Files in GenomicAlignments

Representation and manipulation of short genomic alignments

README.md R/findMateAlignment.R R/coordinate-mapping-methods.R R/GappedReads-class.R R/GAlignments-class.R R/findCompatibleOverlaps-methods.R R/intra-range-methods.R R/cigar-utils.R R/utils.R R/coverage-methods.R R/findSpliceOverlaps-methods.R R/GAlignmentsList-class.R R/summarizeOverlaps-methods.R R/sequenceLayer.R R/stackStringsFromGAlignments.R R/findOverlaps-methods.R R/zzz.R R/pileLettersAt.R R/OverlapEncodings-class.R R/setops-methods.R R/readGAlignments.R R/encodeOverlaps-methods.R R/GAlignmentPairs-class.R R/junctions-methods.R vignettes/summarizeOverlaps-modes.pdf man/setops-methods.Rd man/GAlignmentPairs-class.Rd man/GAlignmentsList-class.Rd man/findCompatibleOverlaps-methods.Rd man/coverage-methods.Rd man/findSpliceOverlaps-methods.Rd man/GAlignments-class.Rd man/stackStringsFromGAlignments.Rd man/junctions-methods.Rd man/intra-range-methods.Rd man/cigar-utils.Rd man/encodeOverlaps-methods.Rd man/coordinate-mapping-methods.Rd man/GappedReads-class.Rd man/OverlapEncodings-class.Rd man/findMateAlignment.Rd man/sequenceLayer.Rd man/readGAlignments.Rd man/pileLettersAt.Rd man/findOverlaps-methods.Rd man/summarizeOverlaps-methods.Rd tests/run_unitTests.R inst/doc/summarizeOverlaps.R inst/doc/summarizeOverlaps.pdf inst/doc/GenomicAlignmentsIntroduction.R inst/doc/GenomicAlignmentsIntroduction.pdf inst/doc/WorkingWithAlignedNucleotides.R inst/doc/WorkingWithAlignedNucleotides.pdf inst/doc/OverlapEncodings.R inst/doc/OverlapEncodings.pdf inst/unitTests/test_coordinate-mapping-methods.R inst/unitTests/test_intra-range-methods.R inst/unitTests/test_GAlignments-class.R inst/unitTests/test_findSpliceOverlaps-methods.R inst/unitTests/test_summarizeOverlaps-methods.R inst/unitTests/test_GAlignmentsList-class.R inst/unitTests/test_readGAlignments.R inst/unitTests/test_cigar-utils.R inst/unitTests/test_readGAlignmentPairs.R inst/unitTests/test_readGAlignmentsList.R