Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities (see 'LICENCE') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

AuthorMartin Morgan, Herv\'e Pag\`es, Valerie Obenchain, Nathaniel Hayden
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0 | file LICENSE
Version1.26.1
http://bioconductor.org/packages/release/bioc/html/Rsamtools.html

View on Bioconductor

Man pages

applyPileups: Apply a user-provided function to calculate pile-up...

ApplyPileupsParam-class: Parameters for creating pileups from BAM files

BamFile-class: Maintain and use BAM files

BamViews-class: Views into a set of BAM files

BcfFile-class: Manipulate BCF files.

defunct: Rsamtools Deprecated and Defunct

deprecated: Deprecated functions

FaFile-class: Manipulate indexed fasta files.

headerTabix: Retrieve sequence names defined in a tabix file.

indexTabix: Compress and index tabix-compatible files.

pileup: Use filters and output formats to calculate pile-up...

PileupFiles-class: Represent BAM files for pileup summaries.

quickBamFlagSummary: Group the records of a BAM file based on their flag bits and...

readPileup: Import samtools 'pileup' files.

RsamtoolsFile-class: A base class for managing file references in Rsamtools

RsamtoolsFileList-class: A base class for managing lists of Rsamtools file references

Rsamtools-package: 'samtools' aligned sequence utilities interface

scanBam: Import, count, index, filter, sort, and merge 'BAM' (binary...

ScanBamParam-class: Parameters for scanning BAM files

scanBcf: Operations on 'BCF' files.

ScanBcfParam-class: Parameters for scanning BCF files

scanFa: Operations on indexed 'fasta' files.

scanTabix: Operations on 'tabix' (indexed, tab-delimited) files.

seqnamesTabix: Retrieve sequence names defined in a tabix file.

TabixFile-class: Manipulate tabix indexed tab-delimited files.

testPairedEndBam: Quickly test if a BAM file has paired end reads

zip: File compression for tabix (bgzip) and fasta (razip) files.

