Commit 1deb5dbd authored by Dan Sheppard's avatar Dan Sheppard
Browse files

Added ability to specify TGA Secs on command line; undefined variable warning bugfix.

parent b2ede769
......@@ -367,7 +367,7 @@ sub check_for_stops {
elsif (defined($offset) && ($offset=~/^\d+$/)){
if ($offset == length($orig_seq)+1) {
if($seen_transcripts->{$tsi}->[1] eq 'known-tga-stop') {
if($seen_transcripts->{$tsi} && $seen_transcripts->{$tsi}->[1] eq 'known-tga-stop') {
$log_object->_save_log('log', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) known to be a stop codon. Ok. [$mod_date]");
} else {
$log_object->_save_log('log_warning', '', $gene->stable_id, 'TRANSCRIPT', $tsi, '', "Annotated stop for transcript $tsi ($tname) \"$offset\" matches actual stop codon yet has no entry in script config to disambiguate it. Please investigate and add appropriate entry. [$mod_date]");
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