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Improving --gencode_primary and --flag_gencode_primary #1734

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merged 3 commits into from
Aug 8, 2024
Merged

Improving --gencode_primary and --flag_gencode_primary #1734

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cec3dcd
Added warnings for incompatible flags; modified header description
likhitha-surapaneni Aug 8, 2024
05973d3
Minor changes
likhitha-surapaneni Aug 8, 2024
822d90c
Added warning for gencode_basic
likhitha-surapaneni Aug 8, 2024
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10 changes: 10 additions & 0 deletions modules/Bio/EnsEMBL/VEP/Config.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -606,6 +606,7 @@ our %INCOMPATIBLE = (
af_gnomade => [qw(af_gnomad)],
quiet => [qw(verbose)],
refseq => [qw(gencode_basic merged)],
gencode_primary => [qw(gencode_basic refseq)],
json => [qw(vcf tab)],
vcf => [qw(json tab)],
tab => [qw(vcf json)],
Expand Down Expand Up @@ -703,7 +704,16 @@ sub new {
$config->{dir_cache} ||= $config->{cache} if -d "$config->{cache}";
$config->{cache} = 1;
}

# throw a warning for GENCODE primary if assembly is not GRCh38
if (defined($config->{'gencode_primary'}) && lc($config->{'gencode_primary'}) && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {
printf("WARNING: --gencode_primary 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($config->{'flag_gencode_primary'}) && lc($config->{'flag_gencode_primary'}) && defined($config->{'assembly'}) && lc($config->{'assembly'}) ne 'grch38') {
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printf("WARNING: --flag_gencode_primary option is currently only available for human on the GRCh38 assembly\n");
}
my $config_command = "";

my @skip_opts = qw(web_output host port stats_file user warning_file input_data);
Expand Down
2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Constants.pm
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Expand Up @@ -259,7 +259,7 @@ our %FIELD_DESCRIPTIONS = (
'CHECK_REF' => 'Reports variants where the input reference does not match the expected reference',
'UPLOADED_ALLELE' => 'The variant allele uploaded',
'SHIFT_LENGTH' => 'Reports the number of bases the insertion or deletion has been shifted relative to the underlying transcript due to right alignment before consequence calculation',
'GENCODE_PRIMARY' => 'Reports if transcript is Gencode Primary'
'GENCODE_PRIMARY' => 'Reports if transcript is GENCODE primary'
);

our @DEFAULT_OUTPUT_COLS = qw(
Expand Down