v2 CN/LOH (WIP): cn build-model and cn call

Cyto model (.simurg-cyto: GC 1 kb/100 kb/1 Mb, PFB from the cluster file, optional
sex-aware batch reference from normal GTCs; IN-051, CYTO-038); GC-wave correction
(CYTO-003); smoothing (CYTO-004); HMM with constitutional, gain-LOH, mosaic and haploid
states, forward-backward QUAL and Viterbi segments (CYTO-005/012); event statistics,
effective size, post-filters, per-type thresholds, promotion/LowFraction, built-in
centromere mask from UCSC cytoBand (CYTO-006..021); sex resolution (CYTO-024), ploidy;
CNV VCF with bgzip+tabix (CYTO-028..031), segments parquet, cn_sample_summary.tsv and
the cn_call_manifest.json sidecar.

docs/messages.md

@@ -8,6 +8,10 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `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_CN_FAILED` | error | CN calling failed for the sample | CYTO-040 |
+| `E_CN_SEX_UNRESOLVED` | error | Sample sex unresolved and --unknown-sex-policy error | CYTO-024 |
+| `E_CN_SIDECAR_MISSING` | error | cn_call_manifest.json not found in the cn call output | CYTO-032 |
+| `E_CN_VCF_UNINDEXED` | error | CNV VCFs must be bgzipped and indexed for annotate | CYTO-032 |
 | `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 |
@@ -32,6 +36,8 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_METH_NO_CONTROLS` | error | Missing control probes in manifest | MET-002 |
 | `E_METH_NO_IDATS` | error | No IDATs found | MET-004 |
 | `E_METH_PREP_FAILED` | error | Prep failed (sample) | MET-010 |
+| `E_MODEL_MANIFEST_MISMATCH` | error | Model was built for a different manifest probe set | IN-051 |
+| `E_MODEL_VERSION` | error | Model schema is too old; rebuild it | IN-051 |
 | `E_NO_INPUT` | error | Neither an input folder nor a sample sheet was given | CLI-006 |
 | `E_NO_INPUT_FOLDER` | error | Sample sheet has no RootFolder and no folder was given | CLI-006 |
 | `E_OUTPUT_EXISTS` | error | Outputs already exist; use --force or --resume | CLI-010 |
@@ -59,7 +65,11 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_SHEET_NO_KEY_COLUMNS` | error | Sample sheet lacks SentrixBarcode_A/SentrixPosition_A | IN-002 |
 | `E_SHEET_RESERVED` | error | Sample sheet column collides with an output column | IN-005 |
 | `E_SHEET_TOO_LONG` | error | Sample sheet name or value longer than 500 characters | IN-006 |
+| `I_CN_SEX_RESOLVED` | info | Sample sex updated from U by the caller | CYTO-024 |
 | `I_UNLISTED_IDATS` | info | IDAT pairs not listed in the sample sheet are ignored | IN-016 |
+| `W_CN_NO_FASTA` | warning | No FASTA: VCF REF padding bases written as N | CYTO-029 |
+| `W_CN_PROBE_FLOOR` | warning | Minimum probe count below 10 raised to 10 | CYTO-008 |
+| `W_CN_THRESHOLD_EXCEEDS_GENOME` | warning | Size threshold exceeds the effective genome; no events | CYTO-009 |
 | `W_CTRL_DEFS_DIFFER` | warning | BPM and CSV control definitions differ; the BPM wins | QC-001 |
 | `W_CTRL_MISSING` | warning | Controls needed by a metric are absent; metric not evaluable | QC-007 |
 | `W_CTRL_ZERO_DIVISOR` | warning | Control metric has a zero denominator (NaN) | QC-008 |