# Generated by roxygen2: do not edit by hand

S3method(print,hapResult)
S3method(print,hapSummary)
export(addINFO)
export(allignSeqs)
export(as.haplotype)
export(displayVarOnGeneModel)
export(filterLargeVCF)
export(filter_vcf)
export(getGenePOS)
export(getGeneRanges)
export(get_hapNet)
export(gffSetATGas0)
export(hapDistribution)
export(hapSetATGas0)
export(hapVsPheno)
export(hapVsPhenos)
export(hap_summary)
export(import_AccINFO)
export(import_MultipleAlignment)
export(import_gff)
export(import_hap)
export(import_seqs)
export(import_vcf)
export(plotEFF)
export(plotHapNet)
export(plotHapTable)
export(seqs2hap)
export(siteEFF)
export(sites)
export(trimSeqs)
export(vcf2hap)
export(write.hap)
import(ggplot2)
import(grDevices)
import(tidyr)
import(vcfR)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,as.matrix)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,width)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,as.data.frame)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,`%over%`)
importFrom(IRanges,end)
importFrom(IRanges,start)
importFrom(ape,as.DNAbin)
importFrom(grDevices,heat.colors)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,locator)
importFrom(graphics,par)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,rect)
importFrom(graphics,strheight)
importFrom(graphics,strwidth)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(maps,map)
importFrom(methods,as)
importFrom(muscle,muscle)
importFrom(pegas,haploNet)
importFrom(rlang,.data)
importFrom(rtracklayer,import)
importFrom(stats,IQR)
importFrom(stats,chisq.test)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,shapiro.test)
importFrom(stats,t.test)
importFrom(stats,wilcox.test)
importFrom(stringdist,stringdist)
importFrom(stringr,str_detect)
importFrom(stringr,str_length)
importFrom(stringr,str_pad)
importFrom(stringr,str_starts)
importFrom(tibble,tibble)
importFrom(trackViewer,lolliplot)
importFrom(utils,read.delim)
importFrom(utils,write.table)
importFrom(vcfR,read.vcfR)
