├── Boucher ├── README └── bnx_to_rmm │ ├── Makefile │ ├── readme │ └── src │ └── bnx_to_rmm.cpp ├── Core ├── Format-description.md ├── Generic-tools.md ├── Library-interface.md ├── Makefile ├── ONE.md ├── ONElib.c ├── ONElib.h ├── ONEstat.c ├── ONEview.c ├── test.aln ├── utils.c └── utils.h ├── Durbin └── Makefile ├── LICENSE ├── Makefile ├── Myers ├── CHECK ├── Dazz2pbr.c ├── Dazz2sxs.c ├── LIBDEFLATE │ ├── .cirrus.yml │ ├── .travis.yml │ ├── COPYING │ ├── Makefile │ ├── Makefile.msc │ ├── NEWS │ ├── README.md │ ├── common │ │ ├── common_defs.h │ │ ├── compiler_gcc.h │ │ └── compiler_msc.h │ ├── lib │ │ ├── adler32.c │ │ ├── adler32_vec_template.h │ │ ├── aligned_malloc.c │ │ ├── aligned_malloc.h │ │ ├── arm │ │ │ ├── adler32_impl.h │ │ │ ├── cpu_features.c │ │ │ ├── cpu_features.h │ │ │ ├── crc32_impl.h │ │ │ └── matchfinder_impl.h │ │ ├── bt_matchfinder.h │ │ ├── crc32.c │ │ ├── crc32_table.h │ │ ├── crc32_vec_template.h │ │ ├── decompress_template.h │ │ ├── deflate_compress.c │ │ ├── deflate_compress.h │ │ ├── deflate_constants.h │ │ ├── deflate_decompress.c │ │ ├── gzip_compress.c │ │ ├── gzip_constants.h │ │ ├── gzip_decompress.c │ │ ├── hc_matchfinder.h │ │ ├── lib_common.h │ │ ├── matchfinder_common.h │ │ ├── unaligned.h │ │ ├── x86 │ │ │ ├── adler32_impl.h │ │ │ ├── cpu_features.c │ │ │ ├── cpu_features.h │ │ │ ├── crc32_impl.h │ │ │ ├── crc32_pclmul_template.h │ │ │ ├── decompress_impl.h │ │ │ └── matchfinder_impl.h │ │ ├── zlib_compress.c │ │ ├── zlib_constants.h │ │ └── zlib_decompress.c │ ├── libdeflate.h │ ├── programs │ │ ├── benchmark.c │ │ ├── checksum.c │ │ ├── detect.sh │ │ ├── gzip.c │ │ ├── prog_util.c │ │ ├── prog_util.h │ │ ├── test_checksums.c │ │ ├── test_incomplete_codes.c │ │ ├── test_slow_decompression.c │ │ ├── test_util.c │ │ ├── test_util.h │ │ └── tgetopt.c │ └── tools │ │ ├── afl-fuzz │ │ ├── Makefile │ │ ├── deflate_compress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ │ └── 0 │ │ ├── deflate_decompress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ │ └── 0 │ │ ├── gzip_decompress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ │ └── 0 │ │ ├── prepare_for_fuzz.sh │ │ └── zlib_decompress │ │ │ ├── fuzz.c │ │ │ └── inputs │ │ │ └── 0 │ │ ├── android_build.sh │ │ ├── checksum_benchmarks.sh │ │ ├── exec_tests.sh │ │ ├── gen_crc32_multipliers.c │ │ ├── gen_crc32_table.c │ │ ├── gzip_tests.sh │ │ ├── make-windows-releases │ │ ├── mips_build.sh │ │ ├── msc_test.bat │ │ ├── pgo_build.sh │ │ ├── produce_gzip_benchmark_table.sh │ │ ├── run_tests.sh │ │ └── windows_build.sh ├── LICENSE ├── Makefile ├── ONElib.c ├── ONElib.h ├── VGP_1_1.def ├── VGPcloud.c ├── VGPpacbio.c ├── VGPpair.c ├── VGPpipe.c ├── VGPschema.h ├── VGPseq.c ├── VGPsimPB.c ├── VGPzip.c ├── cdf.c ├── cdf.h ├── compression.c ├── compression.h ├── frag.c ├── gene_core.c ├── gene_core.h ├── lsd.sort.c ├── lsd.sort.h ├── msd.sort.c ├── msd.sort.h ├── pb_expr.c └── pb_expr.h ├── README.md └── VGP ├── Dazz2pbr.c ├── Dazz2sxs.c ├── HTSLIB ├── INSTALL ├── LICENSE ├── Makefile ├── NEWS ├── README ├── README.large_positions.md ├── aclocal.m4 ├── bcf_sr_sort.c ├── bcf_sr_sort.h ├── bgzf.c ├── bgzip.1 ├── bgzip.c ├── config.h ├── config.mk.in ├── configure.ac ├── cram │ ├── cram.h │ ├── cram_codecs.c │ ├── cram_codecs.h │ ├── cram_decode.c │ ├── cram_decode.h │ ├── cram_encode.c │ ├── cram_encode.h │ ├── cram_external.c │ ├── cram_index.c │ ├── cram_index.h │ ├── cram_io.c │ ├── cram_io.h │ ├── cram_samtools.c │ ├── cram_samtools.h │ ├── cram_stats.c │ ├── cram_stats.h │ ├── cram_structs.h │ ├── mFILE.c │ ├── mFILE.h │ ├── misc.h │ ├── open_trace_file.c │ ├── open_trace_file.h │ ├── os.h │ ├── pooled_alloc.c │ ├── pooled_alloc.h │ ├── rANS_byte.h │ ├── rANS_static.c │ ├── rANS_static.h │ ├── string_alloc.c │ └── string_alloc.h ├── errmod.c ├── faidx.5 ├── faidx.c ├── header.c ├── header.h ├── hfile.c ├── hfile_gcs.c ├── hfile_internal.h ├── hfile_libcurl.c ├── hfile_net.c ├── hfile_s3.c ├── hfile_s3_write.c ├── hts.c ├── hts_internal.h ├── hts_os.c ├── htsfile.1 ├── htsfile.c ├── htslib-s3-plugin.7 ├── htslib-uninstalled.pc ├── htslib.mk ├── htslib.pc.in ├── htslib.pc.tmp ├── htslib │ ├── bgzf.h │ ├── cram.h │ ├── faidx.h │ ├── hfile.h │ ├── hts.h │ ├── hts_defs.h │ ├── hts_endian.h │ ├── hts_log.h │ ├── hts_os.h │ ├── kbitset.h │ ├── kfunc.h │ ├── khash.h │ ├── khash_str2int.h │ ├── klist.h │ ├── knetfile.h │ ├── kroundup.h │ ├── kseq.h │ ├── ksort.h │ ├── kstring.h │ ├── regidx.h │ ├── sam.h │ ├── synced_bcf_reader.h │ ├── tbx.h │ ├── thread_pool.h │ ├── vcf.h │ ├── vcf_sweep.h │ └── vcfutils.h ├── htslib_static.mk ├── htslib_vars.mk ├── kfunc.c ├── knetfile.c ├── kstring.c ├── m4 │ ├── hts_hide_dynamic_syms.m4 │ └── hts_prog_cc_warnings.m4 ├── md5.c ├── multipart.c ├── os │ ├── lzma_stub.h │ └── rand.c ├── plugin.c ├── probaln.c ├── realn.c ├── regidx.c ├── region.c ├── sam.5 ├── sam.c ├── sam_internal.h ├── synced_bcf_reader.c ├── tabix.1 ├── tabix.c ├── tbx.c ├── test │ ├── auxf#values.sam │ ├── auxf#values_java.cram │ ├── auxf.fa │ ├── auxf.fa.fai │ ├── bgziptest.txt │ ├── bgziptest.txt.gz │ ├── bgziptest.txt.gz.gzi │ ├── c1#bounds.sam │ ├── c1#clip.sam │ ├── c1#noseq.sam │ ├── c1#pad1.sam │ ├── c1#pad2.sam │ ├── c1#pad3.sam │ ├── c1#unknown.sam │ ├── c1.fa │ ├── c1.fa.fai │ ├── c2#pad.sam │ ├── c2.fa │ ├── c2.fa.fai │ ├── ce#1.sam │ ├── ce#1000.sam │ ├── ce#2.sam │ ├── ce#5.sam │ ├── ce#5b.sam │ ├── ce#5b_java.cram │ ├── ce#large_seq.sam │ ├── ce#supp.sam │ ├── ce#tag_depadded.sam │ ├── ce#tag_padded.sam │ ├── ce#unmap.sam │ ├── ce#unmap1.sam │ ├── ce#unmap2.sam │ ├── ce.fa │ ├── ce.fa.fai │ ├── colons.bam │ ├── colons.bam.bai │ ├── compare_sam.pl │ ├── cross_validate.sh │ ├── emptyfile │ ├── faidx.fa │ ├── fastqs.fq │ ├── fastqs_README.txt │ ├── fieldarith.c │ ├── fieldarith.sam │ ├── formatcols.vcf │ ├── formatmissing-out.vcf │ ├── formatmissing.vcf │ ├── fuzz │ │ └── hts_open_fuzzer.c │ ├── header_syms.pl │ ├── hfile.c │ ├── hts_endian.c │ ├── index.bam.bai │ ├── index.bam.csi │ ├── index.bcf.csi │ ├── index.cram.crai │ ├── index.sam │ ├── index.sam.gz.bai │ ├── index.sam.gz.csi │ ├── index.vcf │ ├── index.vcf.gz.csi │ ├── index.vcf.gz.tbi │ ├── longrefs │ │ ├── index.expected1.vcf │ │ ├── index.expected2.vcf │ │ ├── index.vcf │ │ ├── longref.sam │ │ ├── longref_itr.expected.sam │ │ └── longref_multi.expected.sam │ ├── maintainer │ │ ├── check_copyright.pl │ │ └── check_spaces.pl │ ├── md#1.sam │ ├── md.fa │ ├── md.fa.fai │ ├── mpileup │ │ ├── c1#pad1.out │ │ ├── c1#pad1.sam │ │ ├── c1#pad2.out │ │ ├── c1#pad2.sam │ │ ├── c1#pad3.out │ │ ├── c1#pad3.sam │ │ ├── mp_D.out │ │ ├── mp_D.sam │ │ ├── mp_DI.out │ │ ├── mp_DI.sam │ │ ├── mp_I.out │ │ ├── mp_I.sam │ │ ├── mp_ID.out │ │ ├── mp_ID.sam │ │ ├── mp_N.out │ │ ├── mp_N.sam │ │ ├── mp_N2.out │ │ ├── mp_N2.sam │ │ ├── mp_P.out │ │ ├── mp_P.sam │ │ ├── mpileup.tst │ │ ├── small.bam │ │ ├── small.out │ │ └── test-pileup.sh │ ├── no_hdr_sq_1.bam │ ├── no_hdr_sq_1.bam.csi │ ├── no_hdr_sq_1.expected.sam │ ├── noroundtrip-out.vcf │ ├── noroundtrip.vcf │ ├── pileup.c │ ├── range.bam │ ├── range.bam.bai │ ├── range.cram │ ├── range.cram.crai │ ├── range.out │ ├── realn01.fa │ ├── realn01.fa.fai │ ├── realn01.sam │ ├── realn01_exp-a.sam │ ├── realn01_exp-e.sam │ ├── realn01_exp.sam │ ├── realn02-r.sam │ ├── realn02.fa │ ├── realn02.fa.fai │ ├── realn02.sam │ ├── realn02_exp-a.sam │ ├── realn02_exp-e.sam │ ├── realn02_exp.sam │ ├── sam.c │ ├── simple_test_driver.sh │ ├── tabix.out │ ├── tabix │ │ ├── bed_file.Y.100200.out │ │ ├── bed_file.bed │ │ ├── gff_file.X.2934832.2935190.out │ │ ├── gff_file.gff │ │ ├── large_chr.20.1.2147483647.out │ │ ├── large_chr.vcf │ │ ├── tabix.tst │ │ ├── test-tabix.sh │ │ ├── vcf_file.1.3000151.out │ │ ├── vcf_file.2.3199812.out │ │ ├── vcf_file.bcf │ │ └── vcf_file.vcf │ ├── test-bcf-sr.c │ ├── test-bcf-sr.pl │ ├── test-bcf-translate.c │ ├── test-bcf-translate.out │ ├── test-logging.pl │ ├── test-parse-reg.c │ ├── test-regidx.c │ ├── test-vcf-api.c │ ├── test-vcf-api.out │ ├── test-vcf-hdr-in.vcf │ ├── test-vcf-hdr.out │ ├── test-vcf-sweep.c │ ├── test-vcf-sweep.out │ ├── test.pl │ ├── test_bgzf.c │ ├── test_index.c │ ├── test_kstring.c │ ├── test_realn.c │ ├── test_str2int.c │ ├── test_view.c │ ├── thrash_threads1.c │ ├── thrash_threads2.c │ ├── thrash_threads3.c │ ├── thrash_threads4.c │ ├── thrash_threads5.c │ ├── thrash_threads6.c │ ├── thrash_threads7.c │ ├── thread_pool.md │ ├── xx#MD.sam │ ├── xx#MD2.sam │ ├── xx#blank.sam │ ├── xx#large_aux.sam │ ├── xx#large_aux2.sam │ ├── xx#large_aux_java.cram │ ├── xx#minimal.sam │ ├── xx#pair.sam │ ├── xx#repeated.sam │ ├── xx#rg.sam │ ├── xx#tlen.sam │ ├── xx#tlen2.sam │ ├── xx#triplet.sam │ ├── xx#unsorted.sam │ ├── xx.fa │ └── xx.fa.fai ├── textutils.c ├── textutils_internal.h ├── thread_pool.c ├── thread_pool_internal.h ├── vcf.5 ├── vcf.c ├── vcf_sweep.c ├── vcfutils.c └── version.sh ├── LIBDEFLATE ├── .cirrus.yml ├── .travis.yml ├── COPYING ├── Makefile ├── Makefile.msc ├── NEWS ├── README.md ├── common │ ├── common_defs.h │ ├── compiler_gcc.h │ └── compiler_msc.h ├── lib │ ├── adler32.c │ ├── adler32_vec_template.h │ ├── aligned_malloc.c │ ├── aligned_malloc.h │ ├── arm │ │ ├── adler32_impl.h │ │ ├── cpu_features.c │ │ ├── cpu_features.h │ │ ├── crc32_impl.h │ │ └── matchfinder_impl.h │ ├── bt_matchfinder.h │ ├── crc32.c │ ├── crc32_table.h │ ├── crc32_vec_template.h │ ├── decompress_template.h │ ├── deflate_compress.c │ ├── deflate_compress.h │ ├── deflate_constants.h │ ├── deflate_decompress.c │ ├── gzip_compress.c │ ├── gzip_constants.h │ ├── gzip_decompress.c │ ├── hc_matchfinder.h │ ├── lib_common.h │ ├── matchfinder_common.h │ ├── unaligned.h │ ├── x86 │ │ ├── adler32_impl.h │ │ ├── cpu_features.c │ │ ├── cpu_features.h │ │ ├── crc32_impl.h │ │ ├── crc32_pclmul_template.h │ │ ├── decompress_impl.h │ │ └── matchfinder_impl.h │ ├── zlib_compress.c │ ├── zlib_constants.h │ └── zlib_decompress.c ├── libdeflate.h ├── programs │ ├── benchmark.c │ ├── checksum.c │ ├── detect.sh │ ├── 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