObject** code, PyFrameObject** frame, const char *funcname, const char *srcfile, int firstlineno); /*proto*/
-#else
- #define __Pyx_TraceDeclarations
- #define __Pyx_TraceCall(funcname, srcfile, firstlineno)
- #define __Pyx_TraceException()
- #define __Pyx_TraceReturn(result)
-#endif /* CYTHON_PROFILE */
-#if CYTHON_TRACE
- #define __Pyx_TraceLine(lineno) \
- if (unlikely(__Pyx_use_tracing) && unlikely(PyThreadState_GET()->use_tracing && PyThreadState_GET()->c_tracefunc)) { \
- PyThreadState* tstate = PyThreadState_GET(); \
- __pyx_frame->f_lineno = lineno; \
- tstate->use_tracing = 0; \
- tstate->c_tracefunc(tstate->c_traceobj, __pyx_frame, PyTrace_LINE, NULL); \
- tstate->use_tracing = 1; \
- }
-#else
- #define __Pyx_TraceLine(lineno)
-#endif
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); /*proto*/
-#else
-#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
-#endif
-
-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*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
-
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name); /*proto*/
-
-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL)
-static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_setattro))
- return tp->tp_setattro(obj, attr_name, value);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_setattr))
- return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
-#endif
- return PyObject_SetAttr(obj, attr_name, value);
-}
-#else
-#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
-#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
-#endif
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); /*proto*/
-
-#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) & likely(len > (L->allocated >> 1))) {
- Py_INCREF(x);
- PyList_SET_ITEM(list, len, x);
- Py_SIZE(list) = len+1;
- return 0;
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- return PyList_Append(list, x);
-}
-#else
-#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
-#endif
-
-static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) {
- PyObject *method, *result = NULL;
- if (unlikely(!args)) return NULL;
- method = __Pyx_PyObject_GetAttrStr(obj, method_name);
- if (unlikely(!method)) goto bad;
- result = __Pyx_PyObject_Call(method, args, NULL);
- Py_DECREF(method);
-bad:
- Py_DECREF(args);
- return result;
-}
-#define __Pyx_PyObject_CallMethod3(obj, name, arg1, arg2, arg3) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(3, arg1, arg2, arg3))
-#define __Pyx_PyObject_CallMethod2(obj, name, arg1, arg2) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(2, arg1, arg2))
-#define __Pyx_PyObject_CallMethod1(obj, name, arg1) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(1, arg1))
-#define __Pyx_PyObject_CallMethod0(obj, name) \
- __Pyx_PyObject_CallMethodTuple(obj, name, (Py_INCREF(__pyx_empty_tuple), __pyx_empty_tuple))
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x); /*proto*/
-
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i))))
-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
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-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
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- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
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-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
-
-#define __Pyx_DelItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
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- CYTHON_UNUSED int is_list, int wraparound);
-
-#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
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-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- 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)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#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;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- } else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
- }
- if (!instance_class) {
- 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 = PyObject_Call(type, args, NULL);
- 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 PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- 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;
- 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, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (result) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
- if (likely(PyList_CheckExact(L))) {
- if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
- } else {
- PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
- if (unlikely(!retval))
- return -1;
- Py_DECREF(retval);
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-static CYTHON_INLINE int __Pyx_DelItem_Generic(PyObject *o, PyObject *j) {
- int r;
- if (!j) return -1;
- r = PyObject_DelItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE int __Pyx_DelItemInt_Fast(PyObject *o, Py_ssize_t i,
- CYTHON_UNUSED int is_list, int wraparound) {
-#if CYTHON_COMPILING_IN_PYPY
- if (is_list || PySequence_Check(o)) {
- return PySequence_DelItem(o, i);
- }
-#else
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return -1;
- }
- }
- return m->sq_ass_item(o, i, (PyObject *)NULL);
- }
-#endif
- return __Pyx_DelItem_Generic(o, PyInt_FromSsize_t(i));
-}
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- const char *ps1, *ps2;
- Py_ssize_t length = PyBytes_GET_SIZE(s1);
- if (length != PyBytes_GET_SIZE(s2))
- return (equals == Py_NE);
- ps1 = PyBytes_AS_STRING(s1);
- ps2 = PyBytes_AS_STRING(s2);
- if (ps1[0] != ps2[0]) {
- return (equals == Py_NE);
- } else if (length == 1) {
- return (equals == Py_EQ);
- } else {
- int result = memcmp(ps1, ps2, (size_t)length);
- 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;
- }
-#endif
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
-#if PY_MAJOR_VERSION < 3
- PyObject* owned_ref = NULL;
-#endif
- int s1_is_unicode, s2_is_unicode;
- if (s1 == s2) {
- goto return_eq;
- }
- s1_is_unicode = PyUnicode_CheckExact(s1);
- s2_is_unicode = PyUnicode_CheckExact(s2);
-#if PY_MAJOR_VERSION < 3
- if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
- owned_ref = PyUnicode_FromObject(s2);
- if (unlikely(!owned_ref))
- return -1;
- s2 = owned_ref;
- s2_is_unicode = 1;
- } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
- owned_ref = PyUnicode_FromObject(s1);
- if (unlikely(!owned_ref))
- return -1;
- s1 = owned_ref;
- s1_is_unicode = 1;
- } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
- return __Pyx_PyBytes_Equals(s1, s2, equals);
- }
-#endif
- if (s1_is_unicode & s2_is_unicode) {
- Py_ssize_t length;
- int kind;
- void *data1, *data2;
- #if CYTHON_PEP393_ENABLED
- if (unlikely(PyUnicode_READY(s1) < 0) || unlikely(PyUnicode_READY(s2) < 0))
- return -1;
- #endif
- length = __Pyx_PyUnicode_GET_LENGTH(s1);
- if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
- goto return_ne;
- }
- kind = __Pyx_PyUnicode_KIND(s1);
- if (kind != __Pyx_PyUnicode_KIND(s2)) {
- goto return_ne;
- }
- data1 = __Pyx_PyUnicode_DATA(s1);
- data2 = __Pyx_PyUnicode_DATA(s2);
- if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
- goto return_ne;
- } else if (length == 1) {
- goto return_eq;
- } else {
- int result = memcmp(data1, data2, length * kind);
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & s2_is_unicode) {
- goto return_ne;
- } else if ((s2 == Py_None) & s1_is_unicode) {
- goto return_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;
- }
-return_eq:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ);
-return_ne:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_NE);
-#endif
-}
-
-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 %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-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) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-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;
- *tb = tstate->exc_traceback;
- 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;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-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;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- 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 (local_tb) {
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- }
- #endif
- Py_XINCREF(local_tb);
- Py_XINCREF(local_type);
- Py_XINCREF(local_value);
- *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;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- 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;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-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_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = *type;
- tstate->exc_value = *value;
- tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
- *type = tmp_type;
- *value = tmp_value;
- *tb = tmp_tb;
-}
-
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
- PyObject* fake_module;
- PyTypeObject* cached_type = NULL;
- fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI);
- if (!fake_module) return NULL;
- Py_INCREF(fake_module);
- cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name);
- if (cached_type) {
- if (!PyType_Check((PyObject*)cached_type)) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s is not a type object",
- type->tp_name);
- goto bad;
- }
- if (cached_type->tp_basicsize != type->tp_basicsize) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s has the wrong size, try recompiling",
- type->tp_name);
- goto bad;
- }
- } else {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
- PyErr_Clear();
- if (PyType_Ready(type) < 0) goto bad;
- if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0)
- goto bad;
- Py_INCREF(type);
- cached_type = type;
- }
-done:
- Py_DECREF(fake_module);
- return cached_type;
-bad:
- Py_XDECREF(cached_type);
- cached_type = NULL;
- goto done;
-}
-
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (unlikely(op->func_doc == NULL)) {
- if (op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- if (unlikely(op->func_doc == NULL))
- return NULL;
- } else {
- Py_INCREF(Py_None);
- return Py_None;
- }
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- value = Py_None; /* Mark as deleted */
- Py_INCREF(value);
- op->func_doc = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_name == NULL)) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- if (unlikely(op->func_name == NULL))
- return NULL;
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_qualname);
- return op->func_qualname;
-}
-static int
-__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__qualname__ must be set to a string object");
- return -1;
- }
- tmp = op->func_qualname;
- Py_INCREF(value);
- op->func_qualname = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_dict == NULL)) {
- op->func_dict = PyDict_New();
- if (unlikely(op->func_dict == NULL))
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (unlikely(value == NULL)) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (unlikely(!PyDict_Check(value))) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_globals);
- return op->func_globals;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (unlikely(!res))
- return -1;
- op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
- Py_INCREF(op->defaults_tuple);
- op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
- Py_INCREF(op->defaults_kwdict);
- Py_DECREF(res);
- return 0;
-}
-static int
-__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value) {
- value = Py_None;
- } else if (value != Py_None && !PyTuple_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__defaults__ must be set to a tuple object");
- return -1;
- }
- Py_INCREF(value);
- tmp = op->defaults_tuple;
- op->defaults_tuple = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) {
- PyObject* result = op->defaults_tuple;
- if (unlikely(!result)) {
- if (op->defaults_getter) {
- if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL;
- result = op->defaults_tuple;
- } else {
- result = Py_None;
- }
- }
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value) {
- value = Py_None;
- } else if (value != Py_None && !PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__kwdefaults__ must be set to a dict object");
- return -1;
- }
- Py_INCREF(value);
- tmp = op->defaults_kwdict;
- op->defaults_kwdict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op) {
- PyObject* result = op->defaults_kwdict;
- if (unlikely(!result)) {
- if (op->defaults_getter) {
- if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL;
- result = op->defaults_kwdict;
- } else {
- result = Py_None;
- }
- }
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value || value == Py_None) {
- value = NULL;
- } else if (!PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__annotations__ must be set to a dict object");
- return -1;
- }
- Py_XINCREF(value);
- tmp = op->func_annotations;
- op->func_annotations = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op) {
- PyObject* result = op->func_annotations;
- if (unlikely(!result)) {
- result = PyDict_New();
- if (unlikely(!result)) return NULL;
- op->func_annotations = result;
- }
- Py_INCREF(result);
- return result;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
- {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0},
- {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
- PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
- if (op == NULL)
- return NULL;
- op->flags = flags;
- op->func_weakreflist = NULL;
- op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
- Py_XINCREF(module);
- op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- Py_INCREF(qualname);
- op->func_qualname = qualname;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- op->func_globals = globals;
- Py_INCREF(op->func_globals);
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_kwdict = NULL;
- op->defaults_getter = NULL;
- op->func_annotations = NULL;
- PyObject_GC_Track(op);
- return (PyObject *) op;
-}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_qualname);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_globals);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- Py_CLEAR(m->defaults_kwdict);
- Py_CLEAR(m->func_annotations);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
-}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
- PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
- PyObject_GC_Del(m);
-}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_qualname);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_globals);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- Py_VISIT(m->defaults_kwdict);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
- if (obj == Py_None)
- obj = NULL;
- return PyMethod_New(func, obj, type);
-}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- op->func_qualname, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(op->func_qualname), (void *)op);
-#endif
-}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-#if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
-#endif
-};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
- __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
- if (__pyx_CyFunctionType == NULL) {
- return -1;
- }
- return 0;
-}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, size);
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_kwdict = dict;
- Py_INCREF(dict);
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->func_annotations = dict;
- Py_INCREF(dict);
-}
-
-static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
- Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases);
- for (i=0; i < nbases; i++) {
- PyTypeObject *tmptype;
- PyObject *tmp = PyTuple_GET_ITEM(bases, i);
- tmptype = Py_TYPE(tmp);
-#if PY_MAJOR_VERSION < 3
- if (tmptype == &PyClass_Type)
- continue;
-#endif
- if (!metaclass) {
- metaclass = tmptype;
- continue;
- }
- if (PyType_IsSubtype(metaclass, tmptype))
- continue;
- if (PyType_IsSubtype(tmptype, metaclass)) {
- metaclass = tmptype;
- continue;
- }
- PyErr_SetString(PyExc_TypeError,
- "metaclass conflict: "
- "the metaclass of a derived class "
- "must be a (non-strict) subclass "
- "of the metaclasses of all its bases");
- return NULL;
- }
- if (!metaclass) {
-#if PY_MAJOR_VERSION < 3
- metaclass = &PyClass_Type;
-#else
- metaclass = &PyType_Type;
-#endif
- }
- Py_INCREF((PyObject*) metaclass);
- return (PyObject*) metaclass;
-}
-
-static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
- PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
- PyObject *ns;
- if (metaclass) {
- PyObject *prep = __Pyx_PyObject_GetAttrStr(metaclass, __pyx_n_s_prepare);
- if (prep) {
- PyObject *pargs = PyTuple_Pack(2, name, bases);
- if (unlikely(!pargs)) {
- Py_DECREF(prep);
- return NULL;
- }
- ns = PyObject_Call(prep, pargs, mkw);
- Py_DECREF(prep);
- Py_DECREF(pargs);
- } else {
- if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError)))
- return NULL;
- PyErr_Clear();
- ns = PyDict_New();
- }
- } else {
- ns = PyDict_New();
- }
- if (unlikely(!ns))
- return NULL;
- if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad;
- if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad;
- if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad;
- return ns;
-bad:
- Py_DECREF(ns);
- return NULL;
-}
-static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases,
- PyObject *dict, PyObject *mkw,
- int calculate_metaclass, int allow_py2_metaclass) {
- PyObject *result, *margs;
- PyObject *owned_metaclass = NULL;
- if (allow_py2_metaclass) {
- owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass);
- if (owned_metaclass) {
- metaclass = owned_metaclass;
- } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) {
- PyErr_Clear();
- } else {
- return NULL;
- }
- }
- if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) {
- metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases);
- Py_XDECREF(owned_metaclass);
- if (unlikely(!metaclass))
- return NULL;
- owned_metaclass = metaclass;
- }
- margs = PyTuple_Pack(3, name, bases, dict);
- if (unlikely(!margs)) {
- result = NULL;
- } else {
- result = PyObject_Call(metaclass, margs, mkw);
- Py_DECREF(margs);
- }
- Py_XDECREF(owned_metaclass);
- return result;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
-#if !CYTHON_COMPILING_IN_PYPY
-#if PY_VERSION_HEX >= 0x02060000
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- #if PY_VERSION_HEX < 0x02060000
- return PyInt_AsSsize_t(b);
- #else
- return PyLong_AsSsize_t(b);
- #endif
- }
- x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/pysam/ctabix.c b/pysam/ctabix.c
deleted file mode 100644
index 266f5cc..0000000
--- a/pysam/ctabix.c
+++ /dev/null
@@ -1,15462 +0,0 @@
-/* Generated by Cython 0.20.1 on Fri Nov 21 19:49:04 2014 */
-
-#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#define CYTHON_ABI "0_20_1"
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #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
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if CYTHON_COMPILING_IN_PYPY
-#define Py_OptimizeFlag 0
-#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_As_int(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)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyClass_Type
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyType_Type
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #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 < 0x02060000
- #define Py_TPFLAGS_HAVE_VERSION_TAG 0
-#endif
-#if PY_VERSION_HEX < 0x02060000 && !defined(Py_TPFLAGS_IS_ABSTRACT)
- #define Py_TPFLAGS_IS_ABSTRACT 0
-#endif
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
- #define Py_TPFLAGS_HAVE_FINALIZE 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
- #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
- #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
- #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
-#else
- #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
- PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
-#endif
-#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
-#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
-#else
- #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
- #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
-#else
- #define __Pyx_PyBaseString_Check(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
- PyString_Check(obj) || PyUnicode_Check(obj))
- #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#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
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
- #define PyNumber_Int PyNumber_Long
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x030200A4
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #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)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (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))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #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))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
-#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
-#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__pysam__ctabix
-#define __PYX_HAVE_API__pysam__ctabix
-#include "stdint.h"
-#include "string.h"
-#include "stdlib.h"
-#include "stdio.h"
-#include "fcntl.h"
-#include "unistd.h"
-#include "zlib.h"
-#include "htslib/kstring.h"
-#include "htslib/hfile.h"
-#include "htslib/bgzf.h"
-#include "htslib/hts.h"
-#include "htslib/sam.h"
-#include "pysam_stream.h"
-#include "htslib/faidx.h"
-#include "htslib/tbx.h"
-#include "errno.h"
-#include "pythread.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
-#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
-#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((char*)s)
-#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
-#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return u_end - u - 1;
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#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))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_d;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-
-static const char *__pyx_f[] = {
- "ctabix.pyx",
- "type.pxd",
- "bool.pxd",
- "complex.pxd",
- "TabProxies.pxd",
-};
-
-/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_BedProxy;
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
-struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator;
-struct __pyx_obj_5pysam_6ctabix_TabixFile;
-struct __pyx_obj_5pysam_6ctabix_Parser;
-struct __pyx_obj_5pysam_6ctabix_asTuple;
-struct __pyx_obj_5pysam_6ctabix_asGTF;
-struct __pyx_obj_5pysam_6ctabix_asBed;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
-struct __pyx_obj_5pysam_6ctabix_TabixIterator;
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_GZIterator;
-struct __pyx_obj_5pysam_6ctabix_GZIteratorHead;
-struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_Tabixfile;
-struct __pyx_opt_args_5pysam_6ctabix__force_str;
-struct __pyx_opt_args_5pysam_6ctabix__force_bytes;
-struct __pyx_opt_args_5pysam_6ctabix__charptr_to_str;
-
-/* "pysam/ctabix.pxd":50
- * ###########################################
- * # used by cvcf.pyx
- * cdef _force_str(object s, encoding=?) # <<<<<<<<<<<<<<
- *
- * ###########################################
- */
-struct __pyx_opt_args_5pysam_6ctabix__force_str {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "pysam/ctabix.pyx":51
- * raise TypeError, u"Argument must be string or unicode."
- *
- * cdef inline bytes _force_bytes(object s, encoding="ascii"): # <<<<<<<<<<<<<<
- * u"""convert string or unicode object to bytes, assuming ascii encoding.
- * """
- */
-struct __pyx_opt_args_5pysam_6ctabix__force_bytes {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "pysam/ctabix.pyx":65
- * raise TypeError, u"Argument must be string, bytes or unicode."
- *
- * cdef inline _charptr_to_str(char* s, encoding="ascii"): # <<<<<<<<<<<<<<
- * if PY_MAJOR_VERSION < 3:
- * return s
- */
-struct __pyx_opt_args_5pysam_6ctabix__charptr_to_str {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "TabProxies.pxd":41
- * ctypedef int uint64_t
- *
- * cdef class TupleProxy: # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_TupleProxy {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
- char *data;
- char **fields;
- int nfields;
- int index;
- int nbytes;
- int offset;
- int is_modified;
- PyObject *encoding;
-};
-
-
-/* "TabProxies.pxd":63
- * cdef update(self, char * buffer, size_t nbytes)
- *
- * cdef class GTFProxy(TupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
-};
-
-
-/* "TabProxies.pxd":73
- * cdef char * getAttributes( self )
- *
- * cdef class NamedTupleProxy(TupleProxy) : # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
-};
-
-
-/* "TabProxies.pxd":76
- * pass
- *
- * cdef class BedProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_BedProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
-};
-
-
-/* "TabProxies.pxd":88
- * cdef update(self, char * buffer, size_t nbytes)
- *
- * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
-};
-
-
-/* "pysam/ctabix.pxd":19
- * kstream_t, kstring_t, gzFile, tbx_t
- *
- * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
- * cdef gzFile fh
- * cdef kstream_t * kstream
- */
-struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtab;
- gzFile fh;
- kstream_t *kstream;
- kstring_t buffer;
- size_t size;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
- int fd;
- int duplicated_fd;
- PyObject *infile;
-};
-
-
-/* "pysam/ctabix.pxd":31
- * cdef __cnext__(self)
- *
- * cdef class TabixFile: # <<<<<<<<<<<<<<
- *
- * # pointer to tabixfile
- */
-struct __pyx_obj_5pysam_6ctabix_TabixFile {
- PyObject_HEAD
- htsFile *tabixfile;
- tbx_t *index;
- int isremote;
- PyObject *_filename;
- PyObject *_filename_index;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
- PyObject *encoding;
-};
-
-
-/* "pysam/ctabix.pxd":53
- *
- * ###########################################
- * cdef class Parser: # <<<<<<<<<<<<<<
- * cdef encoding
- *
- */
-struct __pyx_obj_5pysam_6ctabix_Parser {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtab;
- PyObject *encoding;
-};
-
-
-/* "pysam/ctabix.pxd":58
- * cdef parse(self, char * buffer, int len)
- *
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * cdef parse(self, char * buffer, int len)
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asTuple {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "pysam/ctabix.pxd":61
- * cdef parse(self, char * buffer, int len)
- *
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asGTF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "pysam/ctabix.pxd":64
- * pass
- *
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asBed {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "pysam/ctabix.pxd":67
- * pass
- *
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asVCF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "pysam/ctabix.pxd":70
- * pass
- *
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
- * cdef hts_itr_t * iterator
- * cdef TabixFile tabixfile
- */
-struct __pyx_obj_5pysam_6ctabix_TabixIterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_TabixIterator *__pyx_vtab;
- hts_itr_t *iterator;
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-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
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-#define __Pyx_CyFunction_USED 1
-#include <structmember.h>
-#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
-#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
-#define __Pyx_CYFUNCTION_CCLASS 0x04
-#define __Pyx_CyFunction_GetClosure(f) \
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-#define __Pyx_CyFunction_GetClassObj(f) \
- (((__pyx_CyFunctionObject *) (f))->func_classobj)
-#define __Pyx_CyFunction_Defaults(type, f) \
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-#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
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-static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
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-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
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-static void __Pyx_AddTraceback(const char *funcname, int c_line,
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-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
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-/* Module declarations from 'libc.stdlib' */
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-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_file_iterator = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixFile = 0;
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-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_asTuple = 0;
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-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIterator = 0;
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-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
-static PyObject *__pyx_v_5pysam_6ctabix__FILENAME_ENCODING = 0;
-static PyObject *__pyx_f_5pysam_6ctabix__force_str(PyObject *, struct __pyx_opt_args_5pysam_6ctabix__force_str *__pyx_optional_args); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__encodeFilename(PyObject *); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__force_bytes(PyObject *, struct __pyx_opt_args_5pysam_6ctabix__force_bytes *__pyx_optional_args); /*proto*/
-static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__charptr_to_str(char *, struct __pyx_opt_args_5pysam_6ctabix__charptr_to_str *__pyx_optional_args); /*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;
-static PyObject *__pyx_builtin_ValueError;
-static PyObject *__pyx_builtin_StopIteration;
-static PyObject *__pyx_builtin_OSError;
-static PyObject *__pyx_builtin_ord;
-static PyObject *__pyx_builtin_KeyError;
-static int __pyx_pf_5pysam_6ctabix_6Parser___init__(struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_6Parser_2set_encoding(struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_self, PyObject *__pyx_v_encoding); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_6Parser_4get_encoding(struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_6Parser_6__call__(struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_self, char *__pyx_v_buffer, int __pyx_v_length); /* 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_parser, PyObject *__pyx_v_index, PyObject *__pyx_v_encoding, PyObject *__pyx_v_args, PyObject *__pyx_v_kwargs); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_9TabixFile_2_open(struct __pyx_obj_5pysam_6ctabix_TabixFile *__pyx_v_self, PyObject *__pyx_v_filename, PyObject *__pyx_v_mode, PyObject *__pyx_v_index); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_9TabixFile_4_dup(struct __pyx_obj_5pysam_6ctabix_TabixFile *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_9TabixFile_6_isOpen(struct __pyx_obj_5pysam_6ctabix_TabixFile *__pyx_v_self); /* 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, PyObject *__pyx_v_multiple_iterators); /* 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___init__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self, PyObject *__pyx_v_encoding); /* 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 PyObject *__pyx_pf_5pysam_6ctabix_13TabixIterator_6next(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_6ctabix_13TabixIterator_8__dealloc__(struct __pyx_obj_5pysam_6ctabix_TabixIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_13EmptyIterator___iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_13EmptyIterator_2next(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_13EmptyIterator_4__next__(CYTHON_UNUSED PyObject *__pyx_self, CYTHON_UNUSED PyObject *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_6ctabix_19TabixIteratorParsed___init__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_2__next__(struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_6ctabix_10GZIterator___init__(struct __pyx_obj_5pysam_6ctabix_GZIterator *__pyx_v_self, PyObject *__pyx_v_filename, int __pyx_v_buffer_size, PyObject *__pyx_v_encoding); /* proto */
-static void __pyx_pf_5pysam_6ctabix_10GZIterator_2__dealloc__(struct __pyx_obj_5pysam_6ctabix_GZIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_10GZIterator_4__iter__(struct __pyx_obj_5pysam_6ctabix_GZIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_10GZIterator_6__next__(struct __pyx_obj_5pysam_6ctabix_GZIterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_14GZIteratorHead___next__(struct __pyx_obj_5pysam_6ctabix_GZIteratorHead *__pyx_v_self); /* proto */
-static int __pyx_pf_5pysam_6ctabix_16GZIteratorParsed___init__(struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed *__pyx_v_self, PyObject *__pyx_v_parser); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_16GZIteratorParsed_2__next__(struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed *__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, PyObject *__pyx_v_min_shift); /* proto */
-static int __pyx_pf_5pysam_6ctabix_19tabix_file_iterator___cinit__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self, PyObject *__pyx_v_infile, struct __pyx_obj_5pysam_6ctabix_Parser *__pyx_v_parser, int __pyx_v_buffer_size); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_2__iter__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
-static void __pyx_pf_5pysam_6ctabix_19tabix_file_iterator_4__dealloc__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_6__next__(struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator *__pyx_v_self); /* proto */
