Re-arrange joining on genetic_alteration table to optimize memory con… #11374
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
|
sheridancbio
approved these changes
Feb 6, 2025
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Outdated suggestions cannot be applied.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.
Creation of Clickhouse derived tables based on genetic_alteration table (unpacking delimited strings to CH rows) has been plagued by memory issues, requiring batching of the process. This PR optimizes memory consumption by obeying the "largest table on the left rule". The genetic_alteration table is by far the largest table, so it should be on the left joins. Intuitively, this allows the query optimizer to automatically batch its consumption of that table.