chore: release v0.1.3

[nh13]

🤖 New release

• fgumi-bgzf: 0.1.2 -> 0.1.3
• fgumi-dna: 0.1.2 -> 0.1.3
• fgumi-metrics: 0.1.2 -> 0.1.3
• fgumi-raw-bam: 0.1.2 -> 0.1.3
• fgumi-sam: 0.1.2 -> 0.1.3
• fgumi-consensus: 0.1.2 -> 0.1.3
• fgumi-simd-fastq: 0.1.2 -> 0.1.3
• fgumi-umi: 0.1.2 -> 0.1.3
• fgumi: 0.1.2 -> 0.1.3

Changelog

fgumi-bgzf

[0.1.3] - 2026-04-11

Performance

• Implement N+2 worker-pool model for parallel sort I/O (#242)

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)

fgumi-dna

[0.1.3] - 2026-04-11

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)

fgumi-metrics

[0.1.3] - 2026-04-11

Features

• Add simplex-metrics command for simplex sequencing QC (#195)
• Add position group size metrics and --metrics prefix output (#232)

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)

fgumi-raw-bam

[0.1.3] - 2026-04-11

Bug Fixes

• Use minimal unsigned BAM integer types for non-negative tag values (#213)

Performance

• Optimize sort pipeline with LoserTree merge, EMBEDDED_IN_RECORD, and queryname specifiers (#217)
• Eliminate RecordBuf re-encode bottleneck with raw-byte merge (#228)

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)

fgumi-sam

[0.1.3] - 2026-04-11

Refactor

• Use ClippingMode enum instead of String for --clipping-mode (#218)
• Replace all unwrap() calls in crates/ with expect() (#225)
• Introduce SamTag newtype for two-character BAM tag fields (#241)

fgumi-consensus

[0.1.3] - 2026-04-11

Documentation

• Update bam_codec comments to reflect noodles#364 closure (#182)

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)
• Introduce SamTag newtype for two-character BAM tag fields (#241)

fgumi-simd-fastq

[0.1.3] - 2026-04-11

Features

• Add SIMD-accelerated FASTQ parsing via fgumi-simd-fastq crate (#180)

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)

fgumi-umi

[0.1.3] - 2026-04-11

Refactor

• Replace all unwrap() calls in crates/ with expect() (#225)

fgumi

[0.1.3] - 2026-04-11

Bug Fixes

• Use monotonic counter for chunk file naming during consolidation (#178)
• Exclude BAM bin field from core field comparison (#208)
• Remove unused --sort-order flag from codec and simplex (#209)
• Allow explicit true/false values on all boolean flags (#210)
• Use semantic integer comparison for BAM tag values (#214)
• Dedup --no-umi OOM on production WES data (#231)
• Replace panic!() with graceful error handling in production code (#223)
• Correct Zenodo DOI badge link in README (#250)
• Abort pipeline on deadlock detection when recovery is disabled (#252)
• Prevent pipeline deadlock when held items block reorder buffer progress (#251)
• Prevent OOM and group flush timeout in unified pipeline (#253)

Documentation

• Improve cell barcode documentation for group and dedup commands (#177)
• Update bam_codec comments to reflect noodles#364 closure (#182)
• Update fulcrum genomics logo with light/dark theme support (#194)
• Add trait overview table and extension guide for unified pipeline (#222)
• Add mdBook documentation site with FG branding (#243)
• Describe fgumi as a research preview instead of alpha (#248)

Features

• Add CB (cellular barcode) to template-coordinate sort key (#160)
• Accept BAM input for mapped reads (#181) (#183)
• Add SIMD-accelerated FASTQ parsing via fgumi-simd-fastq crate (#180)
• Add fgumi merge command with loser tree (#186)
• Add --includelist option to simulate fastq-reads (#198)
• Add simplex-metrics command for simplex sequencing QC (#195)
• Add position group size metrics and --metrics prefix output (#232)
• Accept yes/no/y/n/t/f as boolean flag values (#235)
• Add --max-memory=auto with system memory detection (#236)

Miscellaneous Tasks

• Pin GitHub Actions to full-length commit SHAs (#215)
• Add cargo-audit security job to CI workflow (#221)

Performance

• Improve multi-threaded sort scaling (#187)
• Replace LSD with MSD hybrid radix sort for template-coordinate (#191)
• Replace RecordBuf with raw byte comparison for compare-bams (#197)
• Reuse buffers in merge phase to reduce allocations (#219)
• Optimize sort pipeline with LoserTree merge, EMBEDDED_IN_RECORD, and queryname specifiers (#217)
• Eliminate RecordBuf re-encode bottleneck with raw-byte merge (#228)
• Implement N+2 worker-pool model for parallel sort I/O (#242)
• Redesign phase 2 work stealing and bound rayon to --threads (#247)
• Add memory probes and force mimalloc arena collection (#249)
• Bounded BGZF FASTQ pipeline with memory backpressure (#244)

Refactor

• Introduce ChunkNamer to centralize temp file naming (#179)
• Remove vendored BAM decoder, use noodles Reader API (#185)
• Use ClippingMode enum instead of String for --clipping-mode (#218)
• Eliminate RecordBuf duplication by converting to raw-byte processing (#229)
• Replace all unwrap() calls in src/commands/ with expect() (#224)
• Replace all unwrap() calls in src/lib/ with expect() (#226)
• Remove customizable tag options in favor of SAM spec standard tags (#240)
• Remove dead rayon code paths superseded by N+2 pool (#246)
• Introduce SamTag newtype for two-character BAM tag fields (#241)

Revert

• Restore --max-memory default to 768M (#245)

Testing

• Add end-to-end regression tests using simulate and compare (#227)

---

This PR was generated with release-plz.

[coderabbitai]

Note

Reviews paused

It looks like this branch is under active development. To avoid overwhelming you with review comments due to an influx of new commits, CodeRabbit has automatically paused this review. You can configure this behavior by changing the reviews.auto_review.auto_pause_after_reviewed_commits setting.

Use the following commands to manage reviews:

• @coderabbitai resume to resume automatic reviews.
• @coderabbitai review to trigger a single review.

Use the checkboxes below for quick actions:

• ▶️ Resume reviews
• 🔍 Trigger review

📝 Walkthrough

Walkthrough

Workspace version bumped from 0.1.2 to 0.1.3 in the root Cargo.toml and in workspace dependency entries for fgumi-bgzf, fgumi-consensus (retaining default-features = false), fgumi-dna, fgumi-metrics, fgumi-raw-bam, fgumi-sam, and fgumi-umi. Each crate and the root CHANGELOG.md gained a new 0.1.3 entry dated 2026-03-23 documenting: a bug fix using a monotonic counter for chunk file naming during consolidation, documentation updates for cell barcode group and dedup commands, and a feature adding CB (cellular barcode) to the template-coordinate sort key. No code or public API changes.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title 'chore: release v0.1.3' directly and clearly summarizes the main change—a version bump release.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The pull request description directly relates to the changeset, detailing version bumps from 0.1.2 to 0.1.3 for all affected crates and providing changelog entries matching the files modified.

_{✏️ Tip: You can configure your own custom pre-merge checks in the settings.}

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch release-plz-2026-03-06T17-54-36Z

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands and usage tips.}

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.23%. Comparing base (837a760) to head (38cab0c).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #163   +/-   ##
=======================================
  Coverage   89.23%   89.23%           
=======================================
  Files         120      120           
  Lines       58938    58938           
=======================================
+ Hits        52593    52595    +2     
+ Misses       6345     6343    -2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.