COPYING
INSTALL
MANIFEST.in
README.rst
cy_build.py
pysam.py
requirements.txt
setup.cfg
setup.py
bcftools/HMM.c.pysam.c
bcftools/HMM.h
bcftools/bam2bcf.c.pysam.c
bcftools/bam2bcf.h
bcftools/bam2bcf_indel.c.pysam.c
bcftools/bam_sample.c.pysam.c
bcftools/bam_sample.h
bcftools/bcftools.h
bcftools/bin.c.pysam.c
bcftools/bin.h
bcftools/call.h
bcftools/ccall.c.pysam.c
bcftools/consensus.c.pysam.c
bcftools/convert.c.pysam.c
bcftools/convert.h
bcftools/csq.c.pysam.c
bcftools/em.c.pysam.c
bcftools/filter.c.pysam.c
bcftools/filter.h
bcftools/gvcf.c.pysam.c
bcftools/gvcf.h
bcftools/hclust.c.pysam.c
bcftools/hclust.h
bcftools/khash_str2str.h
bcftools/kheap.h
bcftools/kmin.c.pysam.c
bcftools/kmin.h
bcftools/main.c.pysam.c
bcftools/mcall.c.pysam.c
bcftools/mpileup.c.pysam.c
bcftools/mw.h
bcftools/ploidy.c.pysam.c
bcftools/ploidy.h
bcftools/prob1.c.pysam.c
bcftools/prob1.h
bcftools/pysam.h
bcftools/rbuf.h
bcftools/regidx.c.pysam.c
bcftools/regidx.h
bcftools/smpl_ilist.c.pysam.c
bcftools/smpl_ilist.h
bcftools/tabix.c.pysam.c
bcftools/tsv2vcf.c.pysam.c
bcftools/tsv2vcf.h
bcftools/vcfannotate.c.pysam.c
bcftools/vcfcall.c.pysam.c
bcftools/vcfcnv.c.pysam.c
bcftools/vcfconcat.c.pysam.c
bcftools/vcfconvert.c.pysam.c
bcftools/vcffilter.c.pysam.c
bcftools/vcfgtcheck.c.pysam.c
bcftools/vcfindex.c.pysam.c
bcftools/vcfisec.c.pysam.c
bcftools/vcfmerge.c.pysam.c
bcftools/vcfnorm.c.pysam.c
bcftools/vcfplugin.c.pysam.c
bcftools/vcfquery.c.pysam.c
bcftools/vcfroh.c.pysam.c
bcftools/vcfsom.c.pysam.c
bcftools/vcfstats.c.pysam.c
bcftools/vcfview.c.pysam.c
bcftools/vcmp.c.pysam.c
bcftools/vcmp.h
bcftools/version.c.pysam.c
bcftools/version.h
doc/Makefile
doc/api.rst
doc/conf.py
doc/developer.rst
doc/faq.rst
doc/glossary.rst
doc/index.rst
doc/installation.rst
doc/make.bat
doc/release.rst
doc/usage.rst
htslib/Makefile
htslib/bcf_sr_sort.c
htslib/bcf_sr_sort.h
htslib/bgzf.c
htslib/bgzip.c
htslib/config.h.in
htslib/config.mk.in
htslib/configure
htslib/errmod.c
htslib/faidx.c
htslib/hfile.c
htslib/hfile_gcs.c
htslib/hfile_internal.h
htslib/hfile_libcurl.c
htslib/hfile_net.c
htslib/hfile_s3.c
htslib/hts.c
htslib/hts_internal.h
htslib/htsfile.c
htslib/htslib_vars.mk
htslib/kfunc.c
htslib/knetfile.c
htslib/kstring.c
htslib/md5.c
htslib/multipart.c
htslib/plugin.c
htslib/probaln.c
htslib/realn.c
htslib/regidx.c
htslib/sam.c
htslib/synced_bcf_reader.c
htslib/tabix.c
htslib/tbx.c
htslib/textutils.c
htslib/thread_pool.c
htslib/thread_pool_internal.h
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_external.c
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/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/vlen.c
htslib/cram/vlen.h
htslib/cram/zfio.c
htslib/cram/zfio.h
htslib/htslib/bgzf.h
htslib/htslib/cram.h
htslib/htslib/faidx.h
htslib/htslib/hfile.h
htslib/htslib/hts.h
htslib/htslib/hts_defs.h
htslib/htslib/hts_endian.h
htslib/htslib/kbitset.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/thread_pool.h
htslib/htslib/vcf.h
htslib/htslib/vcf_sweep.h
htslib/htslib/vcfutils.h
pysam/Pileup.py
pysam/__init__.py
pysam/bcftools.py
pysam/cbcftools_util.h
pysam/config.py
pysam/csamtools_util.c
pysam/csamtools_util.h
pysam/htslib_util.c
pysam/htslib_util.h
pysam/libcalignedsegment.c
pysam/libcalignedsegment.pxd
pysam/libcalignedsegment.pyx
pysam/libcalignmentfile.c
pysam/libcalignmentfile.pxd
pysam/libcalignmentfile.pyx
pysam/libcbcf.c
pysam/libcbcf.pxd
pysam/libcbcf.pyx
pysam/libcbcftools.c
pysam/libcbcftools.pxd
pysam/libcbcftools.pyx
pysam/libcbgzf.c
pysam/libcbgzf.pyx
pysam/libcfaidx.c
pysam/libcfaidx.pxd
pysam/libcfaidx.pyx
pysam/libchtslib.c
pysam/libchtslib.pxd
pysam/libchtslib.pyx
pysam/libcsamfile.c
pysam/libcsamfile.pxd
pysam/libcsamfile.pyx
pysam/libcsamtools.c
pysam/libcsamtools.pxd
pysam/libcsamtools.pyx
pysam/libctabix.c
pysam/libctabix.pxd
pysam/libctabix.pyx
pysam/libctabixproxies.c
pysam/libctabixproxies.pxd
pysam/libctabixproxies.pyx
pysam/libcutils.c
pysam/libcutils.pxd
pysam/libcutils.pyx
pysam/libcvcf.c
pysam/libcvcf.pxd
pysam/libcvcf.pyx
pysam/namedtuple.py
pysam/pysam_stream.h
pysam/pysam_util.c
pysam/pysam_util.h
pysam/samfile_util.c
pysam/samfile_util.h
pysam/samtools.py
pysam/tabix_util.c
pysam/tabix_util.h
pysam/utils.py
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_addrprg.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_quickcheck.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/bamshuf.c.pysam.c
samtools/bamtk.c.pysam.c
samtools/bedcov.c.pysam.c
samtools/bedidx.c.pysam.c
samtools/cut_target.c.pysam.c
samtools/dict.c.pysam.c
samtools/faidx.c.pysam.c
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_opts.c.pysam.c
samtools/sam_opts.h
samtools/sam_utils.c.pysam.c
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/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/StreamFiledescriptors_test.py
tests/TestUtils.py
tests/VariantFile_test.py
tests/compile_test.py
tests/faidx_test.py
tests/samtools_test.py
tests/tabix_test.py
tests/test_samtools_python.py
tests/x.py
tests/x2.py
tests/x3.py