Modified queries to match Variation schema changes. The sample table was...

Modified queries to match Variation schema changes. The sample table was removed, and the information was pushed into population and individual tables.

modules/Bio/EnsEMBL/Pipeline/Production/NonSense.pm

@@ -73,10 +73,9 @@ sub get_sample_ids {
 
   my ($sample_id, $name);
   my $sql = q{
-     SELECT p.sample_id, s.name
-     FROM sample s, population p
-     WHERE p.sample_id = s.sample_id
-     AND s.name = ? };
+     SELECT p.population_id, p.name
+     FROM population p
+     WHERE p.name = ? };
   foreach my $pop (@$pops) {
     my $result = $helper->execute(-SQL => $sql, -PARAMS => [$pop])->[0] ;
     if ($result) {
@@ -102,7 +101,7 @@ sub get_features {
   my $frequency = $self->param('frequency');
   my $observation = $self->param('observation');
   my $sql = q{
-     SELECT a.sample_id, tv.feature_stable_id, vf.variation_name, substring_index(tv.consequence_types, ",", 1)
+     SELECT a.population_id, tv.feature_stable_id, vf.variation_name, substring_index(tv.consequence_types, ",", 1)
      FROM transcript_variation tv, variation_feature vf, allele_code ac, allele a
      WHERE vf.variation_feature_id = tv.variation_feature_id
      AND vf.variation_id = a.variation_id