How do I change gap length allowed for recombination

[sbeausol]

In practice I see a lot of errors with peptides that aren't contributing to HC-CDR3. Which parameter can I use to shorten the allowed gap when extending CDR3? GapHead/Tail seem to be true or false only

[douweschulte]

To control this you could edit the alphabets/mass_alphabet.txt file and change the affine gap scoring parameters. There are two GapStart default on -12, this is the score applied for openening any gap, and GapExtend default on -1, this controls how much each additional amino acid in a gap is scored. For example you could decrease the GapExtend say to -3, potentially GapStart could be increased a bit (-6?) to still allow reasonably length gaps. So there is no direct parameter to decrease the length, but with these parameters you can score longer gaps lower and so less gaps should be allowed in the data. Let me known if you have any more issues or questions.