Just noting a bug that I think means the PREMATURE_STOP_CODON warning will never be thrown. This gets checked for in the toSFFModel function by iterating over codons in the sequence set by setlongestORF!. The latter function doesn't seem to include stop codons in the chosen ORF, so there will never be a stop codon in the sequence being checked.
Could another option be to check if the length of the CDS falls beneath a percentage of the median_length value for that gene in the references templates.tsv file?
Hi again Ian,
Just noting a bug that I think means the PREMATURE_STOP_CODON warning will never be thrown. This gets checked for in the
toSFFModelfunction by iterating over codons in the sequence set bysetlongestORF!. The latter function doesn't seem to include stop codons in the chosen ORF, so there will never be a stop codon in the sequence being checked.Could another option be to check if the length of the CDS falls beneath a percentage of the median_length value for that gene in the references
templates.tsvfile?Cheers,
Chris