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Fix inconsistencies between --hgvs and --hgvsg #1750

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Sep 6, 2024
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Fix inconsistencies between --hgvs and --hgvsg #1750

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6 changes: 3 additions & 3 deletions modules/Bio/EnsEMBL/VEP/Runner.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -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');
Expand All @@ -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");
}
}
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