-static PyObject *__pyx_pf_5pysam_6ctabix_19tabix_file_iterator_8next(struct __pyx_obj_5pysam_6ctabix_tabix_file_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 PyObject *__pyx_tp_new_5pysam_6ctabix_tabix_file_iterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_Parser(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asTuple(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asGTF(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asBed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_asVCF(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_GZIterator(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_GZIteratorHead(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_GZIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_6ctabix_Tabixfile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static char __pyx_k_b[] = "b";
-static char __pyx_k_c[] = "c";
-static char __pyx_k_r[] = "r";
-static char __pyx_k_s[] = "%s";
-static char __pyx_k_w[] = "w";
-static char __pyx_k_fn[] = "fn";
-static char __pyx_k_fp[] = "fp";
-static char __pyx_k_gz[] = ".gz";
-static char __pyx_k_os[] = "os";
-static char __pyx_k__10[] = "#";
-static char __pyx_k__14[] = ",";
-static char __pyx_k_all[] = "__all__";
-static char __pyx_k_bed[] = "bed";
-static char __pyx_k_cpy[] = "cpy";
-static char __pyx_k_doc[] = "__doc__";
-static char __pyx_k_dup[] = "_dup";
-static char __pyx_k_end[] = "end";
-static char __pyx_k_ftp[] = "ftp:";
-static char __pyx_k_gff[] = "gff";
-static char __pyx_k_ord[] = "ord";
-static char __pyx_k_s_2[] = "s";
-static char __pyx_k_s_i[] = "%s:%i";
-static char __pyx_k_sam[] = "sam";
-static char __pyx_k_sys[] = "sys";
-static char __pyx_k_tbi[] = ".tbi";
-static char __pyx_k_vcf[] = "vcf";
-static char __pyx_k_conf[] = "conf";
-static char __pyx_k_http[] = "http:";
-static char __pyx_k_init[] = "__init__";
-static char __pyx_k_iter[] = "__iter__";
-static char __pyx_k_join[] = "join";
-static char __pyx_k_keys[] = "keys";
-static char __pyx_k_line[] = "line";
-static char __pyx_k_main[] = "__main__";
-static char __pyx_k_mode[] = "mode";
-static char __pyx_k_next[] = "__next__";
-static char __pyx_k_open[] = "_open";
-static char __pyx_k_path[] = "path";
-static char __pyx_k_self[] = "self";
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-static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIterator = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.TabixIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_TabixIterator), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
- #else
- 0, /*reserved*/
- #endif
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- Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
- __Pyx_DOCSTR("TabixIterator(encoding='ascii')\niterates over rows in *tabixfile* in region\n given by *tid*, *start* and *end*.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_6ctabix_TabixIterator, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_TabixIterator, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __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*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- __pyx_pw_5pysam_6ctabix_13TabixIterator_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_TabixIterator, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
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- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
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- 0, /*tp_del*/
- #if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
- #endif
- #if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
- #endif
-};
-static struct __pyx_vtabstruct_5pysam_6ctabix_TabixIteratorParsed __pyx_vtable_5pysam_6ctabix_TabixIteratorParsed;
-
-static PyObject *__pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p;
- PyObject *o = __pyx_tp_new_5pysam_6ctabix_TabixIterator(t, a, k);
- if (unlikely(!o)) return 0;
- p = ((struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o);
- p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_5pysam_6ctabix_TabixIterator*)__pyx_vtabptr_5pysam_6ctabix_TabixIteratorParsed;
- p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- return 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;
- #if PY_VERSION_HEX >= 0x030400a1
- if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
- if (PyObject_CallFinalizerFromDealloc(o)) return;
- }
- #endif
- PyObject_GC_UnTrack(o);
- Py_CLEAR(p->parser);
- PyObject_GC_Track(o);
- __pyx_tp_dealloc_5pysam_6ctabix_TabixIterator(o);
-}
-
-static int __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
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- }
- return 0;
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-
-static int __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed(PyObject *o) {
- PyObject* tmp;
- struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed *)o;
- __pyx_tp_clear_5pysam_6ctabix_TabixIterator(o);
- tmp = ((PyObject*)p->parser);
- p->parser = ((struct __pyx_obj_5pysam_6ctabix_Parser *)Py_None); Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_5pysam_6ctabix_TabixIteratorParsed[] = {
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- {0, 0, 0, 0}
-};
-
-static PyTypeObject __pyx_type_5pysam_6ctabix_TabixIteratorParsed = {
- PyVarObject_HEAD_INIT(0, 0)
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- __pyx_tp_dealloc_5pysam_6ctabix_TabixIteratorParsed, /*tp_dealloc*/
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- #if PY_MAJOR_VERSION < 3
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- __Pyx_DOCSTR("TabixIteratorParsed(Parser parser)\niterates over mapped reads in a region.\n\n The *parser* determines the encoding.\n\n Returns parsed data.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_6ctabix_TabixIteratorParsed, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_TabixIteratorParsed, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_6ctabix_13TabixIterator_3__iter__, /*tp_iter*/
- #else
- 0, /*tp_iter*/
- #endif
- __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_3__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_TabixIteratorParsed, /*tp_methods*/
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- 0, /*tp_descr_set*/
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- __pyx_pw_5pysam_6ctabix_19TabixIteratorParsed_1__init__, /*tp_init*/
- 0, /*tp_alloc*/
- __pyx_tp_new_5pysam_6ctabix_TabixIteratorParsed, /*tp_new*/
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- 0, /*tp_finalize*/
- #endif
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-
-static PyObject *__pyx_tp_new_5pysam_6ctabix_GZIterator(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
- struct __pyx_obj_5pysam_6ctabix_GZIterator *p;
- PyObject *o;
- if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
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- o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
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- p->_filename = Py_None; Py_INCREF(Py_None);
- p->encoding = Py_None; Py_INCREF(Py_None);
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-
-static void __pyx_tp_dealloc_5pysam_6ctabix_GZIterator(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_GZIterator *p = (struct __pyx_obj_5pysam_6ctabix_GZIterator *)o;
- #if PY_VERSION_HEX >= 0x030400a1
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- }
- #endif
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- {
- PyObject *etype, *eval, *etb;
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- ++Py_REFCNT(o);
- __pyx_pw_5pysam_6ctabix_10GZIterator_3__dealloc__(o);
- --Py_REFCNT(o);
- PyErr_Restore(etype, eval, etb);
- }
- Py_CLEAR(p->_filename);
- Py_CLEAR(p->encoding);
- (*Py_TYPE(o)->tp_free)(o);
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-
-static int __pyx_tp_traverse_5pysam_6ctabix_GZIterator(PyObject *o, visitproc v, void *a) {
- int e;
- struct __pyx_obj_5pysam_6ctabix_GZIterator *p = (struct __pyx_obj_5pysam_6ctabix_GZIterator *)o;
- if (p->_filename) {
- e = (*v)(p->_filename, a); if (e) return e;
- }
- if (p->encoding) {
- e = (*v)(p->encoding, a); if (e) return e;
- }
- return 0;
-}
-
-static int __pyx_tp_clear_5pysam_6ctabix_GZIterator(PyObject *o) {
- PyObject* tmp;
- struct __pyx_obj_5pysam_6ctabix_GZIterator *p = (struct __pyx_obj_5pysam_6ctabix_GZIterator *)o;
- tmp = ((PyObject*)p->_filename);
- p->_filename = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- tmp = ((PyObject*)p->encoding);
- p->encoding = Py_None; Py_INCREF(Py_None);
- Py_XDECREF(tmp);
- return 0;
-}
-
-static PyMethodDef __pyx_methods_5pysam_6ctabix_GZIterator[] = {
- {__Pyx_NAMESTR("__next__"), (PyCFunction)__pyx_pw_5pysam_6ctabix_10GZIterator_7__next__, METH_NOARGS|METH_COEXIST, __Pyx_DOCSTR(__pyx_doc_5pysam_6ctabix_10GZIterator_6__next__)},
- {0, 0, 0, 0}
-};
-
-static PyTypeObject __pyx_type_5pysam_6ctabix_GZIterator = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("pysam.ctabix.GZIterator"), /*tp_name*/
- sizeof(struct __pyx_obj_5pysam_6ctabix_GZIterator), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_GZIterator, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
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- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
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- __Pyx_DOCSTR("GZIterator(filename, int buffer_size=65536, encoding='ascii')"), /*tp_doc*/
- __pyx_tp_traverse_5pysam_6ctabix_GZIterator, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_GZIterator, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- __pyx_pw_5pysam_6ctabix_10GZIterator_5__iter__, /*tp_iter*/
- __pyx_pw_5pysam_6ctabix_10GZIterator_7__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_GZIterator, /*tp_methods*/
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-
-static PyObject *__pyx_tp_new_5pysam_6ctabix_GZIteratorHead(PyTypeObject *t, PyObject *a, PyObject *k) {
- struct __pyx_obj_5pysam_6ctabix_GZIteratorHead *p;
- PyObject *o = __pyx_tp_new_5pysam_6ctabix_GZIterator(t, a, k);
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- return o;
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-
-static PyMethodDef __pyx_methods_5pysam_6ctabix_GZIteratorHead[] = {
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- {0, 0, 0, 0}
-};
-
-static PyTypeObject __pyx_type_5pysam_6ctabix_GZIteratorHead = {
- PyVarObject_HEAD_INIT(0, 0)
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- 0, /*tp_itemsize*/
- __pyx_tp_dealloc_5pysam_6ctabix_GZIterator, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
- #if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
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- __Pyx_DOCSTR("iterate line-by-line through gzip (or bgzip)\n compressed file returning comments at top of file.\n "), /*tp_doc*/
- __pyx_tp_traverse_5pysam_6ctabix_GZIterator, /*tp_traverse*/
- __pyx_tp_clear_5pysam_6ctabix_GZIterator, /*tp_clear*/
- 0, /*tp_richcompare*/
- 0, /*tp_weaklistoffset*/
- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_6ctabix_10GZIterator_5__iter__, /*tp_iter*/
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- __pyx_pw_5pysam_6ctabix_14GZIteratorHead_1__next__, /*tp_iternext*/
- __pyx_methods_5pysam_6ctabix_GZIteratorHead, /*tp_methods*/
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- #if CYTHON_COMPILING_IN_PYPY
- __pyx_pw_5pysam_6ctabix_10GZIterator_1__init__, /*tp_init*/
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- struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed *p;
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-
-static void __pyx_tp_dealloc_5pysam_6ctabix_GZIteratorParsed(PyObject *o) {
- struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed *p = (struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed *)o;
- #if PY_VERSION_HEX >= 0x030400a1
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- if (PyObject_CallFinalizerFromDealloc(o)) return;
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- PyObject_GC_UnTrack(o);
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-
-static int __pyx_tp_traverse_5pysam_6ctabix_GZIteratorParsed(PyObject *o, visitproc v, void *a) {
- int e;
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-static int __pyx_tp_clear_5pysam_6ctabix_GZIteratorParsed(PyObject *o) {
- PyObject* tmp;
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- __pyx_tp_clear_5pysam_6ctabix_GZIterator(o);
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-static PyMethodDef __pyx_methods_5pysam_6ctabix_GZIteratorParsed[] = {
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- {0, 0, 0, 0}
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-
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- if (__Pyx_SetAttrString(__pyx_m, "TabixIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_TabixIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 490; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (__Pyx_SetAttrString(__pyx_m, "GZIterator", (PyObject *)&__pyx_type_5pysam_6ctabix_GZIterator) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 598; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- {
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- {
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- __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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- if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
- __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0;
- goto __pyx_L0;
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- __Pyx_XDECREF(__pyx_t_1);
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- if (__pyx_m) {
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- Py_DECREF(__pyx_m); __pyx_m = 0;
- } else if (!PyErr_Occurred()) {
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- }
- __pyx_L0:;
- __Pyx_RefNannyFinishContext();
- #if PY_MAJOR_VERSION < 3
- return;
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- return __pyx_m;
- #endif
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-
-/* Runtime support code */
-#if CYTHON_REFNANNY
-static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) {
- PyObject *m = NULL, *p = NULL;
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- if (!m) goto end;
- p = PyObject_GetAttrString(m, (char *)"RefNannyAPI");
- if (!p) goto end;
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-end:
- Py_XDECREF(p);
- Py_XDECREF(m);
- return (__Pyx_RefNannyAPIStruct *)r;
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-static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
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-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyObject *result;
- ternaryfunc call = func->ob_type->tp_call;
- if (unlikely(!call))
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-#if PY_VERSION_HEX >= 0x02060000
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
-#endif
- result = (*call)(func, arg, kw);
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- Py_LeaveRecursiveCall();
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- PyErr_SetString(
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-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
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- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
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- Py_XDECREF(tmp_type);
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- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- 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)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#if CYTHON_COMPILING_IN_PYPY
- if (!value) {
- Py_INCREF(Py_None);
- value = Py_None;
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-#endif
- PyErr_NormalizeException(&type, &value, &tb);
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- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto raise_error;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- } else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
- }
- if (!instance_class) {
- 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 = PyObject_Call(type, args, NULL);
- 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 PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- 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;
- 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, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
- if (unlikely(!type)) {
- PyErr_SetString(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (likely(PyObject_TypeCheck(obj, type)))
- return 1;
- PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
- Py_TYPE(obj)->tp_name, type->tp_name);
- return 0;
-}
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- const char *ps1, *ps2;
- Py_ssize_t length = PyBytes_GET_SIZE(s1);
- if (length != PyBytes_GET_SIZE(s2))
- return (equals == Py_NE);
- ps1 = PyBytes_AS_STRING(s1);
- ps2 = PyBytes_AS_STRING(s2);
- if (ps1[0] != ps2[0]) {
- return (equals == Py_NE);
- } else if (length == 1) {
- return (equals == Py_EQ);
- } else {
- int result = memcmp(ps1, ps2, (size_t)length);
- 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;
- }
-#endif
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
-#if PY_MAJOR_VERSION < 3
- PyObject* owned_ref = NULL;
-#endif
- int s1_is_unicode, s2_is_unicode;
- if (s1 == s2) {
- goto return_eq;
- }
- s1_is_unicode = PyUnicode_CheckExact(s1);
- s2_is_unicode = PyUnicode_CheckExact(s2);
-#if PY_MAJOR_VERSION < 3
- if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
- owned_ref = PyUnicode_FromObject(s2);
- if (unlikely(!owned_ref))
- return -1;
- s2 = owned_ref;
- s2_is_unicode = 1;
- } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
- owned_ref = PyUnicode_FromObject(s1);
- if (unlikely(!owned_ref))
- return -1;
- s1 = owned_ref;
- s1_is_unicode = 1;
- } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
- return __Pyx_PyBytes_Equals(s1, s2, equals);
- }
-#endif
- if (s1_is_unicode & s2_is_unicode) {
- Py_ssize_t length;
- int kind;
- void *data1, *data2;
- #if CYTHON_PEP393_ENABLED
- if (unlikely(PyUnicode_READY(s1) < 0) || unlikely(PyUnicode_READY(s2) < 0))
- return -1;
- #endif
- length = __Pyx_PyUnicode_GET_LENGTH(s1);
- if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
- goto return_ne;
- }
- kind = __Pyx_PyUnicode_KIND(s1);
- if (kind != __Pyx_PyUnicode_KIND(s2)) {
- goto return_ne;
- }
- data1 = __Pyx_PyUnicode_DATA(s1);
- data2 = __Pyx_PyUnicode_DATA(s2);
- if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
- goto return_ne;
- } else if (length == 1) {
- goto return_eq;
- } else {
- int result = memcmp(data1, data2, length * kind);
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & s2_is_unicode) {
- goto return_ne;
- } else if ((s2 == Py_None) & s1_is_unicode) {
- goto return_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;
- }
-return_eq:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ);
-return_ne:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_NE);
-#endif
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (result) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) {
- PyErr_Format(PyExc_TypeError,
- "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)",
- name, type->tp_name, Py_TYPE(obj)->tp_name);
-}
-static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
- const char *name, int exact)
-{
- if (unlikely(!type)) {
- PyErr_SetString(PyExc_SystemError, "Missing type object");
- return 0;
- }
- if (none_allowed && obj == Py_None) return 1;
- else if (exact) {
- if (likely(Py_TYPE(obj) == type)) return 1;
- #if PY_MAJOR_VERSION == 2
- else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1;
- #endif
- }
- else {
- if (likely(PyObject_TypeCheck(obj, type))) return 1;
- }
- __Pyx_RaiseArgumentTypeInvalid(name, obj, type);
- return 0;
-}
-
-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;
- *tb = tstate->exc_traceback;
- 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;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-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;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- 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 (local_tb) {
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- }
- #endif
- Py_XINCREF(local_tb);
- Py_XINCREF(local_type);
- Py_XINCREF(local_value);
- *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;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- 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;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-#if !CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
- return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL)
-}
-#endif
-
-static CYTHON_INLINE PyObject* __Pyx_PyDict_Keys(PyObject* d) {
- if (PY_MAJOR_VERSION >= 3)
- return __Pyx_PyObject_CallMethod1((PyObject*)&PyDict_Type, __pyx_n_s_keys, d);
- else
- return PyDict_Keys(d);
-}
-
-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 %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-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) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
- PyObject *ob = PyObject_GetItem(dict, __pyx_n_s_pyx_vtable);
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- ptr = PyCapsule_GetPointer(ob, 0);
-#else
- ptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
- Py_DECREF(ob);
- return ptr;
-bad:
- Py_XDECREF(ob);
- return NULL;
-}
-
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
- PyObject* fake_module;
- PyTypeObject* cached_type = NULL;
- fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI);
- if (!fake_module) return NULL;
- Py_INCREF(fake_module);
- cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name);
- if (cached_type) {
- if (!PyType_Check((PyObject*)cached_type)) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s is not a type object",
- type->tp_name);
- goto bad;
- }
- if (cached_type->tp_basicsize != type->tp_basicsize) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s has the wrong size, try recompiling",
- type->tp_name);
- goto bad;
- }
- } else {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
- PyErr_Clear();
- if (PyType_Ready(type) < 0) goto bad;
- if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0)
- goto bad;
- Py_INCREF(type);
- cached_type = type;
- }
-done:
- Py_DECREF(fake_module);
- return cached_type;
-bad:
- Py_XDECREF(cached_type);
- cached_type = NULL;
- goto done;
-}
-
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (unlikely(op->func_doc == NULL)) {
- if (op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- if (unlikely(op->func_doc == NULL))
- return NULL;
- } else {
- Py_INCREF(Py_None);
- return Py_None;
- }
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- value = Py_None; /* Mark as deleted */
- Py_INCREF(value);
- op->func_doc = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_name == NULL)) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- if (unlikely(op->func_name == NULL))
- return NULL;
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_qualname);
- return op->func_qualname;
-}
-static int
-__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__qualname__ must be set to a string object");
- return -1;
- }
- tmp = op->func_qualname;
- Py_INCREF(value);
- op->func_qualname = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_dict == NULL)) {
- op->func_dict = PyDict_New();
- if (unlikely(op->func_dict == NULL))
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (unlikely(value == NULL)) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (unlikely(!PyDict_Check(value))) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_globals);
- return op->func_globals;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (unlikely(!res))
- return -1;
- op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
- Py_INCREF(op->defaults_tuple);
- op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
- Py_INCREF(op->defaults_kwdict);
- Py_DECREF(res);
- return 0;
-}
-static int
-__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value) {
- value = Py_None;
- } else if (value != Py_None && !PyTuple_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__defaults__ must be set to a tuple object");
- return -1;
- }
- Py_INCREF(value);
- tmp = op->defaults_tuple;
- op->defaults_tuple = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) {
- PyObject* result = op->defaults_tuple;
- if (unlikely(!result)) {
- if (op->defaults_getter) {
- if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL;
- result = op->defaults_tuple;
- } else {
- result = Py_None;
- }
- }
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value) {
- value = Py_None;
- } else if (value != Py_None && !PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__kwdefaults__ must be set to a dict object");
- return -1;
- }
- Py_INCREF(value);
- tmp = op->defaults_kwdict;
- op->defaults_kwdict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op) {
- PyObject* result = op->defaults_kwdict;
- if (unlikely(!result)) {
- if (op->defaults_getter) {
- if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL;
- result = op->defaults_kwdict;
- } else {
- result = Py_None;
- }
- }
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value || value == Py_None) {
- value = NULL;
- } else if (!PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__annotations__ must be set to a dict object");
- return -1;
- }
- Py_XINCREF(value);
- tmp = op->func_annotations;
- op->func_annotations = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op) {
- PyObject* result = op->func_annotations;
- if (unlikely(!result)) {
- result = PyDict_New();
- if (unlikely(!result)) return NULL;
- op->func_annotations = result;
- }
- Py_INCREF(result);
- return result;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
- {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0},
- {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
- PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
- if (op == NULL)
- return NULL;
- op->flags = flags;
- op->func_weakreflist = NULL;
- op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
- Py_XINCREF(module);
- op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- Py_INCREF(qualname);
- op->func_qualname = qualname;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- op->func_globals = globals;
- Py_INCREF(op->func_globals);
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_kwdict = NULL;
- op->defaults_getter = NULL;
- op->func_annotations = NULL;
- PyObject_GC_Track(op);
- return (PyObject *) op;
-}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_qualname);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_globals);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- Py_CLEAR(m->defaults_kwdict);
- Py_CLEAR(m->func_annotations);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
-}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
- PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
- PyObject_GC_Del(m);
-}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_qualname);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_globals);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- Py_VISIT(m->defaults_kwdict);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
- if (obj == Py_None)
- obj = NULL;
- return PyMethod_New(func, obj, type);
-}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- op->func_qualname, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(op->func_qualname), (void *)op);
-#endif
-}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-#if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
-#endif
-};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
- __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
- if (__pyx_CyFunctionType == NULL) {
- return -1;
- }
- return 0;
-}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, size);
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_kwdict = dict;
- Py_INCREF(dict);
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->func_annotations = dict;
- Py_INCREF(dict);
-}
-
-static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
- Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases);
- for (i=0; i < nbases; i++) {
- PyTypeObject *tmptype;
- PyObject *tmp = PyTuple_GET_ITEM(bases, i);
- tmptype = Py_TYPE(tmp);
-#if PY_MAJOR_VERSION < 3
- if (tmptype == &PyClass_Type)
- continue;
-#endif
- if (!metaclass) {
- metaclass = tmptype;
- continue;
- }
- if (PyType_IsSubtype(metaclass, tmptype))
- continue;
- if (PyType_IsSubtype(tmptype, metaclass)) {
- metaclass = tmptype;
- continue;
- }
- PyErr_SetString(PyExc_TypeError,
- "metaclass conflict: "
- "the metaclass of a derived class "
- "must be a (non-strict) subclass "
- "of the metaclasses of all its bases");
- return NULL;
- }
- if (!metaclass) {
-#if PY_MAJOR_VERSION < 3
- metaclass = &PyClass_Type;
-#else
- metaclass = &PyType_Type;
-#endif
- }
- Py_INCREF((PyObject*) metaclass);
- return (PyObject*) metaclass;
-}
-
-static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
- PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
- PyObject *ns;
- if (metaclass) {
- PyObject *prep = __Pyx_PyObject_GetAttrStr(metaclass, __pyx_n_s_prepare);
- if (prep) {
- PyObject *pargs = PyTuple_Pack(2, name, bases);
- if (unlikely(!pargs)) {
- Py_DECREF(prep);
- return NULL;
- }
- ns = PyObject_Call(prep, pargs, mkw);
- Py_DECREF(prep);
- Py_DECREF(pargs);
- } else {
- if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError)))
- return NULL;
- PyErr_Clear();
- ns = PyDict_New();
- }
- } else {
- ns = PyDict_New();
- }
- if (unlikely(!ns))
- return NULL;
- if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad;
- if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad;
- if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad;
- return ns;
-bad:
- Py_DECREF(ns);
- return NULL;
-}
-static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases,
- PyObject *dict, PyObject *mkw,
- int calculate_metaclass, int allow_py2_metaclass) {
- PyObject *result, *margs;
- PyObject *owned_metaclass = NULL;
- if (allow_py2_metaclass) {
- owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass);
- if (owned_metaclass) {
- metaclass = owned_metaclass;
- } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) {
- PyErr_Clear();
- } else {
- return NULL;
- }
- }
- if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) {
- metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases);
- Py_XDECREF(owned_metaclass);
- if (unlikely(!metaclass))
- return NULL;
- owned_metaclass = metaclass;
- }
- margs = PyTuple_Pack(3, name, bases, dict);
- if (unlikely(!margs)) {
- result = NULL;
- } else {
- result = PyObject_Call(metaclass, margs, mkw);
- Py_DECREF(margs);
- }
- Py_XDECREF(owned_metaclass);
- return result;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int32_t __Pyx_PyInt_As_int32_t(PyObject *x) {
- const int32_t neg_one = (int32_t) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int32_t) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int32_t");
- return (int32_t) -1;
- }
- return (int32_t) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int32_t)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int32_t) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int32_t");
- return (int32_t) -1;
- }
- if (sizeof(int32_t) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int32_t) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int32_t)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int32_t) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int32_t) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int32_t) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, long, PyLong_AsLong)
- } else if (sizeof(int32_t) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int32_t, long long, PyLong_AsLongLong)
- }
- }
- {
-#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_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int32_t) -1;
- }
- } else {
- int32_t val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int32_t) -1;
- val = __Pyx_PyInt_As_int32_t(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(int) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(int) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(int) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(int),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- return 0;
-}
-
-static int __Pyx_ExportFunction(const char *name, void (*f)(void), const char *sig) {
- PyObject *d = 0;
- PyObject *cobj = 0;
- union {
- void (*fp)(void);
- void *p;
- } tmp;
- d = PyObject_GetAttrString(__pyx_m, (char *)"__pyx_capi__");
- if (!d) {
- PyErr_Clear();
- d = PyDict_New();
- if (!d)
- goto bad;
- Py_INCREF(d);
- if (PyModule_AddObject(__pyx_m, (char *)"__pyx_capi__", d) < 0)
- goto bad;
- }
- tmp.fp = f;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- cobj = PyCapsule_New(tmp.p, sig, 0);
-#else
- cobj = PyCObject_FromVoidPtrAndDesc(tmp.p, (void *)sig, 0);
-#endif
- if (!cobj)
- goto bad;
- if (PyDict_SetItemString(d, name, cobj) < 0)
- goto bad;
- Py_DECREF(cobj);
- Py_DECREF(d);
- return 0;
-bad:
- Py_XDECREF(cobj);
- Py_XDECREF(d);
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
-#if !CYTHON_COMPILING_IN_PYPY
-#if PY_VERSION_HEX >= 0x02060000
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- #if PY_VERSION_HEX < 0x02060000
- return PyInt_AsSsize_t(b);
- #else
- return PyLong_AsSsize_t(b);
- #endif
- }
- x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-
-
-#endif /* Py_PYTHON_H */
diff --git a/pysam/cvcf.c b/pysam/cvcf.c
deleted file mode 100644
index 3e1e1da..0000000
--- a/pysam/cvcf.c
+++ /dev/null
@@ -1,30127 +0,0 @@
-/* Generated by Cython 0.20.1 on Fri Nov 21 19:49:04 2014 */
-
-#define PY_SSIZE_T_CLEAN
-#ifndef CYTHON_USE_PYLONG_INTERNALS
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#else
-#include "pyconfig.h"
-#ifdef PYLONG_BITS_IN_DIGIT
-#define CYTHON_USE_PYLONG_INTERNALS 1
-#else
-#define CYTHON_USE_PYLONG_INTERNALS 0
-#endif
-#endif
-#endif
-#include "Python.h"
-#ifndef Py_PYTHON_H
- #error Python headers needed to compile C extensions, please install development version of Python.
-#elif PY_VERSION_HEX < 0x02040000
- #error Cython requires Python 2.4+.
-#else
-#define CYTHON_ABI "0_20_1"
-#include <stddef.h> /* For offsetof */
-#ifndef offsetof
-#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
-#endif
-#if !defined(WIN32) && !defined(MS_WINDOWS)
- #ifndef __stdcall
- #define __stdcall
- #endif
- #ifndef __cdecl
- #define __cdecl
- #endif
- #ifndef __fastcall
- #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
-#else
-#define CYTHON_COMPILING_IN_PYPY 0
-#define CYTHON_COMPILING_IN_CPYTHON 1
-#endif
-#if CYTHON_COMPILING_IN_PYPY
-#define Py_OptimizeFlag 0
-#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_As_int(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)
- #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size)
- #define PyVarObject_HEAD_INIT(type, size) \
- PyObject_HEAD_INIT(type) size,
- #define PyType_Modified(t)
- typedef struct {
- void *buf;
- PyObject *obj;
- Py_ssize_t len;
- Py_ssize_t itemsize;
- int readonly;
- int ndim;
- char *format;
- Py_ssize_t *shape;
- Py_ssize_t *strides;
- Py_ssize_t *suboffsets;
- void *internal;
- } Py_buffer;
- #define PyBUF_SIMPLE 0
- #define PyBUF_WRITABLE 0x0001
- #define PyBUF_FORMAT 0x0004
- #define PyBUF_ND 0x0008
- #define PyBUF_STRIDES (0x0010 | PyBUF_ND)
- #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES)
- #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES)
- #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES)
- #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES)
- #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE)
- #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE)
- typedef int (*getbufferproc)(PyObject *, Py_buffer *, int);
- typedef void (*releasebufferproc)(PyObject *, Py_buffer *);
-#endif
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyClass_Type
-#else
- #define __Pyx_BUILTIN_MODULE_NAME "builtins"
- #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
- PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
- #define __Pyx_DefaultClassType PyType_Type
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #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 < 0x02060000
- #define Py_TPFLAGS_HAVE_VERSION_TAG 0
-#endif
-#if PY_VERSION_HEX < 0x02060000 && !defined(Py_TPFLAGS_IS_ABSTRACT)
- #define Py_TPFLAGS_IS_ABSTRACT 0
-#endif
-#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
- #define Py_TPFLAGS_HAVE_FINALIZE 0
-#endif
-#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
- #define CYTHON_PEP393_ENABLED 1
- #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
- 0 : _PyUnicode_Ready((PyObject *)(op)))
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
- #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
- #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
- #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
-#else
- #define CYTHON_PEP393_ENABLED 0
- #define __Pyx_PyUnicode_READY(op) (0)
- #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
- #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
- #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
- #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
- #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
-#endif
-#if CYTHON_COMPILING_IN_PYPY
- #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
-#else
- #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
- #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
- PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
-#endif
-#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
-#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
-#else
- #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBaseString_Type PyUnicode_Type
- #define PyStringObject PyUnicodeObject
- #define PyString_Type PyUnicode_Type
- #define PyString_Check PyUnicode_Check
- #define PyString_CheckExact PyUnicode_CheckExact
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PyBytesObject PyStringObject
- #define PyBytes_Type PyString_Type
- #define PyBytes_Check PyString_Check
- #define PyBytes_CheckExact PyString_CheckExact
- #define PyBytes_FromString PyString_FromString
- #define PyBytes_FromStringAndSize PyString_FromStringAndSize
- #define PyBytes_FromFormat PyString_FromFormat
- #define PyBytes_DecodeEscape PyString_DecodeEscape
- #define PyBytes_AsString PyString_AsString
- #define PyBytes_AsStringAndSize PyString_AsStringAndSize
- #define PyBytes_Size PyString_Size
- #define PyBytes_AS_STRING PyString_AS_STRING
- #define PyBytes_GET_SIZE PyString_GET_SIZE
- #define PyBytes_Repr PyString_Repr
- #define PyBytes_Concat PyString_Concat
- #define PyBytes_ConcatAndDel PyString_ConcatAndDel
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
- #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
-#else
- #define __Pyx_PyBaseString_Check(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj) || \
- PyString_Check(obj) || PyUnicode_Check(obj))
- #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
-#endif
-#if PY_VERSION_HEX < 0x02060000
- #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type)
- #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type)
-#endif
-#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
- #define PyInt_Check(op) PyLong_Check(op)
- #define PyInt_CheckExact(op) PyLong_CheckExact(op)
- #define PyInt_FromString PyLong_FromString
- #define PyInt_FromUnicode PyLong_FromUnicode
- #define PyInt_FromLong PyLong_FromLong
- #define PyInt_FromSize_t PyLong_FromSize_t
- #define PyInt_FromSsize_t PyLong_FromSsize_t
- #define PyInt_AsLong PyLong_AsLong
- #define PyInt_AS_LONG PyLong_AS_LONG
- #define PyInt_AsSsize_t PyLong_AsSsize_t
- #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
- #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
- #define PyNumber_Int PyNumber_Long
-#endif
-#if PY_MAJOR_VERSION >= 3
- #define PyBoolObject PyLongObject
-#endif
-#if PY_VERSION_HEX < 0x030200A4
- typedef long Py_hash_t;
- #define __Pyx_PyInt_FromHash_t PyInt_FromLong
- #define __Pyx_PyInt_AsHash_t PyInt_AsLong
-#else
- #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)
- #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b)
-#else
- #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0)))
- #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \
- (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1)))
- #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \
- (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \
- (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))
- #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n)))
-#else
- #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n))
- #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))
-#else
- #define __Pyx_NAMESTR(n) (n)
- #define __Pyx_DOCSTR(n) (n)
-#endif
-#ifndef CYTHON_INLINE
- #if defined(__GNUC__)
- #define CYTHON_INLINE __inline__
- #elif defined(_MSC_VER)
- #define CYTHON_INLINE __inline
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_INLINE inline
- #else
- #define CYTHON_INLINE
- #endif
-#endif
-#ifndef CYTHON_RESTRICT
- #if defined(__GNUC__)
- #define CYTHON_RESTRICT __restrict__
- #elif defined(_MSC_VER) && _MSC_VER >= 1400
- #define CYTHON_RESTRICT __restrict
- #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
- #define CYTHON_RESTRICT restrict
- #else
- #define CYTHON_RESTRICT
- #endif
-#endif
-#ifdef NAN
-#define __PYX_NAN() ((float) NAN)
-#else
-static CYTHON_INLINE float __PYX_NAN() {
- /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
- a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
- a quiet NaN. */
- float value;
- memset(&value, 0xFF, sizeof(value));
- return value;
-}
-#endif
-
-
-#if PY_MAJOR_VERSION >= 3
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
-#else
- #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
- #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
-#endif
-
-#ifndef __PYX_EXTERN_C
- #ifdef __cplusplus
- #define __PYX_EXTERN_C extern "C"
- #else
- #define __PYX_EXTERN_C extern
- #endif
-#endif
-
-#if defined(WIN32) || defined(MS_WINDOWS)
-#define _USE_MATH_DEFINES
-#endif
-#include <math.h>
-#define __PYX_HAVE__pysam__cvcf
-#define __PYX_HAVE_API__pysam__cvcf
-#include "stdlib.h"
-#include "string.h"
-#include "stdint.h"
-#include "stdio.h"
-#include "fcntl.h"
-#include "unistd.h"
-#include "zlib.h"
-#include "htslib/kstring.h"
-#include "htslib/hfile.h"
-#include "htslib/bgzf.h"
-#include "htslib/hts.h"
-#include "htslib/sam.h"
-#include "pysam_stream.h"
-#include "htslib/faidx.h"
-#include "htslib/tbx.h"
-#ifdef _OPENMP
-#include <omp.h>
-#endif /* _OPENMP */
-
-#ifdef PYREX_WITHOUT_ASSERTIONS
-#define CYTHON_WITHOUT_ASSERTIONS
-#endif
-
-#ifndef CYTHON_UNUSED
-# if defined(__GNUC__)
-# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
-# define CYTHON_UNUSED __attribute__ ((__unused__))
-# else
-# define CYTHON_UNUSED
-# endif
-#endif
-typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
- const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/
-
-#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
-#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
-#define __PYX_DEFAULT_STRING_ENCODING ""
-#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
-#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
- (sizeof(type) < sizeof(Py_ssize_t)) || \
- (sizeof(type) > sizeof(Py_ssize_t) && \
- likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX) && \
- (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
- v == (type)PY_SSIZE_T_MIN))) || \
- (sizeof(type) == sizeof(Py_ssize_t) && \
- (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
- v == (type)PY_SSIZE_T_MAX))) )
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
-#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
-#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
-#define __Pyx_PyBytes_FromString PyBytes_FromString
-#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*);
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
-#else
- #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
- #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
-#endif
-#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
-#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s)
-#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s)
-#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((char*)s)
-#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s)
-#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s)
-#if PY_MAJOR_VERSION < 3
-static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
-{
- const Py_UNICODE *u_end = u;
- while (*u_end++) ;
- return u_end - u - 1;
-}
-#else
-#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
-#endif
-#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
-#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
-#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
-#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
-#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
-#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))
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
-static int __Pyx_sys_getdefaultencoding_not_ascii;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- PyObject* ascii_chars_u = NULL;
- PyObject* ascii_chars_b = NULL;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) {
- __Pyx_sys_getdefaultencoding_not_ascii = 0;
- } else {
- const char* default_encoding_c = PyBytes_AS_STRING(default_encoding);
- char ascii_chars[128];
- int c;
- for (c = 0; c < 128; c++) {
- ascii_chars[c] = c;
- }
- __Pyx_sys_getdefaultencoding_not_ascii = 1;
- ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
- if (ascii_chars_u == NULL) goto bad;
- ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
- if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
- PyErr_Format(
- PyExc_ValueError,
- "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
- default_encoding_c);
- goto bad;
- }
- }
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- Py_XDECREF(ascii_chars_u);
- Py_XDECREF(ascii_chars_b);
- return -1;
-}
-#endif
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
-#else
-#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
-#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
-static char* __PYX_DEFAULT_STRING_ENCODING;
-static int __Pyx_init_sys_getdefaultencoding_params(void) {
- PyObject* sys = NULL;
- PyObject* default_encoding = NULL;
- char* default_encoding_c;
- sys = PyImport_ImportModule("sys");
- if (sys == NULL) goto bad;
- default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
- if (default_encoding == NULL) goto bad;
- default_encoding_c = PyBytes_AS_STRING(default_encoding);
- __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
- strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
- Py_DECREF(sys);
- Py_DECREF(default_encoding);
- return 0;
-bad:
- Py_XDECREF(sys);
- Py_XDECREF(default_encoding);
- return -1;
-}
-#endif
-#endif
-
-
-#ifdef __GNUC__
- /* Test for GCC > 2.95 */
- #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))
- #define likely(x) __builtin_expect(!!(x), 1)
- #define unlikely(x) __builtin_expect(!!(x), 0)
- #else /* __GNUC__ > 2 ... */
- #define likely(x) (x)
- #define unlikely(x) (x)
- #endif /* __GNUC__ > 2 ... */
-#else /* __GNUC__ */
- #define likely(x) (x)
- #define unlikely(x) (x)
-#endif /* __GNUC__ */
-
-static PyObject *__pyx_m;
-static PyObject *__pyx_d;
-static PyObject *__pyx_b;
-static PyObject *__pyx_empty_tuple;
-static PyObject *__pyx_empty_bytes;
-static int __pyx_lineno;
-static int __pyx_clineno = 0;
-static const char * __pyx_cfilenm= __FILE__;
-static const char *__pyx_filename;
-
-
-static const char *__pyx_f[] = {
- "cvcf.pyx",
- "ctabix.pxd",
- "TabProxies.pxd",
-};
-
-/*--- Type declarations ---*/
-struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator;
-struct __pyx_obj_5pysam_6ctabix_TabixFile;
-struct __pyx_obj_5pysam_6ctabix_Parser;
-struct __pyx_obj_5pysam_6ctabix_asTuple;
-struct __pyx_obj_5pysam_6ctabix_asGTF;
-struct __pyx_obj_5pysam_6ctabix_asBed;
-struct __pyx_obj_5pysam_6ctabix_asVCF;
-struct __pyx_obj_5pysam_6ctabix_TabixIterator;
-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_GZIterator;
-struct __pyx_obj_5pysam_6ctabix_GZIteratorHead;
-struct __pyx_obj_5pysam_6ctabix_GZIteratorParsed;
-struct __pyx_obj_5pysam_6ctabix_Tabixfile;
-struct __pyx_obj_5pysam_10TabProxies_TupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy;
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy;
-struct __pyx_obj_5pysam_10TabProxies_BedProxy;
-struct __pyx_obj_5pysam_10TabProxies_VCFProxy;
-struct __pyx_obj_5pysam_4cvcf_VCFRecord;
-struct __pyx_obj_5pysam_4cvcf_asVCFRecord;
-struct __pyx_obj_5pysam_4cvcf___pyx_scope_struct___parse;
-struct __pyx_opt_args_5pysam_6ctabix__force_str;
-
-/* "ctabix.pxd":50
- * ###########################################
- * # used by cvcf.pyx
- * cdef _force_str(object s, encoding=?) # <<<<<<<<<<<<<<
- *
- * ###########################################
- */
-struct __pyx_opt_args_5pysam_6ctabix__force_str {
- int __pyx_n;
- PyObject *encoding;
-};
-
-/* "ctabix.pxd":19
- * kstream_t, kstring_t, gzFile, tbx_t
- *
- * cdef class tabix_file_iterator: # <<<<<<<<<<<<<<
- * cdef gzFile fh
- * cdef kstream_t * kstream
- */
-struct __pyx_obj_5pysam_6ctabix_tabix_file_iterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_tabix_file_iterator *__pyx_vtab;
- gzFile fh;
- kstream_t *kstream;
- kstring_t buffer;
- size_t size;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
- int fd;
- int duplicated_fd;
- PyObject *infile;
-};
-
-
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- * cdef class TabixFile: # <<<<<<<<<<<<<<
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- * # pointer to tabixfile
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-struct __pyx_obj_5pysam_6ctabix_TabixFile {
- PyObject_HEAD
- htsFile *tabixfile;
- tbx_t *index;
- int isremote;
- PyObject *_filename;
- PyObject *_filename_index;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
- PyObject *encoding;
-};
-
-
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- * ###########################################
- * cdef class Parser: # <<<<<<<<<<<<<<
- * cdef encoding
- *
- */
-struct __pyx_obj_5pysam_6ctabix_Parser {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_Parser *__pyx_vtab;
- PyObject *encoding;
-};
-
-
-/* "ctabix.pxd":58
- * cdef parse(self, char * buffer, int len)
- *
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * cdef parse(self, char * buffer, int len)
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asTuple {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "ctabix.pxd":61
- * cdef parse(self, char * buffer, int len)
- *
- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asGTF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "ctabix.pxd":64
- * pass
- *
- * cdef class asBed(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
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- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "ctabix.pxd":67
- * pass
- *
- * cdef class asVCF(Parser): # <<<<<<<<<<<<<<
- * pass
- *
- */
-struct __pyx_obj_5pysam_6ctabix_asVCF {
- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
-};
-
-
-/* "ctabix.pxd":70
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- *
- * cdef class TabixIterator: # <<<<<<<<<<<<<<
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- * cdef TabixFile tabixfile
- */
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- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_TabixIterator *__pyx_vtab;
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- struct __pyx_obj_5pysam_6ctabix_TabixFile *tabixfile;
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- PyObject *encoding;
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-struct __pyx_obj_5pysam_6ctabix_TabixIteratorParsed {
- struct __pyx_obj_5pysam_6ctabix_TabixIterator __pyx_base;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
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- * cdef class GZIterator: # <<<<<<<<<<<<<<
- * cdef object _filename
- * cdef gzFile gzipfile
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-struct __pyx_obj_5pysam_6ctabix_GZIterator {
- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_6ctabix_GZIterator *__pyx_vtab;
- PyObject *_filename;
- gzFile gzipfile;
- kstream_t *kstream;
- kstring_t buffer;
- PyObject *encoding;
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- */
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- struct __pyx_obj_5pysam_6ctabix_GZIterator __pyx_base;
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-
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- *
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- struct __pyx_obj_5pysam_6ctabix_GZIterator __pyx_base;
- struct __pyx_obj_5pysam_6ctabix_Parser *parser;
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- struct __pyx_obj_5pysam_6ctabix_TabixFile __pyx_base;
-};
-
-
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- * ctypedef int uint64_t
- *
- * cdef class TupleProxy: # <<<<<<<<<<<<<<
- *
- * cdef:
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- PyObject_HEAD
- struct __pyx_vtabstruct_5pysam_10TabProxies_TupleProxy *__pyx_vtab;
- char *data;
- char **fields;
- int nfields;
- int index;
- int nbytes;
- int offset;
- int is_modified;
- PyObject *encoding;
-};
-
-
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- *
- * cdef class GTFProxy(TupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
- */
-struct __pyx_obj_5pysam_10TabProxies_GTFProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- char *_attributes;
- int hasOwnAttributes;
-};
-
-
-/* "TabProxies.pxd":73
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- * cdef class NamedTupleProxy(TupleProxy) : # <<<<<<<<<<<<<<
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- *
- */
-struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
-};
-
-
-/* "TabProxies.pxd":76
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- *
- * cdef class BedProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
- *
- * cdef:
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-struct __pyx_obj_5pysam_10TabProxies_BedProxy {
- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t start;
- uint32_t end;
- int bedfields;
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- * cdef class VCFProxy(NamedTupleProxy) : # <<<<<<<<<<<<<<
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- * cdef:
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- struct __pyx_obj_5pysam_10TabProxies_NamedTupleProxy __pyx_base;
- char *contig;
- uint32_t pos;
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-
-
-/* "pysam/cvcf.pyx":96
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- *
- * cdef class VCFRecord( TabProxies.TupleProxy): # <<<<<<<<<<<<<<
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-struct __pyx_obj_5pysam_4cvcf_VCFRecord {
- struct __pyx_obj_5pysam_10TabProxies_TupleProxy __pyx_base;
- PyObject *vcf;
- char *contig;
- uint32_t pos;
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-
-/* "pysam/cvcf.pyx":230
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- struct __pyx_obj_5pysam_6ctabix_Parser __pyx_base;
- PyObject *vcffile;
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-
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- *
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- PyObject_HEAD
- PyObject *__pyx_v_d;
- PyObject *__pyx_v_line;
- PyObject *__pyx_v_self;
- PyObject *__pyx_v_stream;
- Py_ssize_t __pyx_t_0;
- PyObject *__pyx_t_1;
- PyObject *(*__pyx_t_2)(PyObject *);
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-/* "ctabix.pxd":53
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- * cdef encoding
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- PyObject *(*parse)(struct __pyx_obj_5pysam_6ctabix_Parser *, char *, int);
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-
-/* "ctabix.pxd":58
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- *
- * cdef class asTuple(Parser): # <<<<<<<<<<<<<<
- * cdef parse(self, char * buffer, int len)
- *
- */
-
-struct __pyx_vtabstruct_5pysam_6ctabix_asTuple {
- struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
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-
-/* "ctabix.pxd":61
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- * cdef class asGTF(Parser): # <<<<<<<<<<<<<<
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- *
- */
-
-struct __pyx_vtabstruct_5pysam_6ctabix_asGTF {
- struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
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-
-/* "ctabix.pxd":64
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- struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
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-/* "ctabix.pxd":67
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-struct __pyx_vtabstruct_5pysam_6ctabix_asVCF {
- struct __pyx_vtabstruct_5pysam_6ctabix_Parser __pyx_base;
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-#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
-#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_getattro))
- return tp->tp_getattro(obj, attr_name);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_getattr))
- return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
-#endif
- return PyObject_GetAttr(obj, attr_name);
-}
-#else
-#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
-#endif
-
-static PyObject *__Pyx_GetBuiltinName(PyObject *name); /*proto*/
-
-static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
- Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/
-
-static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/
-
-static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
- PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
- const char* function_name); /*proto*/
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); /*proto*/
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); /*proto*/
-#else
-#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
-#endif
-
-#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
- __Pyx_GetItemInt_Generic(o, to_py_func(i))))
-#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
- (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck);
-
-static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/
-
-static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-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*/
-
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/
-
-#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) & likely(len > (L->allocated >> 1))) {
- 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
-
-#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 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);
-
-#if PY_MAJOR_VERSION < 3
-#define __Pyx_PyString_Join __Pyx_PyBytes_Join
-#define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v))
-#else
-#define __Pyx_PyString_Join PyUnicode_Join
-#define __Pyx_PyBaseString_Join PyUnicode_Join
-#endif
-#if CYTHON_COMPILING_IN_CPYTHON
- #if PY_MAJOR_VERSION < 3
- #define __Pyx_PyBytes_Join _PyString_Join
- #else
- #define __Pyx_PyBytes_Join _PyBytes_Join
- #endif
-#else
-static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values); /*proto*/
-#endif
-
-#if PY_MAJOR_VERSION >= 3
-static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
- PyObject *value;
- value = PyDict_GetItemWithError(d, key);
- if (unlikely(!value)) {
- if (!PyErr_Occurred()) {
- PyObject* args = PyTuple_Pack(1, key);
- if (likely(args))
- PyErr_SetObject(PyExc_KeyError, args);
- Py_XDECREF(args);
- }
- return NULL;
- }
- Py_INCREF(value);
- return value;
-}
-#else
- #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
-#endif
-
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** py_start, PyObject** py_stop, PyObject** py_slice,
- int has_cstart, int has_cstop, int wraparound);
-
-#if CYTHON_COMPILING_IN_CPYTHON
-#define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL)
-static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) {
- PyTypeObject* tp = Py_TYPE(obj);
- if (likely(tp->tp_setattro))
- return tp->tp_setattro(obj, attr_name, value);
-#if PY_MAJOR_VERSION < 3
- if (likely(tp->tp_setattr))
- return tp->tp_setattr(obj, PyString_AS_STRING(attr_name), value);
-#endif
- return PyObject_SetAttr(obj, attr_name, value);
-}
-#else
-#define __Pyx_PyObject_DelAttrStr(o,n) PyObject_DelAttr(o,n)
-#define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v)
-#endif
-
-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 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_ListComp_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_ListComp_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 */
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
-static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(PyObject* src, Py_ssize_t start, Py_ssize_t stop);
-#else
-#define __Pyx_PyList_GetSlice(seq, start, stop) PySequence_GetSlice(seq, start, stop)
-#define __Pyx_PyTuple_GetSlice(seq, start, stop) PySequence_GetSlice(seq, start, stop)
-#endif
-
-static PyObject* __Pyx_PyObject_CallMethodTuple(PyObject* obj, PyObject* method_name, PyObject* args) {
- PyObject *method, *result = NULL;
- if (unlikely(!args)) return NULL;
- method = __Pyx_PyObject_GetAttrStr(obj, method_name);
- if (unlikely(!method)) goto bad;
- result = __Pyx_PyObject_Call(method, args, NULL);
- Py_DECREF(method);
-bad:
- Py_DECREF(args);
- return result;
-}
-#define __Pyx_PyObject_CallMethod3(obj, name, arg1, arg2, arg3) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(3, arg1, arg2, arg3))
-#define __Pyx_PyObject_CallMethod2(obj, name, arg1, arg2) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(2, arg1, arg2))
-#define __Pyx_PyObject_CallMethod1(obj, name, arg1) \
- __Pyx_PyObject_CallMethodTuple(obj, name, PyTuple_Pack(1, arg1))
-#define __Pyx_PyObject_CallMethod0(obj, name) \
- __Pyx_PyObject_CallMethodTuple(obj, name, (Py_INCREF(__pyx_empty_tuple), __pyx_empty_tuple))
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x); /*proto*/
-
-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, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
- (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
- __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) : \
- (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \
- __Pyx_SetItemInt_Generic(o, to_py_func(i), v)))
-static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v);
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck);
-
-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 void* __Pyx_GetVtable(PyObject *dict); /*proto*/
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name); /*proto*/
-
-static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases);
-
-#if PY_VERSION_HEX < 0x02050000
-#ifndef PyAnySet_CheckExact
-#define PyAnySet_CheckExact(ob) \
- ((ob)->ob_type == &PySet_Type || \
- (ob)->ob_type == &PyFrozenSet_Type)
-#define PySet_New(iterable) \
- PyObject_CallFunctionObjArgs((PyObject *)&PySet_Type, (iterable), NULL)
-#define Pyx_PyFrozenSet_New(iterable) \
- PyObject_CallFunctionObjArgs((PyObject *)&PyFrozenSet_Type, (iterable), NULL)
-#define PySet_Size(anyset) \
- PyObject_Size((anyset))
-#define PySet_Contains(anyset, key) \
- PySequence_Contains((anyset), (key))
-#define PySet_Pop(set) \
- PyObject_CallMethod((set), (char*)"pop", NULL)
-static CYTHON_INLINE int PySet_Clear(PyObject *set) {
- PyObject *ret = PyObject_CallMethod(set, (char*)"clear", NULL);
- if (!ret) return -1;
- Py_DECREF(ret); return 0;
-}
-static CYTHON_INLINE int PySet_Discard(PyObject *set, PyObject *key) {
- PyObject *ret = PyObject_CallMethod(set, (char*)"discard", (char*)"(O)", key);
- if (!ret) return -1;
- Py_DECREF(ret); return 0;
-}
-static CYTHON_INLINE int PySet_Add(PyObject *set, PyObject *key) {
- PyObject *ret = PyObject_CallMethod(set, (char*)"add", (char*)"(O)", key);
- if (!ret) return -1;
- Py_DECREF(ret); return 0;
-}
-#endif /* PyAnySet_CheckExact (<= Py2.4) */
-#endif /* < Py2.5 */
-
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type);
-
-#define __Pyx_CyFunction_USED 1
-#include <structmember.h>
-#define __Pyx_CYFUNCTION_STATICMETHOD 0x01
-#define __Pyx_CYFUNCTION_CLASSMETHOD 0x02
-#define __Pyx_CYFUNCTION_CCLASS 0x04
-#define __Pyx_CyFunction_GetClosure(f) \
- (((__pyx_CyFunctionObject *) (f))->func_closure)
-#define __Pyx_CyFunction_GetClassObj(f) \
- (((__pyx_CyFunctionObject *) (f))->func_classobj)
-#define __Pyx_CyFunction_Defaults(type, f) \
- ((type *)(((__pyx_CyFunctionObject *) (f))->defaults))
-#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \
- ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g)
-typedef struct {
- PyCFunctionObject func;
- PyObject *func_dict;
- PyObject *func_weakreflist;
- PyObject *func_name;
- PyObject *func_qualname;
- PyObject *func_doc;
- PyObject *func_globals;
- PyObject *func_code;
- PyObject *func_closure;
- PyObject *func_classobj; /* No-args super() class cell */
- void *defaults;
- int defaults_pyobjects;
- int flags;
- PyObject *defaults_tuple; /* Const defaults tuple */
- PyObject *defaults_kwdict; /* Const kwonly defaults dict */
- PyObject *(*defaults_getter)(PyObject *);
- PyObject *func_annotations; /* function annotations dict */
-} __pyx_CyFunctionObject;
-static PyTypeObject *__pyx_CyFunctionType = 0;
-#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code) \
- __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code)
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml,
- int flags, PyObject* qualname,
- PyObject *self,
- PyObject *module, PyObject *globals,
- PyObject* code);
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *m,
- size_t size,
- int pyobjects);
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *m,
- PyObject *tuple);
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m,
- PyObject *dict);
-static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m,
- PyObject *dict);
-static int __Pyx_CyFunction_init(void);
-
-static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname,
- PyObject *mkw, PyObject *modname, PyObject *doc); /*proto*/
-static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict,
- PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); /*proto*/
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);
-
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
-
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
-
-static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); /*proto*/
-
-#define __Pyx_Generator_USED
-#include <structmember.h>
-#include <frameobject.h>
-typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *);
-typedef struct {
- PyObject_HEAD
- __pyx_generator_body_t body;
- PyObject *closure;
- PyObject *exc_type;
- PyObject *exc_value;
- PyObject *exc_traceback;
- PyObject *gi_weakreflist;
- PyObject *classobj;
- PyObject *yieldfrom;
- int resume_label;
- char is_running;
-} __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);
-
-#if !defined(__Pyx_PyIdentifier_FromString)
-#if PY_MAJOR_VERSION < 3
- #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
-#else
- #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
-#endif
-#endif
-
-static PyObject *__Pyx_ImportModule(const char *name); /*proto*/
-
-static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/
-
-static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig); /*proto*/
-
-typedef struct {
- int code_line;
- PyCodeObject* code_object;
-} __Pyx_CodeObjectCacheEntry;
-struct __Pyx_CodeObjectCache {
- int count;
- int max_count;
- __Pyx_CodeObjectCacheEntry* entries;
-};
-static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
-static PyCodeObject *__pyx_find_code_object(int code_line);
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
-
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename); /*proto*/
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/
-
-
-/* Module declarations from 'libc.stdint' */
-
-/* Module declarations from 'libc.string' */
-
-/* Module declarations from 'libc.stdlib' */
-
-/* Module declarations from 'libc.stdio' */
-
-/* Module declarations from 'pysam.chtslib' */
-
-/* Module declarations from 'pysam.ctabix' */
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_tabix_file_iterator = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixFile = 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_TabixIterator = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_TabixIteratorParsed = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_GZIterator = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_GZIteratorHead = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_GZIteratorParsed = 0;
-static PyTypeObject *__pyx_ptype_5pysam_6ctabix_Tabixfile = 0;
-static PyObject *(*__pyx_f_5pysam_6ctabix__force_str)(PyObject *, struct __pyx_opt_args_5pysam_6ctabix__force_str *__pyx_optional_args); /*proto*/
-
-/* 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 = 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;
-static PyObject *__pyx_builtin_enumerate;
-static PyObject *__pyx_builtin_map;
-static PyObject *__pyx_builtin_min;
-static PyObject *__pyx_builtin_zip;
-static PyObject *__pyx_builtin_StopIteration;
-static PyObject *__pyx_builtin_KeyError;
-static PyObject *__pyx_builtin_NotImplementedError;
-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_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_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_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_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_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, PyObject *__pyx_v_encoding); /* 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 PyObject *__pyx_tp_new_5pysam_4cvcf_VCFRecord(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_4cvcf_asVCFRecord(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static PyObject *__pyx_tp_new_5pysam_4cvcf___pyx_scope_struct___parse(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
-static char __pyx_k_[] = "";
-static char __pyx_k_0[] = "0";
-static char __pyx_k_A[] = "A";
-static char __pyx_k_D[] = "D";
-static char __pyx_k_G[] = "G";
-static char __pyx_k_I[] = "I";
-static char __pyx_k_N[] = "N";
-static char __pyx_k_a[] = "a";
-static char __pyx_k_c[] = "c";
-static char __pyx_k_d[] = "d";
-static char __pyx_k_f[] = "f";
-static char __pyx_k_i[] = "i";
-static char __pyx_k_k[] = "k";
-static char __pyx_k_l[] = "l";
-static char __pyx_k_n[] = "n";
-static char __pyx_k_r[] = "r";
-static char __pyx_k_s[] = "s";
-static char __pyx_k_t[] = "t";
-static char __pyx_k_v[] = "v";
-static char __pyx_k_x[] = "x";
-static char __pyx_k_y[] = "y";
-static char __pyx_k_DP[] = "DP";
-static char __pyx_k_EC[] = "EC";
-static char __pyx_k_FT[] = "FT";
-static char __pyx_k_GL[] = "GL";
-static char __pyx_k_GP[] = "GP";
-static char __pyx_k_GQ[] = "GQ";
-static char __pyx_k_GT[] = "GT";
-static char __pyx_k_HQ[] = "HQ";
-static char __pyx_k_ID[] = "ID=";
-static char __pyx_k_MQ[] = "MQ";
-static char __pyx_k_PL[] = "PL";
-static char __pyx_k_PQ[] = "PQ";
-static char __pyx_k_PS[] = "PS";
-static char __pyx_k__2[] = ",";
-static char __pyx_k__4[] = ":";
-static char __pyx_k__6[] = "-";
-static char __pyx_k__8[] = ".";
-static char __pyx_k_fa[] = "fa";
-static char __pyx_k_id[] = "id";
-static char __pyx_k_na[] = "na";
-static char __pyx_k_re[] = "re";
-static char __pyx_k_ALT[] = "ALT";
-static char __pyx_k_GLE[] = "GLE";
-static char __pyx_k_POS[] = "POS";
-static char __pyx_k_REF[] = "REF";
-static char __pyx_k_VCF[] = "VCF";
-static char __pyx_k__10[] = ";";
-static char __pyx_k__13[] = "=";
-static char __pyx_k__21[] = "<";
-static char __pyx_k__23[] = ">";
-static char __pyx_k__29[] = "\"";
-static char __pyx_k__46[] = "##";
-static char __pyx_k__51[] = "#";
-static char __pyx_k__55[] = "\t";
-static char __pyx_k__60[] = "\n";
-static char __pyx_k__61[] = "|";
-static char __pyx_k__91[] = "[|/\\\\]";
-static char __pyx_k_add[] = "add";
-static char __pyx_k_all[] = "__all__";
-static char __pyx_k_alt[] = "alt";
-static char __pyx_k_doc[] = "__doc__";
-static char __pyx_k_end[] = "end";
-static char __pyx_k_err[] = "err";
-static char __pyx_k_fmt[] = "fmt";
-static char __pyx_k_get[] = "get";
-static char __pyx_k_gts[] = "gts";
-static char __pyx_k_idx[] = "idx";
-static char __pyx_k_key[] = "key";
-static char __pyx_k_map[] = "map";
-static char __pyx_k_min[] = "min";
-static char __pyx_k_nmb[] = "nmb";
-static char __pyx_k_opt[] = "opt";
-static char __pyx_k_pos[] = "pos";
-static char __pyx_k_ref[] = "ref";
-static char __pyx_k_s_s[] = "%s=%s";
-static char __pyx_k_sys[] = "sys";
-static char __pyx_k_var[] = "var";
-static char __pyx_k_vcf[] = "vcf";
-static char __pyx_k_zip[] = "zip";
-static char __pyx_k_Flag[] = "Flag";
-static char __pyx_k_ID_2[] = "ID";
-static char __pyx_k_INFO[] = "INFO";
-static char __pyx_k_PASS[] = "PASS";
-static char __pyx_k_QUAL[] = "QUAL";
-static char __pyx_k_Type[] = "Type=";
-static char __pyx_k_addn[] = "addn";
-static char __pyx_k_alt1[] = "alt1";
-static char __pyx_k_alt2[] = "alt2";
-static char __pyx_k_args[] = "args";
-static char __pyx_k_cols[] = "cols";
-static char __pyx_k_copy[] = "_copy";
-static char __pyx_k_data[] = "data";
-static char __pyx_k_dict[] = "__dict__";
-static char __pyx_k_elts[] = "elts";
-static char __pyx_k_find[] = "find";
-static char __pyx_k_info[] = "_info";
-static char __pyx_k_init[] = "__init__";
-static char __pyx_k_join[] = "join";
-static char __pyx_k_keys[] = "keys";
-static char __pyx_k_last[] = "last";
-static char __pyx_k_left[] = "left";
-static char __pyx_k_line[] = "line";
-static char __pyx_k_main[] = "__main__";
-static char __pyx_k_pos1[] = "pos1";
-static char __pyx_k_pos2[] = "pos2";
-static char __pyx_k_qual[] = "qual";
-static char __pyx_k_ref1[] = "ref1";
-static char __pyx_k_ref2[] = "ref2";
-static char __pyx_k_rest[] = "rest";
-static char __pyx_k_self[] = "self";
-static char __pyx_k_send[] = "send";
-static char __pyx_k_test[] = "__test__";
-static char __pyx_k_type[] = "type";
-static char __pyx_k_ACGTN[] = "ACGTN";
-static char __pyx_k_CHROM[] = "CHROM";
-static char __pyx_k_Error[] = "Error";
-static char __pyx_k_Float[] = "Float";
-static char __pyx_k_addns[] = "addns";
-static char __pyx_k_ascii[] = "ascii";
-static char __pyx_k_blurp[] = "blurp";
-static char __pyx_k_chrom[] = "chrom";
-static char __pyx_k_close[] = "close";
-static char __pyx_k_descr[] = "descr";
-static char __pyx_k_error[] = "error";
-static char __pyx_k_faref[] = "faref";
-static char __pyx_k_fetch[] = "fetch";
-static char __pyx_k_first[] = "first";
-static char __pyx_k_ielts[] = "ielts";
-static char __pyx_k_label[] = "label";
-static char __pyx_k_lines[] = "lines";
-static char __pyx_k_match[] = "match";
-static char __pyx_k_parse[] = "_parse";
-static char __pyx_k_pysam[] = "pysam";
-static char __pyx_k_range[] = "range";
-static char __pyx_k_s_s_2[] = "##%s=%s\n";
-static char __pyx_k_sdata[] = "sdata";
-static char __pyx_k_split[] = "split";
-static char __pyx_k_start[] = "start";
-static char __pyx_k_strip[] = "strip";
-static char __pyx_k_throw[] = "throw";
-static char __pyx_k_upper[] = "upper";
-static char __pyx_k_value[] = "value";
-static char __pyx_k_write[] = "write";
-static char __pyx_k_FILTER[] = "FILTER";
-static char __pyx_k_FORMAT[] = "FORMAT";
-static char __pyx_k_GTdata[] = "GTdata";
-static char __pyx_k_Number[] = "Number=";
-static char __pyx_k_String[] = "String";
-static char __pyx_k_Type_2[] = "Type";
-static char __pyx_k_allele[] = "allele";
-static char __pyx_k_append[] = "append";
-static char __pyx_k_bisect[] = "bisect";
-static char __pyx_k_copy_2[] = "copy";
-static char __pyx_k_dict_2[] = "dict";
-static char __pyx_k_errors[] = "_errors";
-static char __pyx_k_filter[] = "_filter";
-static char __pyx_k_format[] = "format";
-static char __pyx_k_header[] = "_header";
-static char __pyx_k_import[] = "__import__";
-static char __pyx_k_info_2[] = "info";
-static char __pyx_k_line_2[] = "_line";
-static char __pyx_k_lineno[] = "_lineno";
-static char __pyx_k_module[] = "__module__";
-static char __pyx_k_number[] = "number";
-static char __pyx_k_object[] = "object";
-static char __pyx_k_output[] = "(output)";
-static char __pyx_k_parser[] = "parser";
-static char __pyx_k_record[] = "record";
-static char __pyx_k_region[] = "region";
-static char __pyx_k_result[] = "result";
-static char __pyx_k_sample[] = "sample";
-static char __pyx_k_stream[] = "stream";
-static char __pyx_k_string[] = "string";
-static char __pyx_k_values[] = "values";
-static char __pyx_k_ACGTN_2[] = "^[ACGTN]+$";
-static char __pyx_k_Integer[] = "Integer";
-static char __pyx_k_VCFv3_3[] = "VCFv3.3";
-static char __pyx_k_VCFv4_0[] = "VCFv4.0";
-static char __pyx_k_VCFv4_1[] = "VCFv4.1";
-static char __pyx_k_Warning[] = "Warning";
-static char __pyx_k_alleles[] = "#alleles";
-static char __pyx_k_compile[] = "compile";
-static char __pyx_k_connect[] = "connect";
-static char __pyx_k_errwarn[] = "errwarn";
-static char __pyx_k_getinfo[] = "getinfo";
-static char __pyx_k_lines_2[] = "_lines";
-static char __pyx_k_longest[] = "longest";
-static char __pyx_k_missing[] = "missing";
-static char __pyx_k_movable[] = "movable";
-static char __pyx_k_newalts[] = "newalts";
-static char __pyx_k_parse_2[] = "parse";
-static char __pyx_k_prepare[] = "__prepare__";
-static char __pyx_k_regions[] = "regions";
-static char __pyx_k_replace[] = "replace";
-static char __pyx_k_samples[] = "_samples";
-static char __pyx_k_setinfo[] = "setinfo";
-static char __pyx_k_vcffile[] = "vcffile";
-static char __pyx_k_version[] = "_version";
-static char __pyx_k_GTstring[] = "GTstring";
-static char __pyx_k_Genotype[] = "Genotype";
-static char __pyx_k_KeyError[] = "KeyError";
-static char __pyx_k_Number_2[] = "Number";
-static char __pyx_k_deepcopy[] = "deepcopy";
-static char __pyx_k_encoding[] = "encoding";
-static char __pyx_k_endswith[] = "endswith";
-static char __pyx_k_expected[] = "expected";
-static char __pyx_k_filename[] = "filename";
-static char __pyx_k_filter_2[] = "filter";
-static char __pyx_k_format_2[] = "_format";
-static char __pyx_k_gtsRegEx[] = "gtsRegEx";
-static char __pyx_k_header_2[] = "header";
-static char __pyx_k_headings[] = "headings";
-static char __pyx_k_inregion[] = "inregion";
-static char __pyx_k_operator[] = "operator";
-static char __pyx_k_output_2[] = "output";
-static char __pyx_k_qualname[] = "__qualname__";
-static char __pyx_k_required[] = "_required";
-static char __pyx_k_sequence[] = "sequence";
-static char __pyx_k_shortest[] = "shortest";
-static char __pyx_k_validate[] = "validate";
-static char __pyx_k_Character[] = "Character";
-static char __pyx_k_NT_NUMBER[] = "NT_NUMBER";
-static char __pyx_k_Phase_set[] = "Phase set";
-static char __pyx_k_Tabixfile[] = "Tabixfile";
-static char __pyx_k_VCFRecord[] = "VCFRecord";
-static char __pyx_k_VCF_error[] = "VCF.error";
-static char __pyx_k_VCF_fetch[] = "VCF.fetch";
-static char __pyx_k_VCF_parse[] = "VCF.parse";
-static char __pyx_k_VCF_write[] = "VCF.write";
-static char __pyx_k_WRONG_REF[] = "WRONG_REF";
-static char __pyx_k_convertGT[] = "convertGT";
-static char __pyx_k_enumerate[] = "enumerate";
-static char __pyx_k_genotypes[] = "#genotypes";
-static char __pyx_k_getfilter[] = "getfilter";
-static char __pyx_k_getformat[] = "getformat";
-static char __pyx_k_getheader[] = "getheader";
-static char __pyx_k_last_line[] = "last_line";
-static char __pyx_k_leftalign[] = "leftalign";
-static char __pyx_k_lineparse[] = "lineparse";
-static char __pyx_k_metaclass[] = "__metaclass__";
-static char __pyx_k_reference[] = "reference";
-static char __pyx_k_regions_2[] = "_regions";
-static char __pyx_k_samples_2[] = "samples";
-static char __pyx_k_separator[] = "separator";
-static char __pyx_k_setfilter[] = "setfilter";
-static char __pyx_k_setformat[] = "setformat";
-static char __pyx_k_setheader[] = "setheader";
-static char __pyx_k_tabixfile[] = "tabixfile";
-static char __pyx_k_version_2[] = "version";
-static char __pyx_k_warnerror[] = "warnerror";
-static char __pyx_k_NT_ALLELES[] = "NT_ALLELES";
-static char __pyx_k_NT_UNKNOWN[] = "NT_UNKNOWN";
-static char __pyx_k_VCF___init[] = "VCF.__init__";
-static char __pyx_k_VCF__parse[] = "VCF._parse";
-static char __pyx_k_ValueError[] = "ValueError";
-static char __pyx_k_errorlabel[] = "errorlabel";
-static char __pyx_k_fileformat[] = "fileformat";
-static char __pyx_k_formatdict[] = "formatdict";
-static char __pyx_k_getsamples[] = "getsamples";
-static char __pyx_k_itemgetter[] = "itemgetter";
-static char __pyx_k_itervalues[] = "itervalues";
-static char __pyx_k_namedtuple[] = "namedtuple";
-static char __pyx_k_numbertype[] = "numbertype";
-static char __pyx_k_parse_data[] = "parse_data";
-static char __pyx_k_pysam_cvcf[] = "pysam.cvcf";
-static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
-static char __pyx_k_required_2[] = "required";
-static char __pyx_k_setregions[] = "setregions";
-static char __pyx_k_setsamples[] = "setsamples";
-static char __pyx_k_setversion[] = "setversion";
-static char __pyx_k_startswith[] = "startswith";
-static char __pyx_k_write_data[] = "write_data";
-static char __pyx_k_Description[] = "Description=";
-static char __pyx_k_MISSING_REF[] = "MISSING_REF";
-static char __pyx_k_V33_BAD_REF[] = "V33_BAD_REF";
-static char __pyx_k_VCF_connect[] = "VCF.connect";
-static char __pyx_k_VCF_getinfo[] = "VCF.getinfo";
-static char __pyx_k_VCF_setinfo[] = "VCF.setinfo";
-static char __pyx_k_alleleRegEx[] = "alleleRegEx";
-static char __pyx_k_collections[] = "collections";
-static char __pyx_k_defaultdict[] = "defaultdict";
-static char __pyx_k_description[] = "description";
-static char __pyx_k_errorstring[] = "errorstring";
-static char __pyx_k_ignoreerror[] = "ignoreerror";
-static char __pyx_k_leftalign_2[] = "_leftalign";
-static char __pyx_k_reference_2[] = "_reference";
-static char __pyx_k_warn_errors[] = "_warn_errors";
-static char __pyx_k_writeheader[] = "writeheader";
-static char __pyx_k_BAD_GENOTYPE[] = "BAD_GENOTYPE";
-static char __pyx_k_NT_GENOTYPES[] = "NT_GENOTYPES";
-static char __pyx_k_VCF_inregion[] = "VCF.inregion";
-static char __pyx_k_VCF_validate[] = "VCF.validate";
-static char __pyx_k_get_expected[] = "get_expected";
-static char __pyx_k_get_sequence[] = "get_sequence";
-static char __pyx_k_missingvalue[] = "missingvalue";
-static char __pyx_k_parse_format[] = "parse_format";
-static char __pyx_k_parse_header[] = "parse_header";
-static char __pyx_k_setreference[] = "setreference";
-static char __pyx_k_write_header[] = "write_header";
-static char __pyx_k_Description_2[] = "Description";
-static char __pyx_k_NT_NR_ALLELES[] = "NT_NR_ALLELES";
-static char __pyx_k_StopIteration[] = "StopIteration";
-static char __pyx_k_Undefined_tag[] = "(Undefined tag)";
-static char __pyx_k_VCF_convertGT[] = "VCF.convertGT";
-static char __pyx_k_VCF_getfilter[] = "VCF.getfilter";
-static char __pyx_k_VCF_getformat[] = "VCF.getformat";
-static char __pyx_k_VCF_getheader[] = "VCF.getheader";
-static char __pyx_k_VCF_setfilter[] = "VCF.setfilter";
-static char __pyx_k_VCF_setformat[] = "VCF.setformat";
-static char __pyx_k_VCF_setheader[] = "VCF.setheader";
-static char __pyx_k_VCF_warnerror[] = "VCF.warnerror";
-static char __pyx_k_compare_calls[] = "compare_calls";
-static char __pyx_k_convertGTback[] = "convertGTback";
-static char __pyx_k_datagenerator[] = "datagenerator";
-static char __pyx_k_format_format[] = "format_format";
-static char __pyx_k_parse_heading[] = "parse_heading";
-static char __pyx_k_parse_regions[] = "parse_regions";
-static char __pyx_k_sample2column[] = "_sample2column";
-static char __pyx_k_write_heading[] = "write_heading";
-static char __pyx_k_V33_BAD_ALLELE[] = "V33_BAD_ALLELE";
-static char __pyx_k_V40_BAD_ALLELE[] = "V40_BAD_ALLELE";
-static char __pyx_k_VCF_getsamples[] = "VCF.getsamples";
-static char __pyx_k_VCF_parse_data[] = "VCF.parse_data";
-static char __pyx_k_VCF_setregions[] = "VCF.setregions";
-static char __pyx_k_VCF_setsamples[] = "VCF.setsamples";
-static char __pyx_k_VCF_setversion[] = "VCF.setversion";
-static char __pyx_k_VCF_write_data[] = "VCF.write_data";
-static char __pyx_k_add_definition[] = "_add_definition";
-static char __pyx_k_have_deletions[] = "have_deletions";
-static char __pyx_k_ignored_errors[] = "_ignored_errors";
-static char __pyx_k_nonref_alleles[] = "#nonref_alleles";
-static char __pyx_k_parse_header_2[] = "_parse_header";
-static char __pyx_k_Phasing_quality[] = "Phasing quality";
-static char __pyx_k_VCF_ignoreerror[] = "VCF.ignoreerror";
-static char __pyx_k_VCF_writeheader[] = "VCF.writeheader";
-static char __pyx_k_faref_leftflank[] = "faref_leftflank";
-static char __pyx_k_Genotype_Quality[] = "Genotype Quality";
-static char __pyx_k_POS_NOT_POSITIVE[] = "POS_NOT_POSITIVE";
-static char __pyx_k_VCF_get_expected[] = "VCF.get_expected";
-static char __pyx_k_VCF_parse_format[] = "VCF.parse_format";
-static char __pyx_k_VCF_parse_header[] = "VCF.parse_header";
-static char __pyx_k_VCF_setreference[] = "VCF.setreference";
-static char __pyx_k_VCF_write_header[] = "VCF.write_header";
-static char __pyx_k_parse_formatdata[] = "parse_formatdata";
-static char __pyx_k_phased_genotypes[] = "#phased_genotypes";
-static char __pyx_k_ERROR_INFO_STRING[] = "ERROR_INFO_STRING";
-static char __pyx_k_ERROR_UNKNOWN_KEY[] = "ERROR_UNKNOWN_KEY";
-static char __pyx_k_Haplotype_Quality[] = "Haplotype Quality";
-static char __pyx_k_POS_NOT_NUMERICAL[] = "POS_NOT_NUMERICAL";
-static char __pyx_k_VCF__parse_header[] = "VCF._parse_header";
-static char __pyx_k_VCF_compare_calls[] = "VCF.compare_calls";
-static char __pyx_k_VCF_convertGTback[] = "VCF.convertGTback";
-static char __pyx_k_VCF_format_format[] = "VCF.format_format";
-static char __pyx_k_VCF_parse_heading[] = "VCF.parse_heading";
-static char __pyx_k_VCF_write_heading[] = "VCF.write_heading";
-static char __pyx_k_format_formatdata[] = "format_formatdata";
-static char __pyx_k_in_line_s_s_s_s_s[] = " in line %s: '%s'\n%s %s: %s\n";
-static char __pyx_k_FILTER_NOT_DEFINED[] = "FILTER_NOT_DEFINED";
-static char __pyx_k_FORMAT_NOT_DEFINED[] = "FORMAT_NOT_DEFINED";
-static char __pyx_k_QUAL_NOT_NUMERICAL[] = "QUAL_NOT_NUMERICAL";
-static char __pyx_k_ZERO_LENGTH_ALLELE[] = "ZERO_LENGTH_ALLELE";
-static char __pyx_k_found_s_expected_s[] = "(found %s, expected %s)";
-static char __pyx_k_ERROR_TRAILING_DATA[] = "ERROR_TRAILING_DATA";
-static char __pyx_k_NT_PHASED_GENOTYPES[] = "NT_PHASED_GENOTYPES";
-static char __pyx_k_NotImplementedError[] = "NotImplementedError";
-static char __pyx_k_RMS_mapping_quality[] = "RMS mapping quality";
-static char __pyx_k_UNKNOWN_CHAR_IN_REF[] = "UNKNOWN_CHAR_IN_REF";
-static char __pyx_k_VCF__add_definition[] = "VCF._add_definition";
-static char __pyx_k_fileformat_VCFv_s_s[] = "##fileformat=VCFv%s.%s\n";
-static char __pyx_k_needs_to_be_checked[] = "needs to be checked";
-static char __pyx_k_sth_entry_not_found[] = "(%sth entry not found)";
-static char __pyx_k_BAD_NUMBER_OF_VALUES[] = "BAD_NUMBER_OF_VALUES";
-static char __pyx_k_ERROR_FLAG_HAS_VALUE[] = "ERROR_FLAG_HAS_VALUE";
-static char __pyx_k_Genotype_likelihoods[] = "Genotype likelihoods";
-static char __pyx_k_VCF_parse_formatdata[] = "VCF.parse_formatdata";
-static char __pyx_k_enter_default_format[] = "enter_default_format";
-static char __pyx_k_BAD_NUMBER_OF_COLUMNS[] = "BAD_NUMBER_OF_COLUMNS";
-static char __pyx_k_ERROR_FORMAT_NOT_CHAR[] = "ERROR_FORMAT_NOT_CHAR";
-static char __pyx_k_FORMAT_MISSING_QUOTES[] = "FORMAT_MISSING_QUOTES";
-static char __pyx_k_UNKNOWN_FORMAT_STRING[] = "UNKNOWN_FORMAT_STRING";
-static char __pyx_k_VCF_format_formatdata[] = "VCF.format_formatdata";
-static char __pyx_k_Invalid_error_string_s[] = "Invalid error string: %s";
-static char __pyx_k_Sample_Genotype_Filter[] = "Sample Genotype Filter";
-static char __pyx_k_V33_UNMATCHED_DELETION[] = "V33_UNMATCHED_DELETION";
-static char __pyx_k_BADLY_FORMATTED_HEADING[] = "BADLY_FORMATTED_HEADING";
-static char __pyx_k_ZERO_FOR_NON_FLAG_FIELD[] = "ZERO_FOR_NON_FLAG_FIELD";
-static char __pyx_k_BAD_NUMBER_OF_PARAMETERS[] = "BAD_NUMBER_OF_PARAMETERS";
-static char __pyx_k_ERROR_FORMAT_NOT_INTEGER[] = "ERROR_FORMAT_NOT_INTEGER";
-static char __pyx_k_VCF_enter_default_format[] = "VCF.enter_default_format";
-static char __pyx_k_reference_is_s_VCF_says_s[] = "(reference is %s, VCF says %s)";
-static char __pyx_k_ERROR_FORMAT_NOT_NUMERICAL[] = "ERROR_FORMAT_NOT_NUMERICAL";
-static char __pyx_k_V40_MISSING_ANGLE_BRACKETS[] = "V40_MISSING_ANGLE_BRACKETS";
-static char __pyx_k_WRONG_REF_Wrong_reference_s[] = "WRONG_REF:Wrong reference %s";
-static char __pyx_k_Conditional_genotype_quality[] = "Conditional genotype quality";
-static char __pyx_k_deletion_is_s_reference_is_s[] = "(deletion is %s, reference is %s)";
-static char __pyx_k_BADLY_FORMATTED_FORMAT_STRING[] = "BADLY_FORMATTED_FORMAT_STRING";
-static char __pyx_k_HEADING_NOT_SEPARATED_BY_TABS[] = "HEADING_NOT_SEPARATED_BY_TABS";
-static char __pyx_k_MISSING_INDEL_ALLELE_REF_BASE[] = "MISSING_INDEL_ALLELE_REF_BASE";
-static char __pyx_k_home_andreas_devel_pysam_pysam[] = "/home/andreas/devel/pysam/pysam/cvcf.pyx";
-static char __pyx_k_BADLY_FORMATTED_HEADING_Did_not[] = "BADLY_FORMATTED_HEADING:Did not find 9 required headings (CHROM, POS, ..., FORMAT) %s";
-static char __pyx_k_ERROR_FORMAT_NOT_CHAR_Eexpected[] = "ERROR_FORMAT_NOT_CHAR:Eexpected character in formatted field; got string";
-static char __pyx_k_ERROR_UNKNOWN_KEY_Unknown_key_s[] = "ERROR_UNKNOWN_KEY:Unknown key (%s) found in formatted field (info; format; or filter)";
-static char __pyx_k_Expected_alternate_allel_counts[] = "Expected alternate allel counts";
-static char __pyx_k_FILTER_NOT_DEFINED_Identifier_s[] = "FILTER_NOT_DEFINED:Identifier (%s) in filter found which was not defined in header";
-static char __pyx_k_FORMAT_NOT_DEFINED_Identifier_s[] = "FORMAT_NOT_DEFINED:Identifier (%s) in format found which was not defined in header";
-static char __pyx_k_POS_NOT_POSITIVE_Position_field[] = "POS_NOT_POSITIVE:Position field must be >0";
-static char __pyx_k_Read_depth_at_this_position_for[] = "Read depth at this position for this sample";
-static char __pyx_k_Unknown_number_type_encountered[] = "Unknown number type encountered: %s";
-static char __pyx_k_V33_BAD_ALLELE_Cannot_interpret[] = "V33_BAD_ALLELE:Cannot interpret allele for v3.3 VCF";
-static char __pyx_k_V33_BAD_REF_Reference_should_be[] = "V33_BAD_REF:Reference should be single-character in v3.3 VCF";
-static char __pyx_k_V40_BAD_ALLELE_Bad_allele_found[] = "V40_BAD_ALLELE:Bad allele found for v4.0 VCF (%s)";
-static char __pyx_k_found_s_values_in_element_s_exp[] = "(found %s values in element %s; expected %s)";
-static char __pyx_k_BADLY_FORMATTED_FORMAT_STRING_Fo[] = "BADLY_FORMATTED_FORMAT_STRING:Formatting error in the format string";
-static char __pyx_k_BAD_CHR_TAG_Error_calculating_ch[] = "BAD_CHR_TAG:Error calculating chr tag for %s";
-static char __pyx_k_BAD_GENOTYPE_Cannot_parse_genoty[] = "BAD_GENOTYPE:Cannot parse genotype (%s)";
-static char __pyx_k_BAD_NUMBER_OF_COLUMNS_Wrong_numb[] = "BAD_NUMBER_OF_COLUMNS:Wrong number of columns found (%s)";
-static char __pyx_k_BAD_NUMBER_OF_PARAMETERS_Found_u[] = "BAD_NUMBER_OF_PARAMETERS:Found unexpected number of parameters (%s)";
-static char __pyx_k_BAD_NUMBER_OF_VALUES_Found_too_m[] = "BAD_NUMBER_OF_VALUES:Found too many of values in sample column (%s)";
-static char __pyx_k_Can_only_handle_v3_3_and_v4_0_VC[] = "Can only handle v3.3 and v4.0 VCF files";
-static char __pyx_k_Don_t_understand_region_string_s[] = "Don't understand region string '%s'";
-static char __pyx_k_ERROR_FLAG_HAS_VALUE_Flag_fields[] = "ERROR_FLAG_HAS_VALUE:Flag fields should not have a value";
-static char __pyx_k_ERROR_FORMAT_NOT_INTEGER_Expecte[] = "ERROR_FORMAT_NOT_INTEGER:Expected integer in formatted field; got %s";
-static char __pyx_k_ERROR_FORMAT_NOT_NUMERICAL_Expec[] = "ERROR_FORMAT_NOT_NUMERICAL:Expected integer or float in formatted field; got %s";
-static char __pyx_k_ERROR_INFO_STRING_Error_while_pa[] = "ERROR_INFO_STRING:Error while parsing info field";
-static char __pyx_k_ERROR_TRAILING_DATA_Numerical_fi[] = "ERROR_TRAILING_DATA:Numerical field ('%s') has semicolon-separated trailing data";
-static char __pyx_k_FORMAT_MISSING_QUOTES_Descriptio[] = "FORMAT_MISSING_QUOTES:Description field in format definition is not surrounded by quotes";
-static char __pyx_k_Genotype_posterior_probabilities[] = "Genotype posterior probabilities";
-static char __pyx_k_HEADING_NOT_SEPARATED_BY_TABS_He[] = "HEADING_NOT_SEPARATED_BY_TABS:Heading line appears separated by spaces, not tabs";
-static char __pyx_k_MISSING_INDEL_ALLELE_REF_BASE_In[] = "MISSING_INDEL_ALLELE_REF_BASE:Indel alleles must begin with single reference base";
-static char __pyx_k_MISSING_REF_Reference_allele_mis[] = "MISSING_REF:Reference allele missing";
-static char __pyx_k_POS_NOT_NUMERICAL_Position_colum[] = "POS_NOT_NUMERICAL:Position column is not numerical";
-static char __pyx_k_Phred_scaled_genotype_likelihood[] = "Phred-scaled genotype likelihoods";
-static char __pyx_k_QUAL_NOT_NUMERICAL_Quality_field[] = "QUAL_NOT_NUMERICAL:Quality field must be numerical, or '.'";
-static char __pyx_k_Required_key_s_not_found_in_data[] = "Required key %s not found in data";
-static char __pyx_k_UNKNOWN_CHAR_IN_REF_Unknown_char[] = "UNKNOWN_CHAR_IN_REF:Unknown character in reference field";
-static char __pyx_k_UNKNOWN_FORMAT_STRING_Unknown_fi[] = "UNKNOWN_FORMAT_STRING:Unknown file format identifier";
-static char __pyx_k_V33_UNMATCHED_DELETION_Deleted_s[] = "V33_UNMATCHED_DELETION:Deleted sequence does not match reference (%s)";
-static char __pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS";
-static char __pyx_k_V40_MISSING_ANGLE_BRACKETS_Forma[] = "V40_MISSING_ANGLE_BRACKETS:Format definition is not deliminted by angular brackets";
-static char __pyx_k_ZERO_FOR_NON_FLAG_FIELD_number_s[] = "ZERO_FOR_NON_FLAG_FIELD: number set to 0, but type is not 'FLAG'";
-static char __pyx_k_ZERO_LENGTH_ALLELE_Found_zero_le[] = "ZERO_LENGTH_ALLELE:Found zero-length allele";
-static char __pyx_k_expected_s_for_s_samples_s_got_s[] = "expected %s for %s samples (%s), got %s";
-static char __pyx_k_id_numbertype_number_type_descri[] = "id numbertype number type description missingvalue";
-static char __pyx_k_id_s_expected_s_parameters_got_s[] = "id=%s, expected %s parameters, got %s";
-static char __pyx_k_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2[] = "V40_FORMAT_MUST_HAVE_NAMED_FIELDS:Fields in v4.0 VCF format definition must have named fields";
-static PyObject *__pyx_kp_s_;
-static PyObject *__pyx_kp_b_0;
-static PyObject *__pyx_kp_s_0;
-static PyObject *__pyx_n_s_A;
-static PyObject *__pyx_n_s_ACGTN;
-static PyObject *__pyx_kp_s_ACGTN_2;
-static PyObject *__pyx_n_s_ALT;
-static PyObject *__pyx_n_s_BADLY_FORMATTED_FORMAT_STRING;
-static PyObject *__pyx_kp_s_BADLY_FORMATTED_FORMAT_STRING_Fo;
-static PyObject *__pyx_n_s_BADLY_FORMATTED_HEADING;
-static PyObject *__pyx_kp_s_BADLY_FORMATTED_HEADING_Did_not;
-static PyObject *__pyx_kp_s_BAD_CHR_TAG_Error_calculating_ch;
-static PyObject *__pyx_n_s_BAD_GENOTYPE;
-static PyObject *__pyx_kp_s_BAD_GENOTYPE_Cannot_parse_genoty;
-static PyObject *__pyx_n_s_BAD_NUMBER_OF_COLUMNS;
-static PyObject *__pyx_kp_s_BAD_NUMBER_OF_COLUMNS_Wrong_numb;
-static PyObject *__pyx_n_s_BAD_NUMBER_OF_PARAMETERS;
-static PyObject *__pyx_kp_s_BAD_NUMBER_OF_PARAMETERS_Found_u;
-static PyObject *__pyx_n_s_BAD_NUMBER_OF_VALUES;
-static PyObject *__pyx_kp_s_BAD_NUMBER_OF_VALUES_Found_too_m;
-static PyObject *__pyx_n_s_CHROM;
-static PyObject *__pyx_kp_s_Can_only_handle_v3_3_and_v4_0_VC;
-static PyObject *__pyx_n_s_Character;
-static PyObject *__pyx_kp_s_Conditional_genotype_quality;
-static PyObject *__pyx_n_s_D;
-static PyObject *__pyx_n_s_DP;
-static PyObject *__pyx_kp_s_Description;
-static PyObject *__pyx_n_s_Description_2;
-static PyObject *__pyx_kp_s_Don_t_understand_region_string_s;
-static PyObject *__pyx_n_s_EC;
-static PyObject *__pyx_n_s_ERROR_FLAG_HAS_VALUE;
-static PyObject *__pyx_kp_s_ERROR_FLAG_HAS_VALUE_Flag_fields;
-static PyObject *__pyx_n_s_ERROR_FORMAT_NOT_CHAR;
-static PyObject *__pyx_kp_s_ERROR_FORMAT_NOT_CHAR_Eexpected;
-static PyObject *__pyx_n_s_ERROR_FORMAT_NOT_INTEGER;
-static PyObject *__pyx_kp_s_ERROR_FORMAT_NOT_INTEGER_Expecte;
-static PyObject *__pyx_n_s_ERROR_FORMAT_NOT_NUMERICAL;
-static PyObject *__pyx_kp_s_ERROR_FORMAT_NOT_NUMERICAL_Expec;
-static PyObject *__pyx_n_s_ERROR_INFO_STRING;
-static PyObject *__pyx_kp_s_ERROR_INFO_STRING_Error_while_pa;
-static PyObject *__pyx_n_s_ERROR_TRAILING_DATA;
-static PyObject *__pyx_kp_s_ERROR_TRAILING_DATA_Numerical_fi;
-static PyObject *__pyx_n_s_ERROR_UNKNOWN_KEY;
-static PyObject *__pyx_kp_s_ERROR_UNKNOWN_KEY_Unknown_key_s;
-static PyObject *__pyx_n_s_Error;
-static PyObject *__pyx_kp_s_Expected_alternate_allel_counts;
-static PyObject *__pyx_n_s_FILTER;
-static PyObject *__pyx_n_s_FILTER_NOT_DEFINED;
-static PyObject *__pyx_kp_s_FILTER_NOT_DEFINED_Identifier_s;
-static PyObject *__pyx_n_s_FORMAT;
-static PyObject *__pyx_n_s_FORMAT_MISSING_QUOTES;
-static PyObject *__pyx_kp_s_FORMAT_MISSING_QUOTES_Descriptio;
-static PyObject *__pyx_n_s_FORMAT_NOT_DEFINED;
-static PyObject *__pyx_kp_s_FORMAT_NOT_DEFINED_Identifier_s;
-static PyObject *__pyx_n_s_FT;
-static PyObject *__pyx_n_s_Flag;
-static PyObject *__pyx_n_s_Float;
-static PyObject *__pyx_n_s_G;
-static PyObject *__pyx_n_s_GL;
-static PyObject *__pyx_n_s_GLE;
-static PyObject *__pyx_n_s_GP;
-static PyObject *__pyx_n_s_GQ;
-static PyObject *__pyx_n_s_GT;
-static PyObject *__pyx_n_s_GTdata;
-static PyObject *__pyx_n_s_GTstring;
-static PyObject *__pyx_n_s_Genotype;
-static PyObject *__pyx_kp_s_Genotype_Quality;
-static PyObject *__pyx_kp_s_Genotype_likelihoods;
-static PyObject *__pyx_kp_s_Genotype_posterior_probabilities;
-static PyObject *__pyx_n_s_HEADING_NOT_SEPARATED_BY_TABS;
-static PyObject *__pyx_kp_s_HEADING_NOT_SEPARATED_BY_TABS_He;
-static PyObject *__pyx_n_s_HQ;
-static PyObject *__pyx_kp_s_Haplotype_Quality;
-static PyObject *__pyx_n_s_I;
-static PyObject *__pyx_kp_s_ID;
-static PyObject *__pyx_n_s_ID_2;
-static PyObject *__pyx_n_s_INFO;
-static PyObject *__pyx_n_s_Integer;
-static PyObject *__pyx_kp_s_Invalid_error_string_s;
-static PyObject *__pyx_n_s_KeyError;
-static PyObject *__pyx_n_s_MISSING_INDEL_ALLELE_REF_BASE;
-static PyObject *__pyx_kp_s_MISSING_INDEL_ALLELE_REF_BASE_In;
-static PyObject *__pyx_n_s_MISSING_REF;
-static PyObject *__pyx_kp_s_MISSING_REF_Reference_allele_mis;
-static PyObject *__pyx_n_s_MQ;
-static PyObject *__pyx_n_s_N;
-static PyObject *__pyx_n_s_NT_ALLELES;
-static PyObject *__pyx_n_s_NT_GENOTYPES;
-static PyObject *__pyx_n_s_NT_NR_ALLELES;
-static PyObject *__pyx_n_s_NT_NUMBER;
-static PyObject *__pyx_n_s_NT_PHASED_GENOTYPES;
-static PyObject *__pyx_n_s_NT_UNKNOWN;
-static PyObject *__pyx_n_s_NotImplementedError;
-static PyObject *__pyx_kp_s_Number;
-static PyObject *__pyx_n_s_Number_2;
-static PyObject *__pyx_n_b_PASS;
-static PyObject *__pyx_n_s_PASS;
-static PyObject *__pyx_n_s_PL;
-static PyObject *__pyx_n_s_POS;
-static PyObject *__pyx_n_s_POS_NOT_NUMERICAL;
-static PyObject *__pyx_kp_s_POS_NOT_NUMERICAL_Position_colum;
-static PyObject *__pyx_n_s_POS_NOT_POSITIVE;
-static PyObject *__pyx_kp_s_POS_NOT_POSITIVE_Position_field;
-static PyObject *__pyx_n_s_PQ;
-static PyObject *__pyx_n_s_PS;
-static PyObject *__pyx_kp_s_Phase_set;
-static PyObject *__pyx_kp_s_Phasing_quality;
-static PyObject *__pyx_kp_s_Phred_scaled_genotype_likelihood;
-static PyObject *__pyx_n_s_QUAL;
-static PyObject *__pyx_n_s_QUAL_NOT_NUMERICAL;
-static PyObject *__pyx_kp_s_QUAL_NOT_NUMERICAL_Quality_field;
-static PyObject *__pyx_n_s_REF;
-static PyObject *__pyx_kp_s_RMS_mapping_quality;
-static PyObject *__pyx_kp_s_Read_depth_at_this_position_for;
-static PyObject *__pyx_kp_s_Required_key_s_not_found_in_data;
-static PyObject *__pyx_kp_s_Sample_Genotype_Filter;
-static PyObject *__pyx_n_s_StopIteration;
-static PyObject *__pyx_n_s_String;
-static PyObject *__pyx_n_s_Tabixfile;
-static PyObject *__pyx_kp_s_Type;
-static PyObject *__pyx_n_s_Type_2;
-static PyObject *__pyx_n_s_UNKNOWN_CHAR_IN_REF;
-static PyObject *__pyx_kp_s_UNKNOWN_CHAR_IN_REF_Unknown_char;
-static PyObject *__pyx_n_s_UNKNOWN_FORMAT_STRING;
-static PyObject *__pyx_kp_s_UNKNOWN_FORMAT_STRING_Unknown_fi;
-static PyObject *__pyx_kp_s_Undefined_tag;
-static PyObject *__pyx_kp_s_Unknown_number_type_encountered;
-static PyObject *__pyx_n_s_V33_BAD_ALLELE;
-static PyObject *__pyx_kp_s_V33_BAD_ALLELE_Cannot_interpret;
-static PyObject *__pyx_n_s_V33_BAD_REF;
-static PyObject *__pyx_kp_s_V33_BAD_REF_Reference_should_be;
-static PyObject *__pyx_n_s_V33_UNMATCHED_DELETION;
-static PyObject *__pyx_kp_s_V33_UNMATCHED_DELETION_Deleted_s;
-static PyObject *__pyx_n_s_V40_BAD_ALLELE;
-static PyObject *__pyx_kp_s_V40_BAD_ALLELE_Bad_allele_found;
-static PyObject *__pyx_n_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD;
-static PyObject *__pyx_kp_s_V40_FORMAT_MUST_HAVE_NAMED_FIELD_2;
-static PyObject *__pyx_n_s_V40_MISSING_ANGLE_BRACKETS;
-static PyObject *__pyx_kp_s_V40_MISSING_ANGLE_BRACKETS_Forma;
-static PyObject *__pyx_n_s_VCF;
-static PyObject *__pyx_n_s_VCFRecord;
-static PyObject *__pyx_n_s_VCF___init;
-static PyObject *__pyx_n_s_VCF__add_definition;
-static PyObject *__pyx_n_s_VCF__parse;
-static PyObject *__pyx_n_s_VCF__parse_header;
-static PyObject *__pyx_n_s_VCF_compare_calls;
-static PyObject *__pyx_n_s_VCF_connect;
-static PyObject *__pyx_n_s_VCF_convertGT;
-static PyObject *__pyx_n_s_VCF_convertGTback;
-static PyObject *__pyx_n_s_VCF_enter_default_format;
-static PyObject *__pyx_n_s_VCF_error;
-static PyObject *__pyx_n_s_VCF_fetch;
-static PyObject *__pyx_n_s_VCF_format_format;
-static PyObject *__pyx_n_s_VCF_format_formatdata;
-static PyObject *__pyx_n_s_VCF_get_expected;
-static PyObject *__pyx_n_s_VCF_getfilter;
-static PyObject *__pyx_n_s_VCF_getformat;
-static PyObject *__pyx_n_s_VCF_getheader;
-static PyObject *__pyx_n_s_VCF_getinfo;
-static PyObject *__pyx_n_s_VCF_getsamples;
-static PyObject *__pyx_n_s_VCF_ignoreerror;
-static PyObject *__pyx_n_s_VCF_inregion;
-static PyObject *__pyx_n_s_VCF_parse;
-static PyObject *__pyx_n_s_VCF_parse_data;
-static PyObject *__pyx_n_s_VCF_parse_format;
-static PyObject *__pyx_n_s_VCF_parse_formatdata;
-static PyObject *__pyx_n_s_VCF_parse_header;
-static PyObject *__pyx_n_s_VCF_parse_heading;
-static PyObject *__pyx_n_s_VCF_setfilter;
-static PyObject *__pyx_n_s_VCF_setformat;
-static PyObject *__pyx_n_s_VCF_setheader;
-static PyObject *__pyx_n_s_VCF_setinfo;
-static PyObject *__pyx_n_s_VCF_setreference;
-static PyObject *__pyx_n_s_VCF_setregions;
-static PyObject *__pyx_n_s_VCF_setsamples;
-static PyObject *__pyx_n_s_VCF_setversion;
-static PyObject *__pyx_n_s_VCF_validate;
-static PyObject *__pyx_n_s_VCF_warnerror;
-static PyObject *__pyx_n_s_VCF_write;
-static PyObject *__pyx_n_s_VCF_write_data;
-static PyObject *__pyx_n_s_VCF_write_header;
-static PyObject *__pyx_n_s_VCF_write_heading;
-static PyObject *__pyx_n_s_VCF_writeheader;
-static PyObject *__pyx_kp_s_VCFv3_3;
-static PyObject *__pyx_kp_s_VCFv4_0;
-static PyObject *__pyx_kp_s_VCFv4_1;
-static PyObject *__pyx_n_s_ValueError;
-static PyObject *__pyx_n_s_WRONG_REF;
-static PyObject *__pyx_kp_s_WRONG_REF_Wrong_reference_s;
-static PyObject *__pyx_n_s_Warning;
-static PyObject *__pyx_n_s_ZERO_FOR_NON_FLAG_FIELD;
-static PyObject *__pyx_kp_s_ZERO_FOR_NON_FLAG_FIELD_number_s;
-static PyObject *__pyx_n_s_ZERO_LENGTH_ALLELE;
-static PyObject *__pyx_kp_s_ZERO_LENGTH_ALLELE_Found_zero_le;
-static PyObject *__pyx_kp_s__10;
-static PyObject *__pyx_kp_s__13;
-static PyObject *__pyx_kp_s__2;
-static PyObject *__pyx_kp_s__21;
-static PyObject *__pyx_kp_s__23;
-static PyObject *__pyx_kp_s__29;
-static PyObject *__pyx_kp_s__4;
-static PyObject *__pyx_kp_s__46;
-static PyObject *__pyx_kp_s__51;
-static PyObject *__pyx_kp_s__55;
-static PyObject *__pyx_kp_s__6;
-static PyObject *__pyx_kp_s__60;
-static PyObject *__pyx_kp_s__61;
-static PyObject *__pyx_kp_b__8;
-static PyObject *__pyx_kp_s__8;
-static PyObject *__pyx_kp_s__91;
-static PyObject *__pyx_n_s_a;
-static PyObject *__pyx_n_s_add;
-static PyObject *__pyx_n_s_add_definition;
-static PyObject *__pyx_n_s_addn;
-static PyObject *__pyx_n_s_addns;
-static PyObject *__pyx_n_s_all;
-static PyObject *__pyx_n_s_allele;
-static PyObject *__pyx_n_s_alleleRegEx;
-static PyObject *__pyx_kp_s_alleles;
-static PyObject *__pyx_n_s_alt;
-static PyObject *__pyx_n_s_alt1;
-static PyObject *__pyx_n_s_alt2;
-static PyObject *__pyx_n_s_append;
-static PyObject *__pyx_n_s_args;
-static PyObject *__pyx_n_s_ascii;
-static PyObject *__pyx_n_s_bisect;
-static PyObject *__pyx_n_s_blurp;
-static PyObject *__pyx_n_s_c;
-static PyObject *__pyx_n_s_chrom;
-static PyObject *__pyx_n_s_close;
-static PyObject *__pyx_n_s_collections;
-static PyObject *__pyx_n_s_cols;
-static PyObject *__pyx_n_s_compare_calls;
-static PyObject *__pyx_n_s_compile;
-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_copy_2;
-static PyObject *__pyx_n_s_d;
-static PyObject *__pyx_n_s_data;
-static PyObject *__pyx_n_s_datagenerator;
-static PyObject *__pyx_n_s_deepcopy;
-static PyObject *__pyx_n_s_defaultdict;
-static PyObject *__pyx_kp_s_deletion_is_s_reference_is_s;
-static PyObject *__pyx_n_s_descr;
-static PyObject *__pyx_n_s_description;
-static PyObject *__pyx_n_s_dict;
-static PyObject *__pyx_n_s_dict_2;
-static PyObject *__pyx_n_s_doc;
-static PyObject *__pyx_n_s_elts;
-static PyObject *__pyx_n_s_encoding;
-static PyObject *__pyx_n_s_end;
-static PyObject *__pyx_n_s_endswith;
-static PyObject *__pyx_n_s_enter_default_format;
-static PyObject *__pyx_n_s_enumerate;
-static PyObject *__pyx_n_s_err;
-static PyObject *__pyx_n_s_error;
-static PyObject *__pyx_n_s_errorlabel;
-static PyObject *__pyx_n_s_errors;
-static PyObject *__pyx_n_s_errorstring;
-static PyObject *__pyx_n_s_errwarn;
-static PyObject *__pyx_n_s_expected;
-static PyObject *__pyx_kp_s_expected_s_for_s_samples_s_got_s;
-static PyObject *__pyx_n_s_f;
-static PyObject *__pyx_n_s_fa;
-static PyObject *__pyx_n_s_faref;
-static PyObject *__pyx_n_s_faref_leftflank;
-static PyObject *__pyx_n_s_fetch;
-static PyObject *__pyx_n_s_fileformat;
-static PyObject *__pyx_kp_s_fileformat_VCFv_s_s;
-static PyObject *__pyx_n_s_filename;
-static PyObject *__pyx_n_s_filter;
-static PyObject *__pyx_n_s_filter_2;
-static PyObject *__pyx_n_s_find;
-static PyObject *__pyx_n_s_first;
-static PyObject *__pyx_n_s_fmt;
-static PyObject *__pyx_n_s_format;
-static PyObject *__pyx_n_s_format_2;
-static PyObject *__pyx_n_s_format_format;
-static PyObject *__pyx_n_s_format_formatdata;
-static PyObject *__pyx_n_s_formatdict;
-static PyObject *__pyx_kp_s_found_s_expected_s;
-static PyObject *__pyx_kp_s_found_s_values_in_element_s_exp;
-static PyObject *__pyx_kp_s_genotypes;
-static PyObject *__pyx_n_s_get;
-static PyObject *__pyx_n_s_get_expected;
-static PyObject *__pyx_n_s_get_sequence;
-static PyObject *__pyx_n_s_getfilter;
-static PyObject *__pyx_n_s_getformat;
-static PyObject *__pyx_n_s_getheader;
-static PyObject *__pyx_n_s_getinfo;
-static PyObject *__pyx_n_s_getsamples;
-static PyObject *__pyx_n_s_gts;
-static PyObject *__pyx_n_s_gtsRegEx;
-static PyObject *__pyx_n_s_have_deletions;
-static PyObject *__pyx_n_s_header;
-static PyObject *__pyx_n_s_header_2;
-static PyObject *__pyx_n_s_headings;
-static PyObject *__pyx_kp_s_home_andreas_devel_pysam_pysam;
-static PyObject *__pyx_n_s_i;
-static PyObject *__pyx_n_s_id;
-static PyObject *__pyx_kp_s_id_numbertype_number_type_descri;
-static PyObject *__pyx_kp_s_id_s_expected_s_parameters_got_s;
-static PyObject *__pyx_n_s_idx;
-static PyObject *__pyx_n_s_ielts;
-static PyObject *__pyx_n_s_ignored_errors;
-static PyObject *__pyx_n_s_ignoreerror;
-static PyObject *__pyx_n_s_import;
-static PyObject *__pyx_kp_s_in_line_s_s_s_s_s;
-static PyObject *__pyx_n_s_info;
-static PyObject *__pyx_n_s_info_2;
-static PyObject *__pyx_n_s_init;
-static PyObject *__pyx_n_s_inregion;
-static PyObject *__pyx_n_s_itemgetter;
-static PyObject *__pyx_n_s_itervalues;
-static PyObject *__pyx_n_s_join;
-static PyObject *__pyx_n_s_k;
-static PyObject *__pyx_n_s_key;
-static PyObject *__pyx_n_s_keys;
-static PyObject *__pyx_n_s_l;
-static PyObject *__pyx_n_s_label;
-static PyObject *__pyx_n_s_last;
-static PyObject *__pyx_n_s_last_line;
-static PyObject *__pyx_n_s_left;
-static PyObject *__pyx_n_s_leftalign;
-static PyObject *__pyx_n_s_leftalign_2;
-static PyObject *__pyx_n_s_line;
-static PyObject *__pyx_n_s_line_2;
-static PyObject *__pyx_n_s_lineno;
-static PyObject *__pyx_n_s_lineparse;
-static PyObject *__pyx_n_s_lines;
-static PyObject *__pyx_n_s_lines_2;
-static PyObject *__pyx_n_s_longest;
-static PyObject *__pyx_n_s_main;
-static PyObject *__pyx_n_s_map;
-static PyObject *__pyx_n_s_match;
-static PyObject *__pyx_n_s_metaclass;
-static PyObject *__pyx_n_s_min;
-static PyObject *__pyx_n_s_missing;
-static PyObject *__pyx_n_s_missingvalue;
-static PyObject *__pyx_n_s_module;
-static PyObject *__pyx_n_s_movable;
-static PyObject *__pyx_n_s_n;
-static PyObject *__pyx_n_s_na;
-static PyObject *__pyx_n_s_namedtuple;
-static PyObject *__pyx_kp_s_needs_to_be_checked;
-static PyObject *__pyx_n_s_newalts;
-static PyObject *__pyx_n_s_nmb;
-static PyObject *__pyx_kp_s_nonref_alleles;
-static PyObject *__pyx_n_s_number;
-static PyObject *__pyx_n_s_numbertype;
-static PyObject *__pyx_n_s_object;
-static PyObject *__pyx_n_s_operator;
-static PyObject *__pyx_n_s_opt;
-static PyObject *__pyx_kp_s_output;
-static PyObject *__pyx_n_s_output_2;
-static PyObject *__pyx_n_s_parse;
-static PyObject *__pyx_n_s_parse_2;
-static PyObject *__pyx_n_s_parse_data;
-static PyObject *__pyx_n_s_parse_format;
-static PyObject *__pyx_n_s_parse_formatdata;
-static PyObject *__pyx_n_s_parse_header;
-static PyObject *__pyx_n_s_parse_header_2;
-static PyObject *__pyx_n_s_parse_heading;
-static PyObject *__pyx_n_s_parse_regions;
-static PyObject *__pyx_n_s_parser;
-static PyObject *__pyx_kp_s_phased_genotypes;
-static PyObject *__pyx_n_s_pos;
-static PyObject *__pyx_n_s_pos1;
-static PyObject *__pyx_n_s_pos2;
-static PyObject *__pyx_n_s_prepare;
-static PyObject *__pyx_n_s_pysam;
-static PyObject *__pyx_n_s_pysam_cvcf;
-static PyObject *__pyx_n_s_pyx_vtable;
-static PyObject *__pyx_n_s_qual;
-static PyObject *__pyx_n_s_qualname;
-static PyObject *__pyx_n_s_r;
-static PyObject *__pyx_n_s_range;
-static PyObject *__pyx_n_s_re;
-static PyObject *__pyx_n_s_record;
-static PyObject *__pyx_n_s_ref;
-static PyObject *__pyx_n_s_ref1;
-static PyObject *__pyx_n_s_ref2;
-static PyObject *__pyx_n_s_reference;
-static PyObject *__pyx_n_s_reference_2;
-static PyObject *__pyx_kp_s_reference_is_s_VCF_says_s;
-static PyObject *__pyx_n_s_region;
-static PyObject *__pyx_n_s_regions;
-static PyObject *__pyx_n_s_regions_2;
-static PyObject *__pyx_n_s_replace;
-static PyObject *__pyx_n_s_required;
-static PyObject *__pyx_n_s_required_2;
-static PyObject *__pyx_n_s_rest;
-static PyObject *__pyx_n_s_result;
-static PyObject *__pyx_n_s_s;
-static PyObject *__pyx_kp_s_s_s;
-static PyObject *__pyx_kp_s_s_s_2;
-static PyObject *__pyx_n_s_sample;
-static PyObject *__pyx_n_s_sample2column;
-static PyObject *__pyx_n_s_samples;
-static PyObject *__pyx_n_s_samples_2;
-static PyObject *__pyx_n_s_sdata;
-static PyObject *__pyx_n_s_self;
-static PyObject *__pyx_n_s_send;
-static PyObject *__pyx_n_s_separator;
-static PyObject *__pyx_n_s_sequence;
-static PyObject *__pyx_n_s_setfilter;
-static PyObject *__pyx_n_s_setformat;
-static PyObject *__pyx_n_s_setheader;
-static PyObject *__pyx_n_s_setinfo;
-static PyObject *__pyx_n_s_setreference;
-static PyObject *__pyx_n_s_setregions;
-static PyObject *__pyx_n_s_setsamples;
-static PyObject *__pyx_n_s_setversion;
-static PyObject *__pyx_n_s_shortest;
-static PyObject *__pyx_n_s_split;
-static PyObject *__pyx_n_s_start;
-static PyObject *__pyx_n_s_startswith;
-static PyObject *__pyx_kp_s_sth_entry_not_found;
-static PyObject *__pyx_n_s_stream;
-static PyObject *__pyx_n_s_string;
-static PyObject *__pyx_n_s_strip;
-static PyObject *__pyx_n_s_sys;
-static PyObject *__pyx_n_s_t;
-static PyObject *__pyx_n_s_tabixfile;
-static PyObject *__pyx_n_s_test;
-static PyObject *__pyx_n_s_throw;
-static PyObject *__pyx_n_s_type;
-static PyObject *__pyx_n_s_upper;
-static PyObject *__pyx_n_s_v;
-static PyObject *__pyx_n_s_validate;
-static PyObject *__pyx_n_s_value;
-static PyObject *__pyx_n_s_values;
-static PyObject *__pyx_n_s_var;
-static PyObject *__pyx_n_s_vcf;
-static PyObject *__pyx_n_s_vcffile;
-static PyObject *__pyx_n_s_version;
-static PyObject *__pyx_n_s_version_2;
-static PyObject *__pyx_n_s_warn_errors;
-static PyObject *__pyx_n_s_warnerror;
-static PyObject *__pyx_n_s_write;
-static PyObject *__pyx_n_s_write_data;
