Update SpliceAI.pm

[SouzaBB]

Formated tab output for Ensembl VEP

[dglemos]

Hi @SouzaBB,
Is there a specific use case you need to have the different scores separated in the default VEP format?
In the VCF output format the scores are separated.

Changing the output format implies we also have to change the description here and the headers here.

[SouzaBB]

So, yes.. It makes it easier to see the results in the tab output format. Getting everything into the same cell without a proper header implies that one could interpret the wrong results if looking into the wrong value.
Also, if you want to use those values in any downstream analysis it's also easier rather than formating a vcf output file or parsing data from it.

[dglemos]

Updating the output format makes sense however, changing it by default could impact pipelines running the plugin.

To avoid any problesm, the output format could be updated as an option that way jobs using the plugin would not be impacted.
Could you please update your code to optionally change the output format.

In method new() check new option:

if(defined($param_hash->{split_output})) {
  $self->{split_output} = 1;
}

Update get_header_info()

if($output_vcf || $self->{split_output}) {
  (...)
}

Update run()

if($output_vcf || $self->{config}->{output_format} eq "json" || $self->{config}->{rest} || $self->{split_output})  {
  (...)
}

Finally update the description to reflect the new option.

[dglemos]

The changes should be made against main branch.

Thanks!

[dglemos]

Hi @SouzaBB,
Can you please update this branch against main?

[dglemos]

I'm closing this PR - these updates are included in the following PR #756