MRG: write manysketch --singleton sketches incrementally to reduce memory usage
#375
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
bluegenes
changed the title
manysketch --singletonmanysketch --singleton
|
@ctb ready for review |
ctb
reviewed
Jul 1, 2024
ctb
approved these changes
Jul 1, 2024
Co-authored-by: C. Titus Brown <titus@idyll.org>
bluegenes
changed the title
manysketch --singletonmanysketch --singleton sketches incrementally to reduce memory usage
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Outdated suggestions cannot be applied.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.
I'm running into memory issues with
manysketch--singleton, likely brought on by the fact that we're storing all the singleton sigs in a list until the end of the file, rather than streaming + sending them to be written. This PR fixes that by sending singletons for writing right after signature generation (before going on to the next read/contig). We then avoid writing singletons at the end of the loop, where they would just be empty template sigs.