chore: release v0.2.0

[nh13]

🤖 New release

• fgumi-bgzf: 0.1.3 -> 0.2.0
• fgumi-dna: 0.1.3 -> 0.2.0
• fgumi-raw-bam: 0.1.3 -> 0.2.0
• fgumi-metrics: 0.1.3 -> 0.2.0
• fgumi-sam: 0.1.3 -> 0.2.0
• fgumi-consensus: 0.1.3 -> 0.2.0
• fgumi-simd-fastq: 0.1.3 -> 0.2.0
• fgumi-umi: 0.1.3 -> 0.2.0
• fgumi: 0.1.3 -> 0.2.0

Changelog

fgumi-bgzf

[0.2.0] - 2026-04-22

fgumi-dna

[0.2.0] - 2026-04-22

fgumi-raw-bam

[0.2.0] - 2026-04-22

Bug Fixes

• [breaking] Rename sort-key tag from pa to tc to avoid bwa-mem pa:f collision (#270)

Features

• Add EM-Seq methylation-aware consensus calling (#168)
• Add EM-Seq methylation filters and performance improvements (#169)
• Add --restore-unconverted-bases flag for EM-seq (#170)
• Unified view/editor API + close Complete the raw-byte BAM API in fgumi-raw-bam #272 gaps (#278)
• Additive API surface (#288)
• Raw-byte record_utils + RawRecordClipper (#289)

Performance

• Follow-up speedups + SIMD nibble2base (#282)

Refactor

• Migrate fgumi to new raw-bam view/editor API (#279)
• [breaking] Narrow re-exports + partial free-fn demotion (#280)
• Migrate commands, storage, and pipeline to raw-byte records (#292)
• [breaking] Delete vendored bam_codec; migrate simulate; propagate all remaining 48-commit work (#296)

Testing

• Benchmarks + proptests + edge cases (#281)

fgumi-metrics

[0.2.0] - 2026-04-22

Refactor

• [breaking] Collapse Template/DecodedRecord to raw-only; drop dead RecordBuf helpers (#294)

fgumi-sam

[0.2.0] - 2026-04-22

Bug Fixes

• [breaking] Rename sort-key tag from pa to tc to avoid bwa-mem pa:f collision (#270)
• Stream rejects to disk in simplex/duplex/codec/correct (#293)

Features

• Raw-byte record_utils + RawRecordClipper (#289)

Performance

• Speed up --restore-unconverted-bases hot path (#271)
• Restore unconverted bases on raw BAM bytes (#274)

Refactor

• Migrate fgumi to new raw-bam view/editor API (#279)

fgumi-consensus

[0.2.0] - 2026-04-22

Bug Fixes

• Preserve BA-only orientation for methylation tags (#298)
• Stream rejects to disk in simplex/duplex/codec/correct (#293)

Features

• Add EM-Seq methylation-aware consensus calling (#168)
• Add EM-Seq methylation filters and performance improvements (#169)
• Add --restore-unconverted-bases flag for EM-seq (#170)
• Add --methylation-mode for EM-Seq/TAPs consensus (#172)
• Add --methylation-mode to filter for conversion fraction (#173)
• Add --methylation-mode to simulate subcommands (#263)
• Additive API surface (#288)

Refactor

• Migrate fgumi to new raw-bam view/editor API (#279)
• Migrate internals to RawRecord; drop RecordBuf variants (#291)
• Migrate commands, storage, and pipeline to raw-byte records (#292)
• Rename duplex-filter tier locals to best/worst (#299)
• Migrate workspace tests to fgumi_raw_bam SamBuilder (#295)
• [breaking] Delete vendored bam_codec; migrate simulate; propagate all remaining 48-commit work (#296)

fgumi-simd-fastq

[0.2.0] - 2026-04-22

fgumi-umi

[0.2.0] - 2026-04-22

fgumi

[0.2.0] - 2026-04-22

Bug Fixes

• Add fgumi-simd-fastq to publish list and verify completeness (#257)
• Take last :-separated field as UMI from read name (#264)
• [breaking] Rename sort-key tag from pa to tc to avoid bwa-mem pa:f collision (#270)
• Emit consecutive MI integers 0..N-1 (#273)
• Cap metric memory with per-thread accumulators (#285) (#287)
• Suppress deadlock false positive when all queues empty (#297)
• Stream rejects to disk in simplex/duplex/codec/correct (#293)
• Apply --unmapped-fraction to mapped-reads output (#304)
• Use htsjdk-compatible Murmur3 for downsample selection (#306)
• Preserve /A /B strand suffix in paired-UMI MI keys (#308)

