Rsamtools-package	Rsamtools-package
asBam	scanBam
asBam,character-method	scanBam
bamDirname<-	BamViews-class
bamExperiment	BamViews-class
BamFile	BamFile-class
BamFile-class	BamFile-class
bamFlag	ScanBamParam-class
bamFlag<-	ScanBamParam-class
bamIndicies	BamViews-class
bamPaths	BamViews-class
bamRanges	BamViews-class
bamRanges<-	BamViews-class
bamReverseComplement	ScanBamParam-class
bamReverseComplement<-	ScanBamParam-class
bamSamples	BamViews-class
bamSamples<-	BamViews-class
bamSimpleCigar	ScanBamParam-class
bamSimpleCigar<-	ScanBamParam-class
bamTag	ScanBamParam-class
bamTag<-	ScanBamParam-class
BamViews	BamViews-class
BamViews,GRanges-method	BamViews-class
BamViews,missing-method	BamViews-class
BamViews,RangedData-method	BamViews-class
BamViews-class	BamViews-class
bamWhat	ScanBamParam-class
bamWhat<-	ScanBamParam-class
bamWhich	ScanBamParam-class
bamWhich<-	ScanBamParam-class
BcfFile	BcfFile-class
BcfFile-class	BcfFile-class
bcfGeno	ScanBcfParam-class
bcfInfo	ScanBcfParam-class
bcfMode	BcfFile-class
bcfTrimEmpty	ScanBcfParam-class
bcfWhich	ScanBcfParam-class
bzfile-class	Rsamtools-package
close.BamFile	BamFile-class
close.BcfFile	BcfFile-class
close.FaFile	FaFile-class
countBam	scanBam
countBam,BamFile-method	BamFile-class
countBam,BamViews-method	BamViews-class
countBam,character-method	scanBam
countFa	scanFa
countFa,character-method	scanFa
countFa,FaFile-method	FaFile-class
dim,BamViews-method	BamViews-class
dimnames,BamViews-method	BamViews-class
dimnames<-,BamViews,ANY-method	BamViews-class
FaFile	FaFile-class
FaFile-class	FaFile-class
fifo-class	Rsamtools-package
filterBam	scanBam
filterBam,BamFile-method	BamFile-class
filterBam,character-method	scanBam
gzfile-class	Rsamtools-package
index	RsamtoolsFile-class
indexBam	scanBam
indexBam,BamFile-method	BamFile-class
indexBam,character-method	scanBam
indexFa	scanFa
indexFa,character-method	scanFa
indexFa,FaFile-method	FaFile-class
isOpen,BamFile-method	BamFile-class
isOpen,BcfFile-method	BcfFile-class
isOpen,FaFile-method	FaFile-class
isOpen,RsamtoolsFile-method	RsamtoolsFile-class
names,BamViews-method	BamViews-class
names<-,BamViews-method	BamViews-class
open.BamFile	BamFile-class
open.BcfFile	BcfFile-class
open.FaFile	FaFile-class
path	RsamtoolsFile-class
pipe-class	Rsamtools-package
readBamGappedAlignments	readBamGappedAlignments
readBamGappedAlignments,BamFile-method	BamFile-class
readBamGappedAlignments,BamViews-method	BamViews-class
readBamGappedAlignments,character-method	readBamGappedAlignments
readPileup	readPileup
readPileup,character-method	readPileup
readPileup,connection-method	readPileup
Rsamtools	Rsamtools-package
RsamtoolsFile-class	RsamtoolsFile-class
scanBam	scanBam
scanBam,BamFile-method	BamFile-class
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,GRanges-method	ScanBamParam-class
ScanBamParam,missing-method	ScanBamParam-class
ScanBamParam,RangedData-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,missing-method	ScanBcfParam-class
ScanBcfParam,RangedData-method	ScanBcfParam-class
ScanBcfParam,RangesList-method	ScanBcfParam-class
ScanBcfParam-class	ScanBcfParam-class
scanFa	scanFa
scanFa,character,GRanges-method	scanFa
scanFa,character,missing-method	scanFa
scanFa,FaFile,GRanges-method	FaFile-class
scanFa,FaFile,missing-method	FaFile-class
scanFaIndex	scanFa
scanFaIndex,character-method	scanFa
scanFaIndex,FaFile-method	FaFile-class
show,BamViews-method	BamViews-class
show,RsamtoolsFile-method	RsamtoolsFile-class
show,ScanBamParam-method	ScanBamParam-class
show,ScanBcfParam-method	ScanBcfParam-class
sortBam	scanBam
sortBam,BamFile-method	BamFile-class
sortBam,character-method	scanBam
unz-class	Rsamtools-package
url-class	Rsamtools-package
[,BamViews,ANY,ANY-method	BamViews-class
[,BamViews,ANY,missing-method	BamViews-class
[,BamViews,missing,ANY-method	BamViews-class
