From 5d49c39f9b0e30d45c7fc03db9b7a110320ce799 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 10 Sep 2014 13:10:54 +0100
Subject: [PATCH] ENSCORESW-1025: reinstate phase check ignoring phase creates
more false positives than false negatives also improves the overall exon
mapping
---
modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
index 81c5933526..d45352b591 100644
--- a/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
+++ b/modules/Bio/EnsEMBL/IdMapping/ExonScoreBuilder.pm
@@ -420,9 +420,9 @@ sub calc_overlap_score {
#
## PENALTY:
## penalise by 10% if phase if different
- #if ( $source_exon->phase != $target_exon->phase ) {
- #$score *= 0.9;
- #}
+ 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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