addRead	SFFContainer-class
addRead,SFFContainer,SFFRead-method	SFFContainer-class
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
ava2vcf	ava2vcf
ava2vcf,AVASet-method	ava2vcf
AVASet	AVASet
AVASet,character,character,missing,missing,missing,missing,missing-method	AVASet
AVASet,character,missing,character,character,character,character,character-method	AVASet
AVASet,character,missing,character,character,character,missing,missing-method	AVASet
AVASet,character,missing,missing,missing,missing,missing,missing-method	AVASet
AVASet-class	AVASet-class
avaSetExample	avaSetExample
avaSetFiltered	avaSetFiltered
avaSetFiltered_annot	avaSetFiltered_annot
baseFrequency	baseFrequency
baseFrequency,DNAStringSet-method	baseFrequency
baseFrequency,SFFContainer-method	baseFrequency
baseFrequency,ShortRead-method	baseFrequency
baseQualityHist	baseQualityHist
baseQualityHist,QualityScaledDNAStringSet-method	baseQualityHist
baseQualityHist,SFFContainer-method	baseQualityHist
baseQualityHist,ShortReadQ-method	baseQualityHist
baseQualityStats	baseQualityStats
baseQualityStats,QualityScaledDNAStringSet-method	baseQualityStats
baseQualityStats,SFFContainer-method	baseQualityStats
baseQualityStats,ShortReadQ-method	baseQualityStats
breakpoints	breakpoints
Breakpoints-class	Breakpoints-class
breakpointTable	breakpointTable
breakpointTable,Breakpoints-method	breakpointTable
calculateTiTv	calculateTiTv
calculateTiTv,AVASet-method	calculateTiTv
calculateTiTv,MapperSet-method	calculateTiTv
captureArray	captureArray
clipAdapterLeft	SFFContainer-class
clipAdapterLeft,SFFContainer-method	SFFContainer-class
clipAdapterLeft,SFFRead-method	SFFRead-class
clipAdapterLeft<-	SFFContainer-class
clipAdapterLeft<-,SFFContainer,numeric-method	SFFContainer-class
clipAdapterLeft<-,SFFRead,numeric-method	SFFRead-class
clipAdapterRight	SFFContainer-class
clipAdapterRight,SFFContainer-method	SFFContainer-class
clipAdapterRight,SFFRead-method	SFFRead-class
clipAdapterRight<-	SFFContainer-class
clipAdapterRight<-,SFFContainer,numeric-method	SFFContainer-class
clipAdapterRight<-,SFFRead,numeric-method	SFFRead-class
clipQualityLeft	SFFContainer-class
clipQualityLeft,SFFContainer-method	SFFContainer-class
clipQualityLeft,SFFRead-method	SFFRead-class
clipQualityLeft<-	SFFContainer-class
clipQualityLeft<-,SFFContainer,numeric-method	SFFContainer-class
clipQualityLeft<-,SFFRead,numeric-method	SFFRead-class
clipQualityRight	SFFContainer-class
clipQualityRight,SFFContainer-method	SFFContainer-class
clipQualityRight,SFFRead-method	SFFRead-class
clipQualityRight<-	SFFContainer-class
clipQualityRight<-,SFFContainer,numeric-method	SFFContainer-class
clipQualityRight<-,SFFRead,numeric-method	SFFRead-class
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
complexity.dust	complexity.dust
complexity.dust,DNAStringSet-method	complexity.dust
complexity.dust,SFFContainer-method	complexity.dust
complexity.dust,ShortRead-method	complexity.dust
complexity.entropy	complexity.entropy
complexity.entropy,DNAStringSet-method	complexity.entropy
complexity.entropy,SFFContainer-method	complexity.entropy
complexity.entropy,ShortRead-method	complexity.entropy
convertCigar	convertCigar
coverageOnTarget	coverageOnTarget
coverageOnTarget,list,GRanges-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
