kemal be05793d20 Tidy the repository: remove docs/research and bench, fix references

2026-09-30 08:07:35 +01:00

..

P1_omni2141_summary.json

P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)

2026-09-27 20:22:35 +01:00

P1.md

P1 validated on 1000 Genomes Omni2.5 (2141 vendor GTCs + IDATs)

2026-09-27 20:22:35 +01:00

P2_omni2141_summary.json

P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)

2026-09-27 22:19:28 +01:00

P2.md

P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5)

2026-09-27 22:19:28 +01:00

P3_omni2141_summary.json

P3 validated: normalization bit-identical on 2141 vendor GTCs

2026-09-27 23:41:43 +01:00

P3.md

P3 validated: normalization bit-identical on 2141 vendor GTCs

2026-09-27 23:41:43 +01:00

P4_omni2141_summary.json

P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

2026-09-28 01:21:49 +01:00

P4_preset_omni2141_summary.json

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

2026-09-28 10:25:32 +01:00

P4.md

P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

2026-09-28 01:21:49 +01:00

P5_omni2141_summary.json

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

2026-09-28 10:25:32 +01:00

P5.md

P5 validated on 2141 1000G samples; control-metric fixes (K-021)

2026-09-28 10:25:32 +01:00

P6_gsa36_vs_gtc2vcf.json

P6 validated against GTCtoVCF too: zero unexplained genotype differences

2026-09-28 13:20:44 +01:00

P6_gsa36_vs_gtctovcf.json

P6 validated against GTCtoVCF too: zero unexplained genotype differences

2026-09-28 13:20:44 +01:00

P6.md

P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen

2026-09-28 14:29:42 +01:00

P7.md

P7: differential-testing harness (simurg compare) and nightly run on the Pi

2026-09-28 17:00:37 +01:00

P8_gse165845_summary.json

P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001

2026-09-28 19:47:34 +01:00

P8.md

P8 complete: scientific validation on GSE165845 vs NYGC 30x and GIAB HG001

2026-09-28 19:47:34 +01:00

P9_identity_360.json

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P9_scaling_gp3.json

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P9_scaling_ramdisk.json

P9 complete: compiled kernels validated (byte-identical, 78-80 GSA samples/min/core), scaling report

2026-09-28 22:32:48 +01:00

P9.md

Tidy the repository: remove docs/research and bench, fix references

2026-09-30 08:07:35 +01:00

P10.md

P10 complete: packaging verified on fresh x86_64 and aarch64 VMs

2026-09-28 23:53:59 +01:00

V2_arraytrain_gse165845.json

ArrayTrain: BIC-selected unbounded θ mixtures + HWE-guided labelling

2026-09-29 22:40:19 +01:00

V2_arraytrain.md

ArrayTrain: BIC-selected unbounded θ mixtures + HWE-guided labelling

2026-09-29 22:40:19 +01:00

V2_cn_gse165845_final.json

CN: final full-cohort cloud validation (GSE165845, CYTO-041/042 defaults)

2026-09-29 23:04:16 +01:00

V2_cn_gse165845_q10.json

v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

2026-09-29 07:42:06 +01:00

V2_cn_gse165845_q20.json

v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

2026-09-29 07:42:06 +01:00

V2_cn_synthetic_gsa36.json

v2 CN: synthetic implant evaluation (CYTO-022); reference GTC discovery follows symlinks

2026-09-29 01:30:07 +01:00

V2_cn.md

CN: final full-cohort cloud validation (GSE165845, CYTO-041/042 defaults)

2026-09-29 23:04:16 +01:00

V2_methylation_vs_sesame.json

v2 methylation QC validated on minfiDataEPIC and against sesame (K-026)

2026-09-29 00:41:54 +01:00

V2_methylation.md

v2 methylation QC validated on minfiDataEPIC and against sesame (K-026)

2026-09-29 00:41:54 +01:00

V2_pgx_cn_demo36.json

PGx CN: pgx copy-number train|call (CLI-031/032, PCN-001..017, IN-050), region BED v1, demo identities (K-028)

2026-09-29 13:16:19 +01:00

V2_pgx_cn.md

PGx CN: scan-date batch warning (PCN-006), CN-consistent BAF evidence (PCN-010, --bafs-in-cn),

2026-09-29 17:11:34 +01:00

V2_pgx_star_getrm16.json

PGx: PharmVar genes (CYP1A2, CYP2A6, CYP2A13, CYP2C8, CYP3A4), CYP2A6 *4 from CN (PGX-001/006)

2026-09-29 16:50:27 +01:00

V2_pgx_star_gse165845.json

PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance

2026-09-29 19:00:34 +01:00

V2_pgx_star.md

PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance

2026-09-29 19:00:34 +01:00