bug fix, re-introduced old bug :(

modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm

@@ -295,27 +295,26 @@ sub check_for_stops {
       if ($annot_stops){
 	my $i = 0;
 	foreach my $offset (split(/\s+/, $annot_stops)) {
+    $defined_offset= (defined($offset)) && ($offset=~/^\d+$/);
+	  $defined_found_stop = ( defined(@found_stops) && defined($found_stops[$i]) && defined($found_stops[$i]->[1]));  
     if(not defined($offset)){
       $offset='';
     }
-	  # not a number - ignore
-	  if ($offset!~/^\d+$/){
-	  }
 	  #OK if it matches a known stop
-	  elsif ($found_stops[$i]->[1] == $offset) {
+    if ($defined_offset && $defined_found_stop && ($found_stops[$i]->[1] == $offset)) {    
 	    push  @annotated_stops, $offset;
 	  }
 	  # catch old annotations where number was in DNA not peptide coordinates
-	  elsif (($found_stops[$i]->[1] * 3) == $offset) {
+    elsif ($defined_offset && $defined_found_stop && (($found_stops[$i]->[1] * 3) == $offset)) {
 	    #$support->log_warning("DNA: Annotated stop for transcript tsi ($tname) is in DNA not peptide coordinates) [$mod_date]\n");
       $log_object->_save_log('log_warning', '', $gsi, 'DNA', $tsi, 'VQCT_wrong_selC_coord', "DNA: Annotated stop for transcript tsi ($tname) is in DNA not peptide coordinates) [$mod_date]");  
 	  }
 	  # catch old annotations where number off by one
-	  elsif (($found_stops[$i]->[1]) == $offset+1) {
+    elsif ($defined_offset && $defined_found_stop && (($found_stops[$i]->[1]) == $offset+1)) {
 	    #$support->log_warning("PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one) [$mod_date]\n");
       $log_object->_save_log('log_warning', '', $gsi, 'PEPTIDE', $tsi, 'VQCT_wrong_selC_coord', "PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one) [$mod_date]");  
 	  }
-	  else {
+    elsif($defined_offset) {
 	    #$support->log_warning("Annotated stop for transcript $tsi ($tname) does not match a TGA codon) [$mod_date]\n");
       $log_object->_save_log('log_warning', '', $gsi, 'TRANSCRIPT', $tsi, 'VQCT_wrong_selC_coord', "Annotated stop for transcript $tsi ($tname) does not match a TGA codon) [$mod_date]");
 	    push  @annotated_stops, $offset;