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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(adaptorAlign)
export(barcodeAlign)
export(consensusReadSeq)
export(errorFinder)
export(expectedDist)
export(extractSubseq)
export(filterReads)
export(getAdaptorThresholds)
export(getBarcodeThresholds)
export(homopolymerFinder)
export(homopolymerMatcher)
export(multiReadAlign)
export(qualityAlign)
export(qualityMask)
export(realizeReads)
export(sam2ranges)
export(tuneAlignment)
export(umiGroup)
import(Biostrings)
import(GenomicRanges)
import(IRanges)
import(S4Vectors)
import(XVector)
import(methods)
importClassesFrom(Biostrings,BStringSet)
importClassesFrom(Biostrings,DNAStringSet)
importClassesFrom(Biostrings,PairwiseAlignmentsSingleSubject)
importClassesFrom(Biostrings,QualityScaledDNAStringSet)
importClassesFrom(IRanges,RleList)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,List)
importFrom(BiocGenerics,"rownames<-")
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,score)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,width)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpisup)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpmapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpstart)
importFrom(BiocParallel,bpstop)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,PhredQuality)
importFrom(Biostrings,QualityScaledDNAStringSet)
importFrom(Biostrings,aligned)
importFrom(Biostrings,alignedPattern)
importFrom(Biostrings,alignedSubject)
importFrom(Biostrings,encoding)
importFrom(Biostrings,pattern)
importFrom(Biostrings,quality)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,subject)
importFrom(Biostrings,subseq)
importFrom(Biostrings,type)
importFrom(Biostrings,unaligned)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomeInfoDb,Seqinfo)
importFrom(GenomicAlignments,cigarWidthAlongReferenceSpace)
importFrom(GenomicRanges,GRanges)
importFrom(IRanges,IRanges)
importFrom(IRanges,mad)
importFrom(IRanges,median)
importFrom(Rcpp,sourceCpp)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,"metadata<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,head)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,split)
importFrom(ShortRead,FastqSampler)
importFrom(ShortRead,FastqStreamer)
importFrom(ShortRead,id)
importFrom(ShortRead,sread)
importFrom(ShortRead,yield)
importFrom(XVector,compact)
importFrom(XVector,subseq)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(stats,rbinom)
importFrom(stats,runif)
importFrom(utils,count.fields)
importFrom(utils,read.delim)
useDynLib(sarlacc, .registration=TRUE, .fixes="cxx_")