From 7f5d7a5a69512d849f2f1fd6620cc33a32cff9a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 15 Sep 2010 14:43:00 +0000
Subject: [PATCH] In slice(): Do not transfer supporting features that does not
have an attached slice.
---
modules/Bio/EnsEMBL/Exon.pm | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 7d03eb2019..2181223b15 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -791,7 +791,7 @@ sub slice {
if ( defined($slice) ) {
# If a new slice was provided, flush the internal sequence cache and
- # transcer all supporting evidence to the new slice.
+ # transfer all supporting evidence to the new slice.
delete $self->{'_seq_cache'};
@@ -799,7 +799,17 @@ sub slice {
my @new_features;
for my $old_feature ( @{ $self->{'_supporting_evidence'} } ) {
- my $new_feature = $old_feature->transfer($slice);
+
+ my $new_feature;
+
+ if ( defined( $old_feature->slice() ) ) {
+ $new_feature = $old_feature->transfer($slice);
+ } else {
+ # If the old feature does not have a slice, assume transfer is
+ # not necessary.
+ $new_feature = $old_feature;
+ }
+
push( @new_features, $new_feature );
}
--
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