From 04bb67f945f0a4358c711f7748a0d2a4379555a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 13 Aug 2010 14:32:00 +0000
Subject: [PATCH] Get some of the logic right.
---
modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm | 53 ++++++++++++------------
1 file changed, 26 insertions(+), 27 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index b67a1d38e3..652ce687b8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -672,40 +672,39 @@ FEATURE: while ( $sth->fetch() ) {
} else {
# On the negative strand.
- if ( $dest_slice->is_circular() ) {
+ if ( $dest_slice->is_circular()
+ && $seq_region_start > $seq_region_end )
+ {
# Handle circular chromosomes.
- if ( $seq_region_start > $seq_region_end ) {
- if ( $dest_slice_start > $dest_slice_end ) {
- my $tmp_seq_region_start = $seq_region_start;
+ if ( $dest_slice_start > $dest_slice_end ) {
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start = $dest_slice_end - $seq_region_end + 1;
+ $seq_region_end =
+ $dest_slice_end +
+ $dest_slice->seq_region_length() -
+ $tmp_seq_region_start + 1;
+ } else {
+
+ if ( $seq_region_end > $dest_slice_start ) {
+ # Looking at the region in the beginning of the
+ # chromosome.
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end =
- $dest_slice_end +
+ $seq_region_end -
$dest_slice->seq_region_length() -
- $tmp_seq_region_start + 1;
+ $dest_slice_start + 1;
} else {
-
- if ( $seq_region_end > $dest_slice_start ) {
- # Looking at the region in the beginning of the
- # chromosome.
- $seq_region_start =
- $dest_slice_end - $seq_region_end + 1;
- $seq_region_end =
- $seq_region_end -
- $dest_slice->seq_region_length() -
- $dest_slice_start + 1;
- } else {
- my $tmp_seq_region_start = $seq_region_start;
- $seq_region_start =
- $dest_slice_end -
- $seq_region_end -
- $dest_slice->seq_region_length() + 1;
- $seq_region_end =
- $dest_slice_end - $tmp_seq_region_start + 1;
- }
-
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start =
+ $dest_slice_end -
+ $seq_region_end -
+ $dest_slice->seq_region_length() + 1;
+ $seq_region_end =
+ $dest_slice_end - $tmp_seq_region_start + 1;
}
- } ## end if ( $seq_region_start...)
+
+ }
} else {
# Non-circular chromosome.
--
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