Is your feature request related to a problem? Please describe.
We can expect samples to be contaminated on rare occasions. If a sample should be contaminated by a another sample of the same species, the typing results might be affected. It would be good to have a way of catching these cases and ensure they are not marked as passed.
There are two possible outcomes affecting the typing of such a sample:
One or more loci lack a contig that completely covers the region (currently marked as failed)
One or more loci have several contigs that completely covers the region
Describe the solution you'd like
Implement a check for outcome 2 and mark such samples in the typing report.
pbiology
commented
1 year ago
Is your feature request related to a problem? Please describe. We can expect samples to be contaminated on rare occasions. If a sample should be contaminated by a another sample of the same species, the typing results might be affected. It would be good to have a way of catching these cases and ensure they are not marked as passed.
There are two possible outcomes affecting the typing of such a sample:
Describe the solution you'd like Implement a check for outcome 2 and mark such samples in the typing report.