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useDynLib(Rsamtools, .registration=TRUE)
import(methods)
import(zlibbioc)
importFrom(bitops, bitAnd)
importFrom(utils, read.table) # normalizePath --> base in R-2.13
importFrom(stats, rbinom, setNames)
importClassesFrom(BiocGenerics, url, gzfile, unz, pipe)
importFrom(BiocGenerics, cbind, duplicated, eval, Filter, lapply, Map,
order, path, paste, rbind, Reduce, rep.int, sapply, setdiff,
tapply, union, unique)
importFrom(BiocParallel, bplapply)
import(S4Vectors)
import(IRanges)
importClassesFrom(GenomeInfoDb, Seqinfo)
importFrom(GenomeInfoDb, Seqinfo, seqinfo, seqlevels, sortSeqlevels)
importClassesFrom(GenomicRanges, GRanges, GRangesList)
importFrom(GenomicRanges, GRanges, GRangesList)
importMethodsFrom(GenomicRanges, seqnames, strand)
import(XVector)
importClassesFrom(Biostrings, DNAStringSet, BStringSet, PhredQuality)
importFrom(Biostrings, DNA_ALPHABET, readDNAStringSet,
readRNAStringSet, readAAStringSet,
DNAStringSet, BStringSet, PhredQuality,
getSeq, reverseComplement)
exportPattern("^[^\\.]")
exportMethods(length, names, "[", "[[", show, getSeq, seqinfo)
S3method(close, BamFile)
S3method(close, BcfFile)
S3method(close, FaFile)
S3method(close, TabixFile)
S3method(close, RsamtoolsFileList)
S3method(open, BamFile)
S3method(open, BcfFile)
S3method(open, FaFile)
S3method(open, TabixFile)
S3method(open, RsamtoolsFileList)
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