import("methods")

importFrom("ShortRead",readAligned)

importFrom("rtracklayer", export.bedGraph)

import("data.table")

import("BiocGenerics")
import("S4Vectors")

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

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

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