From f4ce1d991313db76d8db28ebc132860af13b9f42 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Wed, 22 Aug 2012 12:21:08 +0000
Subject: [PATCH] added a get_total method for snp density when counting
features, do not use strict lower/higher
---
.../Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm b/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm
index 7e4325bbda..92a18b6155 100644
--- a/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm
@@ -15,12 +15,21 @@ sub get_density {
my $sql = q{
SELECT count(*) FROM variation_feature
WHERE seq_region_id = ?
- AND seq_region_start < ?
- AND seq_region_end > ? };
+ AND seq_region_start <= ?
+ AND seq_region_end >= ? };
my @params = [$block->get_seq_region_id, $block->end, $block->start];
my $count = $helper->execute_single_result(-SQL => $sql, -PARAMS => @params);
return $count;
}
+sub get_total {
+ my ($self, $option) = @_;
+ my $species = $self->param('species');
+ my $variation_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'variation');
+ my $helper = $variation_adaptor->dbc()->sql_helper();
+ my $sql = "SELECT count(*) FROM variation_feature";
+ return $helper->execute_single_result(-SQL => $sql);
+}
+
return 1;
--
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