Feat/undeletions #1542
Merged
Feat/undeletions #1542
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
Undeletions are inferred mutations from a gap to a base, e.g. `-400A`. In most cases these are bioinformatics errors, so this commit collects them into a separate category to enhance interoperability of lots of mutations. The actual base is visible if you click to copy the mutation list to the clipboard, but in my testing on nCoV datasets this is always the reference base.
Work prompted by the preceeding commit, but I don't think any changes are actually needed. Note that depending on how the dataset was generated you can get what look like undeletions when the root sequence is a gap itself. I think this is rarer than undeletions on branches so not worth categorising at the present time. Added tests as the clearest way to document the behaviour here.
nextstrain-bot
temporarily deployed
to
auspice-feat-undeletion-ghvtvr
|
We could say 'deletion reversion' rather than 'undeletion' - just depends on space I suppose! One could extend the description of gaps to say something like "A change to a '-' character, indicating a missing base. These can indicate deletions but sometimes areas of no coverage are filled with gaps." - but I've no strong feelings and this may be too wordy. Overall I think this looks good, I like the mouseover option to see things more clearly! Thanks James! |
emmahodcroft
approved these changes
Sep 15, 2022
jameshadfield
force-pushed
the
feat/undeletions
branch
from
ff9d0d4 to
8c7b60c
Compare
joverlee521
approved these changes
Sep 15, 2022
jameshadfield
force-pushed
the
feat/undeletions
branch
from
8c7b60c to
ab21e4e
Compare
nextstrain-bot
temporarily deployed
to
auspice-feat-undeletion-ghvtvr
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.
Closes #1537, which has context on the rational for this PR.
Closes #1469
Undeletions (can we think of a better word than "undeletion"?!?) on branches are split out into a separate category and grouped into intervals, like so:
This is not done for tips, as these don't report mutations but rather changes between the root and the tip. While undeletions can be present here, it's rarer and I don't think any of our core builds would have this. See the tests introduced in 9fa1298 for examples of this.
The third commit adds a info-popup detailing what the different categories are and how mutations are grouped into them.