NAMESPACE

# Generated by roxygen2: do not edit by hand

export(MAlignments)
export(MAlignmentsList)
export(MTHGVS)
export(MTcircos)
export(MTcomplex)
export(MTcoverage)
export(MVRanges)
export(MVRangesList)
export(byStrand)
export(decomposeAndCalcConsequences)
export(depthFilterAndHaploMask)
export(exportFilteredAsVcf)
export(filterMT)
export(filterMTvars)
export(fixMetadata)
export(genMTcircos)
export(genesMTcircos)
export(genomeCoverage)
export(genomeLength)
export(getMT)
export(getProteinImpact)
export(getScReads)
export(importVCF)
export(initMTcircos)
export(injectMTVariants)
export(lift_up_to_rCRS)
export(locateMTvariants)
export(newFilterMT)
export(pileupMT)
export(pileupXenograft)
export(plotMTCoverage)
export(plotStrandedMTCoverage)
export(rawMTreads)
export(readLength)
export(s4Methods)
export(scanMT)
export(validMetadata)
export(vcf2mvrl)
exportClasses(MAlignments)
exportClasses(MAlignmentsList)
exportClasses(MVRanges)
exportClasses(MVRangesList)
exportMethods(annotation)
exportMethods(consensusString)
exportMethods(coverage)
exportMethods(encoding)
exportMethods(fileName)
exportMethods(filt)
exportMethods(genes)
exportMethods(genome)
exportMethods(genomeCoverage)
exportMethods(genomeLength)
exportMethods(getAnnotations)
exportMethods(granges)
exportMethods(locateVariants)
exportMethods(plot)
exportMethods(pos)
exportMethods(predictCoding)
exportMethods(readLength)
exportMethods(scanBamHeader)
exportMethods(show)
exportMethods(snpCall)
exportMethods(summarizeVariants)
exportMethods(type)
import(BiocGenerics)
import(BiocParallel)
import(Biostrings)
import(GenomeInfoDb)
import(GenomicAlignments)
import(GenomicRanges)
import(Homo.sapiens)
import(IRanges)
import(Rsamtools)
import(S4Vectors)
import(SummarizedExperiment)
import(VariantAnnotation)
import(VariantTools)
import(circlize)
import(jsonlite)
import(methods)
import(rtracklayer)
import(viridis)
import(xml2)
importFrom(Biobase,snpCall)
importFrom(Biostrings,lcsuffix)
importFrom(GenomicFeatures,genes)
importFrom(S4Vectors,endoapply)
importFrom(VariantAnnotation,filt)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,col2rgb)
importFrom(grDevices,rgb)
importFrom(graphics,legend)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(utils,browseURL)
importFrom(utils,data)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importMethodsFrom(Biostrings,consensusString)
importMethodsFrom(Biostrings,type)
importMethodsFrom(GenomicFeatures,genes)
importMethodsFrom(IRanges,coverage)
importMethodsFrom(VariantAnnotation,filt)