-static PyObject *__pyx_n_s_write_header;
-static PyObject *__pyx_n_s_write_heading;
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-static PyObject *__pyx_getprop_5pysam_4cvcf_9VCFRecord_info(PyObject *o, CYTHON_UNUSED void *x) {
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- * if len(a) == 1: a = a + ref[1:] # SNP; add trailing reference
- * elif a.startswith('I'): a = ref[0] + a[1:] + ref[1:] # insertion just beyond pos; add first and trailing reference
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- * break
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- * # parse sample columns
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- * values = sample.split(':')
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- __Pyx_GIVEREF(__pyx_slice__80);
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- * for sample in cols[9:]:
- * dict = {}
- * values = sample.split(':') # <<<<<<<<<<<<<<
- * if len(values) > len(format):
- * self.error(line,self.BAD_NUMBER_OF_VALUES,"(found %s values in element %s; expected %s)" % (len(values),sample,len(format)))
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- __Pyx_GIVEREF(__pyx_tuple__81);
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- * line = ctabix._force_str(line, self.encoding)
- * self._lineno += 1
- * if line.startswith('##'): # <<<<<<<<<<<<<<
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- * elif line.startswith('#'): # <<<<<<<<<<<<<<
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- * self.enter_default_format()
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- * def _parse(self, line, stream):
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- *
- * def setversion(self, version):
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- __Pyx_GIVEREF(__pyx_tuple__85);
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- * # only when the reference bases are not Ns
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- * while len(ref1)>0 and len(alt1)>0 and ref1[-1] == alt1[-1]:
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- *
- */
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- *
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- * for r in string.split(','):
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- *
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- *
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-
-static PyObject *__Pyx_GetBuiltinName(PyObject *name) {
- PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name);
- if (unlikely(!result)) {
- PyErr_Format(PyExc_NameError,
-#if PY_MAJOR_VERSION >= 3
- "name '%U' is not defined", name);
-#else
- "name '%.200s' is not defined", PyString_AS_STRING(name));
-#endif
- }
- return result;
-}
-
-static void __Pyx_RaiseArgtupleInvalid(
- const char* func_name,
- int exact,
- Py_ssize_t num_min,
- Py_ssize_t num_max,
- Py_ssize_t num_found)
-{
- Py_ssize_t num_expected;
- const char *more_or_less;
- if (num_found < num_min) {
- num_expected = num_min;
- more_or_less = "at least";
- } else {
- num_expected = num_max;
- more_or_less = "at most";
- }
- if (exact) {
- more_or_less = "exactly";
- }
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)",
- func_name, more_or_less, num_expected,
- (num_expected == 1) ? "" : "s", num_found);
-}
-
-static void __Pyx_RaiseDoubleKeywordsError(
- const char* func_name,
- PyObject* kw_name)
-{
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION >= 3
- "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
- #else
- "%s() got multiple values for keyword argument '%s'", func_name,
- PyString_AsString(kw_name));
- #endif
-}
-
-static int __Pyx_ParseOptionalKeywords(
- PyObject *kwds,
- PyObject **argnames[],
- PyObject *kwds2,
- PyObject *values[],
- Py_ssize_t num_pos_args,
- const char* function_name)
-{
- PyObject *key = 0, *value = 0;
- Py_ssize_t pos = 0;
- PyObject*** name;
- PyObject*** first_kw_arg = argnames + num_pos_args;
- while (PyDict_Next(kwds, &pos, &key, &value)) {
- name = first_kw_arg;
- while (*name && (**name != key)) name++;
- if (*name) {
- values[name-argnames] = value;
- 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;
- 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, key);
- goto bad;
-invalid_keyword_type:
- PyErr_Format(PyExc_TypeError,
- "%.200s() keywords must be strings", function_name);
- goto bad;
-invalid_keyword:
- PyErr_Format(PyExc_TypeError,
- #if PY_MAJOR_VERSION < 3
- "%.200s() got an unexpected keyword argument '%.200s'",
- function_name, PyString_AsString(key));
- #else
- "%s() got an unexpected keyword argument '%U'",
- function_name, key);
- #endif
-bad:
- return -1;
-}
-
-static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) {
- PyObject *result;
-#if CYTHON_COMPILING_IN_CPYTHON
- result = PyDict_GetItem(__pyx_d, name);
- if (result) {
- Py_INCREF(result);
- } else {
-#else
- result = PyObject_GetItem(__pyx_d, name);
- if (!result) {
- PyErr_Clear();
-#endif
- result = __Pyx_GetBuiltinName(name);
- }
- return result;
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyObject *result;
- ternaryfunc call = func->ob_type->tp_call;
- if (unlikely(!call))
- return PyObject_Call(func, arg, kw);
-#if PY_VERSION_HEX >= 0x02060000
- if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
- return NULL;
-#endif
- result = (*call)(func, arg, kw);
-#if PY_VERSION_HEX >= 0x02060000
- Py_LeaveRecursiveCall();
-#endif
- if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
- PyErr_SetString(
- PyExc_SystemError,
- "NULL result without error in PyObject_Call");
- }
- return result;
-}
-#endif
-
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
- PyObject *r;
- if (!j) return NULL;
- r = PyObject_GetItem(o, j);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
- PyObject *r = PyList_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
- int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, i);
- Py_INCREF(r);
- return r;
- }
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-#else
- return PySequence_GetItem(o, i);
-#endif
-}
-static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
- if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
- PyObject *r = PyList_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- }
- else if (PyTuple_CheckExact(o)) {
- Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
- if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
- PyObject *r = PyTuple_GET_ITEM(o, n);
- Py_INCREF(r);
- return r;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return NULL;
- }
- }
- return m->sq_item(o, i);
- }
- }
-#else
- if (is_list || PySequence_Check(o)) {
- return PySequence_GetItem(o, i);
- }
-#endif
- return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
-}
-
-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;
- *tb = tstate->exc_traceback;
- 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;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = type;
- tstate->exc_value = value;
- tstate->exc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_SetExcInfo(type, value, tb);
-#endif
-}
-
-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;
- local_value = tstate->curexc_value;
- local_tb = tstate->curexc_traceback;
- 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 (local_tb) {
- if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
- goto bad;
- }
- #endif
- Py_XINCREF(local_tb);
- Py_XINCREF(local_type);
- Py_XINCREF(local_value);
- *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;
- tstate->exc_type = local_type;
- tstate->exc_value = local_value;
- tstate->exc_traceback = local_tb;
- 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;
- *value = 0;
- *tb = 0;
- Py_XDECREF(local_type);
- Py_XDECREF(local_value);
- Py_XDECREF(local_tb);
- return -1;
-}
-
-static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyObject *tmp_type, *tmp_value, *tmp_tb;
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->curexc_type;
- tmp_value = tstate->curexc_value;
- tmp_tb = tstate->curexc_traceback;
- tstate->curexc_type = type;
- tstate->curexc_value = value;
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_type);
- Py_XDECREF(tmp_value);
- Py_XDECREF(tmp_tb);
-#else
- PyErr_Restore(type, value, tb);
-#endif
-}
-static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- *type = tstate->curexc_type;
- *value = tstate->curexc_value;
- *tb = tstate->curexc_traceback;
- tstate->curexc_type = 0;
- tstate->curexc_value = 0;
- tstate->curexc_traceback = 0;
-#else
- PyErr_Fetch(type, value, tb);
-#endif
-}
-
-#if PY_MAJOR_VERSION < 3
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
- CYTHON_UNUSED PyObject *cause) {
- Py_XINCREF(type);
- 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)) {
- #else
- if (PyType_Check(type)) {
- #endif
-#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;
- }
- value = type;
- #if PY_VERSION_HEX < 0x02050000
- if (PyInstance_Check(type)) {
- type = (PyObject*) ((PyInstanceObject*)type)->in_class;
- Py_INCREF(type);
- } else {
- type = 0;
- PyErr_SetString(PyExc_TypeError,
- "raise: exception must be an old-style class or instance");
- goto raise_error;
- }
- #else
- type = (PyObject*) Py_TYPE(type);
- Py_INCREF(type);
- if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: exception class must be a subclass of BaseException");
- goto raise_error;
- }
- #endif
- }
- __Pyx_ErrRestore(type, value, tb);
- return;
-raise_error:
- Py_XDECREF(value);
- Py_XDECREF(type);
- Py_XDECREF(tb);
- return;
-}
-#else /* Python 3+ */
-static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
- PyObject* owned_instance = NULL;
- if (tb == Py_None) {
- tb = 0;
- } else if (tb && !PyTraceBack_Check(tb)) {
- PyErr_SetString(PyExc_TypeError,
- "raise: arg 3 must be a traceback or None");
- goto bad;
- }
- if (value == Py_None)
- value = 0;
- if (PyExceptionInstance_Check(type)) {
- if (value) {
- PyErr_SetString(PyExc_TypeError,
- "instance exception may not have a separate value");
- goto bad;
- }
- value = type;
- type = (PyObject*) Py_TYPE(value);
- } else if (PyExceptionClass_Check(type)) {
- PyObject *instance_class = NULL;
- if (value && PyExceptionInstance_Check(value)) {
- instance_class = (PyObject*) Py_TYPE(value);
- if (instance_class != type) {
- if (PyObject_IsSubclass(instance_class, type)) {
- type = instance_class;
- } else {
- instance_class = NULL;
- }
- }
- }
- if (!instance_class) {
- 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 = PyObject_Call(type, args, NULL);
- 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 PY_VERSION_HEX >= 0x03030000
- if (cause) {
-#else
- if (cause && cause != Py_None) {
-#endif
- PyObject *fixed_cause;
- if (cause == Py_None) {
- fixed_cause = NULL;
- } else if (PyExceptionClass_Check(cause)) {
- fixed_cause = PyObject_CallObject(cause, NULL);
- if (fixed_cause == NULL)
- goto bad;
- } else if (PyExceptionInstance_Check(cause)) {
- fixed_cause = cause;
- Py_INCREF(fixed_cause);
- } else {
- PyErr_SetString(PyExc_TypeError,
- "exception causes must derive from "
- "BaseException");
- goto bad;
- }
- PyException_SetCause(value, fixed_cause);
- }
- PyErr_SetObject(type, value);
- if (tb) {
- PyThreadState *tstate = PyThreadState_GET();
- PyObject* tmp_tb = tstate->curexc_traceback;
- if (tb != tmp_tb) {
- Py_INCREF(tb);
- tstate->curexc_traceback = tb;
- Py_XDECREF(tmp_tb);
- }
- }
-bad:
- Py_XDECREF(owned_instance);
- return;
-}
-#endif
-
-static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
- if (s1 == s2) {
- return (equals == Py_EQ);
- } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
- const char *ps1, *ps2;
- Py_ssize_t length = PyBytes_GET_SIZE(s1);
- if (length != PyBytes_GET_SIZE(s2))
- return (equals == Py_NE);
- ps1 = PyBytes_AS_STRING(s1);
- ps2 = PyBytes_AS_STRING(s2);
- if (ps1[0] != ps2[0]) {
- return (equals == Py_NE);
- } else if (length == 1) {
- return (equals == Py_EQ);
- } else {
- int result = memcmp(ps1, ps2, (size_t)length);
- 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;
- }
-#endif
-}
-
-static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
-#if CYTHON_COMPILING_IN_PYPY
- return PyObject_RichCompareBool(s1, s2, equals);
-#else
-#if PY_MAJOR_VERSION < 3
- PyObject* owned_ref = NULL;
-#endif
- int s1_is_unicode, s2_is_unicode;
- if (s1 == s2) {
- goto return_eq;
- }
- s1_is_unicode = PyUnicode_CheckExact(s1);
- s2_is_unicode = PyUnicode_CheckExact(s2);
-#if PY_MAJOR_VERSION < 3
- if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
- owned_ref = PyUnicode_FromObject(s2);
- if (unlikely(!owned_ref))
- return -1;
- s2 = owned_ref;
- s2_is_unicode = 1;
- } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
- owned_ref = PyUnicode_FromObject(s1);
- if (unlikely(!owned_ref))
- return -1;
- s1 = owned_ref;
- s1_is_unicode = 1;
- } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
- return __Pyx_PyBytes_Equals(s1, s2, equals);
- }
-#endif
- if (s1_is_unicode & s2_is_unicode) {
- Py_ssize_t length;
- int kind;
- void *data1, *data2;
- #if CYTHON_PEP393_ENABLED
- if (unlikely(PyUnicode_READY(s1) < 0) || unlikely(PyUnicode_READY(s2) < 0))
- return -1;
- #endif
- length = __Pyx_PyUnicode_GET_LENGTH(s1);
- if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
- goto return_ne;
- }
- kind = __Pyx_PyUnicode_KIND(s1);
- if (kind != __Pyx_PyUnicode_KIND(s2)) {
- goto return_ne;
- }
- data1 = __Pyx_PyUnicode_DATA(s1);
- data2 = __Pyx_PyUnicode_DATA(s2);
- if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
- goto return_ne;
- } else if (length == 1) {
- goto return_eq;
- } else {
- int result = memcmp(data1, data2, length * kind);
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ) ? (result == 0) : (result != 0);
- }
- } else if ((s1 == Py_None) & s2_is_unicode) {
- goto return_ne;
- } else if ((s2 == Py_None) & s1_is_unicode) {
- goto return_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;
- }
-return_eq:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_EQ);
-return_ne:
- #if PY_MAJOR_VERSION < 3
- Py_XDECREF(owned_ref);
- #endif
- return (equals == Py_NE);
-#endif
-}
-
-static double __Pyx__PyObject_AsDouble(PyObject* obj) {
- PyObject* float_value;
-#if CYTHON_COMPILING_IN_PYPY
- float_value = PyNumber_Float(obj);
-#else
- PyNumberMethods *nb = Py_TYPE(obj)->tp_as_number;
- if (likely(nb) && likely(nb->nb_float)) {
- float_value = nb->nb_float(obj);
- if (likely(float_value) && unlikely(!PyFloat_Check(float_value))) {
- PyErr_Format(PyExc_TypeError,
- "__float__ returned non-float (type %.200s)",
- Py_TYPE(float_value)->tp_name);
- Py_DECREF(float_value);
- goto bad;
- }
- } else if (PyUnicode_CheckExact(obj) || PyBytes_CheckExact(obj)) {
-#if PY_MAJOR_VERSION >= 3
- float_value = PyFloat_FromString(obj);
-#else
- float_value = PyFloat_FromString(obj, 0);
-#endif
- } else {
- PyObject* args = PyTuple_New(1);
- if (unlikely(!args)) goto bad;
- PyTuple_SET_ITEM(args, 0, obj);
- float_value = PyObject_Call((PyObject*)&PyFloat_Type, args, 0);
- 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);
- return value;
- }
-bad:
- return (double)-1;
-}
-
-static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
- PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
-}
-
-#if !CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) {
- return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL)
-}
-#endif
-
-static CYTHON_INLINE PyObject* __Pyx_PyObject_GetSlice(
- PyObject* obj, Py_ssize_t cstart, Py_ssize_t cstop,
- PyObject** _py_start, PyObject** _py_stop, PyObject** _py_slice,
- int has_cstart, int has_cstop, CYTHON_UNUSED int wraparound) {
-#if CYTHON_COMPILING_IN_CPYTHON
- PyMappingMethods* mp;
-#if PY_MAJOR_VERSION < 3
- PySequenceMethods* ms = Py_TYPE(obj)->tp_as_sequence;
- if (likely(ms && ms->sq_slice)) {
- if (!has_cstart) {
- if (_py_start && (*_py_start != Py_None)) {
- cstart = __Pyx_PyIndex_AsSsize_t(*_py_start);
- if ((cstart == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstart = 0;
- }
- if (!has_cstop) {
- if (_py_stop && (*_py_stop != Py_None)) {
- cstop = __Pyx_PyIndex_AsSsize_t(*_py_stop);
- if ((cstop == (Py_ssize_t)-1) && PyErr_Occurred()) goto bad;
- } else
- cstop = PY_SSIZE_T_MAX;
- }
- if (wraparound && unlikely((cstart < 0) | (cstop < 0)) && likely(ms->sq_length)) {
- Py_ssize_t l = ms->sq_length(obj);
- if (likely(l >= 0)) {
- if (cstop < 0) {
- cstop += l;
- if (cstop < 0) cstop = 0;
- }
- if (cstart < 0) {
- cstart += l;
- if (cstart < 0) cstart = 0;
- }
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- goto bad;
- }
- }
- return ms->sq_slice(obj, cstart, cstop);
- }
-#endif
- mp = Py_TYPE(obj)->tp_as_mapping;
- if (likely(mp && mp->mp_subscript))
-#endif
- {
- PyObject* result;
- PyObject *py_slice, *py_start, *py_stop;
- if (_py_slice) {
- py_slice = *_py_slice;
- } else {
- PyObject* owned_start = NULL;
- PyObject* owned_stop = NULL;
- if (_py_start) {
- py_start = *_py_start;
- } else {
- if (has_cstart) {
- owned_start = py_start = PyInt_FromSsize_t(cstart);
- if (unlikely(!py_start)) goto bad;
- } else
- py_start = Py_None;
- }
- if (_py_stop) {
- py_stop = *_py_stop;
- } else {
- if (has_cstop) {
- owned_stop = py_stop = PyInt_FromSsize_t(cstop);
- if (unlikely(!py_stop)) {
- Py_XDECREF(owned_start);
- goto bad;
- }
- } else
- py_stop = Py_None;
- }
- py_slice = PySlice_New(py_start, py_stop, Py_None);
- Py_XDECREF(owned_start);
- Py_XDECREF(owned_stop);
- if (unlikely(!py_slice)) goto bad;
- }
-#if CYTHON_COMPILING_IN_CPYTHON
- result = mp->mp_subscript(obj, py_slice);
-#else
- result = PyObject_GetItem(obj, py_slice);
-#endif
- if (!_py_slice) {
- Py_DECREF(py_slice);
- }
- return result;
- }
- PyErr_Format(PyExc_TypeError,
- "'%.200s' object is unsliceable", Py_TYPE(obj)->tp_name);
-bad:
- return NULL;
-}
-
-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 %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
- index, (index == 1) ? "" : "s");
-}
-
-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) {
- if (unlikely(retval)) {
- Py_DECREF(retval);
- __Pyx_RaiseTooManyValuesError(expected);
- return -1;
- } else {
- return __Pyx_IterFinish();
- }
- return 0;
-}
-
-static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) {
- Py_ssize_t q = a / b;
- Py_ssize_t r = a - q*b;
- q -= ((r != 0) & ((r ^ b) < 0));
- return q;
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON
-static CYTHON_INLINE void __Pyx_crop_slice(Py_ssize_t* _start, Py_ssize_t* _stop, Py_ssize_t* _length) {
- Py_ssize_t start = *_start, stop = *_stop, length = *_length;
- if (start < 0) {
- start += length;
- if (start < 0)
- start = 0;
- }
- if (stop < 0)
- stop += length;
- else if (stop > length)
- stop = length;
- *_length = stop - start;
- *_start = start;
- *_stop = stop;
-}
-static CYTHON_INLINE void __Pyx_copy_object_array(PyObject** CYTHON_RESTRICT src, PyObject** CYTHON_RESTRICT dest, Py_ssize_t length) {
- PyObject *v;
- Py_ssize_t i;
- for (i = 0; i < length; i++) {
- v = dest[i] = src[i];
- Py_INCREF(v);
- }
-}
-static CYTHON_INLINE PyObject* __Pyx_PyList_GetSlice(
- PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
- PyObject* dest;
- Py_ssize_t length = PyList_GET_SIZE(src);
- __Pyx_crop_slice(&start, &stop, &length);
- if (unlikely(length <= 0))
- return PyList_New(0);
- dest = PyList_New(length);
- if (unlikely(!dest))
- return NULL;
- __Pyx_copy_object_array(
- ((PyListObject*)src)->ob_item + start,
- ((PyListObject*)dest)->ob_item,
- length);
- return dest;
-}
-static CYTHON_INLINE PyObject* __Pyx_PyTuple_GetSlice(
- PyObject* src, Py_ssize_t start, Py_ssize_t stop) {
- PyObject* dest;
- Py_ssize_t length = PyTuple_GET_SIZE(src);
- __Pyx_crop_slice(&start, &stop, &length);
- if (unlikely(length <= 0))
- return PyTuple_New(0);
- dest = PyTuple_New(length);
- if (unlikely(!dest))
- return NULL;
- __Pyx_copy_object_array(
- ((PyTupleObject*)src)->ob_item + start,
- ((PyTupleObject*)dest)->ob_item,
- length);
- return dest;
-}
-#endif
-
-static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) {
- if (likely(PyList_CheckExact(L))) {
- if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1;
- } else {
- PyObject* retval = __Pyx_PyObject_CallMethod1(L, __pyx_n_s_append, x);
- if (unlikely(!retval))
- return -1;
- Py_DECREF(retval);
- }
- return 0;
-}
-
-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 = __Pyx_PyObject_CallMethod0(iterable, method_name);
- 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 int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) {
- int r;
- if (!j) return -1;
- r = PyObject_SetItem(o, j, v);
- Py_DECREF(j);
- return r;
-}
-static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v,
- int is_list, int wraparound, int boundscheck) {
-#if CYTHON_COMPILING_IN_CPYTHON
- if (is_list || PyList_CheckExact(o)) {
- Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o));
- if ((!boundscheck) || likely((n >= 0) & (n < PyList_GET_SIZE(o)))) {
- PyObject* old = PyList_GET_ITEM(o, n);
- Py_INCREF(v);
- PyList_SET_ITEM(o, n, v);
- Py_DECREF(old);
- return 1;
- }
- } else {
- PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
- if (likely(m && m->sq_ass_item)) {
- if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
- Py_ssize_t l = m->sq_length(o);
- if (likely(l >= 0)) {
- i += l;
- } else {
- if (PyErr_ExceptionMatches(PyExc_OverflowError))
- PyErr_Clear();
- else
- return -1;
- }
- }
- return m->sq_ass_item(o, i, v);
- }
- }
-#else
-#if CYTHON_COMPILING_IN_PYPY
- if (is_list || (PySequence_Check(o) && !PyDict_Check(o))) {
-#else
- if (is_list || PySequence_Check(o)) {
-#endif
- return PySequence_SetItem(o, i, v);
- }
-#endif
- return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v);
-}
-
-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 void* __Pyx_GetVtable(PyObject *dict) {
- void* ptr;
- PyObject *ob = PyObject_GetItem(dict, __pyx_n_s_pyx_vtable);
- if (!ob)
- goto bad;
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- ptr = PyCapsule_GetPointer(ob, 0);
-#else
- ptr = PyCObject_AsVoidPtr(ob);
-#endif
- if (!ptr && !PyErr_Occurred())
- PyErr_SetString(PyExc_RuntimeError, "invalid vtable found for imported type");
- Py_DECREF(ob);
- return ptr;
-bad:
- Py_XDECREF(ob);
- return NULL;
-}
-
-static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0)
- PyObject *ob = PyCapsule_New(vtable, 0, 0);
-#else
- PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
-#endif
- if (!ob)
- goto bad;
- if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
- goto bad;
- Py_DECREF(ob);
- return 0;
-bad:
- Py_XDECREF(ob);
- return -1;
-}
-
-static PyObject* __Pyx_ImportFrom(PyObject* module, PyObject* name) {
- PyObject* value = __Pyx_PyObject_GetAttrStr(module, name);
- if (unlikely(!value) && PyErr_ExceptionMatches(PyExc_AttributeError)) {
- PyErr_Format(PyExc_ImportError,
- #if PY_MAJOR_VERSION < 3
- "cannot import name %.230s", PyString_AS_STRING(name));
- #else
- "cannot import name %S", name);
- #endif
- }
- return value;
-}
-
-static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) {
- Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases);
- for (i=0; i < nbases; i++) {
- PyTypeObject *tmptype;
- PyObject *tmp = PyTuple_GET_ITEM(bases, i);
- tmptype = Py_TYPE(tmp);
-#if PY_MAJOR_VERSION < 3
- if (tmptype == &PyClass_Type)
- continue;
-#endif
- if (!metaclass) {
- metaclass = tmptype;
- continue;
- }
- if (PyType_IsSubtype(metaclass, tmptype))
- continue;
- if (PyType_IsSubtype(tmptype, metaclass)) {
- metaclass = tmptype;
- continue;
- }
- PyErr_SetString(PyExc_TypeError,
- "metaclass conflict: "
- "the metaclass of a derived class "
- "must be a (non-strict) subclass "
- "of the metaclasses of all its bases");
- return NULL;
- }
- if (!metaclass) {
-#if PY_MAJOR_VERSION < 3
- metaclass = &PyClass_Type;
-#else
- metaclass = &PyType_Type;
-#endif
- }
- Py_INCREF((PyObject*) metaclass);
- return (PyObject*) metaclass;
-}
-
-static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) {
- PyObject* fake_module;
- PyTypeObject* cached_type = NULL;
- fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI);
- if (!fake_module) return NULL;
- Py_INCREF(fake_module);
- cached_type = (PyTypeObject*) PyObject_GetAttrString(fake_module, type->tp_name);
- if (cached_type) {
- if (!PyType_Check((PyObject*)cached_type)) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s is not a type object",
- type->tp_name);
- goto bad;
- }
- if (cached_type->tp_basicsize != type->tp_basicsize) {
- PyErr_Format(PyExc_TypeError,
- "Shared Cython type %.200s has the wrong size, try recompiling",
- type->tp_name);
- goto bad;
- }
- } else {
- if (!PyErr_ExceptionMatches(PyExc_AttributeError)) goto bad;
- PyErr_Clear();
- if (PyType_Ready(type) < 0) goto bad;
- if (PyObject_SetAttrString(fake_module, type->tp_name, (PyObject*) type) < 0)
- goto bad;
- Py_INCREF(type);
- cached_type = type;
- }
-done:
- Py_DECREF(fake_module);
- return cached_type;
-bad:
- Py_XDECREF(cached_type);
- cached_type = NULL;
- goto done;
-}
-
-static PyObject *
-__Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure)
-{
- if (unlikely(op->func_doc == NULL)) {
- if (op->func.m_ml->ml_doc) {
-#if PY_MAJOR_VERSION >= 3
- op->func_doc = PyUnicode_FromString(op->func.m_ml->ml_doc);
-#else
- op->func_doc = PyString_FromString(op->func.m_ml->ml_doc);
-#endif
- if (unlikely(op->func_doc == NULL))
- return NULL;
- } else {
- Py_INCREF(Py_None);
- return Py_None;
- }
- }
- Py_INCREF(op->func_doc);
- return op->func_doc;
-}
-static int
-__Pyx_CyFunction_set_doc(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp = op->func_doc;
- if (value == NULL)
- value = Py_None; /* Mark as deleted */
- Py_INCREF(value);
- op->func_doc = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_name(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_name == NULL)) {
-#if PY_MAJOR_VERSION >= 3
- op->func_name = PyUnicode_InternFromString(op->func.m_ml->ml_name);
-#else
- op->func_name = PyString_InternFromString(op->func.m_ml->ml_name);
-#endif
- if (unlikely(op->func_name == NULL))
- return NULL;
- }
- Py_INCREF(op->func_name);
- return op->func_name;
-}
-static int
-__Pyx_CyFunction_set_name(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__name__ must be set to a string object");
- return -1;
- }
- tmp = op->func_name;
- Py_INCREF(value);
- op->func_name = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_qualname(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_qualname);
