Merge pull request #1750 from nuno-agostinho/hgvsg-error

Fix inconsistencies between --hgvs and --hgvsg

modules/Bio/EnsEMBL/VEP/Runner.pm

@@ -731,11 +731,11 @@ sub post_setup_checks {
     $self->status_msg("INFO: Disabling --hgvs; using --offline and no FASTA file found\n");
     $self->param($_, 0) for qw(hgvs hgvsc hgvsp);
   }
-  
+
   # offline needs cache, can't use HGVS
   if($self->param('offline')) {
     unless($self->fasta_db) {
-      throw("ERROR: Cannot generate HGVS coordinates (--hgvs) in offline mode without a FASTA file (see --fasta)\n") if $self->param('hgvs') || $self->param('hgvsc') || $self->param('hgvsp');
+      throw("ERROR: Cannot generate HGVS coordinates (--hgvs and --hgvsg) in offline mode without a FASTA file (see --fasta)\n") if $self->param('hgvs') || $self->param('hgvsc') || $self->param('hgvsp') || $self->param('hgvsg');
       throw("ERROR: Cannot check reference sequences (--check_ref) without a FASTA file (see --fasta)\n") if $self->param('check_ref');
       throw("ERROR: Cannot look up reference sequences (--lookup_ref) without a FASTA file (see --fasta)\n") if $self->param('lookup_ref');
       throw("ERROR: Cannot use transcript reference sequences (--use_transcript_ref) without a FASTA file (see --fasta); you may wish to use --use_given_ref\n") if $self->param('use_transcript_ref');
@@ -755,7 +755,7 @@ sub post_setup_checks {
 
     # and these depend on either DB or FASTA DB
     unless($self->fasta_db) {
-      foreach my $param(grep {$self->param($_)} qw(hgvs hgvsc hgvsp lookup_ref check_ref use_transcript_ref)) {
+      foreach my $param(grep {$self->param($_)} qw(hgvs hgvsg lookup_ref check_ref use_transcript_ref)) {
         $self->status_msg("INFO: Database will be accessed when using --$param");
       }
     }