NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(autoplot,AlignmentPairsList)
S3method(plot,AlignmentPairsList)
export("query<-")
export("sbjct<-")
export(AlignmentPairs)
export(AlignmentPairsList)
export(breadthOfCoverage)
export(countSubjectsByCoverage)
export(deletions)
export(depthOfCoverage)
export(divergence)
export(geneBodyCoverage)
export(insertionSummary)
export(insertions)
export(matches)
export(mismatches)
export(query)
export(readFastaIndex)
export(readPsl)
export(reduceHitCoverage)
export(repmatches)
export(sbjct)
export(score)
export(summarizeGeneBodyCoverage)
exportClasses(AlignmentPairs)
exportClasses(AlignmentPairsList)
exportMethods("query<-")
exportMethods("sbjct<-")
exportMethods(AlignmentPairs)
exportMethods(AlignmentPairsList)
exportMethods(as.data.frame)
exportMethods(geneBodyCoverage)
exportMethods(matches)
exportMethods(mismatches)
exportMethods(query)
exportMethods(repmatches)
exportMethods(sbjct)
import(GenomeInfoDb)
import(IRanges)
import(S4Vectors)
importFrom(BiocParallel,bplapply)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IntegerList)
importFrom(IRanges,reduce)
importFrom(IRanges,width)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(S4Vectors,subset)
importFrom(dplyr,bind_rows)
importFrom(ggplot2,autoplot)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(graphics,plot)
importFrom(methods,callNextMethod)
importFrom(methods,new)
importFrom(methods,validObject)
importFrom(rlang,as_label)
importFrom(rlang,enquo)
importFrom(rlang,get_expr)
importFrom(rlang,quo_set_expr)
importFrom(tidyr,pivot_longer)
importFrom(utils,read.table)