useDynLib(ShortRead, .registration=TRUE)

importClassesFrom(Biobase, AnnotatedDataFrame, Versioned,
                  ScalarCharacter)

importClassesFrom(Biostrings, BStringSet, DNAStringSet,
                  PairwiseAlignedXStringSet,
                  SolexaQuality, PhredQuality, XStringQuality)

importClassesFrom(IRanges, RangesList)

importFrom(Biobase, selectSome, subListExtract, copySubstitute,
           "dimLabels<-",
           pData, phenoData, varLabels, varMetadata, sampleNames,
           mkScalar)

importFrom(IRanges, append, coverage, narrow, score, start, Views,
           width, rbind, split, "%in%")

importFrom(GenomicRanges, strand)

importFrom(Biostrings, BStringSet, DNAStringSet, compact,
           alphabetFrequency, alphabet, DNA_ALPHABET,
           quality, pairwiseAlignment, pattern,
           trimLRPatterns, unaligned)

importFrom(hwriter, hwrite, hwriteImage)

importFrom(Rsamtools, scanBam, ScanBamParam, bamSimpleCigar,
           bamReverseComplement, bamWhat)

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

exportMethods(show, coerce, dim, length, "[", "[[", alphabetFrequency,
              alphabet, coverage, narrow, strand, trimLRPatterns,
              width, append, rbind, "%in%")

export(pData, phenoData, varLabels, varMetadata)

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