useDynLib(ShortRead, .registration=TRUE)

import(methods, BiocGenerics, S4Vectors, IRanges,
    Seqinfo, GenomicRanges, GenomicAlignments,
    Rsamtools, Biobase)

importFrom(BiocParallel, bplapply)

importFrom(Biostrings, BString, BStringSet, DNAString, DNAStringSet,
           DNA_ALPHABET, PDict, QualityScaledDNAStringSet, alphabet,
           alphabetFrequency, detail, get_seqtype_conversion_lookup,
           mkAllStrings, pattern, quality, readDNAStringSet, reverseComplement,
           trimLRPatterns, vcountPDict, writeXStringSet, xscodes)

importFrom(pwalign, pairwiseAlignment, unaligned)

importFrom(grDevices, colorRampPalette, dev.off, jpeg, pdf, png)

importFrom(hwriter, hwrite, hwriteImage)

importFrom(lattice, dotplot, histogram, levelplot, llines, lsegments,
           ltext, panel.abline, panel.dotplot, panel.grid,
           panel.histogram, panel.levelplot, panel.xyplot,
           strip.custom, xyplot)

importFrom(latticeExtra, xyplot.list)

importFrom(stats, approxfun, setNames)

importFrom(utils, capture.output, packageDescription, read.csv,
           read.table, Sweave)

exportClassPattern("^.*$")

exportMethods(show, coerce, dim, length, "[", "[<-", "[[", alphabetFrequency,
              alphabet, coverage, encoding, narrow, reverse, reverseComplement,
              strand, trimLRPatterns, width, append, rbind, "%in%", c, lapply,
              sapply)

export(pData, phenoData, varLabels, varMetadata)

exportPattern("^[^\\.]")

S3method(close, ShortReadFile)
S3method(open, ShortReadFile)