dinucleotideOddsRatio	dinucleotideOddsRatio
dinucleotideOddsRatio,DNAStringSet-method	dinucleotideOddsRatio
dinucleotideOddsRatio,SFFContainer-method	dinucleotideOddsRatio
dinucleotideOddsRatio,ShortRead-method	dinucleotideOddsRatio
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,IntegerRangesList,DNAString,missing,missing-method	filterChimericReads
filterChimericReads,list,IntegerRangesList,DNAString,numeric,numeric-method	filterChimericReads
filterChimericReads,list,IntegerRangesList,missing,missing,missing-method	filterChimericReads
filterChimericReads,list,IntegerRangesList,missing,numeric,numeric-method	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
flowChars	SFFContainer-class
flowChars,SFFContainer-method	SFFContainer-class
flowChars,SFFRead-method	SFFRead-class
flowChars<-	SFFContainer-class
flowChars<-,SFFContainer,character-method	SFFContainer-class
flowChars<-,SFFRead,character-method	SFFRead-class
flowgram	SFFRead-class
flowgram,SFFRead-method	SFFRead-class
flowgram<-	SFFRead-class
flowgram<-,SFFRead,numeric-method	SFFRead-class
flowgramBarplot	flowgramBarplot
flowgramBarplot,SFFRead-method	flowgramBarplot
flowgramFormat	SFFContainer-class
flowgramFormat,SFFContainer-method	SFFContainer-class
flowgramFormat,SFFRead-method	SFFRead-class
flowgramFormat<-	SFFContainer-class
flowgramFormat<-,SFFContainer,numeric-method	SFFContainer-class
flowgramFormat<-,SFFRead,numeric-method	SFFRead-class
flowgrams	SFFContainer-class
flowgrams,SFFContainer-method	SFFContainer-class
flowgrams<-	SFFContainer-class
flowgrams<-,SFFContainer,list-method	SFFContainer-class
flowIndexes	SFFContainer-class
flowIndexes,SFFContainer-method	SFFContainer-class
flowIndexes,SFFRead-method	SFFRead-class
flowIndexes<-	SFFContainer-class
flowIndexes<-,SFFContainer,list-method	SFFContainer-class
flowIndexes<-,SFFRead,numeric-method	SFFRead-class
gcContent	gcContent
gcContent,DNAStringSet-method	gcContent
gcContent,SFFContainer-method	gcContent
gcContent,ShortRead-method	gcContent
gcContentHist	gcContentHist
gcContentHist,DNAStringSet-method	gcContentHist
gcContentHist,SFFContainer-method	gcContentHist
gcContentHist,ShortRead-method	gcContentHist
gcPerPosition	gcPerPosition
gcPerPosition,DNAStringSet-method	gcPerPosition
gcPerPosition,SFFContainer-method	gcPerPosition
gcPerPosition,ShortRead-method	gcPerPosition
genomeSequencerMIDs	genomeSequencerMIDs
genomeSequencerMIDs,character-method	genomeSequencerMIDs
genomeSequencerMIDs,missing-method	genomeSequencerMIDs
getAlignedReads	getAlignedReads
getAlignedReads,AVASet-method	getAlignedReads
getAminoAbbr	getAminoAbbr
getRead	SFFContainer-class
getRead,SFFContainer,character-method	SFFContainer-class
getReadStatus	MapperSet-class
getReadStatus,MapperSet-method	MapperSet-class
getVariantPercentages	getVariantPercentages
getVariantPercentages,AVASet-method	AVASet-class
getVariantPercentages,MapperSet-method	MapperSet-class
homopolymerHist	homopolymerHist
homopolymerHist,SFFRead-method	homopolymerHist
htmlReport	htmlReport
htmlReport,AVASet-method	AVASet-class
htmlReport,MapperSet-method	MapperSet-class
keySequence	SFFContainer-class
keySequence,SFFContainer-method	SFFContainer-class
keySequence,SFFRead-method	SFFRead-class
keySequence<-	SFFContainer-class
