{AH} parameterize count_coverage tests with new pileup API
@@ -2085,8 +2085,11 @@ class TestCountCoverage(unittest.TestCase):
count_c = array.array('L', [0] * l)
count_g = array.array('L', [0] * l)
count_t = array.array('L', [0] * l)
- for p in bam.pileup(chrom, start, stop, truncate=True,
- stepper='nofilter'):
+ for p in bam.pileup(chrom, start, stop,
+ truncate=True,
+ stepper='nofilter',
+ min_base_quality=quality_threshold,
+ ignore_overlaps=False):
rpos = p.reference_pos - start
for read in p.pileups:
if not read.is_del and not read.is_refskip and \
