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brendanofallon / jovian

Detecting variants in NGS short read data by sequence-to-sequence modeling
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Call bam to vcf #28

Closed durtschi closed 2 years ago

durtschi commented 2 years ago

Updated the command line option "call" to generate vcf given a model, a bam, and a bed file indicating regions for variant calling.

There are some basic elements to track variant phasing in the vcf but they need some work.

The biggest issue that needs to be addressed is that almost all variants are initially placed in the same haplotype (in the _call_vars_region function). I think I'll make that change next.

I was not sure where several functions should go. The vcf.py module, a new module? I left them all in the main module but think I should probably move them before merging.

brendanofallon commented 2 years ago

Looks great, I agree that most of that stuff should be moved to a new module - I think vcf.py is the right place

durtschi commented 2 years ago

Good. Moving that now.

durtschi commented 2 years ago

Ok, I think I moved the functions/classes that make sense to be in vcf.py.