Merge pull request #358 from andrewjpage/dashes_for_missing

change missing gene in core to be dashes rather than Ns
sanger-pathogens · Oct 10, 2017 · 68c77ea · 68c77ea
2 parents 466909f + 802c2aa
commit 68c77ea
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diff --git a/dist.ini b/dist.ini
@@ -3,7 +3,7 @@ author  = Andrew J. Page <[email protected]>
 license = GPL_3
 copyright_holder = Wellcome Trust Sanger Institute
 copyright_year   = 2013
-version = 3.10.2
+version = 3.11.0
 main_module = lib/Bio/Roary.pm
 
 [MetaResources]

diff --git a/lib/Bio/Roary/MergeMultifastaAlignments.pm b/lib/Bio/Roary/MergeMultifastaAlignments.pm
@@ -83,7 +83,7 @@ sub _sequence_for_sample_from_gene_file {
 sub _padded_string_for_gene_file {
     my ( $self, $gene_file ) = @_;
     return '' unless ( defined( $self->_gene_lengths->{$gene_file} ) );
-    return 'N' x ( $self->_gene_lengths->{$gene_file} );
+    return '-' x ( $self->_gene_lengths->{$gene_file} );
 }
 
 sub _create_merged_sequence_for_sample {

diff --git a/t/data/expected_core_gene_alignment_core0.66.aln b/t/data/expected_core_gene_alignment_core0.66.aln
@@ -3,4 +3,4 @@ TTTTT
 >query_2
 GGGGG
 >query_3
-NNNNN
+-----