vdjdb-db

Run QC scripts on a VDJdb chunk, report every error with a suggested fix, verify the output of previous /extract and /format steps, estimate confidence scores, and flag gaps in current py_src QC coverage.

Identify and classify duplicate TCR records across all VDJdb chunks at three resolution levels (beta-only, paired, and same-epitope multi-MHC), categorise by publication source, author overlap, and flag spurious high-frequency records.

Harmonize antigen.gene and antigen.species fields in a VDJdb chunk to canonical VDJdb naming. Detects spurious gene/species names, resolves inconsistencies (same epitope → multiple names), and warns about epitopes that are exact substrings of longer epitopes. Invoked standalone or from /proofread when spurious values are detected.

For each new or changed chunk in chunks/ (by git), find or create a GitHub issue for its PMID, then commit the chunk with "Fixes

Extract TCR:pMHC specificity data from raw source files (papers, supplementary tables, XLS, PDF, 10X output, AIRR-format) and produce a VDJdb-formatted TSV chunk ready for /format and /proofread.

Standardise a raw or partially-formatted VDJdb TSV chunk — normalising species names, IMGT V/D/J gene IDs, IMGT-HLA MHC alleles, and method vocabulary — and produce a properly-named chunk file ready for proofreading.