import(methods)
import(BiocGenerics)
importClassesFrom(IRanges, CompressedIRangesList, IRanges, IRangesList,
                  RangedData, SimpleRleList)
importClassesFrom(ShortRead, AlignedRead)
importMethodsFrom(Biobase, exprs, pData, sampleNames)
importMethodsFrom(GenomicRanges, strand, sort)
importMethodsFrom(IRanges, as.data.frame, as.vector, cor, coverage,
                  disjointBins, end, mean, nchar, nrow, order, quantile,
                  ranges, space, start, unique, unlist, which, width)
importMethodsFrom(ShortRead, chromosome, lapply, position, sapply)
importFrom(parallel, mclapply)
importFrom(graphics, abline, legend, lines, plot, points, rect, text)
importFrom(IRanges, IRanges, IRangesList, RangedData, RleList, findOverlaps,
           queryHits, reduce)
importFrom(GenomicRanges, GRanges)
importFrom(ShortRead, sread)
importFrom(stats, fft, pnorm, runif)
importFrom(Rsamtools, scanBamFlag, ScanBamParam, scanBam)
importFrom(S4Vectors, Rle, values)

exportMethods(export.bed, filterFFT, fragmentLenDetect, peakDetection,
              peakScoring, plotPeaks, processReads, controlCorrection)
export(coverage.rpm, export.wig, processTilingArray, syntheticNucMap,
       pcKeepCompDetect, mergeCalls, readBAM)

