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/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_irods.c
htslib/hfile_net.c
htslib/hts.c
htslib/htsfile.c
htslib/kfunc.c
htslib/knetfile.c
htslib/kstring.c
htslib/regidx.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/rANS_byte.h
htslib/cram/rANS_static.c
htslib/cram/rANS_static.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/regidx.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.pxd
pysam/TabProxies.pyx
pysam/__init__.py
pysam/calignmentfile.c
pysam/calignmentfile.pxd
pysam/calignmentfile.pyx
pysam/cbcf.c
pysam/cbcf.pxd
pysam/cbcf.pyx
pysam/cfaidx.pxd
pysam/cfaidx.pyx
pysam/chtslib.pxd
pysam/chtslib.pyx
pysam/csamfile.pxd
pysam/csamfile.pyx
pysam/csamtools.pxd
pysam/csamtools.pyx
pysam/ctabix.pxd
pysam/ctabix.pyx
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/pbr.json
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/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
tests/AlignedSegment_test.py
tests/AlignmentFile_test.py
tests/SamFile_test.py
tests/TestUtils.py
tests/compile_test.py
tests/cython_flagstat.py
tests/example_btag.bam
tests/faidx_test.py
tests/python_flagstat.py
tests/samtools_test.py
tests/tabix_test.py
tests/x.py