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
Function to test:
Example test function
See #10 for expected behavior.
The fields above map to: