Single variant TabixLD fetching & range bugfix#231
Merged
Conversation
…ion creation. Reduce switch to do whole file scans in annotations.
Lipastomies
changed the title
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
1 participant
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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 takes the main speedup of #230 as well as the annotation file bugfix, and implements them.
On manual testing this branch consistently outperformed the external_sumstats.jk branch, when using a single thread against 2 threads on that branch. While it is possible that with threads upwards of 4-8 would overtake this branch, this is a much smaller change to the codebase and does not muddle up the interfaces with implementations in LD access.
DRAFT:adding tests for annotations as soon as I can manage