# Generated by roxygen2: do not edit by hand

S3method(as.list,AlignmentsExperimentSet)
export("barcodeData<-")
export("experimentData<-")
export("fwdReads<-")
export("fwdReadsType<-")
export("readCounts<-")
export("rveReads<-")
export("rveReadsType<-")
export("unassignedData<-")
export(AlignmentsExperimentSet)
export(amplicanAlign)
export(amplicanConsensus)
export(amplicanFilter)
export(amplicanMap)
export(amplicanNormalize)
export(amplicanOverlap)
export(amplicanPipeline)
export(amplicanPipelineConservative)
export(amplicanReport)
export(amplicanSummarize)
export(amplican_print_reads)
export(assignedCount)
export(barcodeData)
export(cigarsToEvents)
export(comb_along)
export(experimentData)
export(extractEvents)
export(findEOP)
export(findLQR)
export(findPD)
export(fwdReads)
export(fwdReadsType)
export(getEvents)
export(get_seq)
export(is_hdr_strict)
export(lookupAlignment)
export(metaplot_deletions)
export(metaplot_insertions)
export(metaplot_mismatches)
export(pairToEvents)
export(plot_cuts)
export(plot_deletions)
export(plot_height)
export(plot_heterogeneity)
export(plot_insertions)
export(plot_mismatches)
export(plot_variants)
export(readCounts)
export(rveReads)
export(rveReadsType)
export(unassignedCount)
export(unassignedData)
export(waffle)
export(writeAlignments)
exportClasses(AlignmentsExperimentSet)
import(BiocGenerics, except = Position)
import(Rcpp)
import(data.table)
import(ggplot2)
import(ggthemes)
import(knitr)
import(methods)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,extractAt)
importFrom(Biostrings,quality)
importFrom(IRanges,coverage)
importFrom(Rcpp,sourceCpp)
importFrom(ggplot2,Stat)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,layer)
importFrom(pwalign,compareStrings)
importFrom(pwalign,pairwiseAlignment)
importFrom(pwalign,pattern)
importFrom(pwalign,subject)
importFrom(pwalign,unaligned)
importFrom(pwalign,writePairwiseAlignments)
importFrom(rlang,.data)
useDynLib(amplican)
