[maker-devel] Duplicated exons

[Michael Nuhn]

Hello Carson!

I have been trying to get to the bottom of an error message when 
(re)training snap. Snap, or more precisely fathom, was giving me unclear 
error messages about misordered and overlapping exons.

I have looked into the gff files from which these exons originate and 
noticed that a lot of exons in that file were duplicated. For example I 
have found these:

LSalAtl2s75	maker	exon	186317	186936	.	+	. 
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:3;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
LSalAtl2s75	maker	exon	187007	191531	.	+	. 
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:4;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1

and then about four hundred lines later there are these:

LSalAtl2s75	maker	exon	186317	186936	.	+	. 
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:1;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
LSalAtl2s75	maker	exon	187007	191531	.	+	. 
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:2;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1

which are identical except for the order number after "exon:".

This seems to have happened to a lot of features in that file.

How can I avoid this? Or if this is just a rare problem, can I have 
maker recompute the gff file without redoing all the computations again?

Cheers,
Michael.