57353f2d7c9cb6bbb042014c1389578c *DESCRIPTION
4ad7f0e4df2159db6ba8fb3c02baf138 *NAMESPACE
f2c08c8ade0696178a08ec220e322f0e *NEWS
2c0074c331559e48a5e37aba874bcf59 *R/GAlignmentPairs-class.R
a4860a28d76fec5b5ef07c7622b3326d *R/GAlignments-class.R
b725d536c838dcca3f4f83c0c50821d1 *R/GAlignmentsList-class.R
0fb3be6f81953f3a9e64ebb11efe4b7c *R/GappedReads-class.R
b2844da934ce601061be61c072cf5968 *R/OverlapEncodings-class.R
281251b0d6e6eab9c2950175ac15e726 *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
5abacc7cc417d776dcd5100e8e1ec1d2 *R/summarizeOverlaps-methods.R
9f9bed9e94a8626db3f878fd70f012f3 *R/utils.R
49c19615aff54cbcead0ed2a1e410a08 *R/zzz.R
779e0034c6f577700614026cd90a618a *README.md
424ba573338e5f33e6206581cfd9fb34 *build/vignette.rds
bcb46671f9de67f4c98c54cd2fb7b0a6 *inst/CITATION
244300f607fd313bc0f1e12aac6fa8d3 *inst/doc/GenomicAlignmentsIntroduction.R
6e39e7a38e67414501fb32634a4052aa *inst/doc/GenomicAlignmentsIntroduction.Rnw
98ac4ea11c9e156a9414ae6545f03951 *inst/doc/GenomicAlignmentsIntroduction.pdf
a6b943caa621dee3fe79c33c204ca6f6 *inst/doc/OverlapEncodings.R
5d1bb13de397b6d2d60596aaea64ab07 *inst/doc/OverlapEncodings.Rnw
035fdc6eac3bcb00c12c120d982562f6 *inst/doc/OverlapEncodings.pdf
abdff216625c75cdcde9af17016349cf *inst/doc/WorkingWithAlignedNucleotides.R
10c400e5d2948a1b5202e3c387c97990 *inst/doc/WorkingWithAlignedNucleotides.Rmd
64b6b58f2d3a100f0bf4cc5232b63c83 *inst/doc/WorkingWithAlignedNucleotides.html
111d660eb9166747c920a9df9295bfa7 *inst/doc/summarizeOverlaps.R
8d6114b1245e4f25b7db01f3ff3111f5 *inst/doc/summarizeOverlaps.Rnw
75b54d0f3327b6f00e612ea442be4136 *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
2fb44c497e34c02755ad2e06313ef014 *inst/unitTests/test_summarizeOverlaps-methods.R
26455a903312fa90695fd7a4f536737a *man/GAlignmentPairs-class.Rd
6c7284da8f1f35739d68664fcf080450 *man/GAlignments-class.Rd
6b94376b77d2d1168909cbfc53b0b194 *man/GAlignmentsList-class.Rd
5d4578a7b99cc1640355dcb66690e8e4 *man/GappedReads-class.Rd
d4483104b336a8cdd095d2f90034e720 *man/OverlapEncodings-class.Rd
45fbded216bfb8dcb2ca92eb1f50fdd7 *man/cigar-utils.Rd
0cdcf277423e5fdda2ac535e35c43c7c *man/coordinate-mapping-methods.Rd
1002f0230ca8ecd0d159e9ae98912bee *man/coverage-methods.Rd
5284cfc140d20d87ae8b24e2644510f3 *man/encodeOverlaps-methods.Rd
fcee1febfd315c11348ec3667413aea3 *man/findCompatibleOverlaps-methods.Rd
9dfd0b447b9299905ccb29900d1a58e8 *man/findMateAlignment.Rd
3f004b81a4e3e352776012528fb49006 *man/findOverlaps-methods.Rd
f607d40bef8c8aaef1d092ae6a2bf732 *man/findSpliceOverlaps-methods.Rd
57b938d4430976c52a8279df15c7925e *man/intra-range-methods.Rd
68e5dd494eac7235e40056815a1196df *man/junctions-methods.Rd
f01933f6b74fe68756d49e16f89a70f1 *man/pileLettersAt.Rd
31bcbca268b70ef6884cbb8450d705be *man/readGAlignments.Rd
601f4e77ea11748c18e38e89338398d4 *man/sequenceLayer.Rd
058c8ee68f85e5736f08a9726c1e68f8 *man/setops-methods.Rd
9d78c8d57cd379ed37b07d1df700b78c *man/stackStringsFromGAlignments.Rd
5727b55bfd7ac960a349d1463a749dad *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
5d1bb13de397b6d2d60596aaea64ab07 *vignettes/OverlapEncodings.Rnw
10c400e5d2948a1b5202e3c387c97990 *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
