.adjustRelativeInsLocs	selectAlnRegionsHelpers
.checkRelativeLocs	selectAlnRegionsHelpers
.explodeCigarOpCombs	explodeCigarOpCombs
.findMismatches	alleleLabelsHelpers
.formatVarLabels	alleleLabelsHelpers
.getAxisCoords	getAxisCoords
.intersperse	intersperse
.invertKeepRanges	selectAlnRegionsHelpers
.offsetIndices	selectAlnRegionsHelpers
abifToFastq	abifToFastq
addClipped	addClipped
addClipped,GAlignments-method	addClipped
addCodonFrame	addCodonFrame
alleles	alleles
alleles,CrisprSet-method	alleles
alns	alns
alns,CrisprSet-method	alns
annotateGenePlot	annotateGenePlot
arrangePlots	arrangePlots
barplotAlleleFreqs	barplotAlleleFreqs
barplotAlleleFreqs,CrisprSet-method	barplotAlleleFreqs
barplotAlleleFreqs,matrix-method	barplotAlleleFreqs
collapsePairs	collapsePairs
consensusSeqs	consensusSeqs
consensusSeqs,CrisprSet-method	consensusSeqs
countDeletions	indelCounts
countDeletions,GAlignments-method	indelCounts
countIndels	indelCounts
countIndels,GAlignments-method	indelCounts
countInsertions	indelCounts
countInsertions,GAlignments-method	indelCounts
CrisprRun	CrisprRun-class
CrisprRun-class	CrisprRun-class
CrisprSet	CrisprSet-class
CrisprSet-class	CrisprSet-class
dispatchDots	dispatchDots
excludeFromBam	excludeFromBam
findChimeras	findChimeras
findSNVs	findSNVs
findSNVs,CrisprSet-method	findSNVs
getChimeras	getChimeras
getChimeras,CrisprSet-method	getChimeras
getInsertionsTable	getInsertionsTable
gol	gol_clutch1
gol_clutch1	gol_clutch1
indelLabels	indelLabels
indelPercent	indelCounts
indelPercent,GAlignments-method	indelCounts
makeAlignmentTilePlot	makeAlignmentTilePlot
mergeChimeras	mergeChimeras
mergeCrisprSets	mergeCrisprSets
mergeCrisprSets,CrisprSet,CrisprSet-method	mergeCrisprSets
mismatchLabels	mismatchLabels
mutationEfficiency	mutationEfficiency
mutationEfficiency,CrisprSet-method	mutationEfficiency
narrowAlignments	narrowAlignments
narrowAlignments,GAlignments,GRanges-method	narrowAlignments
plotAlignments	plotAlignments
plotAlignments,character-method	plotAlignments
plotAlignments,CrisprSet-method	plotAlignments
plotAlignments,DNAString-method	plotAlignments
plotChimeras	plotChimeras
plotFreqHeatmap	plotFreqHeatmap
plotFreqHeatmap,CrisprSet-method	plotFreqHeatmap
plotFreqHeatmap,matrix-method	plotFreqHeatmap
plotVariants	plotVariants
plotVariants,CrisprSet-method	plotVariants
rcAlns	rcAlns
readsByPCRPrimer	readsByPCRPrimer
readsByPCRPrimer,GAlignments,GRanges-method	readsByPCRPrimer
readsByPCRPrimer,GRanges,GRanges-method	readsByPCRPrimer
readsToTarget	readsToTarget
readsToTarget,character,GRanges-method	readsToTarget
readsToTarget,GAlignments,GRanges-method	readsToTarget
readsToTarget,GAlignmentsList,GRanges-method	readsToTarget
readsToTargets	readsToTarget
readsToTargets,character,GRanges-method	readsToTarget
readsToTargets,GAlignmentsList,GRanges-method	readsToTarget
readTargetBam	readTargetBam
refFromAlns	refFromAlns
refFromAlns,GAlignments,ANY-method	refFromAlns
refFromAlns,GAlignments,GRanges-method	refFromAlns
reverseCigar	reverseCigar
rmMultiPCRChimera	rmMultiPCRChimera
rmMultiPCRChimera,character,Hits,integer-method	rmMultiPCRChimera
selectAlnRegions	seqsToAln
selectOps	selectOps
selectOps,character-method	selectOps
seqsToAln	seqsToAln
setDNATileColours	setDNATileColours
setMismatchTileColours	setMismatchTileColours
transformAlnsToLong	transformAlnsToLong
variantCounts	variantCounts
variantCounts,CrisprSet-method	variantCounts
writeFastq	writeFastq
