Filter support for chimeric alignments

[isthisthat]

Currently it's not straightforward to filter for chimeric alignments in a bam (mate mapped to a different chromosome). It would be very helpful to enable that term in sambamba filtering. It is already reported in flagstat so it would relatively easy to port? :) Thank you very much for your continued support.

[lomereiter]

I'd say it was trivial to port, just want to highlight the tiny difference compared to flagstat in that the new flag allows for secondary and supplementary alignments (those can be filtered out by appending and not (secondary_alignment or supplementary)).

[pjotrp]

@isthisthat do you mind signing up the mailing list so we can discuss the future of sambamba?

[isthisthat]

@pjotrp where do I sign up?

[pjotrp]

https://groups.google.com/forum/#!forum/sambamba-discussion