From 0d954764673487e917c37cf087ff3561ea38de19 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 14 Feb 2014 10:53:13 +0000
Subject: [PATCH] include non_reference chromosomes for mapping stats
---
misc-scripts/assembly/mapping_stats.pl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/misc-scripts/assembly/mapping_stats.pl b/misc-scripts/assembly/mapping_stats.pl
index a66e16ae7c..5a255f9eed 100755
--- a/misc-scripts/assembly/mapping_stats.pl
+++ b/misc-scripts/assembly/mapping_stats.pl
@@ -144,7 +144,7 @@ my $fmt4 = "%-40s%12s%10s\n";
$support->log("Looping over toplevel seq_regions...\n\n");
-foreach my $chr ($support->sort_chromosomes) {
+foreach my $chr ($support->sort_chromosomes(undef, $support->param('assembly'), 1)) {
$support->log_stamped("Toplevel seq_region $chr...\n", 1);
# determine non-N sequence length of alternative toplevel seq_region
--
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