bd6cc26bd3222333378780a1738cebb5f3e14fb395e6e3e55c63c370278119cf 1998 DESCRIPTION
5909948fcd6808d12f09f2ea64d5b0a2e122b65f9494b8fd1b33c7338f57df25 150 INDEX
a2b86f5cdf2d6a344e20b05efff05a7bdf090cd3c99ff0b872d0c171b6b20997 321 Meta/Rd.rds
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6b65c92210ea014c885ab23e69a329ea21bc9e6cda035650300f8d1dad527753 83 NAMESPACE
4a0d1ca29303cac42c12d61eb764a475b8134405a45c17961d34d179c384ce8c 5693 NEWS
570ca456b280cdeb201ef5ebdf22dc8f80092e2c0c68e33c7f73340e420f3759 1058 R/Rhtslib
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48b3abb29fa4ec02cceecb2703b189ebf49f2b29383ef2a496d70fa4e7c85848 1767 include/bedidx.h
267e18aaf00e2646333357011ecc85d3866ae97db34705f360c9957be76917f2 16469 include/htslib/bgzf.h
d91d7e383d5dcbaedcaea054c5b816c32fdd7f630a37bf4cb381589ad0d59095 22175 include/htslib/cram.h
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3583420edd98ae2014183d1f1c6a8b0068a1124e4c91db7c30738fb06c629f7a 13351 include/htslib/hfile.h
f0f6c678d85feccfcfe3818a23d8f2f9ee47860537c21467c4683c62d9d03afe 57515 include/htslib/hts.h
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4db065dca43f85a9480c36efdce3c45ad92a0eb29e4a851e9f1417998a3de6be 3733 include/htslib/knetfile.h
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68d65002e6f7c32ee1293de41e7c0f97f44250dcb10144992153ffdf36181fa9 9224 include/htslib/kseq.h
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4db021a8b3077eee8dd39bb2ba06c1fed745e8ae367bdacb60fe097f6a914970 11462 include/htslib/kstring.h
97f1c5d0e52a059f591bf3b011bcd700df01be092633aaea825349d8b936ebb1 8881 include/htslib/regidx.h
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a78acf91e4a5c394233a2afdb98074df126d427844e5a695495172d6297c136c 16584 include/htslib/synced_bcf_reader.h
844aada4d07b38e246225c1ca99c57d4645095b30357082a468331b82791075c 4956 include/htslib/tbx.h
0d6fb8bc64f10b64295fa9a5a3e112d675003a7f244db3011d0f387f6324aa61 12747 include/htslib/thread_pool.h
9c92b26565b371edec43b01b656eafe6f9d91b80b57dbcdcf5c91041719c9198 68420 include/htslib/vcf.h
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760d2bb171df7069e842f34667226b38285df1a96438c2663ff938bf143a217c 4919 include/htslib/vcfutils.h
7b13b1480d843782c2c2d8ab9a988b461ec39011cd00b51f36456272438395fe 7011 include/sam_opts.c
23693013e68466ed9f02e680f9e5c7e95ee8bd06ac396b8b1c8f064ea51e7e0c 4122 include/sam_opts.h
b358340c8e51cfd35e38a51233265362b969e77caf523559fb36957def58c460 5823 include/sam_utils.c
0786df4f8361e0b63b30b7b74a26b872eea9b02dfd8f02e32be11ec25cf1c4cb 3350 include/sam_utils.h
643eda06f15258ab71a07a741e219bec63cb9bb0f29d60417c6d84a6da7bba4e 5923 include/samtools-1.7-compat.h
2cf764d310825fa5bd00ab9b027b743e21deea83fceab1b1ebf9ca7f85b9f8d2 2111 include/samtools.h
