8c948ffb3f7076f462b3e04e7661e7da *DESCRIPTION
54caee0f6304953f9676c829ad8d6aa8 *INDEX
f82490415db529434053e1c81b4660d4 *Meta/Rd.rds
50a9fa3e1aa2c47fa7bdbd6e6bb8974e *Meta/features.rds
c7a38ea1f02a6ad0c114ce6fb818692b *Meta/hsearch.rds
af16f62da75e8f655744580a08c97ec1 *Meta/links.rds
f64d2b4adb0c365dbee998988f69aa04 *Meta/nsInfo.rds
9ce8062abe7b900ef4ebe5f6540cdc96 *Meta/package.rds
dea3005f4d91fb5a8c42ee56db4190a1 *Meta/vignette.rds
1a75c0ffb3a3852a3c00b65edbb38092 *NAMESPACE
0ab4437a74662d1e768fedb566079790 *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/Rhtslib
0e8decfc60d4e2901f16db3f6e5a758e *R/Rhtslib.rdb
65e773518eca5ed17f90938c88d7c509 *R/Rhtslib.rdx
3f68dc9fc0ab54e240de7f6bdcdd563f *doc/Rhtslib.R
8ff959d176ca1b370f45e475b5b4da88 *doc/Rhtslib.Rmd
051ee9a124ddfcfb12add668cc6ab2b1 *doc/Rhtslib.html
f2c8b6040a730c0548889758d7f74b54 *doc/index.html
08ab35ecf014a5d0cd459d5285ac3020 *help/AnIndex
dcbcd6ba6cf0135ec694b50e3f4bcada *help/Rhtslib.rdb
de565162f1c4ecf9c36061cb88531790 *help/Rhtslib.rdx
e5567b68655c48c3c16ad2ea22272ba7 *help/aliases.rds
31f32f71769fbb920823dddcaf73d18b *help/paths.rds
c900b08f36778e3f26ccb3b7de49bfca *html/00Index.html
ee41876c0116916bb04bcf4fe3e43d78 *html/R.css
0f2567b93f57e6dfb5d94a850b635e53 *include/README
bbd39798c2a6f01f889077f5941f6695 *include/bam.c
f706d5d296391fe4838690b511f8ffd5 *include/bam.h
2408957a062d57805c5dfc2246953d09 *include/bam_cat.c
138b81de73af351558b0b4332e783226 *include/bam_plbuf.c
ad30211f55bc1a4b4186f33144434589 *include/bam_plbuf.h
0e23d952f13fe3fcc8c2ac36dd7726b1 *include/bam_sort.c
029b1020b690176c7830ace95b444596 *include/bam_sort.h
f5d7ac2260f81618da57c298044bdfe3 *include/bedidx.c
f981ce9d176c046d3b2e0f1ad8f3e57d *include/bedidx.h
82fe1d8f80471975416911a01f5fbc57 *include/htslib/bgzf.h
bd6694d333291d27c673df1e85abc90d *include/htslib/cram.h
1b12980a43db8ae6e685582fb6b006f1 *include/htslib/faidx.h
c950d8926745c824df2b5db6ef37003e *include/htslib/hfile.h
4713b87f52521d6a9b6224fcc422b519 *include/htslib/hts.h
b449a7892fe1b88729e6ae1d4d7bc993 *include/htslib/hts_defs.h
7604d88cd00fbcfcc2c26472c899dbbd *include/htslib/hts_endian.h
8a5f58a70ed340e3825294e799b841b6 *include/htslib/hts_expr.h
8fb2df4647dee4d3e4fb3802c924da5f *include/htslib/hts_log.h
3d406f82e08b95aa9a210b336f87cb7f *include/htslib/hts_os.h
cf84c8ac0d1197a3bf11293ca2d19875 *include/htslib/kbitset.h
905afa0bbfc0cae217b909aef543fa93 *include/htslib/kfunc.h
30bf241b355639899d10907da57da573 *include/htslib/khash.h
163c505b6a47b236c04f9455ee4c493c *include/htslib/khash_str2int.h
5b880009152fb7062f2680d401ac7424 *include/htslib/klist.h
12a9d6f435e206d56eaec88ed5215b96 *include/htslib/knetfile.h
06b42704ca4b4b17f448ef9d364b8783 *include/htslib/kroundup.h
515ee402dcd2227985b765219bfca3b4 *include/htslib/kseq.h
c2172de093bc9ba608764386d5f1ed68 *include/htslib/ksort.h
203874d61436e17956eb647b81536b7f *include/htslib/kstring.h
a8d476786a1351aec6445026da0d1ac2 *include/htslib/regidx.h
84894ebf66e9b54432b3ff5de5568724 *include/htslib/sam.h
