28a0883d80f0dcb8c94ea8af621e547b *DESCRIPTION
8042dcb7f1b8242dad58c3ab6dc9e22e *INDEX
bf967ee84084607170e36934a421ca64 *LICENSE
3d1263211b5637154ce16bf293380e8a *Meta/Rd.rds
1d15b8cd6573641f81c4126b0438e9c2 *Meta/features.rds
f62ef0a3d4450c6d154d555ebb1cea22 *Meta/hsearch.rds
544a96157424bdc2172cadabea5fa4d3 *Meta/links.rds
c31a0d27eaa44da5f5b45a2d0d8713f3 *Meta/nsInfo.rds
0d3cbeb12c819ebda271aaa4c9aaf3ce *Meta/package.rds
fc36de6f33a1e0fb3004028a3d5f613d *Meta/vignette.rds
2d2c1c0fa689901e74a8a630709b8901 *NAMESPACE
dc1c40a46e2c3800fc5a20a7ef1c158c *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/Rsamtools
5afc0cdf42461942f6d2db98eb975a77 *R/Rsamtools.rdb
5fac28a4a1d464010d082cf2df8c4d9b *R/Rsamtools.rdx
defff447bde0a37c22f566eb69cda2b0 *doc/Rsamtools-Overview.R
982b79db3356988dbb1245c56bab38e9 *doc/Rsamtools-Overview.Rnw
b1f82582c7ea86f06e7992de0f5f99b0 *doc/Rsamtools-Overview.pdf
a562de7fc0f8aadc9443e9e9a0b5ddcf *doc/index.html
22323232ba2f824ac8db07672145f03d *extdata/ce2dict1.fa
25a019557bb5685d766ed61dc4603a74 *extdata/ce2dict1.fa.fai
7df758adaaf5b6d487ac22e4dba6c31e *extdata/ex1.bam
1888862b9d22ddb8ca663eabc41c78f0 *extdata/ex1.bam.bai
df4a69daba471f2e896bde5f5553ed2a *extdata/ex1.bcf.gz
cab92ee448c41b442150d81fd32a28d9 *extdata/ex1.bcf.gz.csi
96db184679450f1ff65e95a5a6712d27 *extdata/ex1.sam
61da0a60f1e0ada9343497eb6f75abd5 *extdata/ex1.vcf.gz
d2adff4c652e8a9305051539be4f8e4d *extdata/ex1.vcf.gz.csi
f9a7ff6f4b559b5d332e19a30c3f86b0 *extdata/example.gtf.gz
5d8c67b81c8cc21846c6afae879ca705 *extdata/example.gtf.gz.tbi
e52ca02ef4d8de2f1f15b1ac0fa65005 *extdata/example_from_SAM_Spec.bam
c64f2c6168c6aba12b5c82e7dfa74afe *extdata/example_from_SAM_Spec.bam.bai
9d18ffdc11a18e91d5c64b718602c1ac *extdata/example_from_SAM_Spec.sam
0be4721ee2c9f1858c73f0aaa8550f00 *extdata/no_which_buffered_pileup.bam
e1ea162983e5d15bce0d66cdead430bd *extdata/no_which_buffered_pileup.bam.bai
10398b96c08329ee01bd075cfc779132 *extdata/no_which_buffered_pileup.sam
cd09b7d1c482dd798d5ab0b2d411b84d *extdata/no_which_whole_file.bam
b71d4d4736e1071a49190edb922ae5ff *extdata/no_which_whole_file.bam.bai
6f8a5015a9786ce86a965848a9633aa6 *extdata/no_which_whole_file.sam
1da9e8b047ed977ccb5de772b2462696 *extdata/olaps.Rda
715c47c0662b143147324b27bb854dc9 *extdata/pileup.txt
5494fd19934144f67d2a85b4ab89bcd4 *extdata/querybins.bam
f3dfaff77e6fe427770fe389d4a24841 *extdata/querybins.bam.bai
6f871a9c2a93270190defcd22f31cd64 *extdata/querybins.sam
6ddaf935be46e75ca0a88e62fa1093c2 *extdata/revbins.bam
da8444454b8554ca98d7c6e31d0a6f1b *extdata/revbins.bam.bai
c76ac123d3bd572758ff49d8f1ef0303 *extdata/revbins.sam
