NAMESPACE
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 useDynLib(gmapR, .registration = TRUE)
 
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 importFrom(Rsamtools, path, bamPaths, "bamWhich<-", BamFile, BamFileList,
            BamSampler)
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 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
            list_files_with_exts)
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 importFrom(Biobase, createPackage)
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 import(IRanges)
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 import(S4Vectors)
 import(methods)
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 import(GenomicRanges)
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 import(GenomeInfoDb)
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 import(BiocParallel)
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 importMethodsFrom(GenomeInfoDb, genome)
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 importFrom(utils, packageVersion)
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 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
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 importMethodsFrom(GenomicRanges, seqnames, strand)
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 importMethodsFrom(Rsamtools, asBam)
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 importClassesFrom(GenomicFeatures, TxDb)
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 importFrom(GenomicFeatures, transcripts, exons, exonsBy)
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 importClassesFrom(rtracklayer, RTLFile, FastaFile, RTLFileList)
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 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile,
            FileForFormat)
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 importMethodsFrom(rtracklayer, export)
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 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
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            "ref<-", "alt<-", altDepth, refDepth, "vcfWhich<-")
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 importClassesFrom(VariantAnnotation, "VCF", "VRanges")
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 importFrom(BSgenome, getSeq, providerVersion)
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 importFrom(GenomicAlignments, readGAlignments)
 importMethodsFrom(GenomicAlignments, qwidth)
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 ## public API
 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
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        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
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        GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary,
        GmapParam)
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 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
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               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam,
               GmapAlignerParam)
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 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
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               "spliceSites<-", getSeq, gmap)
 
 S3method(as.list, GmapAlignerParam)