Allow duplicates to not count against multiplicity - #5033
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faithokamoto wants to merge 2 commits into
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Changelog Entry
To be copied to the draft changelog by merger:
vg giraffechaining mode removes overlapping chains from multiplicity calculationDescription
Wheee another MAPQ bugfix. I'll run alignment & variant calling comparisons before merging.
We use multiplicity to count the number of independent as-good things. However we only check for independence if we get all the way to alignment; there's an earlier step where we toss out chains if they overlap a previous alignment. That seems like a pretty non-independent event. Thus here we make sure to decrement multiplicity as makes sense.