Added warning for gencode_basic

Ensembl · Aug 8, 2024 · 822d90c · 822d90c
1 parent 05973d3
commit 822d90c
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Config.pm b/modules/Bio/EnsEMBL/VEP/Config.pm
@@ -704,6 +704,11 @@ sub new {
     $config->{dir_cache} ||= $config->{cache} if -d "$config->{cache}";
     $config->{cache} = 1;
   }
+
+   # throw a warning for GENCODE basic if assembly is not GRCh38
+  if (defined($config->{'gencode_basic'}) && $config->{'gencode_basic'} && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {
+    printf("WARNING: --gencode_basic option is currently only available for human on the GRCh38 assembly\n");
+  }
 
   # throw a warning for GENCODE primary if assembly is not GRCh38
   if (defined($config->{'gencode_primary'}) && $config->{'gencode_primary'} && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {