Merge branch 'postreleasefix/99' into release/99

Ensembl · Feb 7, 2020 · 70251e7 · 70251e7
2 parents 26fdcc0 + 8937b3e
commit 70251e7
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Showing 4 changed files with 10 additions and 2 deletions.
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     = 99;
-our $VEP_SUB_VERSION = 0;
+our $VEP_SUB_VERSION = 1;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm
@@ -370,7 +370,7 @@ sub output_hash_to_vcf_info_chunk {
       push @chunk, $data;
     }
     # keep 0 values
-    elsif (defined $hash->{$col}
+    elsif (defined $hash->{$col} && $hash->{$col} ne '' 
            && ($hash->{$col} == 0)) {
       push @chunk, $hash->{$col};
     }

diff --git a/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm b/modules/Bio/EnsEMBL/VEP/Parser/HGVS.pm
@@ -168,6 +168,7 @@ sub create_VariationFeatures {
   my @errors;
 
   foreach my $core_group(@core_groups) {
+    next if (($hgvs =~ /NM_/ || $hgvs =~ /XM_/) && $core_group eq 'core');
     my $sa  = $self->get_adaptor($core_group, 'Slice');
     my $ta  = $self->get_adaptor($core_group, 'Transcript');
 

diff --git a/t/OutputFactory_VCF.t b/t/OutputFactory_VCF.t
@@ -260,6 +260,13 @@ is(
   "output_hash_to_vcf_info_chunk - 0 kept"
 );
 
+is(
+  $of->output_hash_to_vcf_info_chunk({Allele => '', SIFT => 0}),
+  '|0',
+  "output_hash_to_vcf_info_chunk - empty string provided"
+);
+
+
 
 ## get_all_lines_by_InputBuffer
 ###############################