CHANGES.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
cyvcf2/__init__.py
cyvcf2/__main__.py
cyvcf2/cli.py
cyvcf2/cyvcf2.c
cyvcf2/cyvcf2.pxd
cyvcf2/cyvcf2.pyx
cyvcf2/helpers.c
cyvcf2/helpers.h
cyvcf2/relatedness.h
cyvcf2.egg-info/PKG-INFO
cyvcf2.egg-info/SOURCES.txt
cyvcf2.egg-info/dependency_links.txt
cyvcf2.egg-info/entry_points.txt
cyvcf2.egg-info/not-zip-safe
cyvcf2.egg-info/requires.txt
cyvcf2.egg-info/top_level.txt
htslib/LICENSE
htslib/Makefile
htslib/README
htslib/annot-tsv.c
htslib/bcf_sr_sort.c
htslib/bcf_sr_sort.h
htslib/bgzf.c
htslib/bgzip.c
htslib/builddir_vars.mk.in
htslib/config.mk.in
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/htsfile.c
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/synced_bcf_reader.c
htslib/tabix.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/htscodecs/tests/arith_dynamic_fuzz.c
htslib/htscodecs/tests/arith_dynamic_test.c
htslib/htscodecs/tests/entropy.c
htslib/htscodecs/tests/entropy_fuzz.c
htslib/htscodecs/tests/fqzcomp_qual_fuzz.c
htslib/htscodecs/tests/fqzcomp_qual_fuzzrt.c
htslib/htscodecs/tests/fqzcomp_qual_test.c
htslib/htscodecs/tests/rANS_static4x16pr_fuzz.c
htslib/htscodecs/tests/rANS_static4x16pr_test.c
htslib/htscodecs/tests/rANS_static_fuzz.c
htslib/htscodecs/tests/rANS_static_test.c
htslib/htscodecs/tests/tokenise_name3_fuzz.c
htslib/htscodecs/tests/tokenise_name3_fuzzrt.c
htslib/htscodecs/tests/tokenise_name3_test.c
htslib/htscodecs/tests/varint_test.c
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
htslib/samples/add_header.c
htslib/samples/cram.c
htslib/samples/dump_aux.c
htslib/samples/flags_demo.c
htslib/samples/flags_htsopt_field.c
htslib/samples/index_multireg_read.c
htslib/samples/index_reg_read.c
htslib/samples/index_write.c
htslib/samples/mod_aux.c
htslib/samples/mod_aux_ba.c
htslib/samples/mod_bam.c
htslib/samples/modstate.c
htslib/samples/mpileup.c
htslib/samples/pileup.c
htslib/samples/pileup_mod.c
htslib/samples/read_aux.c
htslib/samples/read_bam.c
htslib/samples/read_fast.c
htslib/samples/read_header.c
htslib/samples/read_refname.c
htslib/samples/rem_header.c
htslib/samples/split.c
htslib/samples/split2.c
htslib/samples/split_thread1.c
htslib/samples/split_thread2.c
htslib/samples/update_header.c
htslib/samples/write_fast.c
htslib/test/fieldarith.c
htslib/test/hfile.c
htslib/test/hts_endian.c
htslib/test/pileup.c
htslib/test/pileup_mod.c
htslib/test/plugins-dlhts.c
htslib/test/sam.c
htslib/test/test-bcf-sr.c
htslib/test/test-bcf-translate.c
htslib/test/test-bcf_set_variant_type.c
htslib/test/test-parse-reg.c
htslib/test/test-regidx.c
htslib/test/test-vcf-api.c
htslib/test/test-vcf-sweep.c
htslib/test/test_bgzf.c
htslib/test/test_expr.c
htslib/test/test_faidx.c
htslib/test/test_index.c
htslib/test/test_introspection.c
htslib/test/test_kfunc.c
htslib/test/test_kstring.c
htslib/test/test_mod.c
htslib/test/test_realn.c
htslib/test/test_str2int.c
htslib/test/test_time_funcs.c
htslib/test/test_view.c
htslib/test/thrash_threads1.c
htslib/test/thrash_threads2.c
htslib/test/thrash_threads3.c
htslib/test/thrash_threads4.c
htslib/test/thrash_threads5.c
htslib/test/thrash_threads6.c
htslib/test/thrash_threads7.c
htslib/test/fuzz/hts_open_fuzzer.c