e70143c4e88a9efb9bb587887352612f322526b0e1d56d18a9250135c39773c4 849976 libs/Rhtslib.so
68eda67c6aca0addb4caa2210a0159116fbc2309fd35be108cf47fd1cf926a54 252 libs/symbols.rds
03f9187fc491a704f1b14442abf9e644ef4b9530dbfe62a22308e8ddcb2458c4 751 testdata/auxf#values.sam
e1885105587e59f3e268dfa401eee94ee4057d0accef0ba12b675a27aa092c05 5152 testdata/auxf#values_java.cram
f334eafb55fd48af94d12ceb96f41051d92b3863a2574c30d7594cce8cdd3ec9 29 testdata/auxf.fa
2544da2d952d843a2249d697b5f6b29e4563a7018fe3c3a141290cda973b55b0 18 testdata/auxf.fa.fai
377b09067b88791e8003580f7ac7097e207d2852a635b6482dd31cf43687dbec 148 testdata/c1#bounds.sam
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2d7aa56bdf27fab8615735561b1f9003d9d5351cdd4fa45eb08915a8136b081d 388 testdata/c1#pad1.sam
12e7ca182633b99ea11837410100458e4c343eb52f60c04381d70147cd0430a9 527 testdata/c1#pad2.sam
50aa193502390f97bda55adca62197f687e22e0162d5d916fd00ae75c4b52b7f 665 testdata/c1#pad3.sam
6464ca26e2708f7c6ee5602f7e534b6d7c1b3a77f2d6adfcdbf99ec8d4346300 429 testdata/c1#unknown.sam
1b683e5bc52ea60c21d29161a3ccce7a0d15ac1c927dbc00496bf6c5526dd360 15 testdata/c1.fa
8c0b6165b7bb7bf8eb02d6ec75ce5179974e3ca8f367ec72e78578fa0ee43e88 14 testdata/c1.fa.fai
e2347ae06a891cff70da48ed67ab69b35b97ee07a1d89a809412712a91936216 847 testdata/c2#pad.sam
ff2e023512e6c1bb1798db921bceb4ee99a3b9e0c789632d618e05f6c9912548 14 testdata/c2.fa
2c7cc327c3f3f854c8cd671fc3fd1ebaacff54b253cc8bc310d171965f9cbabc 12 testdata/c2.fa.fai
9aa68ce73f9317022da4ae14b82023cebec204df0aef72bf32d512a2322b48d7 341 testdata/ce#1.sam
2558a8bb8fa15001d9856b6c1a0b5f82ee71cb3a751183b49277cd1384f8d366 322632 testdata/ce#1000.sam
ba74ff7e13d31847018a20a5f18e193d138c806d9619009a59c292063c2ddcf7 645 testdata/ce#2.sam
eca6e1f8c99ed9bf38446142521283bde5d129262cc13f9e801a9648c7af27f3 1872 testdata/ce#5.sam
79312ce880070b9a4b193d4c989523626dda43e061211570faf8532ea690e87c 1836 testdata/ce#5b.sam
12bb51d85161f18136a4df5f6ad9565bd4148e1e01083a95c2d7a8242b1d75e2 6784 testdata/ce#5b_java.cram
71bd64a79379834bcae5d9bb10ba79cec76fbc626210d29d1379848ee1b1be91 2147244 testdata/ce#large_seq.sam
c39f6ee3a930c4e233eac05102d11a7d53021ad2ca963d495c38076cf8444a05 547 testdata/ce#supp.sam
ae7d6c811493a56646432ebe81d4c184bfd4d2e2d8de33479d2721831cd8198c 1638 testdata/ce#tag_depadded.sam
e9801a7438d61018ce0b3748b36f1e04f96756ead533b3f9140c80e95c9e11f5 1650 testdata/ce#tag_padded.sam
8d877799bf8324b98165d09971f2c75ad3e4f3ec34bad4da0f64acb73e19fa65 1325 testdata/ce#unmap.sam
4cf6da6d7c7df3c574afd7dc5f825da0a645d4991fefa8e70f54843b343d7bfe 2747 testdata/ce#unmap1.sam
ccd523651dba55c6bbbe7479edbc67327546ef39fa9b07d7a25d33f6bed91c20 5525 testdata/ce#unmap2.sam
5eca163c91918ada9774080ee2274208155f4d1b2d00700ee950cdd7b269508c 1060702 testdata/ce.fa
445a36da04b64dd49b8b964171c6d4b4cafc12e9bff50f8cf4ce33717fec6ff5 230 testdata/ce.fa.fai
