Reads: linked-pair junction panel for active MAT (only if the ratio test fails its controls) #323

Split from #195 and #196 by the curator ruling of 2026-11-09 on the design note docs/notes/2026-11-09_junction-panel-design.md (PR #321), design B. Do only if the copy-number ratio test (#322) fails its controls.

What

The expressed MAT locus is told apart from its silent cassettes only by sequence outside the homology boxes. In S. cerevisiae, unique chromosome-III sequence lies about 330 bp past Y on the Z side (Z1 plus Z2). The panel counts read pairs with one mate on Ya- or Yalpha-unique k-mers and the other mate on MAT-locus-unique outer flank. That types the active locus directly, whatever the cassette configuration.

Steps

1. Pair-aware counting in reads-type, behind an opt-in policy flag (default off), documented in docs/detect-options.md. About 3–5 days with tests.
2. Panel build: Y-unique k-mers plus the MAT-unique outer flank for each species, from curated records.
3. Acceptance: the same simulated mixes and control strains as Reads: copy-number ratio test for active MAT in cassette yeasts and MTL zygosity #322.
4. Re-download and re-type every paired run of the group (reads are not kept), about 1,000 or more runs.

Limits

Needs paired runs with inserts of about 400 bp or more; single-end runs stay untypable. Switching cultures still read as mixtures.
Related: #195, #196.