make sure dbs flagged as having variation positions changed have a variation db

misc-scripts/density_feature/submit_density_features.pl

@@ -268,6 +268,7 @@ if ($response == 3) {
     #get species for new dbs or changed assembly or where variation positions have changed
     @core_with_variation =  map { $_->[0] }  @{ $prod_dbh->selectall_arrayref("select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where db_release = $current_release and db_type = 'core' and species_id in (select distinct species_id from db where db_release = $current_release and db_type = 'variation');") };
 
+    #this sql relies on variation changed flag in change log
     @chg_variation =  map { $_->[0] }  @{ $prod_dbh->selectall_arrayref("select distinct concat(full_db_name,'|',db_host) from db_list dl join db d using (db_id) where db_type = 'core' and is_current = 1 and species_id in (select distinct species_id from changelog_species cs join changelog c using (changelog_id) where release_id = $current_release and status not in ('cancelled','postponed') and variation_pos_changed = 'Y')") };
 
     my %core_with_variation = map { $_ => 1 } @core_with_variation;
@@ -282,8 +283,16 @@ if ($response == 3) {
 	}
     }
 
+    #make sure dbs flagged having variation positions changed, have a varition db
+    my @chg_var;
+    foreach my $element (@chg_variation) {
+	if (exists($core_with_variation{$element}) ) {
+	    push (@chg_var, $element);
+	}
+    }
+
     my %array_union = ();
-    foreach my $element (@new_sp_assem_var, @chg_variation) { $array_union{$element}++ }
+    foreach my $element (@new_sp_assem_var, @chg_var) { $array_union{$element}++ }
     my @dbnames_hosts = sort(keys %array_union); 
  
     my $file_path = "$outdir/variation_density_data.txt";