useDynLib(gmapR, .registration = TRUE) importFrom(Rsamtools, path, 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(utils, packageVersion) 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) exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory, GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam, GmapAlignerParam) exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-", "spliceSites<-", getSeq, gmap) S3method(as.list, GmapAlignerParam)