Feature Request: Allow Filtering for All Genes

[berntpopp]

Description

The current script filter_variants.sh needs to be extended to allow filtering for all genes. The easiest solution is to run snpEff -Xmx8g genes2bed $reference with an empty gene name. We should implement a new option to allow gene_name to be set to "all" and then handle it by setting $gene_name to an empty value. All relevant checks and processes should be adapted accordingly.

Proposed Changes

1. Allow "all" as a gene_name value:

   • Modify the script to recognize "all" as a special value for the gene_name parameter.
   • When "all" is specified, set $gene_name to an empty string.

2. Adapt genes2bed command:

   • Ensure the genes2bed command is executed with an empty gene name if "all" is specified, which results in creating a BED file for all genes.

3. Update checks and processes:

   • Modify all checks and processes to handle the scenario where gene_name is "all".
   • Ensure the script can handle the filtering and processing of variants for all genes without any issues.

Tasks

• [x] Modify filter_variants.sh to allow "all" as a value for gene_name.
• [x] Adapt the genes2bed command to handle an empty gene name.
• [x] Update all relevant checks and processes in the script to handle filtering for all genes.
• [ ] Test the script thoroughly to ensure it works correctly with the "all" option.

Benefits

• This enhancement will enable users to filter variants across all genes easily.
• It simplifies the process of obtaining a comprehensive set of variants for analysis without specifying individual genes.

Additional Notes

• Ensure backward compatibility with the current usage of specifying individual genes.
• Update the documentation and usage instructions to reflect the new feature.