alignedReadsC1	Breakpoints-class
alignedReadsC1,Breakpoints-method	Breakpoints-class
alignedReadsC1<-	Breakpoints-class
alignedReadsC1<-,Breakpoints,list-method	Breakpoints-class
alignedReadsC2	Breakpoints-class
alignedReadsC2,Breakpoints-method	Breakpoints-class
alignedReadsC2<-	Breakpoints-class
alignedReadsC2<-,Breakpoints,list-method	Breakpoints-class
alignShortReads	alignShortReads
alignShortReads,AVASet,BSgenome,character,logical-method	alignShortReads
alignShortReads,AVASet,BSgenome,character,missing-method	alignShortReads
alignShortReads,AVASet,BSgenome,missing,logical-method	alignShortReads
alignShortReads,AVASet,BSgenome,missing,missing-method	alignShortReads
alignShortReads,AVASet,DNAStringSet,character-method	AVASet-class
alignShortReads,DNAStringSet,BSgenome,character,logical-method	alignShortReads
alignShortReads,DNAStringSet,BSgenome,character,missing-method	alignShortReads
alignShortReads,DNAStringSet,BSgenome,missing,logical-method	alignShortReads
alignShortReads,DNAStringSet,BSgenome,missing,missing-method	alignShortReads
annotatedVariants	AnnotatedVariants-class
annotatedVariants,AnnotatedVariants-method	AnnotatedVariants-class
AnnotatedVariants-class	AnnotatedVariants-class
annotatedVariants<-,AnnotatedVariants,list-method	AnnotatedVariants-class
annotateVariants	annotateVariants
annotateVariants,AVASet,missing-method	annotateVariants
annotateVariants,AVASet-method	AVASet-class
annotateVariants,data.frame,missing-method	annotateVariants
annotateVariants,MapperSet,BSgenome-method	annotateVariants
annotateVariants,MapperSet,missing-method	annotateVariants
annotateVariants,MapperSet-method	MapperSet-class
assayDataAmp	assayDataAmp
assayDataAmp,AVASet-method	AVASet-class
assayDataAmp<-	AVASet-class
assayDataAmp<-,AVASet,AssayData-method	AVASet-class
AVASet	AVASet
AVASet,character-method	AVASet
AVASet-class	AVASet-class
avaSetExample	avaSetExample
avaSetFiltered	avaSetFiltered
avaSetFiltered_annot	avaSetFiltered_annot
breakpoints	breakpoints
Breakpoints-class	Breakpoints-class
calculateTiTv	calculateTiTv
calculateTiTv,AVASet-method	calculateTiTv
calculateTiTv,MapperSet-method	calculateTiTv
captureArray	captureArray
commonAlignC1	Breakpoints-class
commonAlignC1,Breakpoints-method	Breakpoints-class
commonAlignC1<-	Breakpoints-class
commonAlignC1<-,Breakpoints,list-method	Breakpoints-class
commonAlignC2	Breakpoints-class
commonAlignC2,Breakpoints-method	Breakpoints-class
commonAlignC2<-	Breakpoints-class
commonAlignC2<-,Breakpoints,list-method	Breakpoints-class
commonBpsC1	Breakpoints-class
commonBpsC1,Breakpoints-method	Breakpoints-class
commonBpsC1<-	Breakpoints-class
commonBpsC1<-,Breakpoints,list-method	Breakpoints-class
commonBpsC2	Breakpoints-class
commonBpsC2,Breakpoints-method	Breakpoints-class
commonBpsC2<-	Breakpoints-class
commonBpsC2<-,Breakpoints,list-method	Breakpoints-class
convertCigar	convertCigar
coverageOnTarget	coverageOnTarget
coverageOnTarget,list,RangesList-method	coverageOnTarget
demultiplexReads	demultiplexReads
demultiplexReads,XStringSet,XStringSet,missing,logical-method	demultiplexReads
demultiplexReads,XStringSet,XStringSet,missing,missing-method	demultiplexReads
demultiplexReads,XStringSet,XStringSet,numeric,logical-method	demultiplexReads
demultiplexReads,XStringSet,XStringSet,numeric,missing-method	demultiplexReads
detectBreakpoints	detectBreakpoints
detectBreakpoints,list-method	detectBreakpoints
extendedCIGARToList	convertCigar
fDataAmp	fDataAmp
fDataAmp,AVASet-method	AVASet-class
featureDataAmp	featureDataAmp
featureDataAmp,AVASet-method	AVASet-class
featureDataAmp<-	AVASet-class
featureDataAmp<-,AVASet,AnnotatedDataFrame-method	AVASet-class
filterChimericReads	filterChimericReads
