spaln outputs 1-base negative cds gff3

[jesgomez]

Hi,

We have realized that after executing the command pasted below, the output gff3 contains some cds with 4th field 1 base greater than the 5th field. This issue generates some problems when we try to use this gff3 with other programs. Is there any reason for that or is it a bug? It would be nice if spaln produced a valid gff3 file

spaln -O0 -ya1 -M4 -t1 -dgenome -Q7 proteins.fa > proteins.gene.gff3

!!Example

chr6 ALN cds 232268 232267 20 - 0 ID=cds00078;Parent=mRNA00001;Name=chr6_242;Target=AB1IP_DANRE 646 646 +

Thank you, Jèssica