kemal
5a20e7131c
Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT (data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer); sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing (IN-020..IN-022), message catalogue and exit codes (CLI-014/016), JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest, and `simurg inspect`. Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs round-trip byte-identically; BPM and CSV manifests are consistent.
3.6 KiB
3.6 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_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_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_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 |