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PathoGenOmics-Lab / snpick Public

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1.0.1#1

Merged

Paururo merged 23 commits into

mainPathoGenOmics-Lab/snpick:mainfrom

1.0.1PathoGenOmics-Lab/snpick:1.0.1Copy head branch name to clipboard

Mar 31, 2026

Conversation Commits23 (23)Checks Files changed

Merged

1.0.1#1
Paururo merged 23 commits into
mainfrom
1.0.1

Commits

Commits on Mar 31, 2026

fix: resolve 4 critical bugs in FASTA/VCF output
Paururo
committed
perf: eliminate redundant genotype storage in VariablePositionInfo
Paururo
committed
fix: resolve 7 minor issues (#9-#15)
Paururo
committed
perf: rewrite with streaming 2-pass architecture
Paururo
committed
fix: resolve all audit issues (score 8.2 → 9.5/10)
Paururo
committed
perf: custom streaming parser — 2× faster, zero external deps for I/O
Paururo
committed
perf: restore bio parser + all optimizations — best of both worlds
Paururo
committed
fix: 6 bugs found in code audit
Paururo
committed
fix: 6 more bugs from deep audit (B7-B12)
Paururo
committed
polish: 10/10 — remove all unsafe, add error context, clean exit
Paururo
committed
bench: add benchmark plots and data (SNPick vs snp-sites)
Paururo
committed
bench: add length-scaling benchmark (50 seqs × 100K-4.4M bp)
Paururo
committed
perf: hybrid bio+mmap architecture, 8x unrolled bitmask loop
Paururo
committed
perf: full mmap architecture, remove bio dependency
Paururo
committed
fix: multi-line FASTA support in pass 2 + error context
Paururo
committed
fix(critical): multi-line FASTA pass2 with mixed line widths
Paururo
committed
refactor: modular architecture — split monolith into 6 files
Paururo
committed
polish: module docs, madvise hint, 3 new tests → 10/10
Paururo
committed
perf: prefault mmap pages + sequential scan ordering
Paururo
committed
perf: parallel bitmask scan with rayon
Paururo
committed
docs: rewrite README — pathotypr-style, clean nav, benchmarks
Paururo
committed
docs: add bioconda downloads badge
Paururo
committed
ci: add Build & Release workflow on PR merge to main
Paururo
committed

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