Perf: Bundle high-impact optimizations#606
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svdrecbd wants to merge 4 commits intopinellolab:masterfrom
Open
Perf: Bundle high-impact optimizations#606svdrecbd wants to merge 4 commits intopinellolab:masterfrom
svdrecbd wants to merge 4 commits intopinellolab:masterfrom
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- Speed up reverse_complement using str.translate (~3.4x faster). - Optimize find_indels_substitutions using set lookups. - Implement Banded Needleman-Wunsch alignment in CRISPResso2Align.pyx (~2.4x alignment speedup). - Add --needleman_wunsch_bandwidth argument (defaults to -1/off for parity). - Optimize multiprocessing by pre-building key lists. - Add integration tests for bit-exact output verification. - Add performance benchmark script. Note: This commit includes updated C extension files (*.c) generated by Cython, accounting for the large diff size.
kclem
reviewed
Jan 30, 2026
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| variant_file_path = os.path.join(variants_dir, f"variants_{process_id}.pkl") | ||
| with open(variant_file_path, 'wb') as file: |
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Oh right. I updated that block to use pickle as a fallback when I refactored the multiprocessing logic, but since result_queue is now always provided, this file-writing path is indeed dead code. I've removed it along with the unused pickle import and updated the docstrings to reflect the queue-based architecture.
Thank you for catching this!
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Question on Parity & Future Work:
For this PR, I prioritized optimizations that preserve 100% bit-exact consistency with the existing codebase. However, I identified other potential strategies, such as K-mer based pre-filtering for references or swapping the alignment backend, that could yield even larger performance gains. These might introduce negligible differences in edge cases (e.g., handling of extremely poor alignments).
Is strict bit-exact parity a hard requirement for the project, or would you (or whatever entity is responsible for this repo) be open to exploring these kinds of trade-offs in future PRs?
Note on Diff Size: This PR includes updated C extension files (*.c) generated by Cython (CRISPResso2Align.c, etc.). These are tracked in the repo to simplify installation, but they account for the majority of the +16k line diff. The actual logic changes are in the .pyx and .py files.