01d774c7c2c79a0367924f135c6aaf56 *include/htslib/synced_bcf_reader.h
7c2cd3d16fa26876408e65df21898fcf *include/htslib/tbx.h
bbb7040a24c840896ca155533fbc1a30 *include/htslib/thread_pool.h
bfc05ffa7b6c2adb683d18ae71dc2b55 *include/htslib/vcf.h
70eb4c499026fce028f561e6626fff0a *include/htslib/vcf_sweep.h
8c149b90a7de95f0f7fbca92ca9ec218 *include/htslib/vcfutils.h
f5c8356d39d63d07b27552fe9f3c5b6b *include/sam_opts.c
2b38086da37a54b3b8875492f0298c0e *include/sam_opts.h
7401f5b3dc0a6a8a929e5d7c9a5416ee *include/sam_utils.c
5727dec98082662cd01370433019bb50 *include/sam_utils.h
8523a7260604594e68d1cd0633929add *include/samtools-1.7-compat.h
07dadcdc93e781554e8145a6daf1da0c *include/samtools.h
8f2ce34d684d52dcf1ea03117d89b968 *install_time_patches/Rhtslib.diff
89e7630837d725b580f1608ed64d2f2b *libs/x64/Rhtslib.dll
91a3e69a8340550a001d6df2b30ea778 *libs/x64/symbols.rds
aef5fa3c8222ebebd854034b76236538 *testdata/auxf#values.sam
fb2de660e7d5e5238875d628a2aae567 *testdata/auxf#values_java.cram
d28ff5fcc4d0047ec0001e54f2f10e23 *testdata/auxf.fa
7e8fa919cf80797a912221fdeb52f72e *testdata/auxf.fa.fai
1cf3c08841184582e8db4ed483958af3 *testdata/c1#bounds.sam
85fe4fd282e64adb93b5b7789f2632f0 *testdata/c1#clip.sam
1196b53427f8cb7e57028c9a9c316894 *testdata/c1#noseq.sam
71bb8e8c5cb4f86d7dccb4206506ecc0 *testdata/c1#pad1.sam
aba0bb2d0079499b50961c8f0f7c520e *testdata/c1#pad2.sam
ac9b9cf18079d07d61eb6db66384f011 *testdata/c1#pad3.sam
1628e92d4a04185b8dadada2221482e8 *testdata/c1#unknown.sam
d80442fcdb8a146476c4a69c5033befe *testdata/c1.fa
2f537adf9e10a6f3e6445f7f8284bed2 *testdata/c1.fa.fai
225f59dc95977cbc1ecd3adbaa761f00 *testdata/c2#pad.sam
bd0371ae0e2244c7f548852d421ee3f4 *testdata/c2.fa
bacddce6bec3f7da347359cfa7357d72 *testdata/c2.fa.fai
8ed4fdbc2be420fe69537e878b7a9d59 *testdata/ce#1.sam
a2f5549865a33f721aecf835eb4a4dc4 *testdata/ce#1000.sam
877069c3b73a6eba83e7746198c07d85 *testdata/ce#2.sam
ebb33192f142425194f4520b99a28113 *testdata/ce#5.sam
f6974a85bb62f181d547b2758dafe1ad *testdata/ce#5b.sam
a5e7634db2df4aa2925ad9dbdf4dffe0 *testdata/ce#5b_java.cram
7e76d143ad5d0369d81fd2310c394fe7 *testdata/ce#large_seq.sam
a13c2849298e4180bbda657992b647a6 *testdata/ce#supp.sam
84ea6309b8666e83048c9d60e6109f9c *testdata/ce#tag_depadded.sam
d2822558628321aa187fb8eb4acb6fff *testdata/ce#tag_padded.sam
4196c29b1daebf2f072925a32ca930d9 *testdata/ce#unmap.sam
16046e6ba531c379d3d26e0b212b39a3 *testdata/ce#unmap1.sam
966ef7223e7649a99efc5c6029a878ff *testdata/ce#unmap2.sam
cfdd101d3d08fc60f60f2aa63a7055d4 *testdata/ce.fa
caf7cc4f77dcf116369d0b48ff83d5b4 *testdata/ce.fa.fai
9e3faa6aef3fe7c225ef5996cf567c1a *testdata/colons.bam
6685e3a1e6410ca0b421d3c8a56e95b7 *testdata/fieldarith.sam
44dd57afa380887421f862624b0a7c23 *testdata/formatcols.vcf
d5f0f97cc4926cc1df7553dbabe19723 *testdata/formatmissing-out.vcf
d5f0f97cc4926cc1df7553dbabe19723 *testdata/formatmissing.vcf
850cbc11858ea73c2f7d85777bf1807b *testdata/index.sam
0e408b5fdce43c92a43603099f58c8b7 *testdata/index.vcf
f082affb224ff5110ecf52b86fd177eb *testdata/index2.sam
