2d0014309013f425469cfadfc2a630ff *DESCRIPTION
be218ab5f8593f82380357fb87629d5c *NAMESPACE
330af17de9f7670c0478b6a2cf6aa9a1 *NEWS
25582501738a5c09e2f292ec24ce51a9 *R/GAlignmentPairs-class.R
f986263821fc9670e0dbc4211ee4ae8b *R/GAlignments-class.R
b725d536c838dcca3f4f83c0c50821d1 *R/GAlignmentsList-class.R
c5a340897ad4ff0a623f84a5dde4d731 *R/GappedReads-class.R
b2844da934ce601061be61c072cf5968 *R/OverlapEncodings-class.R
d3b79d6d05baef15b3663718a2ca7087 *R/cigar-utils.R
eaa441a6b889ef2b453dbf83cf264ec1 *R/coordinate-mapping-methods.R
44b5f9d7002851fe8f2b90876af641c3 *R/coverage-methods.R
925f41b94b9f5b8a1bfd8910fe5efe0b *R/encodeOverlaps-methods.R
ec77538bb28715a719123c15eb5dc06f *R/findCompatibleOverlaps-methods.R
a53a9a73c3a89fdbbafbab5691b13961 *R/findMateAlignment.R
fc6397a98b201a99efbacc0fdc6a3281 *R/findOverlaps-methods.R
eec5ff414f5348373e46ea55931fa0f9 *R/findSpliceOverlaps-methods.R
078344d32d476cd16da934e35beeb875 *R/intra-range-methods.R
066f29bc0b234ff20f5a8fc106bb79e6 *R/junctions-methods.R
5a8983b0b809eba9fbf6e606f9f7a684 *R/pileLettersAt.R
4c1982831997d9669bf98c46f75afc44 *R/readGAlignments.R
315d89102a9e080ee6dfe5678c93e157 *R/sequenceLayer.R
74ded7794de18e309a852eb7c92cb8a3 *R/setops-methods.R
f1afb176777ee44ca98da411153af910 *R/stackStringsFromGAlignments.R
48de2bb59af5048ffb222b9c82f0a912 *R/summarizeOverlaps-methods.R
9f9bed9e94a8626db3f878fd70f012f3 *R/utils.R
49c19615aff54cbcead0ed2a1e410a08 *R/zzz.R
779e0034c6f577700614026cd90a618a *README.md
76f06521a200377008669bbb5dfe4613 *build/vignette.rds
bcb46671f9de67f4c98c54cd2fb7b0a6 *inst/CITATION
e099f894c81b0cb14abf1dd95d6e6edc *inst/doc/GenomicAlignmentsIntroduction.R
6e39e7a38e67414501fb32634a4052aa *inst/doc/GenomicAlignmentsIntroduction.Rnw
54e5884ea9062e7bb8ddc617dc9170cc *inst/doc/GenomicAlignmentsIntroduction.pdf
e67d3665e733ff5e39e4bfca86f02556 *inst/doc/OverlapEncodings.R
68888481e2bba183e3408e111907d416 *inst/doc/OverlapEncodings.Rnw
8a022839cb0f945109756fdb5b717c07 *inst/doc/OverlapEncodings.pdf
ce6b7e63648a74109c4e351265c9eb26 *inst/doc/WorkingWithAlignedNucleotides.R
5e284095ceea6b18ee2bb1a59c19b8f4 *inst/doc/WorkingWithAlignedNucleotides.Rmd
2ea55375e25ea9417ce2f90f10fda9ab *inst/doc/WorkingWithAlignedNucleotides.html
459876f6a6baca934fcf6c9af7a5b17e *inst/doc/summarizeOverlaps.R
8d6114b1245e4f25b7db01f3ff3111f5 *inst/doc/summarizeOverlaps.Rnw
b03b6d33a67f1092fe298059eaeef323 *inst/doc/summarizeOverlaps.pdf
1c380f8159fda8fad5d0d4902ae9ea23 *inst/extdata/sm_treated1.bam
af83f784077fcced98e3603bb7ad7a4e *inst/extdata/sm_untreated1.bam
a7b36b6b3e11006f2eb35e0c74d36328 *inst/unitTests/test_GAlignments-class.R
154347216f4ba7be01f4202c3981634e *inst/unitTests/test_GAlignmentsList-class.R
8ebc949e316f84ed21c18fdf971de87f *inst/unitTests/test_cigar-utils.R
201ee65c7ea0579dfba6112e0d2d33d9 *inst/unitTests/test_coordinate-mapping-methods.R
