From d2a3a46038925d62e2f9a0024217f8cfabe48923 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 5 Jan 2011 13:14:58 +0000
Subject: [PATCH] Fixed the overlap test in add_Exon().
---
modules/Bio/EnsEMBL/Transcript.pm | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index bc75835138..d7f4bfa238 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1231,17 +1231,17 @@ sub add_Exon {
if ( @{$ea} ) {
if ( $exon->strand() == 1 ) {
- if ( ( $exon->start() > $ea->[$#$ea]->end() )
- && ( $exon->end() > $ea->[$#$ea]->end() ) )
- {
+ if ( $exon->start() > $ea->[$#$ea]->end() ) {
push( @{$ea}, $exon );
$was_added = 1;
} else {
# insert it at correct place
for ( my $i = 0; $i <= $#$ea; $i++ ) {
- if ( ( $exon->start() < $ea->[$i]->start() )
- && ( $exon->end() < $ea->[$i]->start() ) )
- {
+ if ( $exon->start() < $ea->[$i]->start() ) {
+ if ( $exon->end() >= $ea->[$i]->start() ) {
+ # Overlap
+ last;
+ }
splice( @{$ea}, $i, 0, $exon );
$was_added = 1;
last;
@@ -1251,17 +1251,17 @@ sub add_Exon {
} else {
- if ( ( $exon->start() < $ea->[$#$ea]->start() )
- && ( $exon->end() < $ea->[$#$ea]->start() ) )
- {
+ if ( $exon->end() < $ea->[$#$ea]->start() ) {
push( @{$ea}, $exon );
$was_added = 1;
} else {
# insert it at correct place
for ( my $i = 0; $i <= $#$ea; $i++ ) {
- if ( ( $exon->start() > $ea->[$i]->end() )
- && ( $exon->end() > $ea->[$i]->end() ) )
- {
+ if ( $exon->end() > $ea->[$i]->end() ) {
+ if ( $exon->start() <= $ea->[$i]->end() ) {
+ # Overlap
+ last;
+ }
splice( @{$ea}, $i, 0, $exon );
$was_added = 1;
last;
--
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