P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)

- formats/fasta: plain/BGZF FASTA, .fai/.gzi built identical to htslib, index check, build detection,
  contig aliases, mmap genome cache (IN-060..064)
- formats/bgzf, formats/bcf: pure-Python BGZF, tabix .tbi, BCF 2.2 and CSI (OUT-010, OUT-038, OUT-040)
- harmonize/sites: plus-strand mapping with audit rows, indel resolution from SourceSeq (port of GTCtoVCF,
  Apache-2.0) and left normalisation (OUT-014..021, OUT-030, OUT-042)
- harmonize/combine: OUT-031 genotype combination (ploidy-aware, Infinium I/II signal classes, OUT-037)
- pipeline/vcf: `simurg gtc-to-vcf` (per-sample VCF.gz+tbi, --merge cohort BCF+csi, audit parquet)
- pipeline/export: `simurg export bedgraph|finalreport|plink|locus-summary` (OUT-043, OUT-050..052, OUT-071)
- validation: 36 GSA samples vs gtc2vcf: 23.66 M identical calls, 0 unexplained differences; PLINK identical
  to plink2 on 637,397 variants; bcftools validates VCF/BCF and our indexes answer region queries correctly
- fetch_data.sh p6 (Ensembl GRCh38 with checksum), make_oracle_vcf.sh, validate_p6_vcf.py; K-022/K-023

docs/messages.md

@@ -4,8 +4,10 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 
 | Code | Level | Meaning | Spec |
 |---|---|---|---|
+| `E_AUX_INVALID` | error | Auxiliary-loci record is invalid | OUT-035 |
 | `E_BPM_CSV_MISMATCH` | error | BPM and CSV manifests describe different loci | IN-042 |
 | `E_BPM_FORMAT` | error | BPM manifest is malformed or unsupported | IN-040 |
+| `E_BUILD_MISMATCH` | error | Manifest genome build differs from the FASTA build | IN-063 |
 | `E_CONFIG_KEY` | error | Unknown key in --config YAML | CLI-019 |
 | `E_CONFIG_PARSE` | error | --config file is not valid YAML | CLI-019 |
 | `E_CSV_MANIFEST_FORMAT` | error | CSV manifest is malformed | IN-041 |
@@ -13,6 +15,8 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_DUP_IDAT` | error | Several IDAT pairs resolve to the same sample | IN-022 |
 | `E_EGT_LOAD` | error | Cluster (EGT) file cannot be loaded | IN-044 |
 | `E_EGT_MANIFEST_MISMATCH` | error | Cluster file lacks loci of the manifest | IN-043 |
+| `E_FAI_MISMATCH` | error | FASTA index does not match the FASTA | IN-060 |
+| `E_FASTA_FORMAT` | error | FASTA file is malformed | IN-060 |
 | `E_FILE_NOT_FOUND` | error | Input file or folder does not exist | CLI-016 |
 | `E_FILE_UNREADABLE` | error | Input file cannot be read | CLI-016 |
 | `E_GTC_CORRUPT` | warning | GTC file failed validation; sample skipped | IN-032 |
@@ -62,13 +66,30 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `W_IDAT_NAME_MISMATCH` | warning | IDAT barcode/position disagrees with its file name | IN-023 |
 | `W_IDAT_NO_SCAN_TIME` | warning | IDAT has no scan entry in its run info | IN-024 |
 | `W_IDAT_UNPAIRED` | warning | IDAT channel file without its partner | IN-021 |
+| `W_INDEL_PARTIAL_MATCH` | warning | Indel source sequence matches the genome only partially | OUT-019 |
+| `W_INF1_NC_CONFLICT` | warning | Infinium I no-call conflicts with other assays | OUT-037 |
+| `W_LARGE_OUTPUT` | warning | Output will be very large | EDGE-036 |
 | `W_MANIFEST_NO_REFSTRAND` | warning | Manifest lacks RefStrand annotation | IN-040 |
+| `W_MERGE_ALL_NC` | warning | Every probe at a merged site is a no-call | OUT-031 |
+| `W_MERGE_AMBIGUOUS` | warning | Probes at a site allow several genotypes; set missing | OUT-031 |
+| `W_MERGE_INCONSISTENT` | warning | Probes at a site disagree; genotype set missing | OUT-031 |
+| `W_NO_BGZIP` | warning | Uncompressed VCF written; downstream commands need bgzip + index | OUT-010 |
 | `W_QC_LABEL_SANITIZED` | warning | Dataset label was sanitized | QC-042 |
 | `W_QC_NO_BAF` | warning | GTC has no B-allele frequencies; contamination not estimated | QC-064 |
 | `W_QC_PEDIGREE` | warning | Parent1/Parent2/Replicate value does not name a sample in the set | IN-018 |
 | `W_QC_TOO_FEW` | warning | Too few samples or sites for a cohort QC statistic | QC-026 |
 | `W_QC_UNMATCHED_SAMPLES` | warning | Sample IDs present in one QC file but not the other | QC-040 |
+| `W_REF_NOT_QUERIED` | warning | The reference allele is not among the probe's alleles | OUT-015 |
 | `W_SHEET_BARCODE_REPAIRED` | warning | Barcode written as a decimal was repaired | IN-007 |
 | `W_SHEET_EMPTY_COLUMN` | warning | Columns with empty headers are ignored | IN-004 |
 | `W_SHEET_ROOTFOLDER_OVERRIDDEN` | warning | CLI folder overrides the sheet RootFolder | IN-008 |
 | `W_SHEET_SEX_CONFLICT` | warning | Reported-sex columns disagree | IN-014 |
+| `W_SKIP_AMBIGUOUS` | warning | Ambiguous-strand locus dropped by --drop-ambiguous | OUT-042 |
+| `W_SKIP_CONTIG` | warning | Manifest chromosome absent from the FASTA | OUT-019 |
+| `W_SKIP_EXCLUDED` | warning | Locus excluded by --exclude-loci/--include-loci | OUT-019 |
+| `W_SKIP_INDEL_CONTEXT` | warning | Indel sequence cannot be determined (no CSV SourceSeq) | OUT-019 |
+| `W_SKIP_INDEL_REF` | warning | Indel reference allele cannot be determined from the FASTA | OUT-019 |
+| `W_SKIP_INTENSITY_ONLY` | warning | Intensity-only locus was skipped | OUT-019 |
+| `W_SKIP_NO_STRAND` | warning | Locus has neither RefStrand nor a sequence to align | OUT-042 |
+| `W_SKIP_UNMAPPED` | warning | Locus without a genomic position was skipped | OUT-019 |
+| `W_UNKNOWN_LOCI` | warning | Names in a locus list are not in the manifest | OUT-036 |