2a1f46feb805a188710a12477e76c29c *DESCRIPTION
8042dcb7f1b8242dad58c3ab6dc9e22e *INDEX
bf967ee84084607170e36934a421ca64 *LICENSE
9774dc74d51098f0b73499422f63b76d *Meta/Rd.rds
989edc50dffd590a54c8c2ab86576cf9 *Meta/features.rds
86fb627a54f516093aa624901b0caf3a *Meta/hsearch.rds
fc6202a975d6b4a04b3bc6390950a06c *Meta/links.rds
81dbba2429a223ea2fff7f2700e27638 *Meta/nsInfo.rds
59e38f1b4ba9a17b02418b0399313cba *Meta/package.rds
3e36a8d6241f653a0a1e55266c886c9f *Meta/vignette.rds
2d2c1c0fa689901e74a8a630709b8901 *NAMESPACE
ac9cc4301980b8ebf3d57d614bc86e2e *NEWS
ebf0fc819595d631b8bf280c4b049940 *R/Rsamtools
70d34490907ecab91892fdcee8d33e2d *R/Rsamtools.rdb
0e910ad0a764b6c8c92979dc8fbb0197 *R/Rsamtools.rdx
defff447bde0a37c22f566eb69cda2b0 *doc/Rsamtools-Overview.R
a26d3d9be285403c74c335acf9be8035 *doc/Rsamtools-Overview.Rnw
4930a45dd2cf005273b34f4f5dbd7d9d *doc/Rsamtools-Overview.pdf
b47e5d1780052a9d452fe7f686764b54 *doc/Rsamtools-UsingCLibraries.R
b763bda3b8e54d31d9f08e329268a194 *doc/Rsamtools-UsingCLibraries.Rnw
7950b61ad4c463c5d40d2fdab5eaf615 *doc/Rsamtools-UsingCLibraries.pdf
7faf269710aa668f21d694b4a51c794b *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
2579ba9117b0b9ccd0041a1c04105b89 *help/Rsamtools.rdb
67fff201bd8136142df7b7aaf209ace8 *help/Rsamtools.rdx
6b972835c95ff8f583cfe13882a3d464 *help/aliases.rds
f3367d02d438637d28a4105a323ed523 *help/paths.rds
c33f56de133fe650cc5b1b637ded3f2b *html/00Index.html
0649ca906b1bc2badf5b88caf5e2e2eb *html/ApplyPileupsParam-class.html
6cfd2e4e1481c7ff2a1af5e46fa5081b *html/BamFile-class.html
0c51080fd88c9b75cf6872609db3c242 *html/BamViews-class.html
043f5c88b655d461627624f03b17b4e5 *html/BcfFile-class.html
181afdf06f87dd72ee71947350b2f007 *html/FaFile-class.html
cf882e4778480696fbdb0718891b203c *html/PileupFiles-class.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
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723ee51cb5499fc5b0a361f80c7cef3e *html/RsamtoolsFile-class.html
22fdbf32359d6d922f24c01e0857a483 *html/RsamtoolsFileList-class.html
164b65d9a8cf806925e8ace783dd5c6f *html/ScanBamParam-class.html
3e831576a59e7cf7a5c59e597e466ceb *html/ScanBcfParam-class.html
36c386b5719af39ea9350ca15555da20 *html/TabixFile-class.html
21f4b75c42281775c7ae4832e9b81e8c *html/applyPileups.html
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0af5eefcb5a357b5c1c9b647e3ff7430 *html/pileup.html
b4cb9d76b2a30950dc20dd36cb389205 *html/quickBamFlagSummary.html
d6c0989b6d358faa287b9f845cccd9df *html/readPileup.html
e947d471610e2c9d0d2c2e1b5eb64fd6 *html/scanBam.html
a2238511dcb39a08d7de561af691cf2a *html/scanBcf.html
40750d776c2beda0dfeb6da95c066fa3 *html/scanFa.html
c32b30126e1fb95783cf7b6926cba058 *html/scanTabix.html
bae580aaa8256542d197be18b34db577 *html/seqnamesTabix.html
9ce112cbece0ad0a1d5eb207f3b754ad *html/testPairedEndBam.html
07cfbee62f608ce9507168f093e5a152 *html/zip.html
f4e84119e699e3b6d4110de4ae7525d7 *libs/i386/Rsamtools.dll
3e2c084a219f8866f518a210cbcb6348 *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
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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
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7b1f62df6adf251dc2940521ad561e82 *unitTests/test_BcfFile.R
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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
95df6b38a8368a80f830ea449fe8383a *unitTests/test_pileup_querybins.R
343295ff7ce87602517abdecae18c4e2 *unitTests/test_pileup_revbins.R
354a4050b9e0a6cc097f3e0a3804677c *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
