I am using the new tomato ITAG3.0 annotation, but the gff file does not contain the rows for the start and stop codon positions. It only contains ranges for "gene", "transcript", "cds", "exon" and "3' UTR" and "5' UTR". Is there a way to fix that? In other words, is there a way to generate a gff file with the start and stop positions with the information they provided? I was wondering if there is a way to do it with the GenomicRanges or GenomicFeatures packages?