# Generated by roxygen2: do not edit by hand

export(FastQStreamer.getReads)
export(FastQStreamer.init)
export(FastQStreamer.release)
export(TP53GenomicFeatures)
export(alignReads)
export(analyzeVariants)
export(annotateVariants)
export(bamCountUniqueReads)
export(buildConfig)
export(buildGenomicFeaturesFromTxDb)
export(buildTP53FastaGenome)
export(calculateCoverage)
export(calculateTargetLengths)
export(checkConfig)
export(checkGATKJar)
export(checkPicardJar)
export(computeBamStats)
export(computeCoverage)
export(countGenomicFeatures)
export(countGenomicFeaturesChunk)
export(detectAdapterContam)
export(detectQualityInFASTQFile)
export(detectRRNA)
export(filterByLength)
export(filterQuality)
export(findVariantFile)
export(gatk)
export(getBams)
export(getChunkDirs)
export(getConfig)
export(getConfig.integer)
export(getConfig.logical)
export(getConfig.numeric)
export(getConfig.vector)
export(getEndNumber)
export(getMemoryUsage)
export(getNumberOfReadsInFASTQFile)
export(getNumericVectorDataFromFile)
export(getObjectFilename)
export(getPackageFile)
export(getRRNAIds)
export(getTabDataFromFile)
export(getTraceback)
export(hashCoverage)
export(hashVariants)
export(hashVector)
export(initDirs)
export(initLog)
export(initLogger)
export(initPipelineFromConfig)
export(initPipelineFromSaveDir)
export(isAboveQualityThresh)
export(isAdapter)
export(isConfig)
export(listIterator.init)
export(listIterator.next)
export(loadConfig)
export(logdebug)
export(logerror)
export(loginfo)
export(logwarn)
export(makeDir)
export(markDuplicates)
export(markDups)
export(mergeAlignReads)
export(mergeCoverage)
export(mergeLanes)
export(mergePreprocessReads)
export(mergeSummaryAlignment)
export(parseDCF)
export(parseSummaries)
export(plotDF)
export(preprocessReads)
export(processChunks)
export(readInputFiles)
export(readRNASeqEnds)
export(realignIndels)
export(relativeBarPlot)
export(removeChunkDir)
export(resource)
export(rpkm)
export(runAlignment)
export(runPipeline)
export(runPipelineConfig)
export(runPreprocessReads)
export(safe.yield)
export(safeExecute)
export(safeGetObject)
export(safeUnlink)
export(saveWithID)
export(sclapply)
export(setUpDirs)
export(setupTestFramework)
export(statCountFeatures)
export(traceMem)
export(trimReads)
export(trimTailsByQuality)
export(truncateReads)
export(tryKeepTraceback)
export(updateConfig)
export(vcfStat)
export(wrap.callVariants)
export(writeAudit)
export(writeConfig)
export(writeFastQFiles)
export(writeFeatureCountsHTML)
export(writeGenomicFeaturesReport)
export(writePreprocessAlignReport)
export(writeSummary)
export(writeVCF)
import(BiocGenerics)
import(S4Vectors)
import(methods)
importClassesFrom(Biostrings,BStringSet)
importFrom(BiocParallel,MulticoreParam)
importFrom(Biostrings,BStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,DNA_ALPHABET)
importFrom(Biostrings,readDNAStringSet)
importFrom(Cairo,CairoPDF)
importFrom(GenomicRanges,tileGenome)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,bgzip)
importFrom(Rsamtools,indexTabix)
importFrom(Rsamtools,scanBamFlag)
importFrom(ShortRead,FastqSampler)
importFrom(VariantAnnotation,scanVcf)
importFrom(VariantTools,CallGenotypesParam)
importFrom(VariantTools,TallyVariantsParam)
importFrom(VariantTools,VariantCallingFilters)
importFrom(VariantTools,VariantPostFilters)
importFrom(VariantTools,postFilterVariants)
importFrom(gmapR,GmapGenome)
importFrom(gmapR,TP53Genome)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.control)
importFrom(grDevices,dev.copy2pdf)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(grDevices,png)
importFrom(graphics,abline)
importFrom(graphics,barplot)
importFrom(graphics,hist)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,stripchart)
importFrom(graphics,text)
importFrom(hwriter,closePage)
importFrom(hwriter,hwrite)
importFrom(hwriter,hwriteImage)
importFrom(hwriter,openPage)
importFrom(parallel,mccollect)
importFrom(parallel,mclapply)
importFrom(parallel,mcparallel)
importFrom(rtracklayer,BigWigFile)
importFrom(stats,heatmap)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(tools,SIGTERM)
importFrom(utils,capture.output)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,sessionInfo)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importMethodsFrom(Biostrings,pairwiseAlignment)
importMethodsFrom(Biostrings,quality)
importMethodsFrom(Biostrings,unlist)
importMethodsFrom(GenomeInfoDb,"seqlengths<-")
importMethodsFrom(GenomeInfoDb,genome)
importMethodsFrom(GenomeInfoDb,seqlengths)
importMethodsFrom(GenomicAlignments,grglist)
importMethodsFrom(GenomicAlignments,readGAlignments)
importMethodsFrom(GenomicFeatures,cdsBy)
importMethodsFrom(GenomicFeatures,exons)
importMethodsFrom(GenomicFeatures,exonsBy)
importMethodsFrom(GenomicFeatures,genes)
importMethodsFrom(GenomicFeatures,transcripts)
importMethodsFrom(GenomicFeatures,transcriptsBy)
importMethodsFrom(GenomicRanges,end)
importMethodsFrom(GenomicRanges,reduce)
importMethodsFrom(GenomicRanges,seqnames)
importMethodsFrom(GenomicRanges,start)
importMethodsFrom(IRanges,as.vector)
importMethodsFrom(IRanges,disjoin)
importMethodsFrom(IRanges,findOverlaps)
importMethodsFrom(IRanges,length)
importMethodsFrom(IRanges,runLength)
importMethodsFrom(IRanges,unlist)
importMethodsFrom(Rsamtools,ScanBamParam)
importMethodsFrom(Rsamtools,asBam)
importMethodsFrom(Rsamtools,indexBam)
importMethodsFrom(Rsamtools,indexFa)
importMethodsFrom(Rsamtools,mergeBam)
importMethodsFrom(Rsamtools,scanBam)
importMethodsFrom(Rsamtools,sortBam)
importMethodsFrom(ShortRead,FastqQuality)
importMethodsFrom(ShortRead,FastqStreamer)
importMethodsFrom(ShortRead,ShortReadQ)
importMethodsFrom(ShortRead,id)
importMethodsFrom(ShortRead,qa)
importMethodsFrom(ShortRead,readFasta)
importMethodsFrom(ShortRead,readFastq)
importMethodsFrom(ShortRead,report)
importMethodsFrom(ShortRead,sread)
importMethodsFrom(ShortRead,trimEnds)
importMethodsFrom(ShortRead,writeFastq)
importMethodsFrom(ShortRead,yield)
importMethodsFrom(SummarizedExperiment,rowData)
importMethodsFrom(VariantAnnotation,"sampleNames<-")
importMethodsFrom(VariantAnnotation,sampleNames)
importMethodsFrom(VariantAnnotation,writeVcf)
importMethodsFrom(VariantTools,callGenotypes)
importMethodsFrom(VariantTools,callVariants)
importMethodsFrom(VariantTools,tallyVariants)
importMethodsFrom(chipseq,estimate.mean.fraglen)
importMethodsFrom(gmapR,directory)
importMethodsFrom(rtracklayer,export)