count_coverage: ignore reads that have no SEQ field
Occasionally reads are encountered with SEQ = '*'. In this case,
`read.seq` is None and we must skip the `seq[qpos]` loop.
Fixes second instance of
@@ -1578,6 +1578,8 @@ cdef class AlignmentFile(HTSFile):
# count
seq = read.seq
+ if seq is None:
+ continue
quality = read.query_qualities
for qpos, refpos in read.get_aligned_pairs(True):
