Merge pull request #374 from ipilizota/ancestral_leaves

Check the position of ancestral sequences in the genomic align trees

lib/Bio/EnsEMBL/DataCheck/Checks/CheckGenomicAlignTreeTable.pm

@@ -105,7 +105,30 @@ sub tests {
 
   }
 
+  my $sql_4 = qq/
+    SELECT COUNT(*)
+      FROM genomic_align_tree gat
+        JOIN genomic_align ga USING (node_id)
+        JOIN dnafrag df USING (dnafrag_id)
+      WHERE gat.right_index - gat.left_index != 1
+        AND df.coord_system_name != 'ancestralsegment'
+    /;
+
+  my $desc_4 = "All internal nodes link to ancestral sequences";
+  is_rows_zero($dbc, $sql_4, $desc_4);
+
+  my $sql_5 = qq/
+    SELECT COUNT(*)
+      FROM genomic_align_tree gat
+        JOIN genomic_align ga USING (node_id)
+        JOIN dnafrag df USING (dnafrag_id)
+      WHERE gat.right_index - gat.left_index = 1
+        AND df.coord_system_name = 'ancestralsegment'
+  /;
+
+  my $desc_5 = "All leaves are from current genome sequences";
+  is_rows_zero($dbc, $sql_5, $desc_5);
+
 }
 
 1;
-