fix: MA-refactor fallout — qc, track-decorators, filter expressions, mock-fire, stale legacy tags - #123
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…IRE MSPs Same bug class as the fire --extract fix: since the MA-spec refactor (0.10), FIRE quals live on the `fire` annotation type, not the MSPs. `ft qc --m6a-per-msp` read the MSP qual directly, so is_fire was always false, and `ft track-decorators` iterated only fire-type annotations, so precision-0 MSPs (the majority) lost their LINKER decorations relative to 0.6 output. Factor the overlay into FiberseqData::msp_fire_quals() and use it in all three consumers (extract, qc, decorator). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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…legacy tags Three more instances of the 0.10 MA-refactor bug class, found by a systematic sweep: - -x 'qual(msp)' compared against MSP quals, which are always 0 post-MA (the fire-qual path was gated on fire count == msp count, but fire is the p>0 strict subset). '>N' dropped everything including called FIREs; '<N' kept them. Overlay fire quals by molecular start and drop msp/fire by a shared kept-start set; len(msp) now also drops paired fire entries instead of orphaning them. - mock-fire emitted fire-only annotations, invisible to msp-driven consumers; it now writes the msp set alongside fire, matching real fire-scored records. - MA-writing subcommands left consumed legacy tags (ns/nl/as/al/aq, fibertig fs/fl/fa) on the record, so legacy readers saw stale calls forever and convert-tags could never clean them. write_record now strips exactly the tags the reader consumed, with type-checked provenance gates shared with read_record: wrong-typed or un-gated foreign tags reusing the same names are never touched, and records already carrying MA are left alone. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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…A:Z) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ne in MA:Z) Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Keeps this PR scoped to the FIRE-qual overlay fixes (qc, decorators, filter expressions, mock-fire). The write_record legacy-tag hygiene and its tests move to fix/legacy-tag-hygiene, where they ship together with the Ma/Aq/An read-tolerance work. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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… branch Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> # Conflicts: # tests/regression/fire.rs
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## 🤖 New release * `molecular-annotation`: 0.0.2 -> 0.0.3 (✓ API compatible changes) * `fibertools-rs`: 0.12.1 -> 0.13.0 (✓ API compatible changes) <details><summary><i><b>Changelog</b></i></summary><p> ## `molecular-annotation` <blockquote> ## [0.0.3](molecular-annotation-v0.0.2...molecular-annotation-v0.0.3) - 2026-08-13 ### Fixed - [**breaking**] write MA-family tags as Ma/Aq/An (SAM local-use spelling) + legacy-tag hygiene ([#124](#124)) - leading soft clips double-counted in pyMA liftover ([#126](#126)) - MA-refactor fallout — qc, track-decorators, filter expressions, mock-fire ([#123](#123)) </blockquote> ## `fibertools-rs` <blockquote> ## [0.13.0](v0.12.1...v0.13.0) - 2026-08-13 ### Fixed - [**breaking**] write MA-family tags as Ma/Aq/An (SAM local-use spelling) + legacy-tag hygiene ([#124](#124)) - make the Read the Docs (py-ft) build independent of the pyft Rust build ([#127](#127)) - MA-refactor fallout — qc, track-decorators, filter expressions, mock-fire ([#123](#123)) ### Other - cache cargo artifacts, parallelize jobs and tests ([#128](#128)) </blockquote> </p></details> --- This PR was generated with [release-plz](https://github.com/release-plz/release-plz/). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Systematic sweep for the 0.10 MA-refactor bug class (FIRE quals moved off MSPs onto the
firetype). This PR fixes the FIRE-qual overlay consumers:ft qc --m6a-per-msp:is_firewas always false (read MSP quals directly). Now uses the sharedFiberseqData::msp_fire_quals()overlay.ft track-decorators: precision-0 MSPs lost their LINKER decorations vs 0.6 (only thefireview was iterated). All MSPs decorate again, and output ordering is now deterministic (was HashMap-ordered).-x 'qual(msp)'filter expressions: compared against always-zero MSP quals, so>Ndropped every MSP including called FIREs and<Nkept them;len(msp)orphaned paired fire entries. Fire quals are overlaid by molecular start and msp/fire are dropped by a shared kept-start set.ft mock-fire: emitted fire-only annotations invisible to msp-driven consumers; now writes the msp set alongside fire, matching real fire-scored records.AL/separate-lengths references (lengths are inline inMA:Z).Every fix has regression coverage: insta snapshots pin the extract/qc/decorator FIRE rows, plus assertion tests for the filters and mock-fire tag layout. 20 regression tests pass; fmt/clippy clean.
Related PRs: #124 carries the legacy-tag hygiene (provenance-checked stripping of consumed
ns/nl/as/al/aq+ fibertig tags) and theMa/Aq/Anread-tolerance helper, split out of this PR. Still outstanding for their own PRs: the py-ft port (compile-dead since 0.10) and the molecular-annotation python soft-clip liftover offset.🤖 Generated with Claude Code