Files in Bioconductor-mirror/Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/AllClasses.R R/AllGenerics.R R/asBam.R R/countBam.R R/filterBam.R R/idxstatsBam.R R/indexBam.R R/io_bam.R R/mergeBam.R R/methods-ApplyPileupsParam.R R/methods-BamFile.R R/methods-BamFileList.R R/methods-BamSampler.R R/methods-BamViews.R R/methods-BcfFile.R R/methods-FaFile.R R/methods-PileupFiles.R R/methods-RsamtoolsFile.R R/methods-RsamtoolsFileList.R R/methods-ScanBVcfParam.R R/methods-ScanBamParam.R R/methods-TabixFile.R R/phred2ASCIIOffset.R R/pileup.R R/pkgconfig.R R/quickBamFlagSummary.R R/readPileup.R R/scanBam.R R/scanBamHeader.R R/scanBcf.R R/scanBcfHeader.R R/sortBam.R R/testPairedEndBam.R R/utilities.R R/zip_compression.R R/zzz.R
Rsamtools.mk.win
inst/extdata/ce2dict1.fa
inst/extdata/ce2dict1.fa.fai
inst/extdata/ex1.bam
inst/extdata/ex1.bam.bai
inst/extdata/ex1.bcf
inst/extdata/ex1.bcf.bci
inst/extdata/ex1.sam
inst/extdata/example.gtf.gz
inst/extdata/example.gtf.gz.tbi
inst/extdata/example_from_SAM_Spec.bam
inst/extdata/example_from_SAM_Spec.bam.bai
inst/extdata/example_from_SAM_Spec.sam
inst/extdata/no_which_buffered_pileup.bam
inst/extdata/no_which_buffered_pileup.bam.bai
inst/extdata/no_which_buffered_pileup.sam
inst/extdata/no_which_whole_file.bam
inst/extdata/no_which_whole_file.bam.bai
inst/extdata/no_which_whole_file.sam
inst/extdata/olaps.Rda
inst/extdata/pileup.txt
inst/extdata/querybins.bam
inst/extdata/querybins.bam.bai
inst/extdata/querybins.sam
inst/extdata/revbins.bam
inst/extdata/revbins.bam.bai
inst/extdata/revbins.sam
inst/extdata/samtools-github.txt
inst/extdata/slxMaq09_urls.txt
inst/extdata/tagfilter.bam
inst/extdata/tagfilter.bam.bai
inst/extdata/tagfilter.sam
inst/extdata/tiny.bam
inst/extdata/tiny.bam.bai
inst/extdata/tiny.sam
inst/extdata/tophat/README
inst/extdata/tophat/accepted_hits.sam
inst/extdata/tophat/coverage.wig
inst/extdata/tophat/junctions.bed
inst/scripts/BamViews-1000g.R inst/scripts/features.R inst/scripts/remote_test.R
inst/scripts/update-samtools.sh
inst/unitTests/cases/ex1.sam.gz
inst/unitTests/cases/ex1_noindex.bam
inst/unitTests/cases/ex1_shuf1000.bam
inst/unitTests/cases/ex1_shuf1000.bam.bai
inst/unitTests/cases/ex1_unsort.bam
inst/unitTests/cases/ex1_zero_index.bam.bai
inst/unitTests/cases/no_SAMPLE_header.vcf
inst/unitTests/cases/no_header_line.vcf
inst/unitTests/cases/pileup-no-stars.txt
inst/unitTests/cases/plp_refskip.bam
inst/unitTests/cases/plp_refskip.bam.bai
inst/unitTests/test_BamFile.R inst/unitTests/test_BamViews.R inst/unitTests/test_BcfFile.R inst/unitTests/test_FaFile.R inst/unitTests/test_RsamtoolsFile.R inst/unitTests/test_TabixFile.R inst/unitTests/test_applyPileups.R inst/unitTests/test_asBam.R inst/unitTests/test_bam.R inst/unitTests/test_bam_count.R inst/unitTests/test_bam_header.R inst/unitTests/test_compression.R inst/unitTests/test_mapqfilter.R inst/unitTests/test_phred2ASCIIOffset.R inst/unitTests/test_pileup_nowhich.R inst/unitTests/test_pileup_querybins.R inst/unitTests/test_pileup_revbins.R inst/unitTests/test_pileup_single_range.R