Primer Implementation Plan

[averagehat]

Given a reference fasta file, a VCF file, a BAM file, and a primer file:

map primers to reference, creating a new “Primer Bam” file
for each “alt” within the VCF file:
Inspect the “Primer Bam” file to check if that alt overlaps a primer. That is, the alt’s position is between the primer’s map start and map end (a.k.a., it’s mapped region)
count reads that have that alt
count reads that don’t have alt
count reads that have that alt and which end within the primer’s mapped region
count reads that have that don’t have the alt and which end within the primer’s mapped region
return the four counts above

@mousepixels does this match our conclusion today?