Add with_ref and with_query args for get_aligned_pairs.

[y9c]

• with_seq argument is misleading.
• add with_query will make pysam more powerful.

[AndreasHeger]

Thanks, @yech1990 , I agree that with_seq is not a fortunate name and with_ref is better.
However, leaving the query sequence out was intentional as it is easy obtained using the query sequence stored in the read, while getting the reference base is trickier.

[y9c]

More related issues

#1294