AUTHORS
COPYING
INSTALL
MANIFEST.in
NEWS
README.rst
pyproject.toml
requirements-dev.txt
setup.cfg
setup.py
bcftools/HMM.c
bcftools/HMM.c.pysam.c
bcftools/HMM.h
bcftools/LICENSE
bcftools/README
bcftools/abuf.c
bcftools/abuf.c.pysam.c
bcftools/abuf.h
bcftools/bam2bcf.c
bcftools/bam2bcf.c.pysam.c
bcftools/bam2bcf.h
bcftools/bam2bcf_edlib.c
bcftools/bam2bcf_edlib.c.pysam.c
bcftools/bam2bcf_iaux.c
bcftools/bam2bcf_iaux.c.pysam.c
bcftools/bam2bcf_indel.c
bcftools/bam2bcf_indel.c.pysam.c
bcftools/bam_sample.c
bcftools/bam_sample.c.pysam.c
bcftools/bam_sample.h
bcftools/bcftools.h
bcftools/bcftools.pysam.c
bcftools/bcftools.pysam.h
bcftools/bin.c
bcftools/bin.c.pysam.c
bcftools/bin.h
bcftools/call.h
bcftools/ccall.c
bcftools/ccall.c.pysam.c
bcftools/cigar_state.h
bcftools/cols.c
bcftools/cols.c.pysam.c
bcftools/cols.h
bcftools/consensus.c
bcftools/consensus.c.pysam.c
bcftools/convert.c
bcftools/convert.c.pysam.c
bcftools/convert.h
bcftools/csq.c
bcftools/csq.c.pysam.c
bcftools/dbuf.h
bcftools/dist.c
bcftools/dist.c.pysam.c
bcftools/dist.h
bcftools/edlib.c
bcftools/edlib.c.pysam.c
bcftools/edlib.h
bcftools/em.c
bcftools/em.c.pysam.c
bcftools/extsort.c
bcftools/extsort.c.pysam.c
bcftools/extsort.h
bcftools/filter.c
bcftools/filter.c.pysam.c
bcftools/filter.h
bcftools/gff.c
bcftools/gff.c.pysam.c
bcftools/gff.h
bcftools/gvcf.c
bcftools/gvcf.c.pysam.c
bcftools/gvcf.h
bcftools/hclust.c
bcftools/hclust.c.pysam.c
bcftools/hclust.h
bcftools/hex.h
bcftools/khash_str2str.h
bcftools/kheap.h
bcftools/kmin.c
bcftools/kmin.c.pysam.c
bcftools/kmin.h
bcftools/main.c
bcftools/main.c.pysam.c
bcftools/mcall.c
bcftools/mcall.c.pysam.c
bcftools/mpileup.c
bcftools/mpileup.c.pysam.c
bcftools/mw.h
bcftools/ploidy.c
bcftools/ploidy.c.pysam.c
bcftools/ploidy.h
bcftools/prob1.c
bcftools/prob1.c.pysam.c
bcftools/prob1.h
bcftools/rbuf.h
bcftools/read_consensus.c
bcftools/read_consensus.c.pysam.c
bcftools/read_consensus.h
bcftools/regidx.c
bcftools/regidx.c.pysam.c
bcftools/regidx.h
bcftools/reheader.c
bcftools/reheader.c.pysam.c
bcftools/smpl_ilist.c
bcftools/smpl_ilist.c.pysam.c
bcftools/smpl_ilist.h
bcftools/str_finder.c
bcftools/str_finder.c.pysam.c
bcftools/str_finder.h
bcftools/tabix.c
bcftools/tabix.c.pysam.c
bcftools/tsv2vcf.c
bcftools/tsv2vcf.c.pysam.c
bcftools/tsv2vcf.h
bcftools/utlist.h
bcftools/variantkey.h
bcftools/vcfannotate.c
bcftools/vcfannotate.c.pysam.c
bcftools/vcfbuf.c
bcftools/vcfbuf.c.pysam.c
bcftools/vcfbuf.h
bcftools/vcfcall.c
bcftools/vcfcall.c.pysam.c
bcftools/vcfcnv.c
bcftools/vcfcnv.c.pysam.c
bcftools/vcfconcat.c
bcftools/vcfconcat.c.pysam.c
bcftools/vcfconvert.c
bcftools/vcfconvert.c.pysam.c
bcftools/vcffilter.c
bcftools/vcffilter.c.pysam.c
bcftools/vcfgtcheck.c
bcftools/vcfgtcheck.c.pysam.c
bcftools/vcfhead.c
bcftools/vcfhead.c.pysam.c
bcftools/vcfindex.c
bcftools/vcfindex.c.pysam.c
bcftools/vcfisec.c
bcftools/vcfisec.c.pysam.c
bcftools/vcfmerge.c
bcftools/vcfmerge.c.pysam.c
bcftools/vcfnorm.c
bcftools/vcfnorm.c.pysam.c
bcftools/vcfplugin.c
bcftools/vcfplugin.c.pysam.c
bcftools/vcfquery.c
bcftools/vcfquery.c.pysam.c
bcftools/vcfroh.c
bcftools/vcfroh.c.pysam.c
bcftools/vcfsom.c
bcftools/vcfsom.c.pysam.c
bcftools/vcfsort.c
bcftools/vcfsort.c.pysam.c
bcftools/vcfstats.c
bcftools/vcfstats.c.pysam.c
bcftools/vcfview.c
bcftools/vcfview.c.pysam.c
bcftools/vcmp.c
bcftools/vcmp.c.pysam.c
bcftools/vcmp.h
bcftools/version.c
bcftools/version.c.pysam.c
bcftools/version.sh
doc/Makefile
doc/api.rst
doc/benchmarking.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/requirements-rtd.txt
doc/usage.rst
htslib/LICENSE
htslib/Makefile
htslib/README
htslib/bcf_sr_sort.c
htslib/bcf_sr_sort.h
htslib/bgzf.c
htslib/builddir_vars.mk.in
htslib/config.guess
htslib/config.h.in
htslib/config.mk.in
htslib/config.sub
htslib/configure
htslib/configure.ac
htslib/errmod.c
htslib/faidx.c
htslib/fuzz_settings.h
htslib/header.c
htslib/header.h
htslib/hfile.c
htslib/hfile_gcs.c
htslib/hfile_internal.h
htslib/hfile_libcurl.c
htslib/hfile_s3.c
htslib/hfile_s3_write.c
htslib/hts.c
htslib/hts_expr.c
htslib/hts_internal.h
htslib/hts_os.c
htslib/hts_time_funcs.h
htslib/htscodecs_bundled.mk
htslib/htscodecs_external.mk
htslib/htslib.mk
htslib/htslib.pc.in
htslib/htslib_vars.mk
htslib/kfunc.c
htslib/kstring.c
htslib/md5.c
htslib/multipart.c
htslib/plugin.c
htslib/probaln.c
htslib/realn.c
htslib/regidx.c
htslib/region.c
htslib/sam.c
htslib/sam_internal.h
htslib/sam_mods.c
htslib/simd.c
htslib/synced_bcf_reader.c
htslib/tbx.c
htslib/textutils.c
htslib/textutils_internal.h
htslib/thread_pool.c
htslib/thread_pool_internal.h
htslib/vcf.c
htslib/vcf_sweep.c
htslib/vcfutils.c
htslib/version.sh
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.h
htslib/cram/cram_stats.c
htslib/cram/cram_stats.h
htslib/cram/cram_structs.h
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/string_alloc.c
htslib/cram/string_alloc.h
htslib/htscodecs/htscodecs/arith_dynamic.c
htslib/htscodecs/htscodecs/arith_dynamic.h
htslib/htscodecs/htscodecs/c_range_coder.h
htslib/htscodecs/htscodecs/c_simple_model.h
htslib/htscodecs/htscodecs/fqzcomp_qual.c
htslib/htscodecs/htscodecs/fqzcomp_qual.h
htslib/htscodecs/htscodecs/htscodecs.c
htslib/htscodecs/htscodecs/htscodecs.h
htslib/htscodecs/htscodecs/htscodecs_endian.h
htslib/htscodecs/htscodecs/pack.c
htslib/htscodecs/htscodecs/pack.h
htslib/htscodecs/htscodecs/permute.h
htslib/htscodecs/htscodecs/pooled_alloc.h
htslib/htscodecs/htscodecs/rANS_byte.h
