Surject interval crash #3715
Merged
Surject interval crash #3715
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
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Outdated suggestions cannot be applied.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.
Changelog Entry
To be copied to the draft changelog by merger:
vg surjectDescription
vg surjectcould fail an assert statement when re-aligning a read that only intersected a path on its past-the-last position. That situation was encountered because of an edge case in thevg giraffealignments in which a softclip can be placed on the node adjacent to the aligned bases instead of on the same node. We may also want to handle this case better in the tail alignment routine.This PR should make #3714 unnecessary, not that there's any harm to merging both.