I don’t understand why 12 here in utils.py:
Claudiu Creanga

It is a relatively arbitrary choice. When there are multiple SNPs with in the window of interesting (SNP location -/+ 7 bp), the alignments will interfere each others. In this setup, I just want to classify them as “complicated” SNP site. The 12 is roughly corresponds to the window size use. It says if there are two variants within 12 bps, I will classify them as “not-SNP”.