lib/R/library/Rsamtools/DESCRIPTION lib/R/library/Rsamtools/INDEX lib/R/library/Rsamtools/LICENSE lib/R/library/Rsamtools/Meta/Rd.rds lib/R/library/Rsamtools/Meta/features.rds lib/R/library/Rsamtools/Meta/hsearch.rds lib/R/library/Rsamtools/Meta/links.rds lib/R/library/Rsamtools/Meta/nsInfo.rds lib/R/library/Rsamtools/Meta/package.rds lib/R/library/Rsamtools/Meta/vignette.rds lib/R/library/Rsamtools/NAMESPACE lib/R/library/Rsamtools/NEWS lib/R/library/Rsamtools/R/Rsamtools lib/R/library/Rsamtools/R/Rsamtools.rdb lib/R/library/Rsamtools/R/Rsamtools.rdx lib/R/library/Rsamtools/doc/Rsamtools-Overview.R lib/R/library/Rsamtools/doc/Rsamtools-Overview.Rnw lib/R/library/Rsamtools/doc/Rsamtools-Overview.pdf lib/R/library/Rsamtools/doc/index.html lib/R/library/Rsamtools/extdata/ce2dict1.fa lib/R/library/Rsamtools/extdata/ce2dict1.fa.fai lib/R/library/Rsamtools/extdata/ex1.bam lib/R/library/Rsamtools/extdata/ex1.bam.bai lib/R/library/Rsamtools/extdata/ex1.bcf.gz lib/R/library/Rsamtools/extdata/ex1.bcf.gz.csi lib/R/library/Rsamtools/extdata/ex1.sam lib/R/library/Rsamtools/extdata/ex1.vcf.gz lib/R/library/Rsamtools/extdata/ex1.vcf.gz.csi lib/R/library/Rsamtools/extdata/example.gtf.gz lib/R/library/Rsamtools/extdata/example.gtf.gz.tbi lib/R/library/Rsamtools/extdata/example_from_SAM_Spec.bam lib/R/library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai lib/R/library/Rsamtools/extdata/example_from_SAM_Spec.sam lib/R/library/Rsamtools/extdata/no_which_buffered_pileup.bam lib/R/library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai lib/R/library/Rsamtools/extdata/no_which_buffered_pileup.sam lib/R/library/Rsamtools/extdata/no_which_whole_file.bam lib/R/library/Rsamtools/extdata/no_which_whole_file.bam.bai lib/R/library/Rsamtools/extdata/no_which_whole_file.sam lib/R/library/Rsamtools/extdata/olaps.Rda lib/R/library/Rsamtools/extdata/pileup.txt lib/R/library/Rsamtools/extdata/querybins.bam lib/R/library/Rsamtools/extdata/querybins.bam.bai lib/R/library/Rsamtools/extdata/querybins.sam lib/R/library/Rsamtools/extdata/revbins.bam lib/R/library/Rsamtools/extdata/revbins.bam.bai lib/R/library/Rsamtools/extdata/revbins.sam lib/R/library/Rsamtools/extdata/samtools-github.txt lib/R/library/Rsamtools/extdata/slxMaq09_urls.txt lib/R/library/Rsamtools/extdata/tagfilter.bam lib/R/library/Rsamtools/extdata/tagfilter.bam.bai lib/R/library/Rsamtools/extdata/tagfilter.sam lib/R/library/Rsamtools/extdata/tiny.bam lib/R/library/Rsamtools/extdata/tiny.bam.bai lib/R/library/Rsamtools/extdata/tiny.sam lib/R/library/Rsamtools/extdata/tophat/README lib/R/library/Rsamtools/extdata/tophat/accepted_hits.sam lib/R/library/Rsamtools/extdata/tophat/coverage.wig lib/R/library/Rsamtools/extdata/tophat/junctions.bed lib/R/library/Rsamtools/help/AnIndex lib/R/library/Rsamtools/help/Rsamtools.rdb lib/R/library/Rsamtools/help/Rsamtools.rdx lib/R/library/Rsamtools/help/aliases.rds lib/R/library/Rsamtools/help/paths.rds lib/R/library/Rsamtools/html/00Index.html lib/R/library/Rsamtools/html/R.css lib/R/library/Rsamtools/libs/Rsamtools.so lib/R/library/Rsamtools/scripts/BamViews-1000g.R lib/R/library/Rsamtools/scripts/features.R lib/R/library/Rsamtools/scripts/remote_test.R lib/R/library/Rsamtools/scripts/update-samtools.sh lib/R/library/Rsamtools/unitTests/cases/RNEXT.bam lib/R/library/Rsamtools/unitTests/cases/ex1.sam.gz lib/R/library/Rsamtools/unitTests/cases/ex1_noindex.bam lib/R/library/Rsamtools/unitTests/cases/ex1_shuf1000.bam lib/R/library/Rsamtools/unitTests/cases/ex1_shuf1000.bam.bai lib/R/library/Rsamtools/unitTests/cases/ex1_unsort.bam lib/R/library/Rsamtools/unitTests/cases/ex1_zero_index.bam.bai lib/R/library/Rsamtools/unitTests/cases/no_SAMPLE_header.vcf.gz lib/R/library/Rsamtools/unitTests/cases/no_header_line.vcf.gz lib/R/library/Rsamtools/unitTests/cases/pileup-no-stars.txt lib/R/library/Rsamtools/unitTests/cases/plp_refskip.bam lib/R/library/Rsamtools/unitTests/cases/plp_refskip.bam.bai lib/R/library/Rsamtools/unitTests/test_BamFile.R lib/R/library/Rsamtools/unitTests/test_BamViews.R lib/R/library/Rsamtools/unitTests/test_BcfFile.R lib/R/library/Rsamtools/unitTests/test_FaFile.R lib/R/library/Rsamtools/unitTests/test_RsamtoolsFile.R lib/R/library/Rsamtools/unitTests/test_TabixFile.R lib/R/library/Rsamtools/unitTests/test_applyPileups.R lib/R/library/Rsamtools/unitTests/test_asBam.R lib/R/library/Rsamtools/unitTests/test_bam.R lib/R/library/Rsamtools/unitTests/test_bam_count.R lib/R/library/Rsamtools/unitTests/test_bam_header.R lib/R/library/Rsamtools/unitTests/test_compression.R lib/R/library/Rsamtools/unitTests/test_mapqfilter.R lib/R/library/Rsamtools/unitTests/test_phred2ASCIIOffset.R lib/R/library/Rsamtools/unitTests/test_pileup_nowhich.R lib/R/library/Rsamtools/unitTests/test_pileup_querybins.R lib/R/library/Rsamtools/unitTests/test_pileup_revbins.R lib/R/library/Rsamtools/unitTests/test_pileup_single_range.R lib/R/library/Rsamtools/unitTests/test_readPileup.R lib/R/library/Rsamtools/unitTests/test_scanBamFlag.R lib/R/library/Rsamtools/unitTests/test_sortBam_test.R lib/R/library/Rsamtools/unitTests/test_tagfilter.R lib/R/library/Rsamtools/unitTests/test_testPairedEndBam.R lib/R/library/Rsamtools/unitTests/test_utilities.R