1237e725bafb03d9675f734de3d61b74 *ChangeLog
79e759f2c23e78cd6eb3db9cde9ceec1 *DESCRIPTION
ff0c6359ded4fca4d6407714b464e493 *NAMESPACE
dbeb98c50980241139bff7086a0761cc *NEWS
4c19072b4db2ee519a8d29dbec3d3c50 *R/rbamtools.r
8a12bd5e7ed3c86b3eeaf159f6ef84c2 *build/vignette.rds
0c2def85682a89f9e03c9aefca5e568b *inst/doc/rbamtools.R
6f7bbe6b6ec73ba16bbc154cbc3c0e9a *inst/doc/rbamtools.Rnw
e168e4b48a31bdbba4f43b69cbc878e1 *inst/doc/rbamtools.pdf
70636a08b868d8feda7dcb0ad4fd7d7b *inst/extdata/accepted_hits.bam
e402625fa157476dfcd67273bb0f7384 *inst/extdata/accepted_hits.bam.bai
6927ec49f8bf9cc7316d95eb131dfda8 *inst/extdata/test.fastq
fbf1ea4575ab176ed10b4e8aeb037224 *man/GenomePartition-class.Rd
ccaaf2a815c6b0cdaf60153d8a22228b *man/alignDepth-class.Rd
85ddc070f232cfa262913e17d3e49fe2 *man/as.data.frame-methods.Rd
b8c85089332f9e2c2c3cd3a13fce3062 *man/bamAlign-class.Rd
1523e92f06f1d65d422bcdc7b30e2b1e *man/bamAlign.Rd
05f6b66d999a3445d92248c2fa329a97 *man/bamClose-methods.Rd
0f902836fada44d2ba9dab828ab7ff80 *man/bamCount.Rd
1cab1d5a152e0b41890015481843ccf7 *man/bamCountAll.Rd
10401ae9befdf2bb9ce449e61752327e *man/bamGapList-class.Rd
78f8c355543783d44d344b6bd0889cbb *man/bamHeader-class.Rd
035ae21a78bab3d9eee7e148e7caa531 *man/bamHeaderText-class.Rd
cb27afd2caedb4d4847a9c3b64e2b763 *man/bamRange-class.Rd
b3eea2b29fe24282da59743cd622c8ea *man/bamRange.Rd
fdfdd5c8dde9f0609007f7cd4641ef5b *man/bamReader-class.Rd
ed47d230dc6b8808511d88b8682a4fdf *man/bamReader.Rd
848115e228e40ef53711690d07c333f2 *man/bamSort.Rd
75d4befc31fbded1c12f7153cec29785 *man/bamWriter-class.Rd
f223ff40a965799092c6f3e47c2be965 *man/bamWriter.Rd
fb197f9f0f6fdf2dd0e5a66963cd65b9 *man/countNucs.Rd
14a77a17f7689b4bbed8b852f0aa8652 *man/countTextLines.Rd
3285f5f25fbaac846ceb56a644ef2c2b *man/createIdxBatch.Rd
d5fe3bf0e9e34e5e165d61285d66ba42 *man/extractBamRegions.Rd
f12a1f10629f0004a786626bd76b1c75 *man/extractRanges.Rd
05506393a99da388fa6f4fb966d5e009 *man/filename-methods.Rd
cde88ce2ac07a063f0891631f5a8b3bf *man/gapList-class.Rd
d5ef5aee0de29e344ea90b1d6428d3d8 *man/gapSiteList-class.Rd
b57ae07f51c65a5794477418c5d71602 *man/getHeaderText-methods.Rd
f8de3ca22a445bce48a74d8af13994c8 *man/getNextAlign-methods.Rd
d9a7666fd01671024ea375ecfd3ba49b *man/getQualDf.Rd
5d6749b16cef58755f1cd9732b6c8b62 *man/getRefData.Rd
4462b698b3b988d3c6f35d315bc3888b *man/getVal.Rd
14284e31178844ce9c4d4e4dcd5036a0 *man/headerLine-class.Rd
7046b2a5e0fcedc982d9867b808f2d21 *man/headerProgram-class.Rd
4e98356d383985c3beb6ade2b4ba1df0 *man/headerReadGroup-class.Rd
bfb8ab8def344d07644a759af403fbc0 *man/isOpen-methods.Rd
cf2bd12b21ef80dc8a6f123b9883dec2 *man/nucStats.Rd
9fd8b6c9d3fdc4cbcedddd1425210d29 *man/rangeSegCount-class.Rd
bd8cd26b4f571f32660b3893fd2f401f *man/rangeToFastq.Rd
