Fix bug in get_aligned_pairs
I  noticed that in pysam 0.15.1, there is a bug with the get_aligned_pairs function when matches_only=True and with_seq=True.  Basically, the read position gets advanced, but the reference position does not.  This fixes that bug, and I believe it won't involve changing any other portions of the code.
@@ -1952,6 +1952,8 @@ cdef class AlignedSegment:
else:
for i from pos <= i < pos + l:
result.append((None, i))
+ else:
+ r_idx += l
pos += l
elif op == BAM_CHARD_CLIP:
