useDynLib(gmapR, .registration = TRUE)
 

 importFrom(BiocGenerics, path)
 importFrom(Rsamtools, bamPaths, "bamWhich<-", BamFile, BamFileList,

            BamSampler)

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

 importFrom(Biobase, createPackage)

 import(IRanges)

 import(S4Vectors)
 import(methods)

 import(GenomicRanges)

 import(GenomeInfoDb)

 import(BiocParallel)

 importMethodsFrom(GenomeInfoDb, genome)

 importFrom(stats, setNames)
 importFrom(utils, packageVersion, read.table, str)

 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)

 importMethodsFrom(GenomicRanges, seqnames, strand)

 importMethodsFrom(Rsamtools, asBam)

 importClassesFrom(GenomicFeatures, TxDb)

 importFrom(GenomicFeatures, transcripts, exons, exonsBy)

 importClassesFrom(rtracklayer, RTLFile, FastaFile, RTLFileList)

 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile,
            FileForFormat)

 importMethodsFrom(rtracklayer, export)

 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,

            "ref<-", "alt<-", altDepth, refDepth, "vcfWhich<-")

 importClassesFrom(VariantAnnotation, "VCF", "VRanges")

 importFrom(BSgenome, getSeq, providerVersion)

 importFrom(GenomicAlignments, readGAlignments)
 importMethodsFrom(GenomicAlignments, qwidth)

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

        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,

        GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary,

        GmapParam, cmetindex)

 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,

               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam,
               GmapAlignerParam)

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

               "spliceSites<-", getSeq, gmap)
 
 S3method(as.list, GmapAlignerParam)