import(methods)
import(BiocGenerics)
import(S4Vectors)
import(IRanges)
import(GenomicRanges)
import(docopt)
import(BiocIO)

importFrom(tools, file_ext, file_path_sans_ext)
importFrom(stats, as.formula, setNames)
importFrom(utils, read.table)

importFrom(Seqinfo, Seqinfo, seqlevels, "seqlevels<-")
importFrom(rtracklayer, import, path)

exportPattern("(R_)?bedtools_.*")
export(pair, distmode)

## Called by the compiled code, not HelloRanges itself
## We could have these in globalVariables(), but this is more useful.

importFrom(Biostrings, readDNAStringSet, letterFrequency, alphabetFrequency,
           vcountPattern)
importFrom(rtracklayer, asBED, BEDFile)
importFrom(Rsamtools, ScanBamParam)
importFrom(Seqinfo, seqlengths)
importFrom(SummarizedExperiment, SummarizedExperiment)