Functions

applyPileups Man page
ApplyPileupsParam Man page
ApplyPileupsParam-class Man page
applyPileups,PileupFiles,ApplyPileupsParam-method Man page
applyPileups,PileupFiles,missing-method Man page
asBam Man page
asBam,character-method Man page
asBcf Man page
asBcf,character-method Man page
asMates Man page
asMates<- Man page
asMates<-,BamFileList-method Man page
asMates,BamFileList-method Man page
asMates<-,BamFile-method Man page
asMates,BamFile-method Man page
asSam Man page
asSam,character-method Man page
bamDirname<- Man page
bamExperiment Man page
BamFile Man page
BamFile-class Man page
BamFileList Man page
BamFileList-class Man page
bamFlag Man page
bamFlag<- Man page
bamFlagAND Man page
bamFlagAsBitMatrix Man page
bamFlagTest Man page
bamIndicies Man page
bamMapqFilter Man page
bamMapqFilter<- Man page
bamPaths Man page
bamRanges Man page
bamRanges<- Man page
bamReverseComplement Man page
bamReverseComplement<- Man page
BamSampler Man page
BamSampler-class Man page
bamSamples Man page
bamSamples<- Man page
bamSimpleCigar Man page
bamSimpleCigar<- Man page
bamTag Man page
bamTag<- Man page
bamTagFilter Man page
bamTagFilter<- Man page
BamViews Man page
[,BamViews,ANY,ANY-method Man page
[,BamViews,ANY,missing-method Man page
[,BamViews,ANY,missing-method Man page
BamViews-class Man page
BamViews,GRanges-method Man page
[,BamViews,missing,ANY-method Man page
BamViews,missing-method Man page
bamWhat Man page
bamWhat<- Man page
bamWhich Man page
bamWhich<- Man page
bamWhich<-,ScanBamParam,ANY-method Man page
bamWhich<-,ScanBamParam,GRanges-method Man page
bamWhich<-,ScanBamParam,RangesList-method Man page
BcfFile Man page
BcfFile-class Man page
BcfFileList Man page
BcfFileList-class Man page
bcfFixed Man page
bcfGeno Man page
bcfInfo Man page
bcfMode Man page
bcfSamples Man page
bcfTrimEmpty Man page
bcfWhich Man page
bgzip Man page
bgzipTabix Man page
bzfile-class Man page
close.BamFile Man page
close.BcfFile Man page
close.FaFile Man page
close.PileupFiles Man page
close.RsamtoolsFileList Man page
close.TabixFile Man page
countBam Man page
countBam,BamFileList-method Man page
countBam,BamFile-method Man page
countBam,BamViews-method Man page
countBam,character-method Man page
countFa Man page
countFa,character-method Man page
countFa,FaFile-method Man page
countTabix Man page
cycle_bins Man page
dim,BamViews-method Man page
dimnames<-,BamViews,ANY-method Man page
dimnames<-,BamViews-method Man page
dimnames,BamViews-method Man page
distinguish_nucleotides Man page
distinguish_strands Man page
FaFile Man page
FaFile-class Man page
FaFileList Man page
FaFileList-class Man page
fifo-class Man page
filterBam Man page
filterBam,BamFile-method Man page
filterBam,character-method Man page
FLAG_BITNAMES Man page
getSeq,FaFileList-method Man page
getSeq,FaFile-method Man page
gzfile-class Man page
hasUnmappedMate Man page
headerTabix Man page
headerTabix,character-method Man page
headerTabix,TabixFile-method Man page
idxstatsBam Man page
idxstatsBam,BamFile-method Man page
idxstatsBam,character-method Man page
ignore_query_Ns Man page
include_deletions Man page
include_insertions Man page
index Man page
indexBam Man page
indexBam,BamFile-method Man page
indexBam,character-method Man page
indexBcf Man page
indexBcf,BcfFile-method Man page
indexBcf,character-method Man page
indexFa Man page
indexFa,character-method Man page
indexFa,FaFile-method Man page
indexTabix Man page
isDuplicate Man page
isFirstMateRead Man page
isIncomplete,BamFile-method Man page
isMateMinusStrand Man page
isMinusStrand Man page
isNotPassingQualityControls Man page
isNotPrimaryRead Man page
isOpen,BamFile-method Man page
isOpen,BcfFile-method Man page
isOpen,FaFile-method Man page
isOpen,PileupFiles-method Man page
isOpen,RsamtoolsFileList-method Man page
isOpen,RsamtoolsFile-method Man page
isOpen,TabixFile-method Man page
isPaired Man page
isProperPair Man page
isSecondaryAlignment Man page
isSecondMateRead Man page
isUnmappedQuery Man page
left_bins Man page
max_depth Man page
mergeBam Man page
mergeBam,BamFileList-method Man page
mergeBam,character-method Man page
min_base_quality Man page
min_mapq Man page
min_minor_allele_depth Man page
min_nucleotide_depth Man page
names<-,BamViews-method Man page
names,BamViews-method Man page
names,RsamtoolsFileList-method Man page
obeyQname Man page
obeyQname<- Man page
obeyQname<-,BamFileList-method Man page
obeyQname,BamFileList-method Man page
obeyQname<-,BamFile-method Man page
obeyQname,BamFile-method Man page
open.BamFile Man page
open.BcfFile Man page
open.FaFile Man page
open.PileupFiles Man page
open.RsamtoolsFileList Man page
open.TabixFile Man page
