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MAPQ calculation #63

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MAPQ calculation #63

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@jdidion jdidion commented Oct 3, 2023 •
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Implementation of single-end MAPQ algorithm from BWA.

  • Constrains MAPQ between 0-60
  • Sets MAPQ to 0 when the best score is <= the suboptimal score
  • Sets MAPQ to 60 when there is no suboptimal score
  • Otherwise uses a formula based on the ratio between sub-optimal and optimal scores, with various scaling constants.

It seems to work in that it generates different values in the expected range. I need to do more work to compare with Minimap2 to see that the results at least make sense in a relative sense.

@jdidion jdidion requested a review from nh13 October 3, 2023 21:39
@jdidion jdidion marked this pull request as draft October 30, 2023 17:19
@jdidion jdidion self-assigned this Oct 30, 2023
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