Users need to download the PharmCAT positions vcf file by themselves from the PharmCAT releases page.
What is the expected behavior?
PharmCAT will now provide a gzipped file that contains preprocessor scripts and necessary PharmCAT PGx position VCFs. VCF preprocessor will assume a 'pharmcat_positions.vcf.bgz' in the current working directory.
Please tell us about your environment:
PharmCAT Version: v1.0.0
Python Version: python 3.8.7
What actions to take
[x] add the feature in the preprocessor that accommodates the upcoming change in preprocessor releases.
[x] update wiki document
[x] remove the src/scripts/test/pharmcat_pgx_vcf/ once the feature is implemented
feature
Users need to download the PharmCAT positions vcf file by themselves from the PharmCAT releases page.
PharmCAT will now provide a gzipped file that contains preprocessor scripts and necessary PharmCAT PGx position VCFs. VCF preprocessor will assume a 'pharmcat_positions.vcf.bgz' in the current working directory.
Please tell us about your environment:
What actions to take
[x] add the feature in the preprocessor that accommodates the upcoming change in preprocessor releases.
[x] update wiki document
[x] remove the src/scripts/test/pharmcat_pgx_vcf/ once the feature is implemented