Create Primer test cases

[averagehat]

[averagehat]

Function to test:

def primer_annotate(vcf, primerfile, consensus, bamfile, options): 
   # see description of Count object below. Return one count per row in VCF 
    return counts

Example test function

def test_primer_annotate():

  result = primer_annotate(vcf, primerfile, consensus, bamfile, options)
  # parse the vcf, primerfile, consensus, bamfile for the expected values 
  # and compare with `result`

See #10 for expected behavior.

@dataclass
class Count:
    totalWhAlt: int
    totalWithoutAlt: int
    withAltWithinPrimer: int
    withoutAltWithinPrimer: int
example = Count(10, 5, 7, 2)

The fields above map to:

• count total reads that have that alt
• count total 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