Merge pull request #303 from ens-lgil/feature/gff_94

Use MD5 as record ID if there is no 'Name' nor 'ID' in the record
Ensembl · Oct 12, 2018 · 71e793e · 71e793e
2 parents 2879f2b + 6a8665c
commit 71e793e
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Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/File/GFF.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/File/GFF.pm
@@ -197,6 +197,8 @@ sub _record_get_id {
     my $attributes = $record->{attributes};
     $record->{_id} = $attributes->{ID} || $attributes->{Name} || $attributes->{id} || $attributes->{name};
   }
+  # Use MD5 as ID if it's missing in the record
+  $record->{_id} = $record->{md5} if(!exists($record->{_id}) || $record->{_id} !~ /\w+/);
 
   return $record->{_id};
 }

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     = 94;
-our $VEP_SUB_VERSION = 2;
+our $VEP_SUB_VERSION = 3;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS