modify the pairtools-dedup to select the best MAPQ alignment as output of deduplication

[frankyan]

pairtools dedup outputs the first alignment of duplicates. The pull request is trying to output the best MAPQ alignment of duplicates instead of the first one. It can save some alignments when apply pairtools filter with MAPQ threshold after deduplication.

[golobor]

Dear @frankyan ,
apologies for the delayed response!
many thanks for your commit! It looks very clean and well-written.
Before we proceed though, I'd like to learn a bit more about the motivation behind this extra feature. Do you have any quantitative estimate on how many alignments this feature saves/improves? What scenarios does it address? I always assumed that duplicates are already quite similar to each other and thus would have similar MAPQs. The reason I'm asking is that extra features add to the maintenance cost and reduce transparency, so it's important to justify them.
Again, many thanks for your contribution, looking forward to hearing about your experience!
Anton.

[golobor]

closing it for now for the lack of discussion; feel free to reopen!