path Man page
path,RsamtoolsFileList-method Man page
path,RsamtoolsFile-method Man page
phred2ASCIIOffset Man page
pileup Man page
pileup,BamFile-method Man page
pileup,character-method Man page
PileupFiles Man page
PileupFiles,character-method Man page
PileupFiles-class Man page
PileupFiles,list-method Man page
PileupParam Man page
PileupParam-class Man page
pipe-class Man page
plpFiles Man page
plpFlag Man page
plpFlag<- Man page
plpMaxDepth Man page
plpMaxDepth<- Man page
plpMinBaseQuality Man page
plpMinBaseQuality<- Man page
plpMinDepth Man page
plpMinDepth<- Man page
plpMinMapQuality Man page
plpMinMapQuality<- Man page
plpParam Man page
plpWhat Man page
plpWhat<- Man page
plpWhich Man page
plpWhich<- Man page
plpYieldAll Man page
plpYieldAll<- Man page
plpYieldBy Man page
plpYieldBy<- Man page
plpYieldSize Man page
plpYieldSize<- Man page
qnamePrefixEnd Man page
qnamePrefixEnd<- Man page
qnamePrefixEnd<-,BamFileList-method Man page
qnamePrefixEnd,BamFileList-method Man page
qnamePrefixEnd<-,BamFile-method Man page
qnamePrefixEnd,BamFile-method Man page
qnameSuffixStart Man page
qnameSuffixStart<- Man page
qnameSuffixStart<-,BamFileList-method Man page
qnameSuffixStart,BamFileList-method Man page
qnameSuffixStart<-,BamFile-method Man page
qnameSuffixStart,BamFile-method Man page
query_bins Man page
quickBamCounts Man page
quickBamFlagSummary Man page
quickBamFlagSummary,BamFile-method Man page
quickBamFlagSummary,character-method Man page
quickBamFlagSummary,list-method Man page
quickCountBam Man page
razip Man page
readPileup Man page
readPileup,character-method Man page
readPileup,connection-method Man page
Rsamtools Man page
RsamtoolsFile-class Man page
RsamtoolsFileList Man page
RsamtoolsFileList-class Man page
Rsamtools-package Man page
scanBam Man page
scanBam,BamFile-method Man page
scanBam,BamSampler-method Man page
scanBam,BamViews-method Man page
scanBam,character-method Man page
scanBamFlag Man page
scanBamHeader Man page
scanBamHeader,BamFile-method Man page
scanBamHeader,character-method Man page
ScanBamParam Man page
ScanBamParam,ANY-method Man page
ScanBamParam-class Man page
ScanBamParam,GRanges-method Man page
ScanBamParam,missing-method Man page
ScanBamParam,RangesList-method Man page
scanBamWhat Man page
scanBcf Man page
scanBcf,BcfFile-method Man page
scanBcf,character-method Man page
scanBcfHeader Man page
scanBcfHeader,BcfFile-method Man page
scanBcfHeader,character-method Man page
ScanBcfParam Man page
ScanBcfParam-class Man page
ScanBcfParam,GRangesList-method Man page
ScanBcfParam,GRanges-method Man page
ScanBcfParam,missing-method Man page
ScanBcfParam,RangesList-method Man page
ScanBVcfParam-class Man page
scanFa Man page
scanFa,character,GRanges-method Man page
scanFa,character,missing-method Man page
scanFa,character,RangesList-method Man page
scanFa,FaFile,GRanges-method Man page
scanFa,FaFile,missing-method Man page
scanFa,FaFile,RangesList-method Man page
scanFaIndex Man page
scanFaIndex,character-method Man page
scanFaIndex,FaFileList-method Man page
scanFaIndex,FaFile-method Man page
scanTabix Man page
scanTabix,character,ANY-method Man page
scanTabix,character,GRanges-method Man page
scanTabix,character,missing-method Man page
scanTabix,character,RangesList-method Man page
scanTabix,TabixFile,GRanges-method Man page
scanTabix,TabixFile,missing-method Man page
scanTabix,TabixFile,RangesList-method Man page
seqinfo,BamFileList-method Man page
seqinfo,BamFile-method Man page
seqinfo,FaFile-method Man page
seqnamesTabix Man page
seqnamesTabix,character-method Man page
seqnamesTabix,TabixFile-method Man page
show,ApplyPileupsParam-method Man page
show,BamFileList-method Man page
show,BamFile-method Man page
show,BamSampler-method Man page
show,BamViews-method Man page
show,PileupFiles-method Man page
show,PileupParam-method Man page
show,RsamtoolsFile-method Man page
show,ScanBamParam-method Man page
show,ScanBVcfParam-method Man page
sortBam Man page
sortBam,BamFile-method Man page
sortBam,character-method Man page
TabixFile Man page
TabixFile-class Man page
TabixFileList Man page
TabixFileList-class Man page
testPairedEndBam Man page
testPairedEndBam,BamFile-method Man page
testPairedEndBam,character-method Man page
unz-class Man page
url-class Man page
yieldBam Man page
yieldSize Man page
yieldSize<- Man page
yieldSize<-,RsamtoolsFileList-method Man page
yieldSize,RsamtoolsFileList-method Man page
yieldSize<-,RsamtoolsFile-method Man page
yieldSize,RsamtoolsFile-method Man page
yieldTabix Man page
yieldTabix,TabixFile-method Man page

Files

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

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