Discrepancy between "sample-call" and "status" in json

[martinmchugh]

Thanks for releasing aln2type it's a great tool for variant detection.

We've identified some discrepancies in the json files for omicron genomes - sometimes it will list the sample base as the expected variant but the status is listed as "no-detect". The sample-typing-result picks this up as a mutation_ref_call. When we look at the consensus the base is indeed the reference allele.

So it looks like aln2type is doing everything right regarding interpreting whether specific variants are present, but it's sometimes printing an incorrect sample-call in the json which makes troubleshooting a bit more tricky.

Example BA.5 genome (aligned to Wuhan-Hu-1) and json file attached - the problem variants are at 27038 and 27889 for V-22APR-04 specifically.
example_json.txt
example.fasta.txt