Multiple copies detected at the same locus

[mwhitesi]

eci_2792_genome_sequence.zip
For Stx1A gene (possibly others too, haven't checked), VF module reported two overlapping copies of this same gene at the same locus:

e.g.
Contig: https://www.github.com/superphy#00856f353e3710088ec7582e30ce8578bbeb43b1/contigs/lclECI-2792NODE_8_length_178059_cov_24.9142_ID_15
Copy1 start: 174082
Copy2 start: 174073

Only one copy should be reported for the Stx1A gene in this case (probably longest).

I have supplied a genome file to reproduce this, although i would guess this occurs with any Stx1A harboring genome.

[kevinkle]

This is linked to https://github.com/phac-nml/ecoli_vf , will have to curate the reference sequences in that repo.