Handling of incertae sedis output from genbank #174
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
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #174 +/- ##
===========================================
- Coverage 79.04% 77.97% -1.08%
===========================================
Files 13 13
Lines 3741 3854 +113
===========================================
+ Hits 2957 3005 +48
- Misses 784 849 +65 ☔ View full report in Codecov by Sentry. |
|
Making this a draft as it is unlikely we will every publish anything with a |
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Outdated suggestions cannot be applied.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.
This PR adds handling of output containing
Incertae sedisin Genbank/DADA2 format. It's designed to fail if the first or last provided rank areIncertae sedisbecause in this case the taxonomic information is genuinely missing rather than referring to a real uncertainty.The implementation is a little bit rough, let me know if you have ideas for cleaning it up
Fixes #172