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lh3 / miniprot

Align proteins to genomes with splicing and frameshift
https://lh3.github.io/miniprot/
MIT License
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gff rank calculation #20

Closed chklopp closed 1 year ago

chklopp commented 1 year ago

Could you explain how the rank found in the gff format is calculated? What is the frameshift weight? In my test file the rank 1 alignment has not the best Identity or Positive value, but it still corresponds to the reference gene location.

lh3 commented 1 year ago

It is ranked by the Smith-Waterman alignment score without considering introns.