Inconsistent use of operators in the cs tag?

[Percud]

Hi,

According to the PAF format specifications the '*' operator should indicate a substitution, while the '-' operator should indicate a deletion.

However, in this example in which a protein is aligned to the corresponding gene:

efetch -db nucleotide -id NC_041770.1 -format fasta > genome.fasta
efetch -db protein -id NP_001181663.2 -format fasta > protein.fasta
miniprot  --version
#0.12-r237
miniprot genome.fasta protein.fasta 2>/dev/null
#NP_001181663.2	173	0	173	-	NC_041770.1	95433459	7197672	7208553	519	519	0	AS:i:836	ms:i:871	np:i:173	fs:i:0	st:i:0	da:i:0	do:i:0	cg:Z:58M10365U114M	cs:Z::58*gG~gt10362ag-gc:114

The cs tag contains both '*' and a '-' operators:

cs:Z::58*gG~gt10362ag-gc:114

I understand that there is a spliced codon (ggc) here, but I find that the '*' and '-' operators are confounding because there is no substitution or deletion.

[lh3]

Sorry for the late response. PAF is designed for nucleotide alignment. The miniprot PAF is not really PAF anyway. The use of "-" is intentional; otherwise I would need to add new operators for split codons. Note that "-" may also be used for frameshift.