Documentation

• Add EM-Seq user guide (#171)
• Add TAPs guide and update EM-Seq guide for --methylation-mode (#174)
• Correct insert complexity and add micro-bench (#265)
• Fix broken doctests in commands modules (#300)

Features

• Add EM-Seq methylation-aware consensus calling (#168)
• Add EM-Seq methylation filters and performance improvements (#169)
• Add --restore-unconverted-bases flag for EM-seq (#170)
• Add --methylation-mode for EM-Seq/TAPs consensus (#172)
• Add --methylation-mode to filter for conversion fraction (#173)
• Add --methylation-mode to simulate subcommands (#263)
• Auto-detect BAM input on stdin via BGZF magic (#267)
• Replace --mode with orthogonal flags + add --command preset (#276)
• Add --async-reader flag for prefetch I/O on input BAM (#261)
• Distribute spill files across multiple temp dirs (#284)
• Additive API surface (#288)
• Restore --command preset for per-stage compare defaults (#307)

Performance

• Speed up --restore-unconverted-bases hot path (#271)
• Async prefetch reader + POSIX_FADV_SEQUENTIAL for BAM/FASTQ inputs (#258)
• Restore unconverted bases on raw BAM bytes (#274)
• Follow-up speedups + SIMD nibble2base (#282)
• Migrate RecordBuf hot paths to raw-byte accessors (#305)

Refactor

• Migrate fgumi to new raw-bam view/editor API (#279)
• [breaking] Narrow re-exports + partial free-fn demotion (#280)
• Use RawRecord methods in restore_unconverted_bases_in_raw_record (#286)
• PerThreadAccumulator for all per-batch metric collection (#290)
• Migrate internals to RawRecord; drop RecordBuf variants (#291)
• Migrate commands, storage, and pipeline to raw-byte records (#292)
• [breaking] Collapse Template/DecodedRecord to raw-only; drop dead RecordBuf helpers (#294)
• Migrate workspace tests to fgumi_raw_bam SamBuilder (#295)
• [breaking] Delete vendored bam_codec; migrate simulate; propagate all remaining 48-commit work (#296)

Testing

• Benchmarks + proptests + edge cases (#281)

Bug Fixes

• Cap fgumi group metric memory by merging per-position-group counts into per-thread accumulators instead of a SegQueue that grew one AHashMap per position group (#285).
• Replace unbounded SegQueue<CollectedXxxMetrics> buffering in filter, clip, correct, simplex, duplex, and codec with a shared PerThreadAccumulator helper, capping retained metric memory at O(threads × distinct keys) across all pipeline commands. Rejects buffering in the consensus commands is unchanged and tracked separately.

Breaking Changes

• Rename the template-coordinate sort-key tag written by fgumi zipper from pa to tc to avoid collision with bwa-mem's pa:f (primary-alignment score fraction) (#268). The --skip-pa-tags flag on fgumi zipper is renamed to --skip-tc-tags, and the missing_pa_tag dedup metric field is renamed to missing_tc_tag. Existing fgumi-zippered BAMs must be re-zippered (or the tag must be manually renamed) before fgumi dedup will accept them.

---

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📝 Walkthrough

Walkthrough

Bumps workspace/crate versions to 0.2.0 (2026-04-19) and updates workspace dependency version fields in Cargo.toml. Adds 0.2.0 changelog entries across the workspace (root + crates) with git-cliff markers. Changes include: add fgumi-simd-fastq to publish, extract UMI from last colon field, emit consecutive MI values, rename sort-key tag pa → tc (breaking), EM‑Seq/TAPS methylation features and flags (including --restore-unconverted-bases), stdin BGZF auto-detect, --async-reader, CLI flag refactor, and migration to a new raw-bam view/editor API (breaking).

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	Title clearly describes a version release bump (v0.2.0) covering all workspace crates.
Linked Issues check	✅ Passed	PR addresses issue #272 by documenting raw-byte BAM API improvements: unified view/editor API, new raw-byte record utilities, breaking re-export narrowing, and migration to RawRecord-based internals with narrowed surface.
Out of Scope Changes check	✅ Passed	All changes are scoped to version bumping and changelog updates. No unrelated code modifications present; changes align with issue #272 objectives.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description check	✅ Passed	The PR description clearly documents the 0.2.0 release with version bumps for all crates and detailed changelogs organized by categories.

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✨ Finishing Touches

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• Create PR with unit tests
• Commit unit tests in branch release-plz-2026-04-12T05-11-35Z

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.50%. Comparing base (275c09e) to head (bf73ca5).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #259   +/-   ##
=======================================
  Coverage   90.50%   90.50%           
=======================================
  Files         101      101           
  Lines       60160    60160           
=======================================
+ Hits        54448    54449    +1     
+ Misses       5712     5711    -1     

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