keySequence<-,SFFContainer,character-method	SFFContainer-class
keySequence<-,SFFRead,character-method	SFFRead-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
mutationInfo	mutationInfo
name	SFFContainer-class
name,SFFContainer-method	SFFContainer-class
name,SFFRead-method	SFFRead-class
name<-	SFFContainer-class
name<-,SFFContainer,character-method	SFFContainer-class
name<-,SFFRead,character-method	SFFRead-class
names,AnnotatedVariants-method	AnnotatedVariants-class
names,Breakpoints-method	Breakpoints-class
names<-,AnnotatedVariants,character-method	AnnotatedVariants-class
names<-,Breakpoints,ANY-method	Breakpoints-class
nucleotideCharts	nucleotideCharts
nucleotideCharts,DNAStringSet-method	nucleotideCharts
nucleotideCharts,SFFContainer-method	nucleotideCharts
nucleotideCharts,ShortRead-method	nucleotideCharts
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,data.frame,character-method	plotVariants
plotVariationFrequency	plotVariationFrequency
plotVariationFrequency,character,numeric-method	plotVariationFrequency
positionQualityBoxplot	positionQualityBoxplot
positionQualityBoxplot,QualityScaledDNAStringSet-method	positionQualityBoxplot
positionQualityBoxplot,SFFContainer-method	positionQualityBoxplot
positionQualityBoxplot,ShortReadQ-method	positionQualityBoxplot
quality,SFFRead-method	SFFRead-class
quality<-	SFFRead-class
quality<-,SFFRead,BString-method	SFFRead-class
qualityReportSFF	qualityReportSFF
read	SFFRead-class
read,SFFRead-method	SFFRead-class
read<-	SFFRead-class
read<-,SFFRead,QualityScaledDNAStringSet-method	SFFRead-class
readLengthHist	readLengthHist
readLengthHist,DNAStringSet-method	readLengthHist
readLengthHist,SFFContainer-method	readLengthHist
readLengthHist,ShortRead-method	readLengthHist
readLengthStats	readLengthStats
readLengthStats,DNAStringSet-method	readLengthStats
readLengthStats,SFFContainer-method	readLengthStats
readLengthStats,ShortRead-method	readLengthStats
reads	SFFContainer-class
reads,SFFContainer-method	SFFContainer-class
reads<-	SFFContainer-class
reads<-,SFFContainer,QualityScaledDNAStringSet-method	SFFContainer-class
readSFF	readSFF
readsOnTarget	readsOnTarget
readsOnTarget,list,GRanges-method	readsOnTarget
referenceSequences	referenceSequences
referenceSequences,AVASet-method	AVASet-class
referenceSequences<-	AVASet-class
referenceSequences<-,AVASet,AlignedRead-method	AVASet-class
regions	regions
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
sequenceQualityHist	sequenceQualityHist
sequenceQualityHist,QualityScaledDNAStringSet-method	sequenceQualityHist
sequenceQualityHist,SFFContainer-method	sequenceQualityHist
sequenceQualityHist,ShortReadQ-method	sequenceQualityHist
setVariantFilter	setVariantFilter
setVariantFilter,AVASet-method	AVASet-class
setVariantFilter,MapperSet-method	MapperSet-class
sff2fastq	sff2fastq
sff2fastq,SFFContainer-method	sff2fastq
SFFContainer	SFFContainer-class
SFFContainer-class	SFFContainer-class
SFFRead	SFFRead-class
SFFRead-class	SFFRead-class
variants	variants
writeSFF	writeSFF
[,AVASet,ANY,ANY,ANY-method	AVASet-class
[,AVASet,ANY,ANY-method	AVASet-class
[,Breakpoints,ANY,ANY,ANY-method	Breakpoints-class
[,Breakpoints,ANY,ANY-method	Breakpoints-class
[,SFFContainer,ANY,ANY,ANY-method	SFFContainer-class
[,SFFContainer,ANY,ANY-method	SFFContainer-class
