Update BGZF block decode logic and refactor BGZFSplitGuesser on BaseSplitGuesser #179
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
…plitGuesser Stems out of work done in HadoopGenomics#142 and HadoopGenomics#149. Refactors BGZFSplitGuesser to use the logic in the BaseSplitGuesser class. To do this, we need to make BaseSplitGuesser public. Additionally, we replace the logic that is used in BaseSplitGuesser to identify the start of a BGZF block with logic that doesn't require copying bytes from the input stream to a buffer. This improves the performance of identifying the start of a BGZF block; for whatever reason, that copy to the buffer/methods on the buffer are expensive.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.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.
Stems out of work done in #142 and #149. Refactors BGZFSplitGuesser to use the logic in the BaseSplitGuesser class. To do this, we need to make BaseSplitGuesser public. Additionally, we replace the logic that is used in BaseSplitGuesser to identify the start of a BGZF block with logic that doesn't require copying bytes from the input stream to a buffer. This improves the performance of identifying the start of a BGZF block; for whatever reason, that copy to the buffer/methods on the buffer are expensive.
This needs some code style TLC and I'll be back with performance benchmarks.