6423ceb23b9aa2509a64f02c53ff9f57 *inst/unitTests/test_findSpliceOverlaps-methods.R
50ce35ec47c6be35b91c2cc63b9fdbaa *inst/unitTests/test_intra-range-methods.R
a369c93b31e2e090aba36dcab66fa759 *inst/unitTests/test_readGAlignmentPairs.R
d6c4737a308c9831ecaff1d0bbd842d5 *inst/unitTests/test_readGAlignments.R
9610e31d42cdcec687fb5f4fb264b906 *inst/unitTests/test_readGAlignmentsList.R
fff74f636e12162e8d287c1ff1537716 *inst/unitTests/test_summarizeOverlaps-methods.R
0409ef55d4846d990238f05dbac77cb0 *man/GAlignmentPairs-class.Rd
97e265c9f492677afc2730e220a4e164 *man/GAlignments-class.Rd
7a98ae61b25346002e6f8cf238dac5db *man/GAlignmentsList-class.Rd
5d4578a7b99cc1640355dcb66690e8e4 *man/GappedReads-class.Rd
d4483104b336a8cdd095d2f90034e720 *man/OverlapEncodings-class.Rd
f66430144a7a0b8d2a9b8541b94f3a2e *man/cigar-utils.Rd
378d5da17d9768c2b10ba1a8aec2cccc *man/coordinate-mapping-methods.Rd
1002f0230ca8ecd0d159e9ae98912bee *man/coverage-methods.Rd
5284cfc140d20d87ae8b24e2644510f3 *man/encodeOverlaps-methods.Rd
877248543aefb0a3248c3e3971fb48c6 *man/findCompatibleOverlaps-methods.Rd
9dfd0b447b9299905ccb29900d1a58e8 *man/findMateAlignment.Rd
4c649bec22cbbafaa5772ae99e7138f3 *man/findOverlaps-methods.Rd
1867058bd53117af41d1fcd0f4c69f5b *man/findSpliceOverlaps-methods.Rd
f44a8abfea4ce024a1e90d2f36b443d4 *man/intra-range-methods.Rd
68e5dd494eac7235e40056815a1196df *man/junctions-methods.Rd
f01933f6b74fe68756d49e16f89a70f1 *man/pileLettersAt.Rd
c40ad2497b56864169089cab66ef90e9 *man/readGAlignments.Rd
e30655b24161c5685c52b03c58ad16a7 *man/sequenceLayer.Rd
058c8ee68f85e5736f08a9726c1e68f8 *man/setops-methods.Rd
c9b2ba6de692b17af2cebfc90414e6e5 *man/stackStringsFromGAlignments.Rd
e69d02161c0ad2756ed5dec42697f053 *man/summarizeOverlaps-methods.Rd
16a0e36b37708afd25bc082a58bc5264 *src/GenomicAlignments.h
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
b21bbc564b7d01a3088b2b5d3a0a9b35 *src/R_init_GenomicAlignments.c
bab0b4b09cf160fa0109ae25fbb471ef *src/S4Vectors_stubs.c
945d99adb294285a9e15052a4ceb23f7 *src/cigar_utils.c
84956b56d6747273d3d981a1c320cb27 *src/coordinate_mapping_methods.c
592e5bad0692bda898e7daa8f95f08a1 *src/encodeOverlaps_methods.c
d281c6bf21061a53f466ad1e86d2337f *tests/run_unitTests.R
6e39e7a38e67414501fb32634a4052aa *vignettes/GenomicAlignmentsIntroduction.Rnw
68888481e2bba183e3408e111907d416 *vignettes/OverlapEncodings.Rnw
5e284095ceea6b18ee2bb1a59c19b8f4 *vignettes/WorkingWithAlignedNucleotides.Rmd
c4ea62e4f67b91a0e0b023c219d7ceaf *vignettes/precomputed_results/U1.sbcompHITSa.rda
bfa41d04179b4462dd7f27c8ab36f4b1 *vignettes/precomputed_results/U1.sbcompHITSb.rda
eddca1b23bb569ab318ae9f055fb472e *vignettes/precomputed_results/exbytx.rda
93f08c8abf76627655b2995b4ac3d612 *vignettes/summarizeOverlaps-modes.pdf
8d6114b1245e4f25b7db01f3ff3111f5 *vignettes/summarizeOverlaps.Rnw
