[ensembl-dev] empty values in variant_effect_predictor.pl
Will McLaren
wm2 at ebi.ac.uk
Wed Dec 3 16:23:36 GMT 2014
Hi G,
The print_line() subroutine in variant_effect_predictor.pl has the
following code:
$output = join "\t", map {
(defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ?
$extra{$_} : '-'))
} @{$config->{fields}};
So to do as you intend you could change this to
$output = join "\t", map {
(defined $line->{$_} ? $line->{$_} : (defined $extra{$_} ?
$extra{$_} : ''))
} @{$config->{fields}};
Regards
Will McLaren
Ensembl Variation
On 3 December 2014 at 16:17, Genomeo Dev <genomeodev at gmail.com> wrote:
> Hi,
>
> Current VEP script puts dash in empty fields in the default output. Could
> you please point me to the code where I can remove replace dash with an
> empty string? Modifying the output file after it is generated is
> non-trivial for very large files.
>
> --
> G.
>
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