NAMESPACE
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 useDynLib(gmapR, .registration = TRUE)
 
 importFrom(Rsamtools, path, bamPaths, readBamGappedAlignments, "bamWhich<-",
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            BamFile, BamFileList)
 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(methods)
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 import(GenomicRanges)
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 importFrom(utils, packageVersion)
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 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
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 importFrom(GenomicRanges, genome, seqinfo)
 importMethodsFrom(GenomicRanges, seqnames, strand)
 importMethodsFrom(Rsamtools, asBam)
 importClassesFrom(GenomicFeatures, TranscriptDb)
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 importFrom(GenomicFeatures, transcripts, exons)
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 importClassesFrom(rtracklayer, RTLFile, FastaFile)
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile)
 importMethodsFrom(rtracklayer, export)
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 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
            "ref<-", "alt<-")
 importClassesFrom(VariantAnnotation, "VCF", "VRanges")
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 importFrom(BSgenome, getSeq, providerVersion)
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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)
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 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam)
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 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
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               "spliceSites<-", getSeq)