Keep haplotypes in vg chunk that don't extend far enough
#4501
Conversation
This file contains hidden or 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Outdated suggestions cannot be applied.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 chunk --tracewill now produce haplotypes even if they stop before the end of the selected rangeDescription
This refactors haplotype tracing and fixes a problem where haplotypes had to get stopped by the length limit to be visible in
vg chunk.It doesn't pick up new haplotypes that start in a chunk range. And it does some GBWT extensions to select stopping haplotypes that @jltsiren says can't work, and will need to be changed before we merge it.