Fix three validator false positives on real-world data - #36
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Real-fixture verification (GENCODE, GRIDSS) surfaced three validators flagging valid canonical data: - GFF3: comma-separated custom attributes (e.g. GENCODE tag=basic,Ensembl_canonical) were rejected because the multi-value whitelist was treated as exhaustive. Only reserved single-value attributes are now flagged; custom and reserved multi-value attributes may be comma-separated. - GTF: gene-type features were warned for missing transcript_id, which GENCODE/Ensembl legitimately omit on genes. transcript_id is now required only on non-gene features. - VCF: single-breakend ALTs (a contig with a leading/trailing ".", e.g. GRIDSS "TTTT." per VCF 4.2 section 5.4.9) were flagged as non-spec; now accepted. Adds targeted unit tests for each fix and strengthens the real-fixtures suite to assert every canonical fixture validates with zero diagnostics, so a future false positive on real data fails CI.
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Summary
The real-world fixtures added in #35 (now merged) immediately caught three validators flagging valid canonical data as invalid. This fixes all three (each spec-backed) and strengthens the fixture suite so it can't happen again.
What real data exposed
tag=basic,Ensembl_canonical,GENCODE_Primarygene-type features (notranscript_id)transcript_idonly on non-gene features — genes legitimately omit itTTTT./.AATCAfter the fixes, all 11 canonical fixtures validate with zero diagnostics.
The guard (why this can't regress)
The #35 verify suite only asserted "doesn't throw" — which is why those false positives slipped through green. This adds a per-fixture assertion that canonical data produces zero diagnostics (with a
maxDiagnosticsescape hatch for any future genuine advisory). So a new false positive on real GENCODE/GRIDSS/etc. output now fails CI.Tests
tag=a,ballowed; reserved single-valueID=a,bstill flagged; reserved multi-valueParent=a,ballowed.genefeature withouttranscript_idnot warned;exonwithout it still warned. (Updated one existing test that had asserted the old behavior via ageneline.)