Changelog

main (unreleased)

Channels F (C→A), G (C→G), and H (A→T): binomial z-score comparing terminal trinucleotide-context rate (positions 0–4, adapter-adjusted) to a far-interior reference (pos ≥ 30, ≥ 50 counts; mid-read fallback pos 5–14).
channel_h_z_p2plus: secondary H score restricted to positions 2–4; robust when TC hexamer bias is present without a formal position-0 artifact.
ca_pre_interior / ca_stop_interior: pre-aggregated uint64_t counters accumulated at read-scan time, giving Channel F the same symmetric interior reference as Channels G and H.

Channel H adapter skip now uses p0_h5 = position_0_artifact_5prime only. The shared p0_tc_5 gate (which also fires on hexamer_excess_tc < −0.02) was incorrect for Channel H: TC hexamer bias is C→T-specific and does not affect A/T-context trinucleotides. Under strong TC bias the old gate silently excluded p=0 from Channel H, inflating z by ~3×.
Renamed p0_5 → p0_tc_5; comment documents scope to Channels F and G only.
Renamed ca_stop_baseline_3prime → ca_stop_rate_baseline_3prime.
Fixed 17 uint64_t profile fields initialised with float literal 0.0 → 0.

Native paired-end mode: update_sample_profile_pe consumes R1/R2 directly, mapping R2[i] complement to top-strand 3'-end position i (no SE-on-each-mate bleed-through). Insert length M < L detected by R1/R2 overlap (15 bp window, ≤3 mismatches); short-insert pairs are skipped via pe_short_insert_skipped counter, preventing adapter bases from polluting the C→T / G→A signal.
Chemistry-aware Briggs fit: d(i) = d_max·exp(-i/λ) + bg with tail-anchored bg from positions 20..49 (interior background, immune to deamination). Replaces global-mean bg which over-estimated bg in damaged libraries and collapsed d_max.
Area-excess statistic: per-channel sum of (rate - bg) over the first 10 positions, plus a likelihood-ratio score against the bg-only null. Decouples classification from a single d_max point estimate.
Protocol-tag aware library interpretation; chemistry priors flow through library_interpretation.cpp.
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

LV7001884491 PE DS-library misclassified as SS_orig in v8: caused by the 6-base palindrome guard, which only triggered for insert M=6 and let short-insert pairs (≈83% of aDNA pairs at L=101) bleed adapter bases into R2[0..14]. After complement-mapping, the adapter's specific A:G ratio produced a_freq_3prime[0]=0.396 (depleted vs interior 0.466) which the classifier read as M_SS_orig. Replaced with proper R1/R2 overlap detection.
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

78-sample SE regression (33 clay91 + 45 ellesmere; 50 ds + 28 ss truth): 77/78 correct in v9 vs 63/78 in v8; all 14 flips in the correct direction (no regressions). Single remaining miss is a real ambiguity (LV7009022725-20S-IS160: ga3=0.030, ga0=0.047, margin 1.1).
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%)

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)