deals with overlaps in some weird gene structures.

[FredericBGA]

using Maker, we could have two exons or two cds that overlap. exonObjIndx and CDSObjIndx could then be equal to -1, and the plugin fails.

1 maker exon 1591 1852 . + . ID=GENE.1:1;Parent=GENE.1 1 maker CDS 1591 1852 . + 0 ID=GENE.1:cds;Parent=GENE.1 1 maker mRNA 1591 7018 . + . ID=GENE.1;Parent=GENE 1 maker gene 1591 7018 . + . ID=GENE;Name=GENE 1 maker CDS 2091 2220 . + 2 ID=GENE.1:cds;Parent=GENE.1 1 maker exon 2091 2220 . + . ID=GENE.1:2;Parent=GENE.1 1 maker CDS 4636 4743 . + 1 ID=GENE.1:cds;Parent=GENE.1 1 maker exon 4636 4743 . + . ID=GENE.1:3;Parent=GENE.1 1 maker CDS 4847 4949 . + 1 ID=GENE.1:cds;Parent=GENE.1 1 maker exon 4847 4949 . + . ID=GENE.1:4;Parent=GENE.1 1 maker CDS 5024 5188 . + 0 ID=GENE.1:cds;Parent=GENE.1 1 maker exon 5024 6209 . + . ID=GENE.1:5;Parent=GENE.1 1 maker three_prime_UTR 5189 6209 . + . ID=GENE.1:three_prime_utr;Parent=GENE.1 1 maker three_prime_UTR 6547 6679 . + . ID=GENE.1:three_prime_utr;Parent=GENE.1 1 maker exon 6547 6679 . + . ID=GENE.1:6;Parent=GENE.1 1 maker exon 6768 7018 . + . ID=GENE.1:7;Parent=GENE.1 1 maker three_prime_UTR 6768 7018 . + . ID=GENE.1:three_prime_utr;Parent=GENE.1

[twsaari]

Thanks!