import(methods)
import(IRanges)
import(Biostrings)
import(GenomicRanges)
import(GenomicFeatures)

importClassesFrom(ShortRead, AlignedRead)
importFrom(ShortRead, alignData, chromosome, FastqQuality, renew,
           sread, srFilter, varMetadata)

export(renewEatonEtAl, chastityFilter, demultiplex,
       geneBounds, geneIntrons, countExonIdsByTxOverlaps, rpkm)
