From 0c913119ecf33aeb9a6405b450deb75cce189783 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 3 Oct 2013 09:05:02 +0000
Subject: [PATCH] for chromosome Y, we want the whole sequence as one slice, so
use 'include duplicates' (ie, include the duplicated sequence Y has in common
with X rather than the two sequences unique to Y)
---
modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
index 7b004d64af..1e25212c4d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
@@ -397,7 +397,7 @@ sub get_total_length {
sub get_toplevel {
my ($self) = @_;
my $sa = $self->db->get_adaptor('Slice');
- $self->{'toplevel'} = $sa->fetch_all('toplevel');
+ $self->{'toplevel'} = $sa->fetch_all('toplevel', undef, undef, 1);
return $self->{'toplevel'};
}
--
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