Reduce GC to speed up unzip operations #57
Merged
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
cmdcolin
changed the title
|
Nice work! |
|
interestingly this doesn't have an enormous impact on the jb2profile results. it was 5x faster if i was zoomed in very far (large bp per px) but if zoomed out even to 1kbp it becomes pretty slow again (which is probably related to other factors other than this PR) |
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Outdated suggestions cannot be applied.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 can speed up large BAM files significantly
With a test file conjured up for the jb2profile generated with deep (2400x) coverage short reads with wgsim
With this branch: 14seconds
Without this branch: 78seconds
The avoiding of slice, working with more "low level" Uint8Array API (could work with buffer probably but Uint8Array is reliable and not polyfilled) ensures speed
With this change, very little GC occurs while unzipping