[Feature Request] Return query sequence in get_aligned_pairs

[y9c]

get_aligned_pairs(self,  match_only_False, with_ref=True, with_query=True):
    ....

expect output (query_pos, query_seq, ref_pos, ref_seq)

with_seq is a little misleading, and query_seq info is useful for generating per read mutation info. eg T123A for base T at position 123 of ref_seq mutated into A.

[y9c]

I guest one of the purpose in designing of get_algined_pairs is to show mutation info, because subsitutions are in lower case. But only show the ref_sequence is not sufficient.

[y9c]

I add the a very simple commit for this feature. It is just work.

• pysam use looping inside argument checking. To make the code consistent, the code becomes redundant.

• using two argument is not necessary. It is for backward compatibility.

#777

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sorry for wasting such interesting number #777