fixed wrong base qual comparison
@@ -1572,7 +1572,7 @@ cdef class AlignmentFile(HTSFile):
_start <= refpos < _stop:
# only check base quality if _threshold > 0
- if (_threshold and quality and quality[qpos] < _threshold) or not _threshold:
+ if (_threshold and quality and quality[qpos] > _threshold) or not _threshold:
if seq[qpos] == 'A':
count_a.data.as_ulongs[refpos - _start] += 1
if seq[qpos] == 'C':