46d5ed9ac766376dee08e14d107dabfd *extdata/samtools-github.txt
23294b7cc9de134693fe56665ad54ca9 *extdata/slxMaq09_urls.txt
5ab7017a87bd6ba99c768a9155f1d8f6 *extdata/tagfilter.bam
5e643f92d1e20fffae85d626be5b0d95 *extdata/tagfilter.bam.bai
e923e5eab408e6617e72226c7875b974 *extdata/tagfilter.sam
120ab4b3e5c957a44ce695f09af76618 *extdata/tiny.bam
b99c7ee3f818e3ad21ab80198ab09e55 *extdata/tiny.bam.bai
7aee88510e5c4378a271285877a21c66 *extdata/tiny.sam
ce71aff63ec52a72d26cadef6341e0ac *extdata/tophat/README
a3aac6bef3effd53505adb9b2e013d6a *extdata/tophat/accepted_hits.sam
27b6e5502996fbf2dbbc069ee9bf84f7 *extdata/tophat/coverage.wig
4ece538c2a4c0dc91de5e9967b97fd8a *extdata/tophat/junctions.bed
939fa778d90b30419b267b056377242a *help/AnIndex
bd39ea7ae49158560afa0a4682caca83 *help/Rsamtools.rdb
2cb361f4b954f76ba85ba86899ba6d78 *help/Rsamtools.rdx
dcaa9a63b30600c2d5bac8339706bc88 *help/aliases.rds
6bff119f3c2c505c6cf6ef7b9b6f48c3 *help/paths.rds
c3f6c619e6475040a732924ac06b8409 *html/00Index.html
544ded2d2c7dfea05941ad6db309edd3 *html/ApplyPileupsParam-class.html
cff6012a9ab1d68cc5dffa31b17e4da8 *html/BamFile-class.html
e16e30126df91055909ae7249589e09f *html/BamViews-class.html
052dd978ebacc15bf50066a11013d1a5 *html/BcfFile-class.html
3637de4f9b87268b3511ee2d5371e1e5 *html/FaFile-class.html
034c0a9c0cf2b25d5f70fb0fa908c451 *html/PileupFiles-class.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
6b06e92e186751e4197177b478a115bf *html/Rsamtools-package.html
c323c34cf08ccae06268d799a16582bf *html/RsamtoolsFile-class.html
8085c3bc0229848263168509c8e13b4c *html/RsamtoolsFileList-class.html
5244a1c881a670ee059499352d8857a0 *html/ScanBamParam-class.html
250289c9ccd10eb5c48c81f13e750cdd *html/ScanBcfParam-class.html
da42aa8e6737cf32c67e9a2e325a52fd *html/TabixFile-class.html
f6e4c456123497879bd86a9e5e819a21 *html/applyPileups.html
c035e4f44127eb7c4521a67319094a3f *html/defunct.html
bdc79c2bc09137f5134fca6410197cbf *html/deprecated.html
f03f1ceaf8c6b4a18ca2c674bac701fb *html/headerTabix.html
34a1ff82434531b7fbea8a98f6532deb *html/indexTabix.html
44c630de6ab99ba8bcc90a1092dbdc51 *html/pileup.html
88162df03b6427e91b49a36c232ab182 *html/quickBamFlagSummary.html
e250090a180921556c0af3fe54affac2 *html/readPileup.html
014f54b50dbb7865b0a9cad5d2bcf465 *html/scanBam.html
356b2a572a3a8d052d5cd5f399606813 *html/scanBcf.html
d3ab3ec835ced74ab94aa9c162f15b32 *html/scanFa.html
b6953d9cf7a0884ae62be6f7d71d0405 *html/scanTabix.html
871ddaa63ad03c4534d15e2bf15b90ca *html/seqnamesTabix.html
664644e29e48c55fc0865aaaeadff0f4 *html/testPairedEndBam.html
7663b05d52d4664f7aa318e58e45b48a *html/zip.html
