Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Stops counting SNP differences above a certain threshold (default: 9_999_999). Adds nearly negligible overhead by comparing diff to maxdiff (https://github.com/boasvdp/snp-dists/blob/master/main.c#L28).
Comparison on an alignment of 500 simulated (non-masked) TB genomes which differ ~2000 SNPs on average, measured using
/usr/bin/time -v
and 8 threads:Inspired by the -x option in cgmlst-dists.