c1fc34e4173ced07f48fa6f3fe23a7d352b0d7b93749330c0ce0f7074d60ea1d 268 testdata/colons.bam
b8b91517ee1bde7a0d98292cfbf391624367433084dec9e7fca9764fad098226 910 testdata/fieldarith.sam
16b9287d29aaeb250ad093725b5dcf7e9475980d663d1658ac83f820f1c62e0e 241 testdata/formatcols.vcf
f78b2bc15bf27eb2d56173422a841cd9e317f07cf5b58d3118084ab24debc8ba 226 testdata/formatmissing-out.vcf
f78b2bc15bf27eb2d56173422a841cd9e317f07cf5b58d3118084ab24debc8ba 226 testdata/formatmissing.vcf
59f9f23b27bb3e8338f505ae9454b1bc4973eb1ad3bc41e221856681176b842d 54185 testdata/index.sam
d99c0251010dae47b019b85bb732865fb910cb680e7b43ea3a4b49fcf8216304 68888 testdata/index.vcf
9742a10efc186f9c8a61407027df0ed98c18343e940c85e65342f9b9a040dd0f 477 testdata/index2.sam
219d679ae65543600a5a3bcc0a0bfa124cc00e1291fb94077752364ff2b06301 54375 testdata/index_dos.sam
9eff33ff57ed9092e13050e61b3755644ccf39acd73de6bb3a53006d3cf0f69d 1017 testdata/md#1.sam
f5ebe5af58147a2da1b9c3ca4a4c4b6462ad5c0cd7824260f20b559a03c4a956 45 testdata/md.fa
f9771a57e08d0f9a697401b3e0a0261c30d7966283c28622fea891271ce0f309 13 testdata/md.fa.fai
31dabb6356500423ffc3fc2c6f950995c2055558a996a6c40d52460a57cc1b00 148 testdata/modhdr.expected.vcf
47b5113176c53497eef038d5c519c6cee5911f28999aac3e96c3525fef03868f 1691 testdata/no_hdr_sq_1.bam
e5af156b315d4010b4ffcbcc305cdabeaedd4507065aaa0ec88bb1d16a3a6fb9 2019 testdata/no_hdr_sq_1.expected.sam
61c2943f8800b5212e2bc0aa6a745fd8cbfec36a43cc45906952d12bd6ce8108 325 testdata/noroundtrip-out.vcf
f10049c2b304537476322a71423736b3a532081003471df78c57e9a302f04608 271 testdata/noroundtrip.vcf
e15d14e3994027d433431c960bf1c5f2d6939f26b5094cd5a86bc6229a5b2661 13337 testdata/range.bam
ea9217f5a0dd7e57c0f2a94d55d6285d1e8d35cc741de53f12c19eecd0e84326 11182 testdata/range.cram
c4a9cdd9ea9f1acc28cd232489a4a2f3efe6274bca7a4e74772ac5555f21ff00 719 testdata/realn01.fa
52a637e1ea242258f038985f02e53b9ddd986d3a5c20184db0786251d8ea7d50 21 testdata/realn01.fa.fai
ee2b452a807bc45652f099b21e2f2c85c0c0ab5ba8a0569a987ce2c1fd156751 1843 testdata/realn01.sam
f40d994e18dd2a16ea2f0099622726dea7f231c4747ae281789b79be81db7847 2157 testdata/realn01_exp-a.sam
24e3c01376112c9aa8f0cec3c86d163f375685ceb98ec313294e352a66a7ebd3 2157 testdata/realn01_exp-e.sam
24e3c01376112c9aa8f0cec3c86d163f375685ceb98ec313294e352a66a7ebd3 2157 testdata/realn01_exp.sam
6755c73453736f24a0d369e22cae010364665c5471f2de7a2890838ceaa4cc4f 3758 testdata/realn02-r.sam
52e3b93a4d1e614ef2d93b7986dd2f06c8f731f4c0388cdf974cb9014ee10d53 4284 testdata/realn02.fa
d5cb77d98ebf4416094885628e1f7b173289fa78688bc51a96a94894bfb3416c 17 testdata/realn02.fa.fai
d4355e9c58c6109634619547489fbfd4e4e547d0d5e16dd15ab8fa73b7469207 2894 testdata/realn02.sam
36415f73abac3de774e6e9bcaebc557ed5aba9bec0cbc7cdf224d27afb3776fd 3758 testdata/realn02_exp-a.sam
