diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm b/modules/Bio/EnsEMBL/Pipeline/Production/SnpDensity.pm index 7e4325bbda3d30b56491d93bdcedd9ea10b732ad..92a18b61551efc7623e102cd782950ca4eff606f 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;