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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Vectorize error sampling and replace CIGAR aligner with direct walker

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Drop the post-sampling shuffle in cover_dataset

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

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Drop the final pysam.sort in merge_bam; rely on pysam.merge ordering

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

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

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Stitch via pysam.cat with non-overlapping chunks

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

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

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

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ChangeLog: add c_elegans scale-test results and polish details

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