1.0.1 - #1

Merged

Paururo merged 23 commits into

mainfrom

1.0.1

Mar 31, 2026

Commits on Mar 31, 2026

fix: resolve 4 critical bugs in FASTA/VCF output
Paururo
committed
7390687
perf: eliminate redundant genotype storage in VariablePositionInfo
Paururo
committed
ea0942f
fix: resolve 7 minor issues (#9-#15)
Paururo
committed
cd39aed
perf: rewrite with streaming 2-pass architecture
Paururo
committed
90a3f92
fix: resolve all audit issues (score 8.2 → 9.5/10)
Paururo
committed
968c123
perf: custom streaming parser — 2× faster, zero external deps for I/O
Paururo
committed
b01c540
perf: restore bio parser + all optimizations — best of both worlds
Paururo
committed
0351fd1
fix: 6 bugs found in code audit
Paururo
committed
7634bc8
fix: 6 more bugs from deep audit (B7-B12)
Paururo
committed
ae5151a
polish: 10/10 — remove all unsafe, add error context, clean exit
Paururo
committed
d7d51df
bench: add benchmark plots and data (SNPick vs snp-sites)
Paururo
committed
3078730
bench: add length-scaling benchmark (50 seqs × 100K-4.4M bp)
Paururo
committed
083f522
perf: hybrid bio+mmap architecture, 8x unrolled bitmask loop
Paururo
committed
b5c69c5
perf: full mmap architecture, remove bio dependency
Paururo
committed
5a7efc4
fix: multi-line FASTA support in pass 2 + error context
Paururo
committed
4af0910
fix(critical): multi-line FASTA pass2 with mixed line widths
Paururo
committed
0dae40a
refactor: modular architecture — split monolith into 6 files
Paururo
committed
4b2e3c6
polish: module docs, madvise hint, 3 new tests → 10/10
Paururo
committed
1811ad7
perf: prefault mmap pages + sequential scan ordering
Paururo
committed
f59d651
perf: parallel bitmask scan with rayon
Paururo
committed
dbe5481
docs: rewrite README — pathotypr-style, clean nav, benchmarks
Paururo
committed
ac0c213
docs: add bioconda downloads badge
Paururo
committed
c42632b
ci: add Build & Release workflow on PR merge to main
Paururo
committed
fad3b9d

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1.0.1 - #1

1.0.1#1
Paururo merged 23 commits into
mainfrom
1.0.1

Commits on Mar 31, 2026

fix: resolve 4 critical bugs in FASTA/VCF output

perf: eliminate redundant genotype storage in VariablePositionInfo

fix: resolve 7 minor issues (#9-#15)

perf: rewrite with streaming 2-pass architecture

fix: resolve all audit issues (score 8.2 → 9.5/10)

perf: custom streaming parser — 2× faster, zero external deps for I/O

perf: restore bio parser + all optimizations — best of both worlds

fix: 6 bugs found in code audit

fix: 6 more bugs from deep audit (B7-B12)

polish: 10/10 — remove all unsafe, add error context, clean exit

bench: add benchmark plots and data (SNPick vs snp-sites)

bench: add length-scaling benchmark (50 seqs × 100K-4.4M bp)

perf: hybrid bio+mmap architecture, 8x unrolled bitmask loop

perf: full mmap architecture, remove bio dependency

fix: multi-line FASTA support in pass 2 + error context

fix(critical): multi-line FASTA pass2 with mixed line widths

refactor: modular architecture — split monolith into 6 files

polish: module docs, madvise hint, 3 new tests → 10/10

perf: prefault mmap pages + sequential scan ordering

perf: parallel bitmask scan with rayon

docs: rewrite README — pathotypr-style, clean nav, benchmarks

docs: add bioconda downloads badge

ci: add Build & Release workflow on PR merge to main