htslib/htscodecs/htscodecs/rANS_static.c
htslib/htscodecs/htscodecs/rANS_static.h
htslib/htscodecs/htscodecs/rANS_static16_int.h
htslib/htscodecs/htscodecs/rANS_static32x16pr.c
htslib/htscodecs/htscodecs/rANS_static32x16pr.h
htslib/htscodecs/htscodecs/rANS_static32x16pr_avx2.c
htslib/htscodecs/htscodecs/rANS_static32x16pr_avx512.c
htslib/htscodecs/htscodecs/rANS_static32x16pr_neon.c
htslib/htscodecs/htscodecs/rANS_static32x16pr_sse4.c
htslib/htscodecs/htscodecs/rANS_static4x16.h
htslib/htscodecs/htscodecs/rANS_static4x16pr.c
htslib/htscodecs/htscodecs/rANS_word.h
htslib/htscodecs/htscodecs/rle.c
htslib/htscodecs/htscodecs/rle.h
htslib/htscodecs/htscodecs/tokenise_name3.c
htslib/htscodecs/htscodecs/tokenise_name3.h
htslib/htscodecs/htscodecs/utils.c
htslib/htscodecs/htscodecs/utils.h
htslib/htscodecs/htscodecs/varint.h
htslib/htscodecs/htscodecs/varint2.h
htslib/htscodecs/htscodecs/version.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/hts_expr.h
htslib/htslib/hts_log.h
htslib/htslib/hts_os.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/kroundup.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
htslib/m4/hts_check_compile_flags_needed.m4
htslib/m4/hts_hide_dynamic_syms.m4
htslib/m4/hts_prog_cc_warnings.m4
htslib/m4/pkg.m4
htslib/os/lzma_stub.h
htslib/os/rand.c
pysam/Pileup.py
pysam/__init__.py
pysam/bcftools.py
pysam/cbcftools_util.h
pysam/csamtools_util.h
pysam/htslib_util.c
pysam/htslib_util.h
pysam/libcalignedsegment.pxd
pysam/libcalignedsegment.pyi
pysam/libcalignedsegment.pyx
pysam/libcalignmentfile.pxd
pysam/libcalignmentfile.pyi
pysam/libcalignmentfile.pyx
pysam/libcbcf.pxd
pysam/libcbcf.pyi
pysam/libcbcf.pyx
pysam/libcbcftools.pxd
pysam/libcbcftools.pyi
pysam/libcbcftools.pyx
pysam/libcbgzf.pxd
pysam/libcbgzf.pyi
pysam/libcbgzf.pyx
pysam/libcfaidx.pxd
pysam/libcfaidx.pyi
pysam/libcfaidx.pyx
pysam/libchtslib.pxd
pysam/libchtslib.pyi
pysam/libchtslib.pyx
pysam/libcsamfile.pxd
pysam/libcsamfile.pyi
pysam/libcsamfile.pyx
pysam/libcsamtools.pxd
pysam/libcsamtools.pyi
pysam/libcsamtools.pyx
pysam/libctabix.pxd
pysam/libctabix.pyi
pysam/libctabix.pyx
pysam/libctabixproxies.pxd
pysam/libctabixproxies.pyi
pysam/libctabixproxies.pyx
pysam/libcutils.pxd
pysam/libcutils.pyi
pysam/libcutils.pyx
pysam/libcvcf.pxd
pysam/libcvcf.pyi
pysam/libcvcf.pyx
pysam/py.typed
pysam/pysam_stream.h
pysam/pysam_util.c
pysam/pysam_util.h
pysam/samtools.py
pysam/utils.py
pysam/version.h
pysam/version.py
pysam/version.pyi
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/LICENSE
samtools/README
samtools/amplicon_stats.c
samtools/amplicon_stats.c.pysam.c
samtools/bam.c
samtools/bam.c.pysam.c
samtools/bam.h
samtools/bam2depth.c
samtools/bam2depth.c.pysam.c
