Feature request: convex gap penalty

[ksahlin]

Hi again Jeff,

I was wondering if it's possible to implement any convex gap penalty function within this library? This is useful for alignment with longer gaps from exons or SV. For more background, see this issue i posted in an MSA context: convex gap penalties.

I definitely believe such a feature is publishable on its own, since its improves on a problem that is becoming increasingly popular since long DNA/RNA reads: to align with naturally occurring gaps.

Thanks for this library, we used it with great success and cited it here and here, and hopefully more in the future :)

Best,
Kristoffer

[armintoepfer]

I definitely believe such a feature is publishable on its own

NGMLR published it and minimap2 uses a two step approach.

[ksahlin]

Yep, there you go! It would be good to have such functionality in stand alone SW-libraries too for customized alignments. Would there be a lot of work to extract these modules from NLGMR and minimap2 into libraries?

[jeffdaily]

Unfortunately, these days I am stretched too thin to do more than routine maintenance of this project. I would happily consult, test, and accept PRs for this feature if someone was willing to attempt it.