kemalandClaude Opus 5.5
febdd121ef
- genotype/clusters.py: EGT aligned to manifest order (float32 mean R) - genotype/gencall.py: flair, six-case likelihood, priors/posteriors, fuzzy sub-scores and score map, vectorised with the reference's float/double evaluation order and libm transcendentals - genotype/baf_lrr.py, sex.py (rules v1/v2), sample.py (IDAT -> Gtc) - pipeline/inputs.py shared by ingest and genotype - pipeline/genotype.py + CLI: GTC per sample, sample_summary.tsv/json (OUT-060..063), run manifest - GTCs from IDATs are byte-identical to the oracle for 36 GSA samples x 2 normalization versions (NaN sign canonicalised to the x86 pattern) Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
4.0 KiB
4.0 KiB
SimurgArray message catalogue
Generated from src/simurg/core/errors.py — do not edit by hand.
| Code | Level | Meaning | Spec |
|---|---|---|---|
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_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 |
E_DUP_GTC |
error | Several GTC files resolve to the same sample | IN-030 |
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_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 |
E_GTC_UNSUITABLE |
error | GTC lacks fields required by this command | IN-031 |
E_IDAT_ENCRYPTED |
error | Encrypted (version 1) IDATs are not supported | IN-023 |
E_IDAT_FORMAT |
error | IDAT file is malformed | IN-023 |
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_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 |
E_SHEET_BARCODE_FORMAT |
error | Invalid SentrixBarcode_A / SentrixPosition_A value | IN-007 |
E_SHEET_DELIMITER |
error | Sample sheet is not comma-delimited CSV | IN-001 |
E_SHEET_DUP_COLUMN |
error | Duplicate column (column names are case-insensitive) | IN-003 |
E_SHEET_DUP_SAMPLE |
error | The same barcode/position appears in several rows | IN-009 |
E_SHEET_EMPTY |
error | Sample sheet has no data rows | IN-001 |
E_SHEET_NAME_COLLISION |
error | Sample names are not unique or clash with sample IDs | IN-010 |
E_SHEET_NAME_EMPTY |
error | Sample_Name is empty in at least one row | IN-010 |
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_UNLISTED_IDATS |
info | IDAT pairs not listed in the sample sheet are ignored | IN-016 |
W_DUP_IDAT_RESOLVED |
warning | Duplicate IDAT pair resolved by --on-duplicate-idat | IN-022 |
W_EGT_NAME |
warning | Cluster file name is not portable | IN-045 |
W_GTC_FOREIGN |
warning | GTC was produced by another tool | IN-031 |
W_IDAT_LOW_ADDRESS_COVERAGE |
warning | Some manifest addresses are absent from the IDAT | IN-027 |
W_IDAT_MANIFEST_NAME |
warning | IDAT names a different manifest than the BPM | IN-027 |
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_MANIFEST_NO_REFSTRAND |
warning | Manifest lacks RefStrand annotation | IN-040 |
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 |