samtools/bam_addrprg.c
samtools/bam_addrprg.c.pysam.c
samtools/bam_ampliconclip.c
samtools/bam_ampliconclip.c.pysam.c
samtools/bam_ampliconclip.h
samtools/bam_aux.c
samtools/bam_aux.c.pysam.c
samtools/bam_cat.c
samtools/bam_cat.c.pysam.c
samtools/bam_color.c
samtools/bam_color.c.pysam.c
samtools/bam_consensus.c
samtools/bam_consensus.c.pysam.c
samtools/bam_fastq.c
samtools/bam_fastq.c.pysam.c
samtools/bam_flags.c
samtools/bam_flags.c.pysam.c
samtools/bam_import.c
samtools/bam_import.c.pysam.c
samtools/bam_index.c
samtools/bam_index.c.pysam.c
samtools/bam_lpileup.c
samtools/bam_lpileup.c.pysam.c
samtools/bam_lpileup.h
samtools/bam_markdup.c
samtools/bam_markdup.c.pysam.c
samtools/bam_mate.c
samtools/bam_mate.c.pysam.c
samtools/bam_md.c
samtools/bam_md.c.pysam.c
samtools/bam_plbuf.c
samtools/bam_plbuf.c.pysam.c
samtools/bam_plbuf.h
samtools/bam_plcmd.c
samtools/bam_plcmd.c.pysam.c
samtools/bam_quickcheck.c
samtools/bam_quickcheck.c.pysam.c
samtools/bam_reheader.c
samtools/bam_reheader.c.pysam.c
samtools/bam_rmdup.c
samtools/bam_rmdup.c.pysam.c
samtools/bam_rmdupse.c
samtools/bam_rmdupse.c.pysam.c
samtools/bam_samples.c
samtools/bam_samples.c.pysam.c
samtools/bam_sort.c
samtools/bam_sort.c.pysam.c
samtools/bam_split.c
samtools/bam_split.c.pysam.c
samtools/bam_stat.c
samtools/bam_stat.c.pysam.c
samtools/bamshuf.c
samtools/bamshuf.c.pysam.c
samtools/bamtk.c
samtools/bamtk.c.pysam.c
samtools/bedcov.c
samtools/bedcov.c.pysam.c
samtools/bedidx.c
samtools/bedidx.c.pysam.c
samtools/bedidx.h
samtools/consensus_pileup.c
samtools/consensus_pileup.c.pysam.c
samtools/consensus_pileup.h
samtools/coverage.c
samtools/coverage.c.pysam.c
samtools/cram_size.c
samtools/cram_size.c.pysam.c
samtools/cut_target.c
samtools/cut_target.c.pysam.c
samtools/dict.c
samtools/dict.c.pysam.c
samtools/faidx.c
samtools/faidx.c.pysam.c
samtools/padding.c
samtools/padding.c.pysam.c
samtools/phase.c
samtools/phase.c.pysam.c
samtools/reference.c
samtools/reference.c.pysam.c
samtools/reset.c
samtools/reset.c.pysam.c
samtools/sam_opts.c
samtools/sam_opts.c.pysam.c
samtools/sam_opts.h
samtools/sam_utils.c
samtools/sam_utils.c.pysam.c
samtools/sam_utils.h
samtools/sam_view.c
samtools/sam_view.c.pysam.c
samtools/sample.c
samtools/sample.c.pysam.c
samtools/sample.h
samtools/samtools.h
samtools/samtools.pysam.c
samtools/samtools.pysam.h
samtools/splaysort.h
samtools/stats.c
samtools/stats.c.pysam.c
samtools/stats_isize.c
samtools/stats_isize.c.pysam.c
samtools/stats_isize.h
samtools/tmp_file.c
samtools/tmp_file.c.pysam.c
samtools/tmp_file.h
samtools/version.sh
samtools/lz4/LICENSE
samtools/lz4/lz4.c
samtools/lz4/lz4.c.pysam.c
samtools/lz4/lz4.h
win32/getopt.c
win32/getopt.h
win32/stdint.h
win32/unistd.h