diff --git a/modules/Bio/EnsEMBL/VEP/Runner.pm b/modules/Bio/EnsEMBL/VEP/Runner.pm index f01ccb407..b4418d93b 100644 --- a/modules/Bio/EnsEMBL/VEP/Runner.pm +++ b/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"); } }