- return op->func_qualname;
-}
-static int
-__Pyx_CyFunction_set_qualname(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
-#if PY_MAJOR_VERSION >= 3
- if (unlikely(value == NULL || !PyUnicode_Check(value))) {
-#else
- if (unlikely(value == NULL || !PyString_Check(value))) {
-#endif
- PyErr_SetString(PyExc_TypeError,
- "__qualname__ must be set to a string object");
- return -1;
- }
- tmp = op->func_qualname;
- Py_INCREF(value);
- op->func_qualname = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_self(__pyx_CyFunctionObject *m, CYTHON_UNUSED void *closure)
-{
- PyObject *self;
- self = m->func_closure;
- if (self == NULL)
- self = Py_None;
- Py_INCREF(self);
- return self;
-}
-static PyObject *
-__Pyx_CyFunction_get_dict(__pyx_CyFunctionObject *op)
-{
- if (unlikely(op->func_dict == NULL)) {
- op->func_dict = PyDict_New();
- if (unlikely(op->func_dict == NULL))
- return NULL;
- }
- Py_INCREF(op->func_dict);
- return op->func_dict;
-}
-static int
-__Pyx_CyFunction_set_dict(__pyx_CyFunctionObject *op, PyObject *value)
-{
- PyObject *tmp;
- if (unlikely(value == NULL)) {
- PyErr_SetString(PyExc_TypeError,
- "function's dictionary may not be deleted");
- return -1;
- }
- if (unlikely(!PyDict_Check(value))) {
- PyErr_SetString(PyExc_TypeError,
- "setting function's dictionary to a non-dict");
- return -1;
- }
- tmp = op->func_dict;
- Py_INCREF(value);
- op->func_dict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_globals(__pyx_CyFunctionObject *op)
-{
- Py_INCREF(op->func_globals);
- return op->func_globals;
-}
-static PyObject *
-__Pyx_CyFunction_get_closure(CYTHON_UNUSED __pyx_CyFunctionObject *op)
-{
- Py_INCREF(Py_None);
- return Py_None;
-}
-static PyObject *
-__Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op)
-{
- PyObject* result = (op->func_code) ? op->func_code : Py_None;
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) {
- PyObject *res = op->defaults_getter((PyObject *) op);
- if (unlikely(!res))
- return -1;
- op->defaults_tuple = PyTuple_GET_ITEM(res, 0);
- Py_INCREF(op->defaults_tuple);
- op->defaults_kwdict = PyTuple_GET_ITEM(res, 1);
- Py_INCREF(op->defaults_kwdict);
- Py_DECREF(res);
- return 0;
-}
-static int
-__Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value) {
- value = Py_None;
- } else if (value != Py_None && !PyTuple_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__defaults__ must be set to a tuple object");
- return -1;
- }
- Py_INCREF(value);
- tmp = op->defaults_tuple;
- op->defaults_tuple = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_defaults(__pyx_CyFunctionObject *op) {
- PyObject* result = op->defaults_tuple;
- if (unlikely(!result)) {
- if (op->defaults_getter) {
- if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL;
- result = op->defaults_tuple;
- } else {
- result = Py_None;
- }
- }
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_set_kwdefaults(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value) {
- value = Py_None;
- } else if (value != Py_None && !PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__kwdefaults__ must be set to a dict object");
- return -1;
- }
- Py_INCREF(value);
- tmp = op->defaults_kwdict;
- op->defaults_kwdict = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_kwdefaults(__pyx_CyFunctionObject *op) {
- PyObject* result = op->defaults_kwdict;
- if (unlikely(!result)) {
- if (op->defaults_getter) {
- if (__Pyx_CyFunction_init_defaults(op) < 0) return NULL;
- result = op->defaults_kwdict;
- } else {
- result = Py_None;
- }
- }
- Py_INCREF(result);
- return result;
-}
-static int
-__Pyx_CyFunction_set_annotations(__pyx_CyFunctionObject *op, PyObject* value) {
- PyObject* tmp;
- if (!value || value == Py_None) {
- value = NULL;
- } else if (!PyDict_Check(value)) {
- PyErr_SetString(PyExc_TypeError,
- "__annotations__ must be set to a dict object");
- return -1;
- }
- Py_XINCREF(value);
- tmp = op->func_annotations;
- op->func_annotations = value;
- Py_XDECREF(tmp);
- return 0;
-}
-static PyObject *
-__Pyx_CyFunction_get_annotations(__pyx_CyFunctionObject *op) {
- PyObject* result = op->func_annotations;
- if (unlikely(!result)) {
- result = PyDict_New();
- if (unlikely(!result)) return NULL;
- op->func_annotations = result;
- }
- Py_INCREF(result);
- return result;
-}
-static PyGetSetDef __pyx_CyFunction_getsets[] = {
- {(char *) "func_doc", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "__doc__", (getter)__Pyx_CyFunction_get_doc, (setter)__Pyx_CyFunction_set_doc, 0, 0},
- {(char *) "func_name", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__name__", (getter)__Pyx_CyFunction_get_name, (setter)__Pyx_CyFunction_set_name, 0, 0},
- {(char *) "__qualname__", (getter)__Pyx_CyFunction_get_qualname, (setter)__Pyx_CyFunction_set_qualname, 0, 0},
- {(char *) "__self__", (getter)__Pyx_CyFunction_get_self, 0, 0, 0},
- {(char *) "func_dict", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "__dict__", (getter)__Pyx_CyFunction_get_dict, (setter)__Pyx_CyFunction_set_dict, 0, 0},
- {(char *) "func_globals", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "__globals__", (getter)__Pyx_CyFunction_get_globals, 0, 0, 0},
- {(char *) "func_closure", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "__closure__", (getter)__Pyx_CyFunction_get_closure, 0, 0, 0},
- {(char *) "func_code", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "__code__", (getter)__Pyx_CyFunction_get_code, 0, 0, 0},
- {(char *) "func_defaults", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
- {(char *) "__defaults__", (getter)__Pyx_CyFunction_get_defaults, (setter)__Pyx_CyFunction_set_defaults, 0, 0},
- {(char *) "__kwdefaults__", (getter)__Pyx_CyFunction_get_kwdefaults, (setter)__Pyx_CyFunction_set_kwdefaults, 0, 0},
- {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0},
- {0, 0, 0, 0, 0}
-};
-#ifndef PY_WRITE_RESTRICTED /* < Py2.5 */
-#define PY_WRITE_RESTRICTED WRITE_RESTRICTED
-#endif
-static PyMemberDef __pyx_CyFunction_members[] = {
- {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0},
- {0, 0, 0, 0, 0}
-};
-static PyObject *
-__Pyx_CyFunction_reduce(__pyx_CyFunctionObject *m, CYTHON_UNUSED PyObject *args)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromString(m->func.m_ml->ml_name);
-#else
- return PyString_FromString(m->func.m_ml->ml_name);
-#endif
-}
-static PyMethodDef __pyx_CyFunction_methods[] = {
- {__Pyx_NAMESTR("__reduce__"), (PyCFunction)__Pyx_CyFunction_reduce, METH_VARARGS, 0},
- {0, 0, 0, 0}
-};
-static PyObject *__Pyx_CyFunction_New(PyTypeObject *type, PyMethodDef *ml, int flags, PyObject* qualname,
- PyObject *closure, PyObject *module, PyObject* globals, PyObject* code) {
- __pyx_CyFunctionObject *op = PyObject_GC_New(__pyx_CyFunctionObject, type);
- if (op == NULL)
- return NULL;
- op->flags = flags;
- op->func_weakreflist = NULL;
- op->func.m_ml = ml;
- op->func.m_self = (PyObject *) op;
- Py_XINCREF(closure);
- op->func_closure = closure;
- Py_XINCREF(module);
- op->func.m_module = module;
- op->func_dict = NULL;
- op->func_name = NULL;
- Py_INCREF(qualname);
- op->func_qualname = qualname;
- op->func_doc = NULL;
- op->func_classobj = NULL;
- op->func_globals = globals;
- Py_INCREF(op->func_globals);
- Py_XINCREF(code);
- op->func_code = code;
- op->defaults_pyobjects = 0;
- op->defaults = NULL;
- op->defaults_tuple = NULL;
- op->defaults_kwdict = NULL;
- op->defaults_getter = NULL;
- op->func_annotations = NULL;
- PyObject_GC_Track(op);
- return (PyObject *) op;
-}
-static int
-__Pyx_CyFunction_clear(__pyx_CyFunctionObject *m)
-{
- Py_CLEAR(m->func_closure);
- Py_CLEAR(m->func.m_module);
- Py_CLEAR(m->func_dict);
- Py_CLEAR(m->func_name);
- Py_CLEAR(m->func_qualname);
- Py_CLEAR(m->func_doc);
- Py_CLEAR(m->func_globals);
- Py_CLEAR(m->func_code);
- Py_CLEAR(m->func_classobj);
- Py_CLEAR(m->defaults_tuple);
- Py_CLEAR(m->defaults_kwdict);
- Py_CLEAR(m->func_annotations);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_XDECREF(pydefaults[i]);
- PyMem_Free(m->defaults);
- m->defaults = NULL;
- }
- return 0;
-}
-static void __Pyx_CyFunction_dealloc(__pyx_CyFunctionObject *m)
-{
- PyObject_GC_UnTrack(m);
- if (m->func_weakreflist != NULL)
- PyObject_ClearWeakRefs((PyObject *) m);
- __Pyx_CyFunction_clear(m);
- PyObject_GC_Del(m);
-}
-static int __Pyx_CyFunction_traverse(__pyx_CyFunctionObject *m, visitproc visit, void *arg)
-{
- Py_VISIT(m->func_closure);
- Py_VISIT(m->func.m_module);
- Py_VISIT(m->func_dict);
- Py_VISIT(m->func_name);
- Py_VISIT(m->func_qualname);
- Py_VISIT(m->func_doc);
- Py_VISIT(m->func_globals);
- Py_VISIT(m->func_code);
- Py_VISIT(m->func_classobj);
- Py_VISIT(m->defaults_tuple);
- Py_VISIT(m->defaults_kwdict);
- if (m->defaults) {
- PyObject **pydefaults = __Pyx_CyFunction_Defaults(PyObject *, m);
- int i;
- for (i = 0; i < m->defaults_pyobjects; i++)
- Py_VISIT(pydefaults[i]);
- }
- return 0;
-}
-static PyObject *__Pyx_CyFunction_descr_get(PyObject *func, PyObject *obj, PyObject *type)
-{
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- if (m->flags & __Pyx_CYFUNCTION_STATICMETHOD) {
- Py_INCREF(func);
- return func;
- }
- if (m->flags & __Pyx_CYFUNCTION_CLASSMETHOD) {
- if (type == NULL)
- type = (PyObject *)(Py_TYPE(obj));
- return PyMethod_New(func,
- type, (PyObject *)(Py_TYPE(type)));
- }
- if (obj == Py_None)
- obj = NULL;
- return PyMethod_New(func, obj, type);
-}
-static PyObject*
-__Pyx_CyFunction_repr(__pyx_CyFunctionObject *op)
-{
-#if PY_MAJOR_VERSION >= 3
- return PyUnicode_FromFormat("<cyfunction %U at %p>",
- op->func_qualname, (void *)op);
-#else
- return PyString_FromFormat("<cyfunction %s at %p>",
- PyString_AsString(op->func_qualname), (void *)op);
-#endif
-}
-#if CYTHON_COMPILING_IN_PYPY
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- PyCFunctionObject* f = (PyCFunctionObject*)func;
- PyCFunction meth = PyCFunction_GET_FUNCTION(func);
- PyObject *self = PyCFunction_GET_SELF(func);
- Py_ssize_t size;
- switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) {
- case METH_VARARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0)
- return (*meth)(self, arg);
- break;
- case METH_VARARGS | METH_KEYWORDS:
- return (*(PyCFunctionWithKeywords)meth)(self, arg, kw);
- case METH_NOARGS:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 0)
- return (*meth)(self, NULL);
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes no arguments (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- case METH_O:
- if (likely(kw == NULL) || PyDict_Size(kw) == 0) {
- size = PyTuple_GET_SIZE(arg);
- if (size == 1)
- return (*meth)(self, PyTuple_GET_ITEM(arg, 0));
- PyErr_Format(PyExc_TypeError,
- "%.200s() takes exactly one argument (%zd given)",
- f->m_ml->ml_name, size);
- return NULL;
- }
- break;
- default:
- PyErr_SetString(PyExc_SystemError, "Bad call flags in "
- "__Pyx_CyFunction_Call. METH_OLDARGS is no "
- "longer supported!");
- return NULL;
- }
- PyErr_Format(PyExc_TypeError, "%.200s() takes no keyword arguments",
- f->m_ml->ml_name);
- return NULL;
-}
-#else
-static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) {
- return PyCFunction_Call(func, arg, kw);
-}
-#endif
-static PyTypeObject __pyx_CyFunctionType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("cython_function_or_method"), /*tp_name*/
- sizeof(__pyx_CyFunctionObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_CyFunction_dealloc, /*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- (reprfunc) __Pyx_CyFunction_repr, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- __Pyx_CyFunction_Call, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_CyFunction_traverse, /*tp_traverse*/
- (inquiry) __Pyx_CyFunction_clear, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_CyFunctionObject, func_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- 0, /*tp_iternext*/
- __pyx_CyFunction_methods, /*tp_methods*/
- __pyx_CyFunction_members, /*tp_members*/
- __pyx_CyFunction_getsets, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- __Pyx_CyFunction_descr_get, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- offsetof(__pyx_CyFunctionObject, func_dict),/*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
- 0, /*tp_del*/
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-#if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_finalize*/
-#endif
-};
-static int __Pyx_CyFunction_init(void) {
-#if !CYTHON_COMPILING_IN_PYPY
- __pyx_CyFunctionType_type.tp_call = PyCFunction_Call;
-#endif
- __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type);
- if (__pyx_CyFunctionType == NULL) {
- return -1;
- }
- return 0;
-}
-static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults = PyMem_Malloc(size);
- if (!m->defaults)
- return PyErr_NoMemory();
- memset(m->defaults, 0, size);
- m->defaults_pyobjects = pyobjects;
- return m->defaults;
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_tuple = tuple;
- Py_INCREF(tuple);
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *func, PyObject *dict) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->defaults_kwdict = dict;
- Py_INCREF(dict);
-}
-static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, PyObject *dict) {
- __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func;
- m->func_annotations = dict;
- Py_INCREF(dict);
-}
-
-static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name,
- PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) {
- PyObject *ns;
- if (metaclass) {
- PyObject *prep = __Pyx_PyObject_GetAttrStr(metaclass, __pyx_n_s_prepare);
- if (prep) {
- PyObject *pargs = PyTuple_Pack(2, name, bases);
- if (unlikely(!pargs)) {
- Py_DECREF(prep);
- return NULL;
- }
- ns = PyObject_Call(prep, pargs, mkw);
- Py_DECREF(prep);
- Py_DECREF(pargs);
- } else {
- if (unlikely(!PyErr_ExceptionMatches(PyExc_AttributeError)))
- return NULL;
- PyErr_Clear();
- ns = PyDict_New();
- }
- } else {
- ns = PyDict_New();
- }
- if (unlikely(!ns))
- return NULL;
- if (unlikely(PyObject_SetItem(ns, __pyx_n_s_module, modname) < 0)) goto bad;
- if (unlikely(PyObject_SetItem(ns, __pyx_n_s_qualname, qualname) < 0)) goto bad;
- if (unlikely(doc && PyObject_SetItem(ns, __pyx_n_s_doc, doc) < 0)) goto bad;
- return ns;
-bad:
- Py_DECREF(ns);
- return NULL;
-}
-static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases,
- PyObject *dict, PyObject *mkw,
- int calculate_metaclass, int allow_py2_metaclass) {
- PyObject *result, *margs;
- PyObject *owned_metaclass = NULL;
- if (allow_py2_metaclass) {
- owned_metaclass = PyObject_GetItem(dict, __pyx_n_s_metaclass);
- if (owned_metaclass) {
- metaclass = owned_metaclass;
- } else if (likely(PyErr_ExceptionMatches(PyExc_KeyError))) {
- PyErr_Clear();
- } else {
- return NULL;
- }
- }
- if (calculate_metaclass && (!metaclass || PyType_Check(metaclass))) {
- metaclass = __Pyx_CalculateMetaclass((PyTypeObject*) metaclass, bases);
- Py_XDECREF(owned_metaclass);
- if (unlikely(!metaclass))
- return NULL;
- owned_metaclass = metaclass;
- }
- margs = PyTuple_Pack(3, name, bases, dict);
- if (unlikely(!margs)) {
- result = NULL;
- } else {
- result = PyObject_Call(metaclass, margs, mkw);
- Py_DECREF(margs);
- }
- Py_XDECREF(owned_metaclass);
- return result;
-}
-
-static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
- PyObject *empty_list = 0;
- PyObject *module = 0;
- PyObject *global_dict = 0;
- PyObject *empty_dict = 0;
- PyObject *list;
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_import;
- py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
- if (!py_import)
- goto bad;
- #endif
- if (from_list)
- list = from_list;
- else {
- empty_list = PyList_New(0);
- if (!empty_list)
- goto bad;
- list = empty_list;
- }
- global_dict = PyModule_GetDict(__pyx_m);
- if (!global_dict)
- goto bad;
- empty_dict = PyDict_New();
- if (!empty_dict)
- goto bad;
- #if PY_VERSION_HEX >= 0x02050000
- {
- #if PY_MAJOR_VERSION >= 3
- if (level == -1) {
- if (strchr(__Pyx_MODULE_NAME, '.')) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(1);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, 1);
- #endif
- if (!module) {
- if (!PyErr_ExceptionMatches(PyExc_ImportError))
- goto bad;
- PyErr_Clear();
- }
- }
- level = 0; /* try absolute import on failure */
- }
- #endif
- if (!module) {
- #if PY_VERSION_HEX < 0x03030000
- PyObject *py_level = PyInt_FromLong(level);
- if (!py_level)
- goto bad;
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, py_level, NULL);
- Py_DECREF(py_level);
- #else
- module = PyImport_ImportModuleLevelObject(
- name, global_dict, empty_dict, list, level);
- #endif
- }
- }
- #else
- if (level>0) {
- PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4.");
- goto bad;
- }
- module = PyObject_CallFunctionObjArgs(py_import,
- name, global_dict, empty_dict, list, NULL);
- #endif
-bad:
- #if PY_VERSION_HEX < 0x03030000
- Py_XDECREF(py_import);
- #endif
- Py_XDECREF(empty_list);
- Py_XDECREF(empty_dict);
- return module;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(long) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(long) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(long) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(long),
- little, !is_unsigned);
- }
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value) {
- const uint32_t neg_one = (uint32_t) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
- if (is_unsigned) {
- if (sizeof(uint32_t) < sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(uint32_t) <= sizeof(unsigned long)) {
- return PyLong_FromUnsignedLong((unsigned long) value);
- } else if (sizeof(uint32_t) <= sizeof(unsigned long long)) {
- return PyLong_FromUnsignedLongLong((unsigned long long) value);
- }
- } else {
- if (sizeof(uint32_t) <= sizeof(long)) {
- return PyInt_FromLong((long) value);
- } else if (sizeof(uint32_t) <= sizeof(long long)) {
- return PyLong_FromLongLong((long long) value);
- }
- }
- {
- int one = 1; int little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&value;
- return _PyLong_FromByteArray(bytes, sizeof(uint32_t),
- little, !is_unsigned);
- }
-}
-
-#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \
- { \
- func_type value = func(x); \
- if (sizeof(target_type) < sizeof(func_type)) { \
- if (unlikely(value != (func_type) (target_type) value)) { \
- func_type zero = 0; \
- PyErr_SetString(PyExc_OverflowError, \
- (is_unsigned && unlikely(value < zero)) ? \
- "can't convert negative value to " #target_type : \
- "value too large to convert to " #target_type); \
- return (target_type) -1; \
- } \
- } \
- return (target_type) value; \
- }
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
- const long neg_one = (long) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(long) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- return (long) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to long");
- return (long) -1;
- }
- if (sizeof(long) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(long) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(long)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(long) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(long) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(long) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong)
- } else if (sizeof(long) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- long val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (long) -1;
- }
- } else {
- long val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (long) -1;
- val = __Pyx_PyInt_As_long(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
- const int neg_one = (int) -1, const_zero = 0;
- const int is_unsigned = neg_one > const_zero;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_Check(x))) {
- if (sizeof(int) < sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG)
- } else {
- long val = PyInt_AS_LONG(x);
- if (is_unsigned && unlikely(val < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- return (int) val;
- }
- } else
-#endif
- if (likely(PyLong_Check(x))) {
- if (is_unsigned) {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return (int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (unlikely(Py_SIZE(x) < 0)) {
- PyErr_SetString(PyExc_OverflowError,
- "can't convert negative value to int");
- return (int) -1;
- }
- if (sizeof(int) <= sizeof(unsigned long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong)
- } else if (sizeof(int) <= sizeof(unsigned long long)) {
- __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong)
- }
- } else {
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- if (sizeof(digit) <= sizeof(int)) {
- switch (Py_SIZE(x)) {
- case 0: return 0;
- case 1: return +(int) ((PyLongObject*)x)->ob_digit[0];
- case -1: return -(int) ((PyLongObject*)x)->ob_digit[0];
- }
- }
- #endif
-#endif
- if (sizeof(int) <= sizeof(long)) {
- __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong)
- } else if (sizeof(int) <= sizeof(long long)) {
- __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong)
- }
- }
- {
-#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
- PyErr_SetString(PyExc_RuntimeError,
- "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
-#else
- int val;
- PyObject *v = __Pyx_PyNumber_Int(x);
- #if PY_MAJOR_VERSION < 3
- if (likely(v) && !PyLong_Check(v)) {
- PyObject *tmp = v;
- v = PyNumber_Long(tmp);
- Py_DECREF(tmp);
- }
- #endif
- if (likely(v)) {
- int one = 1; int is_little = (int)*(unsigned char *)&one;
- unsigned char *bytes = (unsigned char *)&val;
- int ret = _PyLong_AsByteArray((PyLongObject *)v,
- bytes, sizeof(val),
- is_little, !is_unsigned);
- Py_DECREF(v);
- if (likely(!ret))
- return val;
- }
-#endif
- return (int) -1;
- }
- } else {
- int val;
- PyObject *tmp = __Pyx_PyNumber_Int(x);
- if (!tmp) return (int) -1;
- val = __Pyx_PyInt_As_int(tmp);
- Py_DECREF(tmp);
- return val;
- }
-}
-
-static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
- PyObject *tmp_type, *tmp_value, *tmp_tb;
-#if CYTHON_COMPILING_IN_CPYTHON
- PyThreadState *tstate = PyThreadState_GET();
- tmp_type = tstate->exc_type;
- tmp_value = tstate->exc_value;
- tmp_tb = tstate->exc_traceback;
- tstate->exc_type = *type;
- tstate->exc_value = *value;
- tstate->exc_traceback = *tb;
-#else
- PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
- PyErr_SetExcInfo(*type, *value, *tb);
-#endif
- *type = tmp_type;
- *value = tmp_value;
- *tb = tmp_tb;
-}
-
-static 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_GetAttr(ev, __pyx_n_s_args);
- Py_DECREF(ev);
- if (likely(args)) {
- value = PyObject_GetItem(args, 0);
- Py_DECREF(args);
- }
- if (unlikely(!value)) {
- __Pyx_ErrRestore(NULL, NULL, NULL);
- Py_INCREF(Py_None);
- value = Py_None;
- }
- }
-#endif
- *pvalue = value;
- return 0;
-}
-#endif
-static CYTHON_INLINE
-void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) {
- PyObject *exc_type = self->exc_type;
- PyObject *exc_value = self->exc_value;
- PyObject *exc_traceback = self->exc_traceback;
- self->exc_type = NULL;
- self->exc_value = NULL;
- self->exc_traceback = NULL;
- Py_XDECREF(exc_type);
- Py_XDECREF(exc_value);
- Py_XDECREF(exc_traceback);
-}
-static CYTHON_INLINE
-int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) {
- if (unlikely(gen->is_running)) {
- PyErr_SetString(PyExc_ValueError,
- "generator already executing");
- 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,
- "can't send non-None value to a "
- "just-started generator");
- return NULL;
- }
- }
- if (unlikely(self->resume_label == -1)) {
- PyErr_SetNone(PyExc_StopIteration);
- return NULL;
- }
- 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);
-#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 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) {
- __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 = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value);
- }
- gen->is_running = 0;
- if (likely(ret)) {
- return ret;
- }
- return __Pyx_Generator_FinishDelegation(gen);
- }
- return __Pyx_Generator_SendEx(gen, value);
-}
-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_GetAttr(yf, __pyx_n_s_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);
-#else
- PyErr_SetNone(PyExc_GeneratorExit);
-#endif
- retval = __Pyx_Generator_SendEx(gen, NULL);
- if (retval) {
- Py_DECREF(retval);
- PyErr_SetString(PyExc_RuntimeError,
- "generator ignored GeneratorExit");
- return NULL;
- }
- 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))
- {
- 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 *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_GetAttr(yf, __pyx_n_s_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(gen, NULL);
-}
-static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_VISIT(gen->closure);
- Py_VISIT(gen->classobj);
- Py_VISIT(gen->yieldfrom);
- Py_VISIT(gen->exc_type);
- Py_VISIT(gen->exc_value);
- Py_VISIT(gen->exc_traceback);
- return 0;
-}
-static int __Pyx_Generator_clear(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- Py_CLEAR(gen->closure);
- Py_CLEAR(gen->classobj);
- Py_CLEAR(gen->yieldfrom);
- Py_CLEAR(gen->exc_type);
- Py_CLEAR(gen->exc_value);
- Py_CLEAR(gen->exc_traceback);
- return 0;
-}
-static void __Pyx_Generator_dealloc(PyObject *self) {
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- PyObject_GC_UnTrack(gen);
- if (gen->gi_weakreflist != NULL)
- PyObject_ClearWeakRefs(self);
- if (gen->resume_label > 0) {
- PyObject_GC_Track(self);
-#if PY_VERSION_HEX >= 0x030400a1
- if (PyObject_CallFinalizerFromDealloc(self))
-#else
- Py_TYPE(gen)->tp_del(self);
- if (self->ob_refcnt > 0)
-#endif
- return; /* resurrected. :( */
- PyObject_GC_UnTrack(self);
- }
- __Pyx_Generator_clear(self);
- PyObject_GC_Del(gen);
-}
-static void __Pyx_Generator_del(PyObject *self) {
- PyObject *res;
- PyObject *error_type, *error_value, *error_traceback;
- __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self;
- if (gen->resume_label <= 0)
- return ;
-#if PY_VERSION_HEX < 0x030400a1
- assert(self->ob_refcnt == 0);
- self->ob_refcnt = 1;
-#endif
- __Pyx_ErrFetch(&error_type, &error_value, &error_traceback);
- res = __Pyx_Generator_Close(self);
- if (res == NULL)
- PyErr_WriteUnraisable(self);
- else
- Py_DECREF(res);
- __Pyx_ErrRestore(error_type, error_value, error_traceback);
-#if PY_VERSION_HEX < 0x030400a1
- /* Undo the temporary resurrection; can't use DECREF here, it would
- * cause a recursive call.
- */
- assert(self->ob_refcnt > 0);
- if (--self->ob_refcnt == 0)
- return; /* this is the normal path out */
- /* close() resurrected it! Make it look like the original Py_DECREF
- * never happened.
- */
- {
- Py_ssize_t refcnt = self->ob_refcnt;
- _Py_NewReference(self);
- self->ob_refcnt = refcnt;
- }
-#if CYTHON_COMPILING_IN_CPYTHON
- assert(PyType_IS_GC(self->ob_type) &&
- _Py_AS_GC(self)->gc.gc_refs != _PyGC_REFS_UNTRACKED);
- /* If Py_REF_DEBUG, _Py_NewReference bumped _Py_RefTotal, so
- * we need to undo that. */
- _Py_DEC_REFTOTAL;
-#endif
- /* If Py_TRACE_REFS, _Py_NewReference re-added self to the object
- * chain, so no more to do there.
- * If COUNT_ALLOCS, the original decref bumped tp_frees, and
- * _Py_NewReference bumped tp_allocs: both of those need to be
- * undone.
- */
-#ifdef COUNT_ALLOCS
- --Py_TYPE(self)->tp_frees;
- --Py_TYPE(self)->tp_allocs;
-#endif
-#endif
-}
-static PyMemberDef __pyx_Generator_memberlist[] = {
- {(char *) "gi_running",
-#if PY_VERSION_HEX >= 0x02060000
- T_BOOL,
-#else
- T_BYTE,
-#endif
- offsetof(__pyx_GeneratorObject, is_running),
- READONLY,
- NULL},
- {0, 0, 0, 0, 0}
-};
-static PyMethodDef __pyx_Generator_methods[] = {
- {__Pyx_NAMESTR("send"), (PyCFunction) __Pyx_Generator_Send, METH_O, 0},
- {__Pyx_NAMESTR("throw"), (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0},
- {__Pyx_NAMESTR("close"), (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0},
- {0, 0, 0, 0}
-};
-static PyTypeObject __pyx_GeneratorType_type = {
- PyVarObject_HEAD_INIT(0, 0)
- __Pyx_NAMESTR("generator"), /*tp_name*/
- sizeof(__pyx_GeneratorObject), /*tp_basicsize*/
- 0, /*tp_itemsize*/
- (destructor) __Pyx_Generator_dealloc,/*tp_dealloc*/
- 0, /*tp_print*/
- 0, /*tp_getattr*/
- 0, /*tp_setattr*/
-#if PY_MAJOR_VERSION < 3
- 0, /*tp_compare*/
-#else
- 0, /*reserved*/
-#endif
- 0, /*tp_repr*/
- 0, /*tp_as_number*/
- 0, /*tp_as_sequence*/
- 0, /*tp_as_mapping*/
- 0, /*tp_hash*/
- 0, /*tp_call*/
- 0, /*tp_str*/
- 0, /*tp_getattro*/
- 0, /*tp_setattro*/
- 0, /*tp_as_buffer*/
- Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE, /* tp_flags*/
- 0, /*tp_doc*/
- (traverseproc) __Pyx_Generator_traverse, /*tp_traverse*/
- 0, /*tp_clear*/
- 0, /*tp_richcompare*/
- offsetof(__pyx_GeneratorObject, gi_weakreflist), /* tp_weaklistoffse */
- 0, /*tp_iter*/
- (iternextfunc) __Pyx_Generator_Next, /*tp_iternext*/
- __pyx_Generator_methods, /*tp_methods*/
- __pyx_Generator_memberlist, /*tp_members*/
- 0, /*tp_getset*/
- 0, /*tp_base*/
- 0, /*tp_dict*/
- 0, /*tp_descr_get*/
- 0, /*tp_descr_set*/
- 0, /*tp_dictoffset*/
- 0, /*tp_init*/
- 0, /*tp_alloc*/
- 0, /*tp_new*/
- 0, /*tp_free*/
- 0, /*tp_is_gc*/
- 0, /*tp_bases*/
- 0, /*tp_mro*/
- 0, /*tp_cache*/
- 0, /*tp_subclasses*/
- 0, /*tp_weaklist*/
-#if PY_VERSION_HEX >= 0x030400a1
- 0, /*tp_del*/
-#else
- __Pyx_Generator_del, /*tp_del*/
-#endif
-#if PY_VERSION_HEX >= 0x02060000
- 0, /*tp_version_tag*/
-#endif
-#if PY_VERSION_HEX >= 0x030400a1
- __Pyx_Generator_del, /*tp_finalize*/
-#endif
-};
-static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body,
- PyObject *closure) {
- __pyx_GeneratorObject *gen =
- PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type);
- if (gen == NULL)
- return NULL;
- gen->body = body;
- gen->closure = closure;
- Py_XINCREF(closure);
- gen->is_running = 0;
- gen->resume_label = 0;
- gen->classobj = NULL;
- gen->yieldfrom = NULL;
- gen->exc_type = NULL;
- gen->exc_value = NULL;
- gen->exc_traceback = NULL;
- gen->gi_weakreflist = NULL;
- PyObject_GC_Track(gen);
- return gen;
-}
-static int __pyx_Generator_init(void) {
- __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr;
- __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter;
- __pyx_GeneratorType = __Pyx_FetchCommonType(&__pyx_GeneratorType_type);
- if (__pyx_GeneratorType == NULL) {
- return -1;
- }
- return 0;
-}
-
-static int __Pyx_check_binary_version(void) {
- char ctversion[4], rtversion[4];
- PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
- PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
- if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
- char message[200];
- PyOS_snprintf(message, sizeof(message),
- "compiletime version %s of module '%.100s' "
- "does not match runtime version %s",
- ctversion, __Pyx_MODULE_NAME, rtversion);
- #if PY_VERSION_HEX < 0x02050000
- return PyErr_Warn(NULL, message);
- #else
- return PyErr_WarnEx(NULL, message, 1);
- #endif
- }
- 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,
- size_t size, int strict)
-{
- PyObject *py_module = 0;
- PyObject *result = 0;
- PyObject *py_name = 0;
- char warning[200];
- Py_ssize_t basicsize;
-#ifdef Py_LIMITED_API
- PyObject *py_basicsize;
-#endif
- py_module = __Pyx_ImportModule(module_name);
- if (!py_module)
- goto bad;
- py_name = __Pyx_PyIdentifier_FromString(class_name);
- if (!py_name)
- goto bad;
- result = PyObject_GetAttr(py_module, py_name);
- Py_DECREF(py_name);
- py_name = 0;
- Py_DECREF(py_module);
- py_module = 0;
- if (!result)
- goto bad;
- if (!PyType_Check(result)) {
- PyErr_Format(PyExc_TypeError,
- "%.200s.%.200s is not a type object",
- module_name, class_name);
- goto bad;
- }
-#ifndef Py_LIMITED_API
- basicsize = ((PyTypeObject *)result)->tp_basicsize;
-#else
- py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
- if (!py_basicsize)
- goto bad;
- basicsize = PyLong_AsSsize_t(py_basicsize);
- Py_DECREF(py_basicsize);
- py_basicsize = 0;
- if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
- goto bad;
-#endif
- if (!strict && (size_t)basicsize > size) {
- PyOS_snprintf(warning, sizeof(warning),
- "%s.%s size changed, may indicate binary incompatibility",
- module_name, class_name);
- #if PY_VERSION_HEX < 0x02050000
- if (PyErr_Warn(NULL, warning) < 0) goto bad;
- #else
- if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
- #endif
- }
- else if ((size_t)basicsize != size) {
- PyErr_Format(PyExc_ValueError,
- "%.200s.%.200s has the wrong size, try recompiling",
- module_name, class_name);
- goto bad;
- }
- return (PyTypeObject *)result;
-bad:
- Py_XDECREF(py_module);
- Py_XDECREF(result);
- return NULL;
-}
-#endif
-
-#ifndef __PYX_HAVE_RT_ImportFunction
-#define __PYX_HAVE_RT_ImportFunction
-static int __Pyx_ImportFunction(PyObject *module, const char *funcname, void (**f)(void), const char *sig) {
- PyObject *d = 0;
- PyObject *cobj = 0;
- union {
- void (*fp)(void);
- void *p;
- } tmp;
- d = PyObject_GetAttrString(module, (char *)"__pyx_capi__");
- if (!d)
- goto bad;
- cobj = PyDict_GetItemString(d, funcname);
- if (!cobj) {
- PyErr_Format(PyExc_ImportError,
- "%.200s does not export expected C function %.200s",
- PyModule_GetName(module), funcname);
- goto bad;
- }
-#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3 && PY_MINOR_VERSION==0)
- if (!PyCapsule_IsValid(cobj, sig)) {
- PyErr_Format(PyExc_TypeError,
- "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
- PyModule_GetName(module), funcname, sig, PyCapsule_GetName(cobj));
- goto bad;
- }
- tmp.p = PyCapsule_GetPointer(cobj, sig);
-#else
- {const char *desc, *s1, *s2;
- desc = (const char *)PyCObject_GetDesc(cobj);
- if (!desc)
- goto bad;
- s1 = desc; s2 = sig;
- while (*s1 != '\0' && *s1 == *s2) { s1++; s2++; }
- if (*s1 != *s2) {
- PyErr_Format(PyExc_TypeError,
- "C function %.200s.%.200s has wrong signature (expected %.500s, got %.500s)",
- PyModule_GetName(module), funcname, sig, desc);
- goto bad;
- }
- tmp.p = PyCObject_AsVoidPtr(cobj);}
-#endif
- *f = tmp.fp;
- if (!(*f))
- goto bad;
- Py_DECREF(d);
- return 0;
-bad:
- Py_XDECREF(d);
- return -1;
-}
-#endif
-
-static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
- int start = 0, mid = 0, end = count - 1;
- if (end >= 0 && code_line > entries[end].code_line) {
- return count;
- }
- while (start < end) {
- mid = (start + end) / 2;
- if (code_line < entries[mid].code_line) {
- end = mid;
- } else if (code_line > entries[mid].code_line) {
- start = mid + 1;
- } else {
- return mid;
- }
- }
- if (code_line <= entries[mid].code_line) {
- return mid;
- } else {
- return mid + 1;
- }
-}
-static PyCodeObject *__pyx_find_code_object(int code_line) {
- PyCodeObject* code_object;
- int pos;
- if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
- return NULL;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
- return NULL;
- }
- code_object = __pyx_code_cache.entries[pos].code_object;
- Py_INCREF(code_object);
- return code_object;
-}
-static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
- int pos, i;
- __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
- if (unlikely(!code_line)) {
- return;
- }
- if (unlikely(!entries)) {
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
- if (likely(entries)) {
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = 64;
- __pyx_code_cache.count = 1;
- entries[0].code_line = code_line;
- entries[0].code_object = code_object;
- Py_INCREF(code_object);
- }
- return;
- }
- pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
- if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
- PyCodeObject* tmp = entries[pos].code_object;
- entries[pos].code_object = code_object;
- Py_DECREF(tmp);
- return;
- }
- if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
- int new_max = __pyx_code_cache.max_count + 64;
- entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
- __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry));
- if (unlikely(!entries)) {
- return;
- }
- __pyx_code_cache.entries = entries;
- __pyx_code_cache.max_count = new_max;
- }
- for (i=__pyx_code_cache.count; i>pos; i--) {
- entries[i] = entries[i-1];
- }
- entries[pos].code_line = code_line;
- entries[pos].code_object = code_object;
- __pyx_code_cache.count++;
- Py_INCREF(code_object);
-}
-
-#include "compile.h"
-#include "frameobject.h"
-#include "traceback.h"
-static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
- const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_srcfile = 0;
- PyObject *py_funcname = 0;
- #if PY_MAJOR_VERSION < 3
- py_srcfile = PyString_FromString(filename);
- #else
- py_srcfile = PyUnicode_FromString(filename);
- #endif
- if (!py_srcfile) goto bad;
- if (c_line) {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #else
- py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
- #endif
- }
- else {
- #if PY_MAJOR_VERSION < 3
- py_funcname = PyString_FromString(funcname);
- #else
- py_funcname = PyUnicode_FromString(funcname);
- #endif
- }
- if (!py_funcname) goto bad;
- py_code = __Pyx_PyCode_New(
- 0, /*int argcount,*/
- 0, /*int kwonlyargcount,*/
- 0, /*int nlocals,*/
- 0, /*int stacksize,*/
- 0, /*int flags,*/
- __pyx_empty_bytes, /*PyObject *code,*/
- __pyx_empty_tuple, /*PyObject *consts,*/
- __pyx_empty_tuple, /*PyObject *names,*/
- __pyx_empty_tuple, /*PyObject *varnames,*/
- __pyx_empty_tuple, /*PyObject *freevars,*/
- __pyx_empty_tuple, /*PyObject *cellvars,*/
- py_srcfile, /*PyObject *filename,*/
- py_funcname, /*PyObject *name,*/
- py_line, /*int firstlineno,*/
- __pyx_empty_bytes /*PyObject *lnotab*/
- );
- Py_DECREF(py_srcfile);
- Py_DECREF(py_funcname);
- return py_code;
-bad:
- Py_XDECREF(py_srcfile);
- Py_XDECREF(py_funcname);
- return NULL;
-}
-static void __Pyx_AddTraceback(const char *funcname, int c_line,
- int py_line, const char *filename) {
- PyCodeObject *py_code = 0;
- PyObject *py_globals = 0;
- PyFrameObject *py_frame = 0;
- py_code = __pyx_find_code_object(c_line ? c_line : py_line);
- if (!py_code) {
- py_code = __Pyx_CreateCodeObjectForTraceback(
- funcname, c_line, py_line, filename);
- if (!py_code) goto bad;
- __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
- }
- py_globals = PyModule_GetDict(__pyx_m);
- if (!py_globals) goto bad;
- py_frame = PyFrame_New(
- PyThreadState_GET(), /*PyThreadState *tstate,*/
- py_code, /*PyCodeObject *code,*/
- py_globals, /*PyObject *globals,*/
- 0 /*PyObject *locals*/
- );
- if (!py_frame) goto bad;
- py_frame->f_lineno = py_line;
- PyTraceBack_Here(py_frame);
-bad:
- Py_XDECREF(py_code);
- Py_XDECREF(py_frame);
-}
-
-static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
- while (t->p) {
- #if PY_MAJOR_VERSION < 3
- if (t->is_unicode) {
- *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
- } else if (t->intern) {
- *t->p = PyString_InternFromString(t->s);
- } else {
- *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
- }
- #else /* Python 3+ has unicode identifiers */
- if (t->is_unicode | t->is_str) {
- if (t->intern) {
- *t->p = PyUnicode_InternFromString(t->s);
- } else if (t->encoding) {
- *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
- } else {
- *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
- }
- } else {
- *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
- }
- #endif
- if (!*t->p)
- return -1;
- ++t;
- }
- return 0;
-}
-
-static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) {
- return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str));
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
- Py_ssize_t ignore;
- return __Pyx_PyObject_AsStringAndSize(o, &ignore);
-}
-static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
- if (
-#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- __Pyx_sys_getdefaultencoding_not_ascii &&
-#endif
- PyUnicode_Check(o)) {
-#if PY_VERSION_HEX < 0x03030000
- char* defenc_c;
- PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
- if (!defenc) return NULL;
- defenc_c = PyBytes_AS_STRING(defenc);
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- {
- char* end = defenc_c + PyBytes_GET_SIZE(defenc);
- char* c;
- for (c = defenc_c; c < end; c++) {
- if ((unsigned char) (*c) >= 128) {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
- }
- }
-#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/
- *length = PyBytes_GET_SIZE(defenc);
- return defenc_c;
-#else /* PY_VERSION_HEX < 0x03030000 */
- if (PyUnicode_READY(o) == -1) return NULL;
-#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
- if (PyUnicode_IS_ASCII(o)) {
- *length = PyUnicode_GET_DATA_SIZE(o);
- return PyUnicode_AsUTF8(o);
- } else {
- PyUnicode_AsASCIIString(o);
- return NULL;
- }
-#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
- return PyUnicode_AsUTF8AndSize(o, length);
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */
-#endif /* PY_VERSION_HEX < 0x03030000 */
- } else
-#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */
-#if !CYTHON_COMPILING_IN_PYPY
-#if PY_VERSION_HEX >= 0x02060000
- if (PyByteArray_Check(o)) {
- *length = PyByteArray_GET_SIZE(o);
- return PyByteArray_AS_STRING(o);
- } else
-#endif
-#endif
- {
- char* result;
- int r = PyBytes_AsStringAndSize(o, &result, length);
- if (unlikely(r < 0)) {
- return NULL;
- } else {
- return result;
- }
- }
-}
-static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
- int is_true = x == Py_True;
- if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
- else return PyObject_IsTrue(x);
-}
-static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
- PyNumberMethods *m;
- const char *name = NULL;
- PyObject *res = NULL;
-#if PY_MAJOR_VERSION < 3
- if (PyInt_Check(x) || PyLong_Check(x))
-#else
- if (PyLong_Check(x))
-#endif
- return Py_INCREF(x), x;
- m = Py_TYPE(x)->tp_as_number;
-#if PY_MAJOR_VERSION < 3
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Int(x);
- }
- else if (m && m->nb_long) {
- name = "long";
- res = PyNumber_Long(x);
- }
-#else
- if (m && m->nb_int) {
- name = "int";
- res = PyNumber_Long(x);
- }
-#endif
- if (res) {
-#if PY_MAJOR_VERSION < 3
- if (!PyInt_Check(res) && !PyLong_Check(res)) {
-#else
- if (!PyLong_Check(res)) {
-#endif
- PyErr_Format(PyExc_TypeError,
- "__%.4s__ returned non-%.4s (type %.200s)",
- name, name, Py_TYPE(res)->tp_name);
- Py_DECREF(res);
- return NULL;
- }
- }
- else if (!PyErr_Occurred()) {
- PyErr_SetString(PyExc_TypeError,
- "an integer is required");
- }
- return res;
-}
-#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- #include "longintrepr.h"
- #endif
-#endif
-static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
- Py_ssize_t ival;
- PyObject *x;
-#if PY_MAJOR_VERSION < 3
- if (likely(PyInt_CheckExact(b)))
- return PyInt_AS_LONG(b);
-#endif
- if (likely(PyLong_CheckExact(b))) {
- #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
- #if CYTHON_USE_PYLONG_INTERNALS
- switch (Py_SIZE(b)) {
- case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
- case 0: return 0;
- case 1: return ((PyLongObject*)b)->ob_digit[0];
- }
- #endif
- #endif
- #if PY_VERSION_HEX < 0x02060000
- return PyInt_AsSsize_t(b);
- #else
- return PyLong_AsSsize_t(b);
- #endif
- }
- x = PyNumber_Index(b);
- if (!x) return -1;
- ival = PyInt_AsSsize_t(x);
- Py_DECREF(x);
- return ival;
-}
-static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
-#if PY_VERSION_HEX < 0x02050000
- if (ival <= LONG_MAX)
- return PyInt_FromLong((long)ival);
- else {
- unsigned char *bytes = (unsigned char *) &ival;
- int one = 1; int little = (int)*(unsigned char*)&one;
- return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0);
- }
-#else
- return PyInt_FromSize_t(ival);
-#endif
-}
-
-
-#endif /* Py_PYTHON_H */
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pysam.git
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