# Generated by roxygen2: do not edit by hand

export(BAIT)
export(ChrTable)
export(ContigOrdering)
export(LibraryGroupList)
export(LinkageGroupList)
export(StrandFreqMatrix)
export(StrandReadMatrix)
export(StrandStateList)
export(StrandStateMatrix)
export(barplotLinkageGroupCalls)
export(clusterContigs)
export(contiBAIT)
export(findSexGroups)
export(findSimilarLibraries)
export(fixLinkageGroups)
export(flipOrderedLinkageGroups)
export(highlightAssemblyErrors)
export(ideogramPlot)
export(locateMisorients)
export(makeBoxPlot)
export(makeChrTable)
export(mapGapFromOverlap)
export(mergeFlankedLGs)
export(orderAllLinkageGroups)
export(plotContigOrder)
export(plotLGDistances)
export(plotWCdistribution)
export(preprocessStrandTable)
export(reorientAndMergeLGs)
export(strandSeqFreqTable)
export(thoroughBed)
export(writeBed)
exportClasses(ChrTable)
exportClasses(ContigOrdering)
exportClasses(LibraryGroupList)
exportClasses(LinkageGroupList)
exportClasses(StrandFreqMatrix)
exportClasses(StrandReadMatrix)
exportClasses(StrandStateList)
exportClasses(StrandStateMatrix)
exportMethods(barplotLinkageGroupCalls)
exportMethods(clusterContigs)
exportMethods(findSexGroups)
exportMethods(findSimilarLibraries)
exportMethods(fixLinkageGroups)
exportMethods(flipOrderedLinkageGroups)
exportMethods(ideogramPlot)
exportMethods(locateMisorients)
exportMethods(makeBoxPlot)
exportMethods(mergeFlankedLGs)
exportMethods(orderAllLinkageGroups)
exportMethods(plotContigOrder)
exportMethods(plotLGDistances)
exportMethods(plotWCdistribution)
exportMethods(preprocessStrandTable)
exportMethods(reorientAndMergeLGs)
exportMethods(show)
exportMethods(thoroughBed)
exportMethods(writeBed)
import(BH)
import(BiocParallel)
import(DNAcopy)
import(GenomicAlignments)
import(GenomicFiles)
import(GenomicRanges)
import(IRanges)
import(Rcpp)
import(Rsamtools)
import(TSP)
import(clue)
import(diagram)
import(ggplot2)
import(grDevices)
import(methods)
importFrom(BiocGenerics,"%in%")
importFrom(S4Vectors,DataFrame)
importFrom(cluster,daisy)
importFrom(colorspace,rainbow_hcl)
importFrom(data.table,":=")
importFrom(data.table,data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,tstrsplit)
importFrom(exomeCopy,subdivideGRanges)
importFrom(gplots,heatmap.2)
importFrom(graphics,boxplot)
importFrom(graphics,hist)
importFrom(graphics,lines)
importFrom(graphics,text)
importFrom(gtools,chr)
importFrom(gtools,mixedsort)
importFrom(reshape2,melt)
importFrom(rtracklayer,export.bed)
importFrom(stats,aggregate)
importFrom(stats,rbinom)
importFrom(stats,runif)
importFrom(utils,head)
importFrom(utils,tail)
useDynLib(contiBAIT)
