Haplotype sampling improvements #4329
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Changelog Entry
To be copied to the draft changelog by merger:
Description
This PR adds an experimental haploid scoring model for haplotype sampling. There are two differences to the current (diploid) model: most common kmer count is always used as an estimate of kmer coverage, and heterozygous kmers are reclassified as homozygous.
There is also an optional non-greedy approach for selecting subchain boundaries. The approach tries to make sure each haplotype visits each subchain only once. If a haplotype visits both orientations of a potential end node of a subchain, the subchain will be extended until we find a node where this does not happen. This way, we should be able to avoid sequence loss from haplotypes that reverse their orientation, return to a previous subchain, reverse again, and continue forward.
The PR also includes some improvements to
WFAExtenderused in long-read Giraffe.