P5a: QC — control metrics, thresholds, status, contamination, relatedness, locus summary

- qc/controls: canonical control names (QC-002), bkg/offset (QC-003), 13 genotyping metrics (QC-004/005),
  missing/zero-divisor handling (QC-007/008); controls_raw.tsv / controls_qc.tsv (QC-009/011) incl. compat CSVs
- qc/thresholds + profiles: YAML schema, validation codes, precedence, shipped profiles, auto (QC-020..025)
- qc/status: functional PASS/FAIL/NA, control CLEAR/FLAGGED, flags (QC-030..033)
- qc/contamination: BAF regression; bit-compatible with gtc2vcf BAFregress (36/36, K-017), exact mode too
- qc/relatedness: KING-robust, duplicates, Mendelian errors, pedigree from sheet (IN-018)
- qc/locus_summary: OUT-072, bit-identical to BeadArrayFiles except ChiTest (K-018)
- qc/suggest: suggest-thresholds (QC-026)
- pipeline/qc: disk-backed cohort store; CLI qc controls|samples|contamination|relatedness|loci|suggest-thresholds
- genotype: control tables (OUT-070), het_rate, QC columns, cohort QC
- tests: unit + oracle (BAFregress plugin, BeadArrayFiles locus summary)

THIRD_PARTY_NOTICES.md

@@ -5,8 +5,9 @@ used only as external subprocess oracles and are not copied or linked.
 
 | Source | Licence | How it is used |
 |---|---|---|
-| [Illumina BeadArrayFiles](https://github.com/Illumina/BeadArrayFiles) — Copyright (c) 2020, Illumina | BSD-2-Clause | File-format layouts (GTC, BPM, EGT), normalization-bin rule, `GTC_File_Format_v5.pdf`; test oracle |
-| [gtc2vcf / idat2gtc](https://github.com/freeseek/gtc2vcf) — Copyright (C) 2018-2025 Giulio Genovese | MIT | IDAT field codes, BPM locus-entry order, EGT data-block variants, GTC write order, assay-type inference (`infer_assay_type`); test oracle |
+| [Illumina BeadArrayFiles](https://github.com/Illumina/BeadArrayFiles) — Copyright (c) 2020, Illumina | BSD-2-Clause | File-format layouts (GTC, BPM, EGT), normalization-bin rule, `GTC_File_Format_v5.pdf`; locus-summary formulas (`examples/locus_summary.py`, ported to `simurg/qc/locus_summary.py`); test oracle |
+| [gtc2vcf / idat2gtc](https://github.com/freeseek/gtc2vcf) — Copyright (C) 2018-2025 Giulio Genovese | MIT | IDAT field codes, BPM locus-entry order, EGT data-block variants, GTC write order, assay-type inference (`infer_assay_type`); BAF-regression numerics (`BAFregress.c`, `simurg/qc/contamination.py`); test oracle |
+| [klib `ksort.h`](https://github.com/attractivechaos/klib) as shipped in htslib — Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd | MIT | Quickselect `ks_ksmall` partition order, ported to `simurg/qc/contamination.py` (`ks_ksmall`) to reproduce BAFregress medians |
 | [Illumina GTCtoVCF](https://github.com/Illumina/GTCtoVCF) | Apache-2.0 | VCF conversion rules (phase P6) |
 | [Picard `picard.arrays`](https://github.com/broadinstitute/picard) | MIT | Second format reference |
 | [illuminaio](https://github.com/HenrikBengtsson/illuminaio) | GPL-2 | Documentation of IDAT field codes only; oracle via subprocess |
@@ -67,3 +68,31 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 THE SOFTWARE.
 ```
+
+## MIT (klib `ksort.h` in htslib, licence header verbatim)
+
+```
+The MIT License
+
+Copyright (c) 2008, 2012-2013, 2017-2019 Genome Research Ltd (GRL).
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+```