# Generated by roxygen2: do not edit by hand

export(GenotypeBreaks)
export(breakSeekr)
export(breakpointr)
export(breakpointr2UCSC)
export(deltaWCalculator)
export(exportRegions)
export(genotype.binom)
export(genotype.fisher)
export(hotspotter)
export(loadFromFiles)
export(plotBreakpoints)
export(plotBreakpointsPerChr)
export(plotHeatmap)
export(ranges2UCSC)
export(readBamFileAsGRanges)
export(removeReadPileupSpikes)
export(runBreakpointr)
export(summarizeBreaks)
export(synchronizeReadDir)
import(GenomeInfoDb)
import(GenomicRanges)
import(IRanges)
import(breakpointRdata)
import(doParallel)
import(foreach)
import(ggplot2)
importFrom(BiocGenerics,as.vector)
importFrom(BiocGenerics,table)
importFrom(GenomicAlignments,first)
importFrom(GenomicAlignments,last)
importFrom(GenomicAlignments,readGAlignmentPairs)
importFrom(GenomicAlignments,readGAlignments)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,scanBamHeader)
importFrom(S4Vectors,endoapply)
importFrom(S4Vectors,subjectHits)
importFrom(cowplot,plot_grid)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(gtools,mixedorder)
importFrom(gtools,mixedsort)
importFrom(methods,as)
importFrom(methods,is)
importFrom(stats,dbinom)
importFrom(stats,density)
importFrom(stats,ecdf)
importFrom(stats,fisher.test)
importFrom(stats,runif)
importFrom(utils,flush.console)
importFrom(utils,read.table)
importFrom(utils,write.table)
