Adjusting penalty scores in the miniprot splice model

[RNA-ROB]

For minimap2 (versions 2.25 and above), it seems like the miniprot splice model is used for aligning RNA-seq reads by default. According to the miniprot paper, there are fixed penalty scores associated with read alignments against different donor/acceptor splice site dinucleotides (see screenshots below):

Would it be possible for users to adjust these specific penalty scores when running minimap2? Thanks!

[lh3]

The miniprot scoring is unfortunately hard coded for now. I thought to add an option to rescale the penalty on the command line but I didn't do that for some reason I forgot. That said, you can still use the old model with option -J0.