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

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65
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Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
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API

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

Global functions
.BamFile_guessIndex Source code
.BamViews_delegate Source code
.BamViews_which Source code
.RsamtoolsFile Source code
.ScanBcfParam Source code
.apply_bin_levels Source code
.as.data.frame_list_of_lists Source code
.as.factor_bin Source code
.as.list_PileupParam Source code
.ascii_offset Source code
.bcfHeaderAsSimpleList Source code
.bcf_template Source code
.bin_levels Source code
.build_path Source code
.calcBitPos Source code
.checkPrefixSuffix Source code
.check_qname_arg Source code
.countBam_postprocess Source code
.detailedSummary Source code
.extptr Source code
.file.rename Source code
.filterBam_FilterRules Source code
.filterBam_preprocess Source code
.findMateWithinGroups Source code
.has.wholenumbers Source code
.headerTabix Source code
.io_bam Source code
.io_bcf Source code
.io_check_exists Source code
.isValidHit Source code
.load_bamcols_from_scanBam_res Source code
.make_unique Source code
.metacols_run_lengths Source code
.normalizePath Source code
.normalizeRangesList Source code
.normalize_tagFilter Source code
.onLoad Source code
.phred2ascii_char Source code
.phred2ascii_int Source code
.pileup Source code
.pileupWhat Source code
.pkgLd Source code
.pkgMk Source code
.ppath Source code
.preprocess_bins Source code
.printDetailedSummary Source code
.printMainSummary Source code
.printSummaryHeader Source code
.printSummaryLine Source code
.readPileup_SNP Source code
.readPileup_indel Source code
.readPileup_indel_idx Source code
.readPileup_table Source code
.runlen Source code
.scanBamTemplate Source code
.scanBam_extract_which_labels Source code
.scanBam_postprocess Source code
.scanBam_template Source code
.scanFa Source code
.schemaBuilder Source code
.seqnamesTabix Source code
.show_classname Source code
.strandHelper Source code
.tabix_scan Source code
.uunlist Source code
.zip Source code
ApplyPileupsParam Man page Source code
ApplyPileupsParam-class Man page
BamFile Man page Source code
BamFile-class Man page
BamFileList Man page Source code
BamFileList-class Man page
BamSampler Man page
BamSampler-class Man page
BamViews Man page
BamViews,GRanges-method Man page
BamViews,missing-method Man page
BamViews-class Man page
BcfFile Man page Source code
BcfFile-class Man page
BcfFileList Man page Source code
BcfFileList-class Man page
FLAG_BITNAMES Man page
FaFile Man page Source code
FaFile-class Man page
FaFileList Man page Source code
FaFileList-class Man page
PileupFiles Man page Source code
PileupFiles,character-method Man page
PileupFiles,list-method Man page
PileupFiles-class Man page
PileupParam Man page Source code
PileupParam-class Man page
Rsamtools Man page
Rsamtools-package Man page
RsamtoolsFile Man page
RsamtoolsFile-class Man page
RsamtoolsFileList Man page
RsamtoolsFileList-class Man page
ScanBVcfParam-class Man page
ScanBamParam Man page
ScanBamParam,ANY-method Man page
ScanBamParam,GRanges-method Man page
ScanBamParam,IntegerRangesList-method Man page
ScanBamParam,missing-method Man page
ScanBamParam-class Man page
ScanBcfParam Man page
ScanBcfParam,GRanges-method Man page
ScanBcfParam,GRangesList-method Man page
ScanBcfParam,IntegerRangesList-method Man page
ScanBcfParam,missing-method Man page
ScanBcfParam-class Man page
TabixFile Man page Source code
TabixFile-class Man page
TabixFileList Man page Source code
TabixFileList-class Man page
[,BamViews,ANY,ANY-method Man page
[,BamViews,ANY,missing-method Man page Man page
