cyvcf2-test.py

from cyvcf2 import VCFReader

from snv_spectrum import Snv

reader = VCFReader(str(root / 'all.ann.vcf'))
samples = reader.samples

for variant in reader:
    for sample, depth, alt_depth, gt_base in zip(
        samples,
        variant.gt_depths,
        variant.gt_alt_depths,
        variant.gt_bases
    ):
        ref, alt = gt_base.split('/')
        if alt == ref == '.': continue
        snv = Snv(ref, alt)
        snv.set_context_from_fasta_locus(reference, variant.CHROM, variant.POS)
        snv = snv.with_pyrimidine_reference()

        print(snv.context)
    break