Merge pull request #358 from andrewjpage/dashes_for_missing

andrewjpage · web-flow · commit 68c77ea91f36 · 2017-10-10T17:03:00.000+01:00
change missing gene in core to be dashes rather than Ns
diff --git a/dist.ini b/dist.ini
@@ -3,7 +3,7 @@ author  = Andrew J. Page <ap13@sanger.ac.uk>
 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
+-----

Original file line number	Diff line number	Diff line change
`@@ -83,7 +83,7 @@ sub _sequence_for_sample_from_gene_file {`
`83`	`83`	`sub _padded_string_for_gene_file {`
`84`	`84`	`my ( $self, $gene_file ) = @_;`
`85`	`85`	`return '' unless ( defined( $self->_gene_lengths->{$gene_file} ) );`
`86`		`- return 'N' x ( $self->_gene_lengths->{$gene_file} );`
	`86`	`+ return '-' x ( $self->_gene_lengths->{$gene_file} );`
`87`	`87`	`}`
`88`	`88`
`89`	`89`	`sub _create_merged_sequence_for_sample {`