Optimize BAM parsing #74
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
Georgehe4
pushed a commit
to Georgehe4/pileup.js
that referenced
this pull request
Apr 28, 2017
Major Feature Upgrades
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Outdated suggestions cannot be applied.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 speeds up
BamFile.getAlignmentsInRangein a few ways:SamReadclass for lazy parsing and type safety (Fixes Create a SAMRead class #71)SamReads directly usingArrayBuffer, bypassing the jBinary overhead.The latter optimization is particularly effective. Overall the "should fetch from a large, dense BAM file" test case went from taking ~1450ms/run on my machine to taking ~550ms/run.
See #26