Force the order of transcripts in /tmp/ALL_transcripts.ctgs

src/CroCo_v1.2.sh

@@ -115,6 +115,9 @@ echo
  esac
  echo -e "\nIndex built : $out/$toolidx\n"
 
+ refseqALL=$out/ALL_transcripts.ctgs
+ echo '' > $refseqALL
+
  #for (( j=0; j <i; j++ ))
  for ref in "${orders[@]}"
  do
@@ -128,10 +131,11 @@ echo
     Seqlength = length($2) ;
     print a[1]"\t"Seqlength > refseqs
    }' $out/$ref".fasta_mod"
- done
+  
   # regroup all samples 
- refseqALL=$out/ALL_transcripts.ctgs
- cat $out/*.ctgs > $refseqALL
+  cat $out/*.ctgs >> $refseqALL
+ done
+
  
  # mapping successively every read sets on all transcripts.
  #for (( k=0; k <i; k++ ))