lib/R/library/GenomicAlignments/CITATION lib/R/library/GenomicAlignments/DESCRIPTION lib/R/library/GenomicAlignments/INDEX lib/R/library/GenomicAlignments/Meta/Rd.rds lib/R/library/GenomicAlignments/Meta/features.rds lib/R/library/GenomicAlignments/Meta/hsearch.rds lib/R/library/GenomicAlignments/Meta/links.rds lib/R/library/GenomicAlignments/Meta/nsInfo.rds lib/R/library/GenomicAlignments/Meta/package.rds lib/R/library/GenomicAlignments/Meta/vignette.rds lib/R/library/GenomicAlignments/NAMESPACE lib/R/library/GenomicAlignments/NEWS lib/R/library/GenomicAlignments/R/GenomicAlignments lib/R/library/GenomicAlignments/R/GenomicAlignments.rdb lib/R/library/GenomicAlignments/R/GenomicAlignments.rdx lib/R/library/GenomicAlignments/doc/GenomicAlignmentsIntroduction.R lib/R/library/GenomicAlignments/doc/GenomicAlignmentsIntroduction.Rnw lib/R/library/GenomicAlignments/doc/GenomicAlignmentsIntroduction.pdf lib/R/library/GenomicAlignments/doc/OverlapEncodings.R lib/R/library/GenomicAlignments/doc/OverlapEncodings.Rnw lib/R/library/GenomicAlignments/doc/OverlapEncodings.pdf lib/R/library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.R lib/R/library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.Rnw lib/R/library/GenomicAlignments/doc/WorkingWithAlignedNucleotides.pdf lib/R/library/GenomicAlignments/doc/index.html lib/R/library/GenomicAlignments/doc/summarizeOverlaps.R lib/R/library/GenomicAlignments/doc/summarizeOverlaps.Rnw lib/R/library/GenomicAlignments/doc/summarizeOverlaps.pdf lib/R/library/GenomicAlignments/extdata/sm_treated1.bam lib/R/library/GenomicAlignments/extdata/sm_untreated1.bam lib/R/library/GenomicAlignments/help/AnIndex lib/R/library/GenomicAlignments/help/GenomicAlignments.rdb lib/R/library/GenomicAlignments/help/GenomicAlignments.rdx lib/R/library/GenomicAlignments/help/aliases.rds lib/R/library/GenomicAlignments/help/paths.rds lib/R/library/GenomicAlignments/html/00Index.html lib/R/library/GenomicAlignments/html/R.css lib/R/library/GenomicAlignments/libs/GenomicAlignments.so lib/R/library/GenomicAlignments/unitTests/test_GAlignments-class.R lib/R/library/GenomicAlignments/unitTests/test_GAlignmentsList-class.R lib/R/library/GenomicAlignments/unitTests/test_cigar-utils.R lib/R/library/GenomicAlignments/unitTests/test_coordinate-mapping-methods.R lib/R/library/GenomicAlignments/unitTests/test_findSpliceOverlaps-methods.R lib/R/library/GenomicAlignments/unitTests/test_intra-range-methods.R lib/R/library/GenomicAlignments/unitTests/test_readGAlignmentPairs.R lib/R/library/GenomicAlignments/unitTests/test_readGAlignments.R lib/R/library/GenomicAlignments/unitTests/test_readGAlignmentsList.R lib/R/library/GenomicAlignments/unitTests/test_summarizeOverlaps-methods.R