Nucmer block bug fix #52
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…0.1. Issue was that nucmer reported two matches with an overlap, where ref and query had different lengths, but no indels were reported (and the two matches probably ought to have been reported as one whole match. Workaround doesn't use the projection to get the overlapping intervals coordinates in split_match function anymore.
… nucmer is run with fixes the issue. Switched from using dnadiff to using nucmer directly, and to run with --breaklen 500 and --diagdiff 20, which (anecdotely) should prevent breaking up matches like in the pair NZ_CP029142.1, NZ_CP060660.1.
… loop in resolve_overlaps goes over 100000 to make catching issues quicker in future. Cleaned up mess from debugging.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Found bug where nucmer was reporting a single match without indels as two matches with disparate lengths, which broke coordinate projection and made the overlap splitting get stuck. Switched from using dnadiff to nucmer with suitable parameters, which appears to have fixed all issues.