Purpose: To check for amplicon coverage dropouts
Expected inputs:
- bam file
- primer scheme file --> determine amplicons based on it
- bam files of old samples to compare against (to set regional thresholds rather than a generic constant value)
What to base thresholds on:
- exact minimum coverage threshold
- minimum coverage as a percent of sample's highest coverage regions
- observed typical coverage in region based on older data
Potential outputs:
- list of regions (based on windows) with lower than threshold coverage
- List of amplicons (based on primers) containing any dropouts (by windows)
- List of amplicons (based on primers) fully dropped out
- pass/fail boolean