Commit bad74a17 authored by khalid's avatar khalid
Browse files

debug radsex_map_region plot

parent 52b183ad
......@@ -19,9 +19,12 @@ if ( chromosome_file == ""){
radsex_map_circos(fichiers, output_file = output_file, chromosomes_file= chromosome_file)
if (file.exists(signi_out_file) )
{
regions = read.table(signi_out_file, header= TRUE, sep="\t")
regions = read.table(signi_out_file, header= TRUE, sep=" ")
chromosomes = read.table(chromosome_file, header= FALSE, sep="\t")
reg = chromosomes[which(chomosomes[,1]==regions[1,2]),2]
radsex_map_region(fichiers, region = reg, chromosomes_file = chromosome_file, output_file = "mapping_to_first_contig_mqc.png")
contigs = unique(regions[,2])
for (ctg in contigs){
reg = chromosomes[which(chromosomes[,1]==ctg),2]
radsex_map_region(fichiers, region = reg, chromosomes_file = chromosome_file, output_file = paste0(parameters$results_dir,"/",parameters$<step_name>__radsex_map_output_dir,"/mapping_to_",reg,"_mqc.png") )
}
}
}
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