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