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The interval join skipped every record with a `*` ALT, though `*` (an allele spanning an upstream deletion) leaves the record's REF span as written. A skipped record has no gene link, so a vcfp:LinkedSelector never selects it, and a prohibition on a gene panel does not reach it. vcf-rdfizer-testing experiment 17's arm 4 found this by comparing the records each release view kept with a bcftools baseline, record by record. NB72462M has 13 `*` records in the 28 cancer-predisposition genes; the rule withholding those genes from research released all 13 to a general-research view. Its 17 `*` records in cardiac genes were also withheld from a view limited to those genes, the fail-closed side of the same gap. `*` and `.` now key by the REF span. Symbolic alleles and breakends are still skipped: their extent is END or a mate, which needs a different coordinate policy. The SPDI join is unchanged; `*` has no allele sequence to express. The docs say what a rule over links does not reach: a record a linker could not key, counted in the link report's skipped_records. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
A patch: the gene linkers (`ensembl-genes-grch38`, `gene-demo`) link records whose ALT is `*`, by their REF span. Up to v3.3.0 they were skipped, so a policy rule over gene links did not reach them. Nothing changes what a v3.3.0 conversion writes. The conda sha256 stays a placeholder until the tag exists. Populate it with `python3 scripts/release.py 3.3.1 --fetch-conda-sha256` after pushing v3.3.1. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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The validator's q01-q13 have been thirteen since the identity digests (q11-q13) were added; docs/ already says thirteen. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
The gene linkers (
ensembl-genes-grch38,gene-demo) skipped every record whose ALT is*, though*(an allele spanning an upstream deletion) leaves the record's REF span as written. A skipped record has no gene link, so avcfp:LinkedSelectornever selects it, and a prohibition on a gene panel does not reach it.How it was found
vcf-rdfizer-testing experiment 17, arm 4, compares the records each release view keeps with a bcftools baseline, record by record. That comparison is new; earlier arms compared carriers only. On NB72462M:
*records in cancer-predisposition genes released*records in cardiac genes withheld (fails closed)The same 13, plus 11 from NG131FQA1I, were in arm 1's research views. Arms 2 and 3 are unaffected: the cohort files have no
*records, and HG005's research views released nothing.Changes
keys_for: in an interval join,*and.ALTs key by the REF span. Symbolic alleles and breakends are still skipped, because their extent is END or a mate. The SPDI join is unchanged, since*has no allele sequence.limitations.md,policy-demonstrator.md,datalinking.md, linker READMEs) say what a rule over links does not reach: records a linker could not key, which the link report counts inskipped_records.scripts/release.py 3.3.1).Tests
test/test_linking_unit.py:*,G,*and.key by REF span;<DEL>, breakends and mixed*,<DEL>are still skipped; an end-to-end link run puts a*record in a gene. Both fail without the fix.Ran 1211 tests … OK (skipped=24).After merge
Tag
v3.3.1from main, thenpython3 scripts/release.py 3.3.1 --fetch-conda-sha256(seescripts/RELEASING.md).🤖 Generated with Claude Code