allow missssing contigs in correspondance file when running convert_G…

…FF_coord.sh
cmdoret · Aug 6, 2018 · 64341b9 · 64341b9
1 parent e20f8c0
commit 64341b9
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/src/convert_coord/convert_GFF_coord.sh b/src/convert_coord/convert_GFF_coord.sh
@@ -118,6 +118,8 @@ eval $run_fun <<CONV_COORD
  track=( \$line )
  # Getting line of corresp file for the contig on current line
  corresp=( \$(grep "^\${track[0]}" $CORRESP_GFF | sed 's/,/ /g') )
+ # If track is not on a chromosome (i.e. contig is not anchored), skip it
+ if [ -z "\$corresp" ]; then continue; fi
  # Replacing contig of current record in memory
  track[0]=\${corresp[1]}
  # Shift start and end if necessary and flip,