bamSummarise	bamSummarise
bamSummariseByChr	bamSummariseByChr
bamSummaryToCoverage	bamSummaryToCoverage
chromosomeMappingSummary	chromosomeMappingSummary
cleanReferenceGenome	cleanReferenceGenome
fastqCheckup	fastqCheckup
fastqValidator	fastqValidator
fixFastq	fixFastq
getChromosomeIds	getChromosomeIds
getChromosomeSequence	getChromosomeSequence
getFastqBases	getFastqBases
getFastqCount	getFastqCount
getFastqPlusErrorCount	getFastqPlusErrorCount
getMalformedFastqHeaderCount	getMalformedFastqHeaderCount
getReferenceGenome	getReferenceGenome
getRpath	getRpath
getSeqLengths	getSeqLengths
getSequenceQualityMismatchCount	getSequenceQualityMismatchCount
getSkippedLineCount	getSkippedLineCount
getStringSetId	getStringSetId
getZeroLengthSequenceCount	getZeroLengthSequenceCount
infoGraphicPlot3	infoGraphicPlot3
infoGraphicPlot4	infoGraphicPlot4
init	init
isInitialised	isInitialised
lcalc	lcalc
LeftRightPlot	LeftRightPlot
listCachedObjects	listCachedObjects
loadReferenceGenome	loadReferenceGenome
md5sum	md5sum
ncalc	ncalc
parallelBamSummarise	parallelBamSummarise
phredmean	phredmean
plotAlignmentAccuracy	plotAlignmentAccuracy
plotAlignmentIdentity	plotAlignmentIdentity
plotDepthOfCoverageMegablock	plotDepthOfCoverageMegablock
plotOverallCovHistogram	plotOverallCovHistogram
qualToMeanQ	qualToMeanQ
setReferenceGenome	setReferenceGenome
setRpath	setRpath
snifflesKaryogram	snifflesKaryogram
svLengthDistribution	svLengthDistribution
testBam	testBam
Vcf2FilteredGranges	Vcf2FilteredGranges
Vcf2GRanges	Vcf2GRanges