9e7147f44c8489fcd42e6320cc5bf5bd *libs/i386/Rsamtools.dll
293aa12d9dc1a9f00ba976b9536ea12f *libs/x64/Rsamtools.dll
d1167f1edb9728e01f1dbb33c4f84b03 *scripts/BamViews-1000g.R
09e38a9cf5301e08d2908ef80d6cfcc3 *scripts/features.R
11f2c54c085e7eba3b0af7f465af7458 *scripts/remote_test.R
0bf0afc1ae9722c9554c6f6dbd8999f7 *scripts/update-samtools.sh
7b400651565e7a8ecb8f6635023f13a6 *unitTests/cases/RNEXT.bam
7b8ce960ff8555ae68a9c51007e1542c *unitTests/cases/ex1.sam.gz
7df758adaaf5b6d487ac22e4dba6c31e *unitTests/cases/ex1_noindex.bam
6a5958f08f38d0ec9edaa102fdef65d3 *unitTests/cases/ex1_shuf1000.bam
7c1ac84cf8c553c0503ac44ec535ef39 *unitTests/cases/ex1_shuf1000.bam.bai
0dd5eed996f57fa6cabc6e61912b7f6d *unitTests/cases/ex1_unsort.bam
d41d8cd98f00b204e9800998ecf8427e *unitTests/cases/ex1_zero_index.bam.bai
aae2954740e639838abe34f01300d4bf *unitTests/cases/no_SAMPLE_header.vcf.gz
c7113cd55b6fb5722580727d3f114d4a *unitTests/cases/no_header_line.vcf.gz
ac02584ece063693f76c7de3a6c26ef3 *unitTests/cases/pileup-no-stars.txt
7f2ccec39e20c8cc23ce7514a454c803 *unitTests/cases/plp_refskip.bam
b276362cd73352494e2ea78cecef09ee *unitTests/cases/plp_refskip.bam.bai
326a0b105ae40f30036f94a2253597d5 *unitTests/test_BamFile.R
e05c7ac367b4155ee915bf08ddbf5c7a *unitTests/test_BamViews.R
7b1f62df6adf251dc2940521ad561e82 *unitTests/test_BcfFile.R
85af3e7fa8973cdc88298c45f526d285 *unitTests/test_FaFile.R
a07725b677e0ab35c082484c84f65861 *unitTests/test_RsamtoolsFile.R
ff45daefd835b2e12445d44261e6f9fe *unitTests/test_TabixFile.R
54e550e4f9ed1add7d824c06e7bf42c4 *unitTests/test_applyPileups.R
71ba57d7c4774a0cd3cf82f7311aff49 *unitTests/test_asBam.R
58f49c4a0d44b5c98be0e8bd2e5c2403 *unitTests/test_bam.R
e592a2f2c295340cff8a5b6f13ecfa99 *unitTests/test_bam_count.R
289a01b62bdccc1ffb49c73473e3f610 *unitTests/test_bam_header.R
ca78f7656ad33707cbf04b9c28728b38 *unitTests/test_compression.R
10e0663a7fbccfbb25b4c343280960f3 *unitTests/test_mapqfilter.R
589f3f7e3a7e8f8f8ccfc1ab28b1d452 *unitTests/test_phred2ASCIIOffset.R
e3954c5dcfe78977342c9f2a98947ac8 *unitTests/test_pileup_nowhich.R
a0c649d152813ec5331ff427f4daad57 *unitTests/test_pileup_querybins.R
ab4c0994b2c1d8276335dc4828777348 *unitTests/test_pileup_revbins.R
d99f7b5f0574bd2238093ebe1a2cc17f *unitTests/test_pileup_single_range.R
26597ca7fdf80e4a07d99cfa78717939 *unitTests/test_readPileup.R
c845a4269940541c04f8349fbe23f92c *unitTests/test_scanBamFlag.R
e8ba000c556d2b8458957e61b57eb220 *unitTests/test_sortBam_test.R
0700f9e7951020e83d3633412a68d9cc *unitTests/test_tagfilter.R
36f997e813e6c6a5b9e14745c2a138fd *unitTests/test_testPairedEndBam.R
a120850700c502ee932186b3dd0be6cf *unitTests/test_utilities.R
