debug radsex_map_region plot

tools/radsex_map/radsex_map.prepare.report.R

@@ -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") )
+ }
  }
 }