[Seqan-dev] Asymmetric Scoring of Insertions / Deletions in Alignments

[Brett Bowman <bnbowman@gmail.com>]

I'd like to create some scoring schemes with asymmetric weights for insertion / deletion errors for working with single-molecule sequencing data.  Raw data from both PacBio and Oxford Nanopore have known insertion-biases, and so optimal scoring schemes need to penalize those errors less than deletions. 

This appears to be partially supported by the SeqAn API already, since the "Score" class has separate interface functions for "scoreGapHorizontal" and "scoreGapVertical", but I can't see any existing specifications that utilize them.

Is there an allowed / recommended way to do this currently, or do I need to create my own Score specialization?

Sincerely,

-Brett