Develop - #286

Merged

joshfactorial merged 16 commits into

mainfrom

May 19, 2026

Commits on May 18, 2026

Speed up read simulation by ~2.4x on multi-thread ecoli benchmark

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claude
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be411aa
Vectorize error sampling and replace CIGAR aligner with direct walker

joshfactorial
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claude
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6759026
Drop the post-sampling shuffle in cover_dataset

joshfactorial
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908115e
Sort BAM records at the worker write boundary; drop per-worker pysam.sort

joshfactorial
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claude
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08730da
Drop the final pysam.sort in merge_bam; rely on pysam.merge ordering

joshfactorial
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3f7a208
Vectorize get_quality_scores; eliminate per-base scalar rng.normal calls

joshfactorial
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61d678d
Stream BAM and FASTQ inline; drop the per-chunk reads_to_write buffer

joshfactorial
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6df862e
Stitch via pysam.cat with non-overlapping chunks

joshfactorial
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4f69ae1
Auto-tune chunk size from genome length; parallelize stitch steps

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363b786
Document multi-node HPC deployment; record v4.4.3 perf overhaul in ChangeLog

joshfactorial
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9eb182d
Polish hot path: drop redundant deepcopies, one-pass apply_errors, byte-level FASTQ concat

joshfactorial
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a4dfa0d
ChangeLog: add c_elegans scale-test results and polish details

joshfactorial
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claude
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6c0c2cb

Commits on May 19, 2026