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Changelog

main (unreleased)

Added

  • UNKNOWN library-type category when no model beats M_bias (zero-damage libraries)
  • GA0 bilateral rescue: spike_is_ss && d5 ≤ 0.005 → SS, validated on 24 DS controls (all d5 ≥ 0.11)
  • Channel B₃′: G→A stop codon conversion at 3' end for SS library damage validation

Fixed

  • Bug: missing best = bic_M_DS_spike update in spike_is_ss branch of waterfall
  • Bug: best_ss included M_SS_orig without applying the ct3.ΔBIC > 0 gate
  • Bug: M_DS_spike rescue could fire when M_DS_symm_art won via joint fit with marginal ct5/ga3 ΔBIC ≤ 0, now restricted to ds_spike_won

Validation

  • Dataset 1 (46 DS + 45 SS): 88/91 correct, 3 UNKNOWN (100% on determined calls)
  • Dataset 2 (78 DS + 146 SS): 193/196 correct on determined calls, 28 UNKNOWN (98.5%)

Previous milestones

BIC library-type classifier (initial)

  • 4-channel joint BIC model: ct5, ga3, ga0, ct3
  • 7 composite BIC models: M_bias, M_DS_symm, M_DS_spike, M_DS_symm_art, M_SS_comp, M_SS_orig, M_SS_asym
  • spike_is_ss gate: ga0.amplitude ≥ 0.10 routes M_DS_spike to SS model set
  • Post-hoc symmetry check: ct5.ΔBIC / ga3.ΔBIC < 0.50 with ga3.ΔBIC > 30,000 → SS
  • M_DS_spike rescue using max_damage_5prime ≤ 0.005 (d5 bilateral gate)

Initial release

  • Briggs-model exponential decay fitting (WLS, fixed λ)
  • GC-stratified damage estimation (10 bins, EM mixture)
  • Channel A/B cross-validation
  • Channel C (8-oxoG uniformity) and Channel D (G→T / C→A)
  • Hexamer-based damage LLR
  • Alignability-weighted D_max estimation