kemalandClaude Opus 5.5
df41569f64
- formats/fasta: plain/BGZF FASTA, .fai/.gzi built identical to htslib, index check, build detection, contig aliases, mmap genome cache (IN-060..064) - formats/bgzf, formats/bcf: pure-Python BGZF, tabix .tbi, BCF 2.2 and CSI (OUT-010, OUT-038, OUT-040) - harmonize/sites: plus-strand mapping with audit rows, indel resolution from SourceSeq (port of GTCtoVCF, Apache-2.0) and left normalisation (OUT-014..021, OUT-030, OUT-042) - harmonize/combine: OUT-031 genotype combination (ploidy-aware, Infinium I/II signal classes, OUT-037) - pipeline/vcf: `simurg gtc-to-vcf` (per-sample VCF.gz+tbi, --merge cohort BCF+csi, audit parquet) - pipeline/export: `simurg export bedgraph|finalreport|plink|locus-summary` (OUT-043, OUT-050..052, OUT-071) - validation: 36 GSA samples vs gtc2vcf: 23.66 M identical calls, 0 unexplained differences; PLINK identical to plink2 on 637,397 variants; bcftools validates VCF/BCF and our indexes answer region queries correctly - fetch_data.sh p6 (Ensembl GRCh38 with checksum), make_oracle_vcf.sh, validate_p6_vcf.py; K-022/K-023 Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
7.7 KiB
7.7 KiB
SimurgArray message catalogue
Generated from src/simurg/core/errors.py — do not edit by hand.
| Code | Level | Meaning | Spec |
|---|---|---|---|
E_AUX_INVALID |
error | Auxiliary-loci record is invalid | OUT-035 |
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_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_FAI_MISMATCH |
error | FASTA index does not match the FASTA | IN-060 |
E_FASTA_FORMAT |
error | FASTA file is malformed | IN-060 |
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_QC_CONFIG_EXT |
error | QC config file must be .yaml or .yml | QC-021 |
E_QC_CONFIG_MISSING |
error | QC config file does not exist | QC-021 |
E_QC_CONFIG_PARSE |
error | QC config file is not valid YAML | QC-021 |
E_QC_CONFIG_STRUCTURE |
error | QC config lacks the qc/report (QC/Report) wrapper | QC-021 |
E_QC_DATASET_INCOMPLETE |
error | Dataset folder lacks a required file | QC-041 |
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 |
E_QC_THRESHOLD_KEY |
error | Unknown QC threshold key | QC-021 |
E_QC_THRESHOLD_RANGE |
error | QC threshold value out of range | QC-021 |
E_QC_THRESHOLD_VALUE |
error | QC threshold value is not numeric or null | QC-021 |
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_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 |
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_INDEL_PARTIAL_MATCH |
warning | Indel source sequence matches the genome only partially | OUT-019 |
W_INF1_NC_CONFLICT |
warning | Infinium I no-call conflicts with other assays | OUT-037 |
W_LARGE_OUTPUT |
warning | Output will be very large | EDGE-036 |
W_MANIFEST_NO_REFSTRAND |
warning | Manifest lacks RefStrand annotation | IN-040 |
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_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 |
W_QC_PEDIGREE |
warning | Parent1/Parent2/Replicate value does not name a sample in the set | IN-018 |
W_QC_TOO_FEW |
warning | Too few samples or sites for a cohort QC statistic | QC-026 |
W_QC_UNMATCHED_SAMPLES |
warning | Sample IDs present in one QC file but not the other | QC-040 |
W_REF_NOT_QUERIED |
warning | The reference allele is not among the probe's alleles | OUT-015 |
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 |
W_SKIP_AMBIGUOUS |
warning | Ambiguous-strand locus dropped by --drop-ambiguous | OUT-042 |
W_SKIP_CONTIG |
warning | Manifest chromosome absent from the FASTA | OUT-019 |
W_SKIP_EXCLUDED |
warning | Locus excluded by --exclude-loci/--include-loci | OUT-019 |
W_SKIP_INDEL_CONTEXT |
warning | Indel sequence cannot be determined (no CSV SourceSeq) | OUT-019 |
W_SKIP_INDEL_REF |
warning | Indel reference allele cannot be determined from the FASTA | OUT-019 |
W_SKIP_INTENSITY_ONLY |
warning | Intensity-only locus was skipped | OUT-019 |
W_SKIP_NO_STRAND |
warning | Locus has neither RefStrand nor a sequence to align | OUT-042 |
W_SKIP_UNMAPPED |
warning | Locus without a genomic position was skipped | OUT-019 |
W_UNKNOWN_LOCI |
warning | Names in a locus list are not in the manifest | OUT-036 |