alignReads	alignReads
alignReadsChunk	alignReadsChunk
analyzeVariants	analyzeVariants
annotateVariants	annotateVariants
bamCountUniqueReads	bamCountUniqueReads
buildConfig	buildConfig
buildGenomicFeaturesFromTxDb	buildGenomicFeaturesFromTxDb
buildShortReadReports	buildShortReadReports
buildTallyParam	buildTallyParam
buildTP53FastaGenome	buildTP53FastaGenome
buildTP53GenomeTemplate	buildTP53GenomeTemplate
calculateCoverage	calculateCoverage
calculateTargetLengths	calculateTargetLengths
callVariantsGATK	callVariantsGATK
checkConfig	checkConfig
checkGATKJar	checkGATKJar
checkPicardJar	checkPicardJar
computeBamStats	computeBamStats
computeCoverage	computeCoverage
countFeatures	countFeatures
countGenomicFeatures	countGenomicFeatures
countGenomicFeaturesChunk	countGenomicFeaturesChunk
createTmpDir	createTmpDir
detectAdapterContam	detectAdapterContam
detectQualityInFASTQFile	detectQualityInFASTQFile
detectRRNA	detectRRNA
excludeVariantsByRegions	excludeVariantsByRegions
FastQStreamer.getReads	FastQStreamer.getReads
FastQStreamer.init	FastQStreamer.init
FastQStreamer.release	FastQStreamer.release
filterByLength	filterByLength
filterQuality	filterQuality
findVariantFile	findVariantFile
gatk	gatk
generateSingleGeneDERs	generateSingleGeneDERs
getAdapterSeqs	getAdapterSeqs
getBams	getBams
getChunkDirs	getChunkDirs
getConfig	getConfig
getConfig.integer	getConfig.integer
getConfig.logical	getConfig.logical
getConfig.numeric	getConfig.numeric
getConfig.vector	getConfig.vector
getEndNumber	getEndNumber
getMemoryUsage	getMemoryUsage
getNumberOfReadsInFASTQFile	getNumberOfReadsInFASTQFile
getNumericVectorDataFromFile	getNumericVectorDataFromFile
getObjectFilename	getObjectFilename
getPackageFile	getPackageFile
getRandomAlignCutoff	getRandomAlignCutoff
getRRNAIds	getRRNAIds
getTabDataFromFile	getTabDataFromFile
getTraceback	getTraceback
hashCoverage	hashCoverage
hashVariants	hashVariants
hashVector	hashVector
HTSeqGenie	HTSeqGenie
initDirs	initDirs
initLog	initLog
initLogger	initLogger
initPipelineFromConfig	initPipelineFromConfig
initPipelineFromSaveDir	initPipelineFromSaveDir
isAboveQualityThresh	isAboveQualityThresh
isAdapter	isAdapter
isConfig	isConfig
isFirstFragment	isFirstFragment
isSparse	isSparse
listIterator.init	listIterator.init
listIterator.next	listIterator.next
loadConfig	loadConfig
logdebug	logdebug
logerror	logerror
loginfo	loginfo
logwarn	logwarn
makeDir	makeDir
makeRandomSreads	makeRandomSreads
markDuplicates	markDuplicates
markDups	markDups
mergeAlignReads	mergeAlignReads
mergeCoverage	mergeCoverage
mergeLanes	mergeLanes
mergePreprocessReads	mergePreprocessReads
mergeSummaryAlignment	mergeSummaryAlignment
parseDCF	parseDCF
parseSummaries	parseSummaries
picard	picard
plotDF	plotDF
preprocessReads	preprocessReads
preprocessReadsChunk	preprocessReadsChunk
processChunks	processChunks
readInputFiles	readInputFiles
readRNASeqEnds	readRNASeqEnds
realignIndels	realignIndels
realignIndelsGATK	realignIndelsGATK
relativeBarPlot	relativeBarPlot
removeChunkDir	removeChunkDir
resource	resource
rpkm	rpkm
runAlignment	runAlignment
runPipeline	runPipeline
runPipelineConfig	runPipelineConfig
runPreprocessReads	runPreprocessReads
safe.yield	safe.yield
safeExecute	safeExecute
safeGetObject	safeGetObject
safeUnlink	safeUnlink
saveWithID	saveWithID
sclapply	sclapply
setChunkDir	setChunkDir
setUpDirs	setUpDirs
setupTestFramework	setupTestFramework
statCountFeatures	statCountFeatures
TP53GenomicFeatures	TP53GenomicFeatures
traceMem	traceMem
trimReads	trimReads
trimTailsByQuality	trimTailsByQuality
truncateReads	truncateReads
tryKeepTraceback	tryKeepTraceback
updateConfig	updateConfig
vcfStat	vcfStat
wrap.callVariants	wrap.callVariants
writeAudit	writeAudit
writeConfig	writeConfig
writeFastQFiles	writeFastQFiles
writeFeatureCountsHTML	writeFeatureCountsHTML
writeGenomicFeaturesReport	writeGenomicFeaturesReport
writePreprocessAlignHTML	writePreprocessAlignHTML
writePreprocessAlignReport	writePreprocessAlignReport
writeSummary	writeSummary
writeVCF	writeVCF