3615c1c68983ce8754139ac5f5839bae *testdata/index_dos.sam
9621fcaa95ed603b13ef585dd869d57b *testdata/md#1.sam
25e3af5db6506317564059876ee08fc0 *testdata/md.fa
b14c43520985e77e0898f1c9ecd0637c *testdata/md.fa.fai
1a2ed042710fc52c7da871672016bc35 *testdata/modhdr.expected.vcf
875889b957af6d82dddc32488f319192 *testdata/no_hdr_sq_1.bam
79f024f93052b404912a2fb6e801032a *testdata/no_hdr_sq_1.expected.sam
8a8a4c82dfe06e48d0ae7407332a5f39 *testdata/noroundtrip-out.vcf
fc5c8cff45f39fc42681d0e502e3c86c *testdata/noroundtrip.vcf
1c23eaabeb31d8cbafe19d6e5b3a5999 *testdata/range.bam
f3802d15f9b780fef5427c356353bd85 *testdata/range.cram
745c9d977ff8b0962a4d2db9934e233b *testdata/realn01.fa
fa751c736ab697698a577ec1fcdecf2f *testdata/realn01.fa.fai
d39d1b211437a547ab29100f21659af9 *testdata/realn01.sam
e7577869b1c3dec7ee938b878c74c8ab *testdata/realn01_exp-a.sam
9a92badfe49d198bc8f9b8b0fa32ca99 *testdata/realn01_exp-e.sam
9a92badfe49d198bc8f9b8b0fa32ca99 *testdata/realn01_exp.sam
2f4fdcb4ae88352dcba27b1c08bd9a8c *testdata/realn02-r.sam
775792a1fdf307b406598a61cf4d9610 *testdata/realn02.fa
e5db0b04f87cccd586e94733f6ec24b4 *testdata/realn02.fa.fai
622728558d4d94fde284d401cb44e4d6 *testdata/realn02.sam
4bd7e39a7584234ebb142e44df92e0f0 *testdata/realn02_exp-a.sam
286a79b00726ce8ce5d558ea4f22c150 *testdata/realn02_exp-e.sam
bbafb340c76a1cd651344494b9df0b99 *testdata/realn02_exp.sam
d0cf3b31ce612cf25828c7b0633ab928 *testdata/realn03.fa
cd42d622187a1c85e7b89f7da4f66c12 *testdata/realn03.fa.fai
0470c2f7eb2bcd8d83ac28592bf441b4 *testdata/realn03.sam
d761298ef73e55140e42dc579a54b893 *testdata/realn03_exp.sam
91e7e591625b466e22d59cd479e83a69 *testdata/tabix/bed_file.bed
a3ca4493f951df2467fed1d68b931beb *testdata/tabix/gff_file.gff
75c420357c4d787e7972bc7a8882cc6e *testdata/tabix/large_chr.vcf
dac6b73f431e51a58577cd7b251471bc *testdata/tabix/vcf_file.bcf
5f98d67bb203f2f77a56d5eea6bdeba5 *testdata/tabix/vcf_file.vcf
e30fafaf3430f91d0a6df845f6ee8ac0 *testdata/test-vcf-hdr-in.vcf
a4c1907f5ad5be3f63b0c9aaad810b43 *testdata/vcf_meta_meta.vcf
9bdb8a927048138ebff3e6cc453c2014 *testdata/xx#MD.sam
730692f9db3b7cef0d705f6b0e303c4c *testdata/xx#MD2.sam
a95108fcd08a9366e15246ac80c9289a *testdata/xx#blank.sam
4707816d39fb24851b4a55b4da1bb7a2 *testdata/xx#large_aux.sam
6915beff0fd50f3e3e3615ef0fa111fa *testdata/xx#large_aux2.sam
687f33311fa7ab69e03632a172139ad0 *testdata/xx#large_aux_java.cram
e7cfb90690ba8b0b3123b5750fca4810 *testdata/xx#minimal.sam
2349b1bbbb2e5af5e81a786e3a1c72b1 *testdata/xx#pair.sam
3fb60cb838a2f0b4c91fbdc7095247a8 *testdata/xx#repeated.sam
2d298fb75099fbf0c1eda326536df856 *testdata/xx#rg.sam
10a75a063b03e018b1e0093e448dfacd *testdata/xx#tlen.sam
3b15464da6d57edf3a03211f42b190dd *testdata/xx#tlen2.sam
ca2c1dbbc1f49e7e77310ed1769d2a43 *testdata/xx#triplet.sam
e89624b6e9e818d60134c747418eb5ce *testdata/xx#unsorted.sam
fa89a7556f0a9d332564f7bd5bb5d874 *testdata/xx.fa
39cb4f1855c06993a9628b114c449e0f *testdata/xx.fa.fai
aee78caeb41475b39665169d9e4b8910 *usrlib/x64/libhts.a
