v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018)

Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking
(MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye
bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006,
bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the
detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation
datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style
Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some
control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878).

docs/messages.md

@@ -26,6 +26,12 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_IDAT_MANIFEST_MISMATCH` | error | IDATs and manifest belong to different products | IN-027 |
 | `E_IDAT_PAIR_MISMATCH` | error | Red and Grn IDATs of a sample do not match | IN-023 |
 | `E_INTERNAL` | error | Internal error (bug); rerun with --debug and report | CLI-014 |
+| `E_METH_CONTROLS_FORMAT` | error | Controls not formatted correctly. Must have 4 columns (Address,Type,Color_Channel,Name) | MET-002 |
+| `E_METH_MISSING_COLUMNS` | error | Missing required columns in the methylation manifest | MET-002 |
+| `E_METH_NO_ASSAY` | error | Probe section not found | MET-002 |
+| `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_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 |
@@ -37,7 +43,6 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `E_QC_FORMAT` | error | Invalid --output-format value | QC-063 |
 | `E_QC_LABEL_COUNT` | error | Number of labels does not match number of datasets | QC-042 |
 | `E_QC_LABEL_DUPLICATE` | error | Dataset labels are not unique | QC-042 |
-| `E_QC_METHYLATION` | error | Methylation control metrics are not available yet (v2) | QC-006 |
 | `E_QC_MIXED_TYPES` | error | Genotyping and methylation datasets cannot be mixed | QC-043 |
 | `E_QC_NO_DATASETS` | error | No QC dataset folder found | QC-041 |
 | `E_QC_PROFILE` | error | Unknown QC profile | QC-024 |
@@ -73,6 +78,10 @@ Generated from `src/simurg/core/errors.py` — do not edit by hand.
 | `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_METH_MISSING_CONTROL_NAMES` | warning | Control names missing from the manifest; metric set to NA | MET-009 |
+| `W_METH_MISSING_CONTROL_TYPES` | warning | Control types missing from the manifest; metric set to NA | MET-009 |
+| `W_METH_MISSING_SAMPLE` | warning | Missing sample: IDATs absent; the sample fails, the run continues | MET-015 |
+| `W_METH_NO_FEATURES` | warning | No features, skipping PCA plot | MET-013 |
 | `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 |