inst/unitTests/test_readPileup.R inst/unitTests/test_scanBamFlag.R inst/unitTests/test_sortBam_test.R inst/unitTests/test_tagfilter.R inst/unitTests/test_testPairedEndBam.R inst/unitTests/test_utilities.R man/ApplyPileupsParam-class.Rd man/BamFile-class.Rd man/BamViews-class.Rd man/BcfFile-class.Rd man/FaFile-class.Rd man/PileupFiles-class.Rd man/Rsamtools-package.Rd man/RsamtoolsFile-class.Rd man/RsamtoolsFileList-class.Rd man/ScanBamParam-class.Rd man/ScanBcfParam-class.Rd man/TabixFile-class.Rd man/applyPileups.Rd man/defunct.Rd man/deprecated.Rd man/headerTabix.Rd man/indexTabix.Rd man/pileup.Rd man/quickBamFlagSummary.Rd man/readPileup.Rd man/scanBam.Rd man/scanBcf.Rd man/scanFa.Rd man/scanTabix.Rd man/seqnamesTabix.Rd man/testPairedEndBam.Rd man/zip.Rd
src/BamFileIterator.h
src/BamIterator.h
src/BamRangeIterator.h
src/Biostrings_stubs.c
src/GenomicPosition.h
src/IRanges_stubs.c
src/Makevars
src/Makevars.common
src/Makevars.win
src/PileupBuffer.cpp
src/PileupBuffer.h
src/PileupBufferShim.h
src/PosCache.h
src/PosCacheColl.cpp
src/PosCacheColl.h
src/R_init_Rsamtools.c
src/ResultManager.cpp
src/ResultManager.h
src/S4Vectors_stubs.c
src/Template.h
src/XVector_stubs.c
src/as_bam.c
src/as_bam.h
src/bam_data.c
src/bam_data.h
src/bam_mate_iter.cpp
src/bam_mate_iter.h
src/bambuffer.c
src/bambuffer.h
src/bamfile.c
src/bamfile.h
src/bcffile.c
src/bcffile.h
src/encode.c
src/encode.h
src/fafile.c
src/fafile.h
src/idxstats.c
src/idxstats.h
src/io_sam.c
src/io_sam.h
src/pbuffer_wrapper.cpp
src/pbuffer_wrapper.h
src/pileup.cpp
src/pileup.h
src/pileupbam.c
src/pileupbam.h
src/samtools/bam.c
src/samtools/bam.h
src/samtools/bam_aux.c
src/samtools/bam_endian.h
src/samtools/bam_import.c
src/samtools/bam_index.c
src/samtools/bam_lpileup.c
src/samtools/bam_md.c
src/samtools/bam_pileup.c
src/samtools/bam_reheader.c
src/samtools/bam_sort.c
src/samtools/bcftools/bcf.c
src/samtools/bcftools/bcf.h
src/samtools/bcftools/bcf2qcall.c
src/samtools/bcftools/bcfutils.c
src/samtools/bcftools/fet.c
src/samtools/bcftools/index.c
src/samtools/bcftools/prob1.c
src/samtools/bcftools/prob1.h
src/samtools/bcftools/vcf.c
src/samtools/bgzf.c
src/samtools/bgzf.h
src/samtools/faidx.c
src/samtools/faidx.h
src/samtools/kaln.h
src/samtools/khash.h
src/samtools/knetfile.c
src/samtools/knetfile.h
src/samtools/kprobaln.c
src/samtools/kprobaln.h
src/samtools/kseq.h
src/samtools/ksort.h
src/samtools/kstring.c
src/samtools/kstring.h
src/samtools/razf.c
src/samtools/razf.h
src/samtools/sam.c
src/samtools/sam.h
src/samtools/sam_header.c
src/samtools/sam_header.h
src/samtools_patch.c
src/samtools_patch.h
src/scan_bam_data.c
src/scan_bam_data.h
src/tabix/bedidx.c
src/tabix/index.c
src/tabix/tabix.h
src/tabixfile.c
src/tabixfile.h
src/tagfilter.c
src/tagfilter.h
src/utilities.c
src/utilities.h
src/zip_compression.c
src/zip_compression.h
tests/Rsamtools_unit_tests.R
vignettes/Rsamtools-Overview.Rnw
vignettes/Rsamtools-UsingCLibraries.Rnw
Bioconductor-mirror/Rsamtools documentation built on June 1, 2017, 1:10 a.m.