Merge pull request #605 from helensch/fix/vcf_zero_values_97

Keep zero values in VCF - 97
Ensembl · Sep 20, 2019 · 2e1aacb · 2e1aacb
2 parents d896ba4 + 7492fd2
commit 2e1aacb
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Showing 3 changed files with 22 additions and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 97;
-our $VEP_SUB_VERSION = 3;
+our $VEP_SUB_VERSION = 4;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm
@@ -369,6 +369,11 @@ sub output_hash_to_vcf_info_chunk {
 
       push @chunk, $data;
     }
+    # keep 0 values
+    elsif (defined $hash->{$col}
+           && ($hash->{$col} == 0)) {
+      push @chunk, $hash->{$col};
+    }
     else {
       push @chunk, '';
     }

diff --git a/t/OutputFactory_VCF.t b/t/OutputFactory_VCF.t
@@ -244,6 +244,22 @@ is(
   'output_hash_to_vcf_info_chunk - whitespace converted'
 );
 
+$of = Bio::EnsEMBL::VEP::OutputFactory::VCF->new({
+  config => Bio::EnsEMBL::VEP::Config->new({fields => 'Allele,SIFT'})
+});
+
+is(
+  $of->output_hash_to_vcf_info_chunk({Allele => 'A', SIFT => '0'}),
+  'A|0',
+  "output_hash_to_vcf_info_chunk - '0' kept"
+);
+
+is(
+  $of->output_hash_to_vcf_info_chunk({Allele => 'A', SIFT => 0}),
+  'A|0',
+  "output_hash_to_vcf_info_chunk - 0 kept"
+);
+
 
 ## get_all_lines_by_InputBuffer
 ###############################