Update to abpoa 1.2.0 #479
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abPOA 1.2.0 can align longer sequences via minimizer-based seeding. This is very interesting for Cactus which presently relies on some repurporsed stitching code for >10kb alignments that is a suspected sources of misalignments in some complex regions.
In Cactus, this logic is controlled by
partialOrderAlignmentWindow, so increasing it should be a good test of what this improves.Speaking of the config, now is also probably a good time to add all the abPOA parameters for scoring and seeding so they can overridden if desired.