COMSIC VCF

[atimms]

Describe the issue
Thanks for this great tool.

Later versions of COSMIC have replaced CNT with SAMPLE_COUNT so COMSIC VCF is not being used by purecn.

To Reproduce
supplying cosmic vcf like this.

--cosmic-vcf-file $work_dir/COSMICv97.GRCh38.Variants.normalized.dedup.vcf.gz

or
--cosmic-vcf-file $work_dir/COSMICv100.GRCh38.Variants.normalized.dedup.vcf.gz

Expected behavior
When using COSMICv97 works as expected, but from versions 99 onwards there is no CNT field and counts now seem to be represented by SAMPLE_COUNT.

Log file
INFO [2025-01-10 08:21:10] Reading COSMIC VCF...
WARN [2025-01-10 08:21:40] Cosmic VCF has no CNT info field. Giving up COSMIC annotation.

[lima1]

Thanks @atimms for reporting. I will fix this in the next days.