bd2064166e421fa1609c6438074e4a51 *ChangeLog
050a0c8ee5172bb5574da27426493fda *DESCRIPTION
4f2484069550c107d299d6d681905dd2 *NAMESPACE
f63c83f98e4e0055ff4b5dbc18a9b81b *NEWS
c6236133d976dfc3568ea1293368cb4f *R/rbamtools.R
0061268e35669606e7e1b0dd7de463d9 *R/sampleBamFiles.R
a80de5e269af91d72e06119c411d4a54 *R/segmentize.R
0e07bb651321e9352dd022ee464f1d3a *build/vignette.rds
63ad847ccc4b279f8530171d6a9c4d4e *inst/COPYRIGHTS
54a677b499bfa7f910cb17782ad7f603 *inst/doc/rbamtools.R
5d7cebfadefe0c4c2c62ec1d718f50d7 *inst/doc/rbamtools.Rnw
fffdf2c2d1cfd602d4abe734af62a964 *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
bab9876b529627a1f3b5bfffff7affc8 *man/bamAlign-class.Rd
1523e92f06f1d65d422bcdc7b30e2b1e *man/bamAlign.Rd
05f6b66d999a3445d92248c2fa329a97 *man/bamClose-methods.Rd
0f902836fada44d2ba9dab828ab7ff80 *man/bamCount.Rd
48a1efe5bd83a461afa41688c77e0b4f *man/bamCountAll.Rd
10401ae9befdf2bb9ce449e61752327e *man/bamGapList-class.Rd
779f81d0125e0824eda9f32a0bcfe352 *man/bamHeader-class.Rd
035ae21a78bab3d9eee7e148e7caa531 *man/bamHeaderText-class.Rd
c5d807ab6053bb954cc60dafb2e946c9 *man/bamRange-class.Rd
abcf0de2bfe92090ce3f6969dfad014c *man/bamRange.Rd
5d7c2227b5851c3cebb78ddd2b8927d8 *man/bamReader-class.Rd
ed47d230dc6b8808511d88b8682a4fdf *man/bamReader.Rd
30c234c856a1b10bd5f8b84290e55736 *man/bamSave.Rd
4f2f7a8df47fffb7d9a9a0ba1440dc19 *man/bamSort.Rd
14dce93bed5d33a32147b0709d317f1f *man/bamWriter-class.Rd
bbc0c163f0264c812b308ec9dd4f121c *man/bamWriter.Rd
fb197f9f0f6fdf2dd0e5a66963cd65b9 *man/countNucs.Rd
14a77a17f7689b4bbed8b852f0aa8652 *man/countTextLines.Rd
07bcbe3f7fb589fa5fa8f237cca9ce36 *man/createIdxBatch.Rd
dfe65ce7f34b1ee1fb72448f63bfd2b2 *man/exonAlignDepth-class.Rd
074ea94d48753d837e434c2cb0fa89fb *man/exonLoessModel-class.Rd
501fc6e4ff0ab94c7dfd13f3767d1902 *man/extractBamRegions.Rd
70f1063ba75abf4abf0dcd1ca23e4174 *man/extractGeneRegions.Rd
ebc8b9ef24893e5b9d58e694412f92c4 *man/extractRanges.Rd
05506393a99da388fa6f4fb966d5e009 *man/filename-methods.Rd
a6b0a6fc35d39ab6cd27029793bc5310 *man/gapList-class.Rd
f33cd1cfbef20555a9a9c46097219345 *man/gapSiteList-class.Rd
6224f1b6da84d7f3ec6e866522cc1767 *man/geneAlignDepth-class.Rd
e465265ac8e267d0c4e17a7ff5ae7eb4 *man/getHeaderText-methods.Rd
f8de3ca22a445bce48a74d8af13994c8 *man/getNextAlign-methods.Rd
d82775a557f44d5093bfdd6bc0283034 *man/getQualDf.Rd
c77851450649ababa7eb4ebb88e35ac5 *man/getRefData.Rd
4462b698b3b988d3c6f35d315bc3888b *man/getVal.Rd
30d7148c81cbd0a11852d9788dcf6743 *man/groupRatio.Rd
14284e31178844ce9c4d4e4dcd5036a0 *man/headerLine-class.Rd
8310190874263e0f83a42f14d1246d08 *man/headerProgram-class.Rd
e623ed04c858c83f8316af60869542bc *man/headerReadGroup-class.Rd
