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.

src/simurg/core/errors.py

@@ -135,6 +135,22 @@ CATALOGUE: dict[str, MessageDef] = dict(
         _m("W_QC_PEDIGREE", "warning", "Parent1/Parent2/Replicate value does not name a sample in the set", "IN-018"),
         _m("W_QC_NO_BAF", "warning", "GTC has no B-allele frequencies; contamination not estimated", "QC-064"),
         _m("W_QC_TOO_FEW", "warning", "Too few samples or sites for a cohort QC statistic", "QC-026"),
+        # --- cytogenetics CNV/LOH (CYTO-001 .. CYTO-040) -------------------------------------------------
+        _m("E_MODEL_MANIFEST_MISMATCH", "error", "Model was built for a different manifest probe set", "IN-051"),
+        _m("E_MODEL_VERSION", "error", "Model schema is too old; rebuild it", "IN-051"),
+        _m("W_CN_PROBE_FLOOR", "warning", "Minimum probe count below 10 raised to 10", "CYTO-008"),
+        _m(
+            "W_CN_THRESHOLD_EXCEEDS_GENOME",
+            "warning",
+            "Size threshold exceeds the effective genome; no events",
+            "CYTO-009",
+        ),
+        _m("I_CN_SEX_RESOLVED", "info", "Sample sex updated from U by the caller", "CYTO-024"),
+        _m("E_CN_SEX_UNRESOLVED", "error", "Sample sex unresolved and --unknown-sex-policy error", "CYTO-024"),
+        _m("W_CN_NO_FASTA", "warning", "No FASTA: VCF REF padding bases written as N", "CYTO-029"),
+        _m("E_CN_SIDECAR_MISSING", "error", "cn_call_manifest.json not found in the cn call output", "CYTO-032"),
+        _m("E_CN_VCF_UNINDEXED", "error", "CNV VCFs must be bgzipped and indexed for annotate", "CYTO-032"),
+        _m("E_CN_FAILED", "error", "CN calling failed for the sample", "CYTO-040"),
         # --- methylation control QC (MET-001 .. MET-018) -------------------------------------------------
         _m("E_METH_NO_ASSAY", "error", "Probe section not found", "MET-002"),
         _m("E_METH_NO_CONTROLS", "error", "Missing control probes in manifest", "MET-002"),