NAMESPACE
b22faf0d
 useDynLib(gmapR, .registration = TRUE)
 
c67b519b
 importFrom(BiocGenerics, path)
 importFrom(Rsamtools, bamPaths, "bamWhich<-", BamFile, BamFileList,
6cca01e8
            BamSampler)
c78be696
 importFrom(tools, file_path_as_absolute, file_ext, file_path_sans_ext,
            list_files_with_exts)
b22faf0d
 importFrom(Biobase, createPackage)
97bf6d3e
 import(IRanges)
c78be696
 import(S4Vectors)
 import(methods)
97bf6d3e
 import(GenomicRanges)
c9319fcf
 import(GenomeInfoDb)
c78be696
 import(BiocParallel)
8418591e
 importMethodsFrom(GenomeInfoDb, genome)
c67b519b
 importFrom(stats, setNames)
 importFrom(utils, packageVersion, read.table, str)
0dbb11f8
 importFrom(Biostrings, getSeq, readDNAStringSet, DNAStringSet)
8418591e
 importMethodsFrom(GenomicRanges, seqnames, strand)
b22faf0d
 importMethodsFrom(Rsamtools, asBam)
8418591e
 importClassesFrom(GenomicFeatures, TxDb)
f053c5f3
 importFrom(GenomicFeatures, transcripts, exons, exonsBy)
ead94b30
 importClassesFrom(rtracklayer, RTLFile, FastaFile, RTLFileList)
f053c5f3
 importFrom(rtracklayer, "referenceSequence<-", import, export, FastaFile,
            FileForFormat)
b22faf0d
 importMethodsFrom(rtracklayer, export)
59c36844
 importFrom(VariantAnnotation, readVcf, ScanVcfParam, fixed, VRanges, ref, alt,
f053c5f3
            "ref<-", "alt<-", altDepth, refDepth, "vcfWhich<-")
59c36844
 importClassesFrom(VariantAnnotation, "VCF", "VRanges")
248ed950
 importFrom(BSgenome, getSeq, providerVersion)
30f3bfda
 importFrom(GenomicAlignments, readGAlignments)
 importMethodsFrom(GenomicAlignments, qwidth)
b22faf0d
 
 ## public API
 
 export(bam_tally, GmapGenome, GmapGenomeDirectory, GsnapParam,
d99f8059
        directory, BamTallyParam, makeGmapGenomePackage, GsnapOutput,
ead94b30
        GmapSnps, GmapSnpDirectory, TP53Genome, TP53Which, variantSummary,
1cb2c805
        GmapParam, cmetindex)
0a4b811e
 
b22faf0d
 exportClasses(GmapGenome, GmapGenomeDirectory, GmapSnpDirectory,
ead94b30
               GsnapOutput, GmapSnps, BamTallyParam, GsnapParam, GmapParam,
               GmapAlignerParam)
cc3f47cf
 
5fdf6426
 exportMethods(bamPaths, path, genome, seqinfo, gsnap, "snps<-",
ead94b30
               "spliceSites<-", getSeq, gmap)
 
 S3method(as.list, GmapAlignerParam)