b4b7b30c2cf7720459f0e3e7d0f89631 *man/rbamtools-package.Rd
70749e9ae7321a64c6e832ae269ce38d *man/readPooledBamGapDf.Rd
ac66ec150f4777b47f1c79451e4e08ed *man/readPooledBamGaps.Rd
43c9459c9c4030cf14a82135fcf04345 *man/readerToFastq.Rd
c8e535c71f80d4ea74e48b177313f7c9 *man/refSeqDict-class.Rd
d5cd1a6c7f2e020c70b9a6d5a21d793f *man/setVal.Rd
e6579ecae98750915f5a88a341599675 *src/Makevars
02df778c95890ab6d735549582f4766f *src/Makevars.win
938c927c11d8db5b8ed6fc5f48efdf78 *src/align_counts.h
4d91b83a77c36cffad704841f65e75e2 *src/align_list.h
a083444dcfe1bc04dd7a78f8342b876d *src/bitmask.h
953a4df7f40eb5327ef516f2bfe9dcc6 *src/data_frame.h
4083104482995a028af267c52f922cd2 *src/extptr.h
0fc2bf25a1d398361a99b2c2b1a27be7 *src/gapSiteList.h
14964b9ca4339434ad612fc7fdd321a6 *src/gapSiteListList.h
55d9b2ebdf6a1601ea7f2640f9668f04 *src/gap_list.h
c0a38b37169806e7728ebce66cf7b4c0 *src/grange.h
c9956ca58facde6896a6f176cc243996 *src/range_partition.h
8fbf8cd87c36e437a329566aa03865d6 *src/rbamtools.cpp
e764393a6914790c7b1193d81e578458 *src/rbamtools.h
2e4c02f66ddf5b45e5f82ff579740386 *src/samtools/LICENSE
23c9b76a283050fa883cdad563c2ddf1 *src/samtools/bam.c
19ace9b9bc1df84573e6905ffa330dd6 *src/samtools/bam.h
e83437966ea850ce728c7464829c4e4b *src/samtools/bam_aux.c
f7cefb3e7547d4e411f9ea11cd69754b *src/samtools/bam_endian.h
54497f00431189eff6fa691a2c67ab04 *src/samtools/bam_import.c
a44ce4f09609b5166a5e50875ae5127b *src/samtools/bam_index.c
d9e850fd4c45aea2b16f3c414653fa37 *src/samtools/bam_sort.c
b4a65020d204657209e2f2e350bf3636 *src/samtools/bgzf.c
86d5cb10e9aa3142f9ce23bfc95d72a0 *src/samtools/bgzf.h
f0b28f833b42283648305b1e22bcdfbb *src/samtools/faidx.c
4cb1218daa2c840cf4433f75ed1fb63b *src/samtools/faidx.h
3c669fdbd041832bd5e7e137cc83cf95 *src/samtools/khash.h
955405f73508c3f12c7292bff32ed39b *src/samtools/kseq.h
885022ecd86e6650582b1b085a097059 *src/samtools/ksort.h
55910d3ccbc5c155f4e0d9d1b6899480 *src/samtools/kstring.c
6f641b01f25a2531f39b6fb0a24143fa *src/samtools/kstring.h
8958057d288712db4892f8b49fd74aa5 *src/samtools/razf.c
f811b63e4de097b427ad3d23d91e5c3a *src/samtools/razf.h
21c4655f97bb92a99d502d1a964d428f *src/samtools/rdef.h
b1a99b6b2a0d8a6af94c38167f8077a5 *src/samtools/sam.c
eb06482d20c8cbceead50f119c2a0229 *src/samtools/sam.h
9d9bfd529368210ce4287e24379a29f0 *src/samtools/sam_header.c
d07492fd02fcbcddeb159e19b7bc22f3 *src/samtools/sam_header.h
cda4fe5baa2dff1314647e76ad850f38 *tests/test-all.R
dd64d5cdbc30868d35965a8e6512fac7 *tests/test_bam_align.r
348aba8692dcc96ce9a37b3201c19ee1 *tests/test_bam_header.r
0d6ec743d9d90c46faca6486755f8c39 *tests/test_bam_range.r
d643ff2a32ee153ac08e07640377ece0 *tests/test_range_seg_count.r
6f7bbe6b6ec73ba16bbc154cbc3c0e9a *vignettes/rbamtools.Rnw
5f41defa7a3d35054572556e7cfd899e *vignettes/rbamtools.bib
