reducing memory required in IntervalMergerIterator when not concatting names #1711
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
|
@lbergelson can you please take a look when you have a moment? |
lbergelson
approved these changes
Jul 3, 2024
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Outdated suggestions cannot be applied.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.
When using
IntervalMergerIteratorto merge many small intervals over a whole contig it can take quite a bit of memory to store each interval. This can happen when trying to convert a GVCF with many reference blocks that are only a few bases in length into an interval list. The intervals are stored only to concat the names of each interval, which is not useful when merging so many intervals. This change keeps memory usage lower by not adding each interval that is iterated over totoBeMergedwhenconcatenateNamesis false.