phac-nml / cladeomatic Goto Github PK

This seems to occur in the larger shigella dataset for some positions. It is hard to track down but it is found when testing and the genotype results based on the kmer data give different results than the snp data.

Testing has shown that some samples are not assigned any genotype based on the kmer scheme file but are correctly typed using the SNP scheme. This is likely the result of a missing partial assignment for these genotypes in the kmer scheme but the snp based scheme preserves this information.

Occasionally there is a non multiple of three passed to the translation, this needs to be prevented