Repository navigation
sort: add --threads and phase-timing output - #2591
Merged
Merged
Conversation
hiruna72
marked this pull request as ready for review
September 14, 2026 22:42
Member
|
Thank you for the pull request |
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
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
Adds
--threads INTtobcftools sort, threading the final merge-to-output BGZF/BCF compression (same convention asview/concat/norm: compression of the output stream only). Also adds phase 1 / phase 2 elapsed-time lines on stderr (sort-to-temp-files vs. final-merge-and-write), using the samegettimeofdaypattern already used invcfconcat.c/vcfgtcheck.c.Motivation: sorting very large VCFs was bottlenecked on the single-threaded final write. On a 333MB/382k-record real SV VCF,
--threads 8cut phase 2 from 37.2s to 9.4s (output verified byte-identical to the unthreaded run). Full test suite passes, no new failures.Assisted-by: Claude:claude