From 932cd31bb6867d56bca2831294ebaf35a899a393 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 15 Sep 2011 07:59:16 +0000
Subject: [PATCH] Rolling back the code to 1.20 because of issues with
re-binning the human Y chromsome density values resulting in a -ve value.
---
misc-scripts/density_feature/variation_density.pl | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index 3bf3e56b5e..c1ad66f6fd 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/misc-scripts/density_feature/variation_density.pl
@@ -49,7 +49,11 @@ $sth->execute();
my @sorted_slices = sort( {
$a->coord_system()->rank() <=> $b->coord_system()->rank()
|| $b->seq_region_length() <=> $a->seq_region_length()
-} @{ $slice_adaptor->fetch_all('toplevel', '', undef, 1) } );
+} @{ $slice_adaptor->fetch_all('toplevel')} );
+# Cannot use this due to PAR regions & basefeatureadaptor's fetch method
+#understanding par region translation
+#} @{ $slice_adaptor->fetch_all('toplevel', '', undef, 1) } );
+
my $analysis = $analysis_adaptor->fetch_by_logic_name('snpdensity');
# new Bio::EnsEMBL::Analysis(
--
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