From c2f4a16a9c4e08f2f92b091ffabfa98de52053de Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 3 Jun 2011 12:20:51 +0000
Subject: [PATCH] overlapping exon check bug fix
---
modules/Bio/EnsEMBL/Transcript.pm | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 4974e63c96..7aedfaa5ae 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1306,6 +1306,10 @@ sub add_Exon {
# Overlap
last;
}
+ if ( $i and $exon_start <= $ea->[$i-1]->end() ) {
+ # Overlap
+ last;
+ }
splice( @{$ea}, $i, 0, $exon );
$was_added = 1;
last;
@@ -1332,6 +1336,10 @@ sub add_Exon {
# Overlap
last;
}
+ if ( $i and $exon_end >= $ea->[$i-1]->start() ) {
+ # Overlap
+ last;
+ }
splice( @{$ea}, $i, 0, $exon );
$was_added = 1;
last;
--
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