6ee0158a68699dc7428d359753377913 *DESCRIPTION
fc869ee2ea4207aedc3b58907a28f0af *NAMESPACE
c81905d4a08d014e2d2103b55c974dae *NEWS
79b2a5d684d0f1b5374d3501c7f94931 *R/GAlignmentPairs-class.R
a4860a28d76fec5b5ef07c7622b3326d *R/GAlignments-class.R
b725d536c838dcca3f4f83c0c50821d1 *R/GAlignmentsList-class.R
0fb3be6f81953f3a9e64ebb11efe4b7c *R/GappedReads-class.R
b2844da934ce601061be61c072cf5968 *R/OverlapEncodings-class.R
c0cf428c74dfe55733db77d32ec81c68 *R/cigar-utils.R
e38ab509f323e11a56f4b24049da08b6 *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
92c678775b4cc1d5f891f0d0eb66203b *R/intra-range-methods.R
869e1a4d3628b203d2e3cb8c2d4bfe81 *R/junctions-methods.R
2835af57981575323ed47fa226ae1e8f *R/pileLettersAt.R
4c1982831997d9669bf98c46f75afc44 *R/readGAlignments.R
324b58438c19135686c31e43d9fa33a5 *R/sequenceLayer.R
74ded7794de18e309a852eb7c92cb8a3 *R/setops-methods.R
52c6719c10cb3205d64def425dc6953c *R/stackStringsFromGAlignments.R
48de2bb59af5048ffb222b9c82f0a912 *R/summarizeOverlaps-methods.R
9f9bed9e94a8626db3f878fd70f012f3 *R/utils.R
49c19615aff54cbcead0ed2a1e410a08 *R/zzz.R
779e0034c6f577700614026cd90a618a *README.md
cef5c1e2744c475783788936272fd4ed *build/vignette.rds
bcb46671f9de67f4c98c54cd2fb7b0a6 *inst/CITATION
e099f894c81b0cb14abf1dd95d6e6edc *inst/doc/GenomicAlignmentsIntroduction.R
6e39e7a38e67414501fb32634a4052aa *inst/doc/GenomicAlignmentsIntroduction.Rnw
591f60b7e1a32d2443c12437974cc322 *inst/doc/GenomicAlignmentsIntroduction.pdf
e67d3665e733ff5e39e4bfca86f02556 *inst/doc/OverlapEncodings.R
68888481e2bba183e3408e111907d416 *inst/doc/OverlapEncodings.Rnw
0afb1fb28b2108d1574abaeac3a589e3 *inst/doc/OverlapEncodings.pdf
ce6b7e63648a74109c4e351265c9eb26 *inst/doc/WorkingWithAlignedNucleotides.R
5e284095ceea6b18ee2bb1a59c19b8f4 *inst/doc/WorkingWithAlignedNucleotides.Rmd
f3fd10505a9bd28a65a33898029a691f *inst/doc/WorkingWithAlignedNucleotides.html
459876f6a6baca934fcf6c9af7a5b17e *inst/doc/summarizeOverlaps.R
8d6114b1245e4f25b7db01f3ff3111f5 *inst/doc/summarizeOverlaps.Rnw
920bb83efa2dcfa5c2d514dfabe030b7 *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
4bcd8177a9a9003a0c3a606a332682f5 *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
f56b45755ceccecbcac2895d9b38fc6c *man/GAlignmentPairs-class.Rd
dafcf613c99627ee3886a22e337ca2ec *man/GAlignments-class.Rd
d735da37b74e3a21e168b9a60ae6ab99 *man/GAlignmentsList-class.Rd
5d4578a7b99cc1640355dcb66690e8e4 *man/GappedReads-class.Rd
d4483104b336a8cdd095d2f90034e720 *man/OverlapEncodings-class.Rd
08f3a360c6936ed4c4ff0e4621b404bb *man/cigar-utils.Rd
f8fb5f6f8bce84b12e36ad0a5e98f85e *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
f607d40bef8c8aaef1d092ae6a2bf732 *man/findSpliceOverlaps-methods.Rd
117432d7d54e45b733c0fae87d80f919 *man/intra-range-methods.Rd
68e5dd494eac7235e40056815a1196df *man/junctions-methods.Rd
f01933f6b74fe68756d49e16f89a70f1 *man/pileLettersAt.Rd
c40ad2497b56864169089cab66ef90e9 *man/readGAlignments.Rd
2766ceb4bb35899cd7dd1ecdff240dc6 *man/sequenceLayer.Rd
058c8ee68f85e5736f08a9726c1e68f8 *man/setops-methods.Rd
c9b2ba6de692b17af2cebfc90414e6e5 *man/stackStringsFromGAlignments.Rd
e69d02161c0ad2756ed5dec42697f053 *man/summarizeOverlaps-methods.Rd
4c3d0706c7fc38abfbf9f12c4c56dc50 *src/GenomicAlignments.h
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
c1447a8c12b80e50df97da384d72354c *src/R_init_GenomicAlignments.c
bab0b4b09cf160fa0109ae25fbb471ef *src/S4Vectors_stubs.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
bfc74687c14cfd8e5286a1a3b7674d76 *vignettes/precomputed_results/exbytx.rda
93f08c8abf76627655b2995b4ac3d612 *vignettes/summarizeOverlaps-modes.pdf
8d6114b1245e4f25b7db01f3ff3111f5 *vignettes/summarizeOverlaps.Rnw
