variant code duplication

Question

variant code duplication

Opened this issue 8 years ago · 2 comments

gene_expression and activity both use the same or similar Variant class. Also sequence.py has similar logic which is used by motifs.py and others.
Need to merge these for combined vcf read utility. See vcf.py for start.

Answer 1 · 2017-01-29T23:44:39.000Z

Note: vcf combined class being created with the intent of doing analytics on the final results files more easily.

Answer 2 · 2017-10-02T20:06:45.000Z

I may convert much of this code to instead use pysam, which should drastically simplify this and make reading/writing the VCF files much easier. I'm sure the file reading will work, but I want to test it and see how it handles adding INFO fields before implementing anything.