[,BamViews,missing,ANY-method Man page
`bamDirname<-` Source code
`bamRanges<-` Source code
`bamSamples<-` Source code
applyPileups 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,BamFile-method Man page
asMates,BamFileList-method Man page
asMates<- Man page
asMates<-,BamFile-method Man page
asMates<-,BamFileList-method Man page
asSam Man page
asSam,character-method Man page
bamDirname<- Man page
bamExperiment Man page Source code
bamFlag Man page Source code
bamFlag<- Man page
bamFlagAND Man page Source code
bamFlagAsBitMatrix Man page Source code
bamFlagTest Man page Source code
bamIndicies Man page Source code
bamMapqFilter Man page Source code
bamMapqFilter<- Man page
bamPaths Man page Source code
bamRanges Man page Source code
bamRanges<- Man page
bamReverseComplement Man page Source code
bamReverseComplement<- Man page
bamSamples Man page Source code
bamSamples<- Man page
bamSimpleCigar Man page Source code
bamSimpleCigar<- Man page
bamTag Man page Source code
bamTag<- Man page
bamTagFilter Man page Source code
bamTagFilter<- Man page
bamWhat Man page Source code
bamWhat<- Man page
bamWhich Man page Source code
bamWhich<- Man page
bamWhich<-,ScanBamParam,ANY-method Man page
bamWhich<-,ScanBamParam,GRanges-method Man page
bamWhich<-,ScanBamParam,IntegerRangesList-method Man page
bcfFixed Man page Source code
bcfGeno Man page Source code
bcfInfo Man page Source code
bcfMode Man page Source code
bcfSamples Man page Source code
bcfTrimEmpty Man page Source code
bcfWhich Man page Source code
bgzip Man page Source code
bgzipTabix Man page Source code
bzfile-class Man page
close.BamFile Man page Source code
close.BcfFile Man page Source code
close.FaFile Man page Source code
close.RsamtoolsFileList Man page Source code
close.TabixFile Man page Source code
countBam Man page
countBam,BamFile-method Man page
countBam,BamFileList-method Man page
countBam,BamViews-method Man page
countBam,character-method Man page
countFa Man page
countFa,FaFile-method Man page
countFa,character-method Man page
countTabix Man page Source code
cycle_bins Man page
dim,BamViews-method Man page
dimnames,BamViews-method Man page
dimnames<-,BamViews,ANY-method Man page
dimnames<-,BamViews-method Man page
distinguish_nucleotides Man page
distinguish_strands Man page
fifo-class Man page
filterBam Man page
filterBam,BamFile-method Man page
filterBam,character-method Man page
getSeq,FaFile-method Man page
getSeq,FaFileList-method Man page
gzfile-class Man page
gzindex Man page
gzindex,FaFile-method Man page
gzindex,FaFileList-method Man page
gzindex<- Man page
gzindex<-,FaFile-method Man page
gzindex<-,FaFileList-method Man page
hasUnmappedMate Man page
headerTabix Man page
headerTabix,TabixFile-method Man page
headerTabix,character-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
index,RsamtoolsFile-method Man page
index,RsamtoolsFileList-method Man page
index<- Man page
index<-,RsamtoolsFile-method Man page
index<-,RsamtoolsFileList-method 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,FaFile-method Man page
indexFa,character-method Man page
indexTabix Man page Source code
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,RsamtoolsFile-method Man page
isOpen,RsamtoolsFileList-method Man page
isOpen,TabixFile-method Man page
isPaired Man page
isProperPair Man page
isSecondMateRead Man page
isSecondaryAlignment 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,RsamtoolsFileList-method Man page
names<-,BamViews-method Man page
obeyQname Man page
obeyQname,BamFile-method Man page
obeyQname,BamFileList-method Man page
obeyQname<- Man page
obeyQname<-,BamFile-method Man page
obeyQname<-,BamFileList-method Man page
open.BamFile Man page Source code
open.BcfFile Man page Source code
open.FaFile Man page Source code
