vg giraffe no longer produces alignments with deletions on one end
Description
The dozeu pair rescue algorithm in vg giraffe uses a simple and error-prone heuristic to find a location to anchor the dozeu alignment on whenever there are no local minimizer hits. It's possible for the heuristic to initially miss the correct alignment but then find it in the subsequent alignment steps. In this case, it can produce essentially the correct alignment, except that it is misanchored on a nearby position, which can lead to deletions that seem to go off to nowhere. The dozeu seeding heuristic can't be easily fixed to avoid these cases, so instead I implemented a post-processing algorithm to remove the erroneous deletions.
Changelog Entry
To be copied to the draft changelog by merger:
vg giraffeno longer produces alignments with deletions on one endDescription
The
dozeupair rescue algorithm invg giraffeuses a simple and error-prone heuristic to find a location to anchor thedozeualignment on whenever there are no local minimizer hits. It's possible for the heuristic to initially miss the correct alignment but then find it in the subsequent alignment steps. In this case, it can produce essentially the correct alignment, except that it is misanchored on a nearby position, which can lead to deletions that seem to go off to nowhere. Thedozeuseeding heuristic can't be easily fixed to avoid these cases, so instead I implemented a post-processing algorithm to remove the erroneous deletions.Resolves https://github.com/vgteam/vg/issues/4204