Incorrect mapping of a read to an incorrect gene as the true gene has no minimizer hits (with minimal example)

[Danderson123]

Hey Leandro!

This is another issue related to #332. I have noticed there are quite a few cases where Pandora incorrectly annotates one gene as another and there are no minimizer hits to the true gene, even when the allele is identical to one in the PRG for the missed gene. You can see this in the .png file in the gzipped directory attached. This plot shows k-mers for each gene on the x-axis with the colours showing the minimizer hits from the pandora .minimatches file (red shows hits in the incorrect gene and blue shows hits in the correct gene). The true gene is "glpG" but Pandora annotates it as "group_18516" as there are no minimizers mapping to the PRG of the true gene. I have compiled a minimal example for these genes in the directory attached. This includes the MSAs, the panRG, the query sequences and the Pandora map output.

I used make_prg v0.4.0 and pandora_b19d26.

Best wishes,
Daniel

no_minimisers_for_true_gene.tar.gz