From f8a84e46beb5b5e1477c3fafcdd328d67d254da6 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Fri, 30 Mar 2012 16:16:27 +0000
Subject: [PATCH] order by orientation to avoid merging rows with different
 strands

---
 misc-scripts/assembly/merge_cmp_gaps.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/misc-scripts/assembly/merge_cmp_gaps.pl b/misc-scripts/assembly/merge_cmp_gaps.pl
index e29a642f05..d9adeeaec6 100755
--- a/misc-scripts/assembly/merge_cmp_gaps.pl
+++ b/misc-scripts/assembly/merge_cmp_gaps.pl
@@ -119,7 +119,7 @@ my $sql = qq(
   AND cs1.version = '$assembly'
   AND cs2.version = '$altassembly'
   AND sr2.name = ?
-  ORDER BY a.cmp_start
+  ORDER BY a.ori, a.cmp_start
 );
 
 my $sth = $dbh->prepare($sql);
-- 
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