useDynLib(gmapR, .registration = TRUE)
 
 importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments, "bamWhich<-",

            BamFile, BamFileList)
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
            list_files_with_exts)

 importFrom(Biobase, createPackage)

 import(IRanges)

 import(methods)

 import(GenomicRanges)

 importFrom(utils, packageVersion)

 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)

 importFrom(GenomicRanges, genome, seqinfo)
 importMethodsFrom(GenomicRanges, seqnames, strand)
 importMethodsFrom(Rsamtools, asBam)
 importClassesFrom(GenomicFeatures, TranscriptDb)

 importFrom(GenomicFeatures, transcripts, exons)

 importClassesFrom(rtracklayer, RTLFile, FastaFile)
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
 importMethodsFrom(rtracklayer, export)

 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
            "ref<-", "alt<-")
 importClassesFrom(VariantAnnotation, "VCF", "VRanges")

 importFrom(BSgenome, getSeq, providerVersion)

 
 ## public API
 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,

        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,

        GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary)

 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)

 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",

               "spliceSites<-", getSeq)