2026-07-04 — v26 manual assembly controls: strand override + overlap/match tuning

July 4, 2026

Until now the contig assembler was a one-shot black box: load two reads, click Assemble, and hope the auto-orientation logic picks the right strand and a 20 bp minimum overlap works for your amplicon. That is fine for a classic F+R Sanger pair — but the moment you have an unusual run, a very short amplicon, or a re-sequenced read that was stored reversed, you had no lever to pull. Today that changed.

What I shipped

Strand A / Strand B override selects. Each read can now be set to Auto (existing behaviour), Force Forward (pass the sequence as-is regardless of what auto-detection would choose), or Force Reverse (pre-apply reverse complement before the assembler sees the read). This is the fix for the "I know read B came off the reverse primer but the assembler keeps mis-orienting it" case.
Min overlap (bp) control. A numeric input (range 5–200, default 20) lets you tighten the minimum overlap length. Short amplicons now assemble cleanly at 10–15 bp instead of silently failing at the 20 bp hard-code; long, repeat-heavy amplicons can be tightened to 50+ bp to avoid spurious matches.
Min match % control. A percentage input (range 0–100, default 0 = accept any positive-scoring overlap) adds a score-quality floor. Setting it to 70 % means at least 70 % of the overlap positions must contribute a positive match score — useful for rejecting chimeric overlaps that only pass because the overlap region happens to be short.
Live re-assembly on control change. Once a contig has been assembled, any change to a control immediately triggers a fresh assembly pass, so you can scrub the overlap-length slider and watch the consensus update in real time without pressing Assemble again.
Informative error messages. When no qualifying overlap is found the status line now shows the exact min-overlap and min-match values that were active, so there is no ambiguity about why the assembly failed.

Architecture

src/consensus/assemblyControls.ts — pure TypeScript, no DOM. Defines AssemblyControlState, DEFAULT_ASSEMBLY_CONTROLS, applyStrandOverride() (reverse-complements seq + qual when 'reverse'), and assembleWithControls() which orchestrates the full pipeline: strand pre-processing → minMatchFraction gate → buildPairedContig. Everything is client-side; no data leaves the browser.
src/components/ContigPanel.ts — extended with a .contig-panel__controls section above the action buttons, containing four labelled widgets (data-testid anchors for tests). Added getAssemblyControls() to read the current widget state as an AssemblyControlState object.
src/components/TraceViewer.ts — runContigAssembly() now calls assembleWithControls() instead of buildPairedContig() directly, passing the controls from getAssemblyControls(). Change listeners on all four controls fire runContigAssembly() when a contig is already resident.

Tests

tests/core/assemblyControls.test.ts — exact-value unit tests:
- applyStrandOverride — exact RC sequences and reversed quality arrays for the 'reverse' case; identity for 'auto' and 'forward'.
- assembleWithControls — storing a read as RC of the correct sequence, then setting strandA='reverse', recovers the exact consensus AAAAAACCCCCGGGGG with contigLength=16, mismatchCount=0, and coverage=2 at overlap positions 6–10.
- minMatchFraction — overlap score 2/4 = 0.5 is accepted at threshold 0.5 and rejected at 0.6; exact IUPAC mismatch base K at position 10 is verified.
- minOverlap — assembly fails with minOverlap=10 on a 5-base overlap pair and succeeds at minOverlap=5.
tests/e2e/assembly-controls.e2e.test.ts — Playwright tests: default values, option sets, range attributes, label wiring, keyboard focus, assembly round-trips with min-overlap=5 and min-overlap=200, live re-assembly on control change.