75e181fe91f34ec65af6b5f0cde99e45ff81a5c5e908a0f23ee0f4898d884855 3758 testdata/realn02_exp-e.sam
eea2010995e089b9d0e148d0c0ece1ce82a2325b7f79fa5e57f72d19b671a54e 3758 testdata/realn02_exp.sam
17ef457815edcbc98231947846666ca141d1e2e4408200f40d346af728824324 16 testdata/realn03.fa
2ef8ba9ef2bbdfbeb941b67ce5e0f1b16ce02bb558820fcfcaf23853656fd933 14 testdata/realn03.fa.fai
289174a957f13cab71541656eec6b2fe379b1b1951c223c225432b1cc249aa7c 138 testdata/realn03.sam
73ffe7140dfe9e20cb0039846107975485418c2c646bd4d184a4d31ac10ae851 172 testdata/realn03_exp.sam
872ae56363e74fb860d1c4e8ceb3beaf65fd77d2598fc97331ae9d0671cedd2b 1857 testdata/tabix/bed_file.bed
926e8db2311965cbb5b827e7996308f4aff90f696f0556e17069f73b25cc331d 5618 testdata/tabix/gff_file.gff
b3eb6d0f7b807a858acf0bd0b6065d67923a1dfce52ebc1d21fd03b00e7daeec 622 testdata/tabix/large_chr.vcf
93bda0b0ad4efb45f3aa97672e9030b4c8fbe8440159ef85b2a6f4a6cd83f6f5 4485 testdata/tabix/vcf_file.bcf
ce983955ffef237b4a36adf16b9322b1ccfc0c4e05714a11efe2ed3ca3e4a0de 4302 testdata/tabix/vcf_file.vcf
96c01419aaa466e8bea034da890181119fbe933804078e9dc007e30ce3c3f876 2024 testdata/test-vcf-hdr-in.vcf
043b6e3c91bca8a34f3036e69d8e199a151f53ffd06f75b58efa2de83e3f74d6 427 testdata/vcf_meta_meta.vcf
c32f82a9d4eaee4fcad4ebdfef6aae5b2120a097ff78f0486239a9e7a316ec2e 1070 testdata/xx#MD.sam
32fa3590d966935e8fd6acecd09f0184885c2a9690abd6fa262e8864615a270c 1159 testdata/xx#MD2.sam
60b0c8faa6c2bad7ca3685d37a7fc4f01675ac8c5629b9ee45df0fa12fde4214 71 testdata/xx#blank.sam
e0a2a36434ec631ef185ff64eff6686efedc5e7237f94d61b94eb03718b37412 905485 testdata/xx#large_aux.sam
29d4b25fd86454756bf0ae17a8e362bec730279b2d7c3c22e6cab2858884c9e0 651 testdata/xx#large_aux2.sam
ab178652b846ee71fb986c484523ba09c997cbd6e29b9e0eeb6bc8bc1c92150e 22668 testdata/xx#large_aux_java.cram
22ac5e640f8b592b1225a061929ee2833410d8fa6091014b656ba2f31582b849 254 testdata/xx#minimal.sam
361ab11e0210c4fab42d27be4c86b7b11db534e0e9edad8da75e5c73466298ca 304 testdata/xx#pair.sam
ff24949ba4988c97da59f6d420b7fde4e7b5636f99d5bc44ca0ecebfad005115 298 testdata/xx#repeated.sam
82e3b5cfb195203366b212ff2fbab9e25e66d090938abe2eb238476e49afbee0 517 testdata/xx#rg.sam
5950c84a734ed97599456e28d69994a11431c144582b9d5b49caa81f06ee6930 1028 testdata/xx#tlen.sam
6f977d8e1fd7b61c04bdd418385a22cf9902b068e096a38fae0463fdb65069e8 1096 testdata/xx#tlen2.sam
4da3423cede424ce83193e4691b8dc02deae0b8e86d0b8fffc40e090f8d2f8a0 267 testdata/xx#triplet.sam
6601c6d79e0d6acba18865fe896e2a81973decf6dd624394cadf3bdfddda301a 320 testdata/xx#unsorted.sam
a1d5ccb865dc067319836cc6e50eb9a176ae3c1917745b93e70a55a83f4cfccb 86 testdata/xx.fa
9b4eaa63d723625fc6c89b17d423b1ffe5c49a59d7d2020114ee807c08fee5e4 44 testdata/xx.fa.fai
f8ae8753d8627ebc078d6deefdbf9fd13c97cc0364c3420471377da5b1982941 4682296 usrlib/libhts.a
