Merge pull request sanger-pathogens#31 from andrewjpage/master

use new st
CraigPorter · Mar 8, 2013 · c42c5ae · c42c5ae
2 parents 3e885a0 + eeb7754
commit c42c5ae
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Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/lib/Bio/MLST/CompareAlleles.pm b/lib/Bio/MLST/CompareAlleles.pm
@@ -159,8 +159,8 @@ sub _build_matching_sequences
     # more than 1 allele has 100% match
     if(defined($top_blast_hit{contamination}))
     {
-      $self->contamination(1);      
-      $self->contamination_sequence_names($top_blast_hit{contamination});
+      $self->contamination(1);
+      $self->_translate_contamination_names_into_sequence_types($top_blast_hit{contamination},$top_blast_hit{allele_name});
     }
 
     $top_blast_hit{allele_name} =~ s![-_]+!-!g;
@@ -195,7 +195,7 @@ sub _build_matching_sequences
 
 sub _translate_contamination_names_into_sequence_types
 {
-  my ($self, $contamination_names) = @_;
+  my ($self, $contamination_names, $main_allele_name) = @_;
   my @contamination_sequence_types;
 
   for my $allele_number (@{ $contamination_names})
@@ -205,7 +205,7 @@ sub _translate_contamination_names_into_sequence_types
       sequence_names => [$allele_number]
     );
 
-    if(defined($st->sequence_type()))
+    if(defined($st->sequence_type()) && $main_allele_name ne $st->sequence_type())
     {
       push(@contamination_sequence_types, $st->sequence_type());
     }

diff --git a/t/SequenceTypes/CompareAlleles.t b/t/SequenceTypes/CompareAlleles.t
@@ -37,7 +37,6 @@ ok(($compare_alleles = Bio::MLST::CompareAlleles->new(
 is_deeply( $compare_alleles->found_sequence_names,sort(['adk-3']), 'last top hit returned if more than 1 is 100%');
 is($compare_alleles->new_st, 0, 'existing ST found');
 is($compare_alleles->contamination, 1, 'contamination found');
-is_deeply($compare_alleles->contamination_sequence_names, ['adk-3','adk-2'], 'Names of other contamination sequences');
 
 
 ok(($compare_alleles = Bio::MLST::CompareAlleles->new(