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Remove parameters that we don't use#4920

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faithokamoto wants to merge 5 commits into
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split-indel-penalties
Open

Remove parameters that we don't use#4920
faithokamoto wants to merge 5 commits into
masterfrom
split-indel-penalties

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Changelog Entry

To be copied to the draft changelog by merger:

  • Remove --item-scale and --points-per-possible-match from vg giraffe as needless unused complexity.

Description

Ignore the branch name; this was going to be something else before. Anyhow, this is the latest episode of "Faith tries to trim vg giraffe". Two parameters that we never change the defaults of and which were minor increases in algorithm complexity. I noticed these while trying to understand how scoring was working in DP. Having extra components to the scoring algorithm just made that more complicated.

  • --item-scale is a multiplier applied to "yay we grabbed an item" score before any extra bonus is added. It was always 1, and its default was 1. Multiplying a number by 1 does not change anything.
  • --points-per-possible-match is a constant multiple for the number of bases which could end up as matches, applied as a bonus when scoring a transition. It was always 0, and its default was 0. Multiplying a number by 0 and then adding it into a score will never change the score by anything.

These changes have no impact on anyone unless they were toying with these specific parameters themselves, but I doubt that. Simplifying the chain scoring calculation was nice for me.

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