bug fixes

misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm

@@ -486,6 +486,8 @@ sub adjust_coords {
 sub filter_overlaps {
     my $self = shift;
     my $id = $self->id;
+    
+    return unless ($self->{'_match'});
 
     foreach my $R_chr (sort keys %{ $self->{'_match'} }) {
         # rearrange the datastructure so that we can find overlaps

misc-scripts/assembly/align_nonident_regions.pl

@@ -183,8 +183,8 @@ $support->log_stamped("Looping over non-aligned blocks...\n");
 
 $sql = qq(SELECT * FROM tmp_align);
 if ($support->param('chromosomes')) {
-  my $chr_string = join(", ", $support->param('chromosomes'));
-  $sql .= " WHERE ref_seq_region_name IN ($chr_string)";
+  my $chr_string = join("', '", $support->param('chromosomes'));
+  $sql .= " WHERE ref_seq_region_name IN ('$chr_string')";
 }
 $sth = $R_dbh->prepare($sql);
 $sth->execute;