import("methods")
import("stats")

importFrom("ShortRead",readAligned)

importFrom("rtracklayer", export.bedGraph)

import("data.table")

import("GenomicRanges")

importMethodsFrom(BiocGenerics, cbind, get, lapply, mapply, rbind, sapply, strand)

importMethodsFrom(IRanges, append, as.factor, as.list, as.vector, colnames, "colnames<-", coverage, diff, endoapply, eval, gsub, head, ifelse, "%in%", levels, median, metadata, "metadata<-", narrow, ncol, nrow, order, paste, pmin, quantile, Rle, rownames, "rownames<-", runLength, runValue, score, sort, split, start, sub,  table, tapply, toupper, unique, unlist, update, which, width, with)

import("Biostrings")
import("BSgenome")
import("ggplot2")

export("pairReads")
export("mapReadsToRestrictionSites")
export("GOTHiC")
