Support disjoint assembling features for mid-region germline imputation (FR3 gap)

[PoslavskySV]

What

Adds support for a disjoint assembling feature to the MiXCR Amplicon Alignment block, so clonotypes can be assembled across an uncovered mid-region window.

• Workflow — assemblingFeature may now be a disjoint, comma-separated list of pieces with explicit reference points, e.g. FR1Begin:FR3Begin(+40),FR3Begin(+46):FR4End. formatAssemblingFeature emits the MiXCR --assemble-clonotypes-by [{…},{…}] form; parseAssemblingFeature classifies fully-covered regions as exported-as-is and the partially-covered gap region, flanks, and full VDJRegion as germline-imputed.
• UI — the "Assembling feature" dropdown gains a Custom (advanced) option that reveals a free-text field for entering an arbitrary MiXCR gene feature (including a disjoint one). UI-only; the model already types assemblingFeature as a free string.

Why

With 2×150 sequencing, long-CDR3 clones can have paired reads that don't overlap, leaving a short uncovered window in FR3. Default full-VDJRegion assembly drops those clones. A disjoint assembling feature that brackets the gap lets each mate fully cover one piece, so the clone survives; enabling "Impute non-covered parts from germline" reconstructs the skipped window (and the full VDJRegion) from the assigned V/J germline — the same way the parental/reference sequence fills the gap.

Testing

• exportSpecs unit tests (grammar + region classification): 37/37, incl. 6 new disjoint cases.
• Tengo compiles (pl-tengo check); UI type-check + lint + build green.
• Added a wf.test e2e case (disjoint FR3-gap feature with imputation) exercising a disjoint feature end-to-end on the s1 fixture. Not yet run in a dev backend (native-module / registry-auth gap in the local env) — relying on CI to run it here.

Notes

• The one behavior to confirm on a real MiXCR run: the exported column names for a disjoint feature (nSeq[{…}], isProductive[{…}]). The code extends the existing braced-range pattern (nSeq{CDR1Begin:CDR3End}, already covered by tests); if MiXCR names them differently, the wf.test surfaces it and the outputProductiveFeature/key wiring is the adjustment point.
• Model untouched → no collision with the in-flight structurer migration.
• @platforma-sdk/block-tools in the workspace catalog is 2.12.0 (latest 2.12.9) — pre-existing on main, not bumped here.

Greptile Summary

Adds configurable disjoint clonotype assembly across uncovered mid-region windows.

• Workflow formatting now converts comma-separated feature pieces into MiXCR disjoint-feature syntax and classifies fully covered versus germline-imputed regions.
• Export specifications now use the disjoint feature for clonotype keys and productivity while imputing the skipped regions and full VDJRegion.
• The settings UI adds a Custom (advanced) assembling-feature input.
• Unit and workflow tests cover formatting, region classification, column expectations, and an end-to-end FR3-gap configuration.
• Important touched terms:
  • Assembling feature — the gene feature MiXCR uses to define clonotype sequences; changed from preset contiguous features to also support custom disjoint features.
  • Disjoint assembling feature — multiple separated feature pieces assembled as one clonotype key; newly formatted as MiXCR [{…},{…}] syntax.
  • Reference point — a named feature boundary with an optional nucleotide offset, such as FR3Begin(+40); newly parsed to determine whole-region coverage.
  • Germline imputation — reconstruction of uncovered sequence from assigned V/J germline genes; extended to the skipped gap, partially covered regions, flanks, and full VDJRegion.
  • Clonotype key — columns identifying a unique assembled clone; changed to use the exported disjoint-feature nucleotide sequence with best V and J genes.
  • VDJRegion — the full variable-diversity-joining region; classified as imputed whenever assembly uses a disjoint feature.

Confidence Score: 4/5

The empty custom assembling-feature path must be rejected or defaulted before merging because it currently causes the workflow to panic.

The new clearable custom field can persist an empty assemblingFeature, argument validation allows it through, and the export-spec parser then panics on the invalid shape.

ui/src/pages/SettingsPanel.vue, workflow/src/calculate-export-specs.lib.tengo

Important Files Changed

Filename	Overview
ui/src/pages/SettingsPanel.vue	Adds custom assembling-feature selection and input, but permits an empty value that reaches the workflow and fails.
workflow/src/calculate-export-specs.lib.tengo	Formats and classifies disjoint features, constructs export columns, and selects the disjoint sequence as the clonotype key.
workflow/src/mixcr-analyze.tpl.tengo	Converts comma-separated feature pieces into MiXCR disjoint-feature command syntax.
test/src/exportSpecs.test.ts	Adds focused tests for disjoint formatting, coverage classification, clonotype keys, and productivity-column expectations.
test/src/wf.test.ts	Adds an end-to-end workflow case using a disjoint FR3-gap feature with germline imputation.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  UI[Custom assembling feature] --> F[Format comma-separated pieces]
  F --> A[MiXCR assemble-clonotypes-by]
  F --> C[Classify covered regions]
  C --> N[Export covered regions as-is]
  C --> I[Impute gaps and VDJRegion]
  A --> K[Disjoint sequence clonotype key]
  N --> O[Clonotype outputs]
  I --> O
  K --> O

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Prompt To Fix All With AI

Fix the following 1 code review issue. Work through them one at a time, proposing concise fixes.

---

### Issue 1 of 1
ui/src/pages/SettingsPanel.vue:475-481
**Empty custom feature crashes workflow**

When a user selects Custom (advanced) and leaves or clears this field, the empty string passes argument validation and reaches `parseAssemblingFeature`, which panics because the value has no valid endpoints, causing the analysis run to fail.

_{Reviews (1): Last reviewed commit: "Add a "Custom (advanced)" assembling-fea..." | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

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[greptile-apps]

Empty custom feature crashes workflow

When a user selects Custom (advanced) and leaves or clears this field, the empty string passes argument validation and reaches parseAssemblingFeature, which panics because the value has no valid endpoints, causing the analysis run to fail.

Prompt To Fix With AI

This is a comment left during a code review.
Path: ui/src/pages/SettingsPanel.vue
Line: 475-481

Comment:
**Empty custom feature crashes workflow**

When a user selects Custom (advanced) and leaves or clears this field, the empty string passes argument validation and reaches `parseAssemblingFeature`, which panics because the value has no valid endpoints, causing the analysis run to fail.

How can I resolve this? If you propose a fix, please make it concise.