I uncovered some shortcomings in the pinned alignment interface, specifically with the heuristic of pinning to all sink nodes. Turns out that this can force the alignment to take an indel that it would be otherwise not inclined to in some cases. I'm circumventing the problem by providing the option for the calling environment to specify pinning points rather than having gssw choose them automatically.
I uncovered some shortcomings in the pinned alignment interface, specifically with the heuristic of pinning to all sink nodes. Turns out that this can force the alignment to take an indel that it would be otherwise not inclined to in some cases. I'm circumventing the problem by providing the option for the calling environment to specify pinning points rather than having gssw choose them automatically.