# Generated by roxygen2: do not edit by hand

export(MmapprParam)
export(calculateDistance)
export(generateCandidates)
export(loessFit)
export(mmappr)
export(outputMmapprData)
export(peakRefinement)
export(prePeak)
export(tempOutputFolder)
exportClasses(MmapprData)
exportClasses(MmapprParam)
exportMethods("distancePower<-")
exportMethods("fileAggregation<-")
exportMethods("homozygoteCutoff<-")
exportMethods("loessOptCutFactor<-")
exportMethods("loessOptResolution<-")
exportMethods("minBaseQuality<-")
exportMethods("minDepth<-")
exportMethods("minMapQuality<-")
exportMethods("mutFiles<-")
exportMethods("naCutoff<-")
exportMethods("outputFolder<-")
exportMethods("peakIntervalWidth<-")
exportMethods("refFasta<-")
exportMethods("refGenome<-")
exportMethods("species<-")
exportMethods("vepFlags<-")
exportMethods("wtFiles<-")
exportMethods(candidates)
exportMethods(distance)
exportMethods(distancePower)
exportMethods(fileAggregation)
exportMethods(homozygoteCutoff)
exportMethods(loessOptCutFactor)
exportMethods(loessOptResolution)
exportMethods(minBaseQuality)
exportMethods(minDepth)
exportMethods(minMapQuality)
exportMethods(mutFiles)
exportMethods(naCutoff)
exportMethods(outputFolder)
exportMethods(param)
exportMethods(peakIntervalWidth)
exportMethods(peaks)
exportMethods(refFasta)
exportMethods(refGenome)
exportMethods(species)
exportMethods(vepFlags)
exportMethods(wtFiles)
import(methods)
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,mergeBam)
importFrom(VariantTools,TallyVariantsParam)
importFrom(VariantTools,callVariants)
importFrom(ensemblVEP,VEPFlags)
importFrom(gmapR,GmapGenome)
importFrom(grDevices,dev.list)
importFrom(grDevices,dev.off)
importFrom(grDevices,graphics.off)
importFrom(grDevices,pdf)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,legend)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,polygon)
importFrom(magrittr,"%>%")
importFrom(stats,approxfun)
importFrom(stats,density.default)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,var)
importFrom(utils,capture.output)
importFrom(utils,object.size)
importFrom(utils,sessionInfo)
importFrom(utils,str)
importFrom(utils,tail)
importFrom(utils,write.table)
