Commit 082259b6 authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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The penalty on the position-based score for exons when an exon had a

phase change was removed because it meant that an exon whose sequence
and position had not changed would become a candidate for similarity
mapping.  This caused lots of criss-crossing stable ID history entries
between genes/transcripts/translations in some gene families.
parent 52088706
......@@ -402,11 +402,17 @@ sub calc_overlap_score {
my $score = ( $overlap/$source_length + $overlap/$target_length )/2;
# PENALTY:
# penalise by 10% if phase if different
if ( $source_exon->phase != $target_exon->phase ) {
$score *= 0.9;
}
# The following penalty was removed because it meant that an exon
# whose sequence and position had not changed would become a
# candidate for similarity mapping when its phase changed. This
# caused lots of criss-crossing stable ID history entries between
# genes/transcripts/translations in some gene families.
#
## PENALTY:
## penalise by 10% if phase if different
#if ( $source_exon->phase != $target_exon->phase ) {
#$score *= 0.9;
#}
# add score to scoring matrix if it's at least 0.5
if ( $score >= 0.5 ) {
......
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