filterChimericReads,list,missing,DNAString,missing,missing-method	filterChimericReads
filterChimericReads,list,missing,DNAString,numeric,numeric-method	filterChimericReads
filterChimericReads,list,missing,missing,missing,missing-method	filterChimericReads
filterChimericReads,list,missing,missing,numeric,numeric-method	filterChimericReads
filterChimericReads,list,RangesList,DNAString,missing,missing-method	filterChimericReads
filterChimericReads,list,RangesList,DNAString,numeric,numeric-method	filterChimericReads
filterChimericReads,list,RangesList,missing,missing,missing-method	filterChimericReads
filterChimericReads,list,RangesList,missing,numeric,numeric-method	filterChimericReads
genomeSequencerMIDs	genomeSequencerMIDs
genomeSequencerMIDs,character-method	genomeSequencerMIDs
genomeSequencerMIDs,missing-method	genomeSequencerMIDs
getAlignedReads	getAlignedReads
getAlignedReads,AVASet-method	getAlignedReads
getAminoAbbr	getAminoAbbr
getReadStatus	MapperSet-class
getReadStatus,MapperSet-method	MapperSet-class
getVariantPercentages	getVariantPercentages
getVariantPercentages,AVASet-method	AVASet-class
getVariantPercentages,MapperSet-method	MapperSet-class
htmlReport	htmlReport
htmlReport,AVASet-method	AVASet-class
htmlReport,MapperSet-method	MapperSet-class
length,Breakpoints-method	Breakpoints-class
listToExtendedCIGAR	convertCigar
MapperSet	MapperSet
MapperSet,character-method	MapperSet
MapperSet-class	MapperSet-class
mapperSetExample	mapperSetExample
mergeBreakpoints	mergeBreakpoints
mergeBreakpoints,Breakpoints,missing,list-method	Breakpoints-class
mergeBreakpoints,Breakpoints,missing,missing-method	Breakpoints-class
mergeBreakpoints,Breakpoints,numeric,missing-method	Breakpoints-class
names,AnnotatedVariants-method	AnnotatedVariants-class
names,Breakpoints-method	Breakpoints-class
names<-,AnnotatedVariants,character-method	AnnotatedVariants-class
names<-,Breakpoints,ANY-method	Breakpoints-class
plotAmpliconCoverage	plotAmpliconCoverage
plotAmpliconCoverage,AVASet,character,logical-method	plotAmpliconCoverage
plotAmpliconCoverage,AVASet,character,missing-method	plotAmpliconCoverage
plotAmpliconCoverage,AVASet,missing,logical-method	plotAmpliconCoverage
plotAmpliconCoverage,AVASet,missing,missing-method	plotAmpliconCoverage
plotChimericReads	plotChimericReads
plotChimericReads,Breakpoints-method	Breakpoints-class
plotVariants	plotVariants
plotVariants,AnnotatedVariants,character-method	plotVariants
plotVariants,AnnotatedVariants,data.frame-method	plotVariants
plotVariationFrequency	plotVariationFrequency
plotVariationFrequency,character,numeric-method	plotVariationFrequency
readsOnTarget	readsOnTarget
readsOnTarget,list,RangesList-method	readsOnTarget
referenceSequences	referenceSequences
referenceSequences,AVASet-method	AVASet-class
referenceSequences<-	AVASet-class
referenceSequences<-,AVASet,AlignedRead-method	AVASet-class
removeLinker	removeLinker
removeLinker,XStringSet,DNAString,logical,numeric,numeric-method	removeLinker
removeLinker,XStringSet,DNAString,missing,missing,missing-method	removeLinker
seqsC1	Breakpoints-class
seqsC1,Breakpoints-method	Breakpoints-class
seqsC1<-	Breakpoints-class
seqsC1<-,Breakpoints,list-method	Breakpoints-class
seqsC2	Breakpoints-class
seqsC2,Breakpoints-method	Breakpoints-class
seqsC2<-	Breakpoints-class
seqsC2<-,Breakpoints,list-method	Breakpoints-class
sequenceCaptureLinkers	sequenceCaptureLinkers
sequenceCaptureLinkers,character-method	sequenceCaptureLinkers
sequenceCaptureLinkers,missing-method	sequenceCaptureLinkers
setVariantFilter	setVariantFilter
setVariantFilter,AVASet-method	AVASet-class
setVariantFilter,MapperSet-method	MapperSet-class
transcriptdf	transcriptdf
[,AVASet,ANY,ANY-method	AVASet-class
[,Breakpoints,ANY,ANY-method	Breakpoints-class
