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…he scoring and MAPQ stuff into their own classes
…mise to give you a score matrix
…r QualAdjAlignmentScorer
…cover the log base immediately
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Changelog Entry
To be copied to the draft changelog by merger:
GSSWAlignerand moved toAlignmentScorerandMappingQualityCalculator.Description
This breaks the alignment-scoring and mapping quality computation responsibilities off of the aligner class hierarchy and gives them their own class hierarchies.
Now there's alignment scorers for normal, quality-adjusted, and Minimap2-style logged-gap approaches. Each of them knows how to produce the "log base" that we use for mapping quality computation and hand it off to the MAPQ calculator. The aligners can use the appropriate ones of these scoring classes for the actual DP.
A lot of this code was synthesized via Anthropic Claude, and I've gone over most of it to try and make it acceptable.
This should produce exactly the same answers as before.