bfb8ab8def344d07644a759af403fbc0 *man/isOpen-methods.Rd
ff743e1f74aeb6698c6b0d8b8af89e93 *man/multseq.Rd
cf2bd12b21ef80dc8a6f123b9883dec2 *man/nucStats.Rd
08de7538348e33e17f8c46097d8f9aa0 *man/rangeSegCount-class.Rd
b829f7938ffba97257d9538e6ea25e41 *man/rangeToFastq.Rd
d738d5315f9cfe2c63c3f02508b687bb *man/rbamtools-package.Rd
70749e9ae7321a64c6e832ae269ce38d *man/readPooledBamGapDf.Rd
ac66ec150f4777b47f1c79451e4e08ed *man/readPooledBamGaps.Rd
9f6e98ef161b72c4d624bf994c7d24aa *man/readerToFastq.Rd
e4465d59348de30d9a76a7bf9621290f *man/refSeqDict-class.Rd
6fe1d444162401ce6cb2252dd35378ab *man/sampleBamFiles-class.Rd
2855c7b75ece73eb67798f1311340b4c *man/saveAldData.Rd
7bd4d0cdc5283170f66486a119f2ee22 *man/segmentize.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
b2a32b5aaea10358e8949a9503e93f31 *src/data_frame.h
fa717743bfb2d7e1c5e54c2babe3036e *src/extptr.h
0fc2bf25a1d398361a99b2c2b1a27be7 *src/gapSiteList.h
14964b9ca4339434ad612fc7fdd321a6 *src/gapSiteListList.h
2074bb218ea5da582e525013651a3f47 *src/gap_list.h
c0a38b37169806e7728ebce66cf7b4c0 *src/grange.h
c17367da42c6e438110f06dfa24116e4 *src/range_partition.h
0d2616136255272fb9e9efce08a2d64e *src/rbamtools.cpp
223837d733b494d87127c8129392df81 *src/rbamtools.h
2e4c02f66ddf5b45e5f82ff579740386 *src/samtools/LICENSE
5e89cee97f20a8148203663737b7b7f4 *src/samtools/bam.c
19ace9b9bc1df84573e6905ffa330dd6 *src/samtools/bam.h
1bb511beab109f86d3f7dd3b637f26da *src/samtools/bam_aux.c
f7cefb3e7547d4e411f9ea11cd69754b *src/samtools/bam_endian.h
7f1a04708ae5bc992a3d046936ab3d1e *src/samtools/bam_import.c
80ab8f1eb28b484187288f599db24be2 *src/samtools/bam_index.c
46d7abae8e0a57cdde381de7d5f1f2b4 *src/samtools/bam_sort.c
647da8736d366ac074e5458ca1be0642 *src/samtools/bgzf.c
86d5cb10e9aa3142f9ce23bfc95d72a0 *src/samtools/bgzf.h
9690fa3510e0261d92f8af6e31167eb9 *src/samtools/faidx.c
4cb1218daa2c840cf4433f75ed1fb63b *src/samtools/faidx.h
3c669fdbd041832bd5e7e137cc83cf95 *src/samtools/khash.h
955405f73508c3f12c7292bff32ed39b *src/samtools/kseq.h
c40244e065ec507d5c910673f7d32e46 *src/samtools/ksort.h
8cf2b5c70f741236d4e0ba50d0e28dcc *src/samtools/kstring.c
422869dacc5b68bfac5ac6877cef492b *src/samtools/kstring.h
f78db41816faa4e488e976b341516bd1 *src/samtools/razf.c
f811b63e4de097b427ad3d23d91e5c3a *src/samtools/razf.h
21c4655f97bb92a99d502d1a964d428f *src/samtools/rdef.h
317b04f8a39fc2430c8f97b07c05ef1e *src/samtools/sam.c
eb06482d20c8cbceead50f119c2a0229 *src/samtools/sam.h
a40bf11a9a09fc0986a8669c2da02d2d *src/samtools/sam_header.c
d07492fd02fcbcddeb159e19b7bc22f3 *src/samtools/sam_header.h
225ee6edfb8ac583213af1c5beef336a *tests/test-all.R
5d7cebfadefe0c4c2c62ec1d718f50d7 *vignettes/rbamtools.Rnw
5f41defa7a3d35054572556e7cfd899e *vignettes/rbamtools.bib