open.RsamtoolsFileList Man page Source code
open.TabixFile Man page Source code
path Man page
path,RsamtoolsFile-method Man page
path,RsamtoolsFileList-method Man page
phred2ASCIIOffset Man page Source code
pileup Man page
pileup,BamFile-method Man page
pileup,character-method Man page
pipe-class Man page
plpFiles Man page Source code
plpFlag Man page Source code
plpFlag<- Man page
plpMaxDepth Man page Source code
plpMaxDepth<- Man page
plpMinBaseQuality Man page Source code
plpMinBaseQuality<- Man page
plpMinDepth Man page Source code
plpMinDepth<- Man page
plpMinMapQuality Man page Source code
plpMinMapQuality<- Man page
plpParam Man page Source code
plpWhat Man page Source code
plpWhat<- Man page
plpWhich Man page Source code
plpWhich<- Man page
plpYieldAll Man page Source code
plpYieldAll<- Man page
plpYieldBy Man page Source code
plpYieldBy<- Man page
plpYieldSize Man page Source code
plpYieldSize<- Man page
qnamePrefixEnd Man page
qnamePrefixEnd,BamFile-method Man page
qnamePrefixEnd,BamFileList-method Man page
qnamePrefixEnd<- Man page
qnamePrefixEnd<-,BamFile-method Man page
qnamePrefixEnd<-,BamFileList-method Man page
qnameSuffixStart Man page
qnameSuffixStart,BamFile-method Man page
qnameSuffixStart,BamFileList-method Man page
qnameSuffixStart<- Man page
qnameSuffixStart<-,BamFile-method Man page
qnameSuffixStart<-,BamFileList-method Man page
query_bins Man page
quickBamCounts Man page Source code
quickBamFlagSummary Man page
quickBamFlagSummary,BamFile-method Man page
quickBamFlagSummary,character-method Man page
quickBamFlagSummary,list-method Man page
quickCountBam Man page Source code
razip Man page Source code
readPileup Man page
readPileup,character-method Man page
readPileup,connection-method 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 Source code
scanBamHeader Man page
scanBamHeader,BamFile-method Man page
scanBamHeader,character-method Man page
scanBamWhat Man page Source code
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
scanFa Man page
scanFa,FaFile,GRanges-method Man page
scanFa,FaFile,IntegerRangesList-method Man page
scanFa,FaFile,missing-method Man page
scanFa,character,GRanges-method Man page
scanFa,character,IntegerRangesList-method Man page
scanFa,character,missing-method Man page
scanFaIndex Man page
scanFaIndex,FaFile-method Man page
scanFaIndex,FaFileList-method Man page
scanFaIndex,character-method Man page
scanTabix Man page
scanTabix,TabixFile,GRanges-method Man page
scanTabix,TabixFile,IntegerRangesList-method Man page
scanTabix,TabixFile,missing-method Man page
scanTabix,character,ANY-method Man page
scanTabix,character,GRanges-method Man page
scanTabix,character,IntegerRangesList-method Man page
scanTabix,character,missing-method Man page
seqinfo,BamFile-method Man page
seqinfo,BamFileList-method Man page
seqinfo,FaFile-method Man page
seqnamesTabix Man page
seqnamesTabix,TabixFile-method Man page
seqnamesTabix,character-method Man page
show,ApplyPileupsParam-method Man page
show,BamFile-method Man page
show,BamFileList-method Man page
show,BamSampler-method Man page
show,BamViews-method Man page
show,FaFile-method Man page
show,PileupFiles-method Man page
show,PileupParam-method Man page
show,RsamtoolsFile-method Man page
show,ScanBVcfParam-method Man page
show,ScanBamParam-method Man page
sortBam Man page
sortBam,BamFile-method Man page
sortBam,character-method 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,RsamtoolsFile-method Man page
yieldSize,RsamtoolsFileList-method Man page
yieldSize<- Man page
yieldSize<-,RsamtoolsFile-method Man page
yieldSize<-,RsamtoolsFileList-method Man page
yieldTabix Man page
yieldTabix,TabixFile-method Man page
Rsamtools documentation built on Nov. 8, 2020, 8:11 p.m.

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