[ensembl-dev] empty values in variant_effect_predictor.pl

[Genomeo Dev]

Excellent thanks Will!


On 3 December 2014 at 16:23, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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>>
>
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>


-- 
G.
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