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2.36.0 — a junction naming neither V nor J gets a locus proposed too - #146
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2.34.0 proposed the missing side from the junction, but only within the locus the *other* side named. A record naming neither came back refused: no locus, no boundary, nothing for a nucleotide stage to work on. No new rule. Every locus the organism ships now competes, scored by the same `anchor_depth` from each germline's own anchor, and a locus only wins by explaining residues at BOTH ends -- which is what keeps a TRA junction out of TRD, where the V genes are shared and the J genes are not. 522 of VDJdb's curated `chunks` records name neither side (461 distinct keys). All 461 get a locus and 459 come back `good`, against none before. The proposed locus agrees with the `cdr3.alpha`/`cdr3.beta` column the record was filed under on 457 of 461 (99.13 %) -- 318 TRB, 139 TRA -- and all four disagreements are `CACD...DKLIF`: TRDV2's own anchor and TRDJ1's own ending, in a schema with no delta column. Each end must explain its own anchor residue or no locus is named. Without that floor `QQQQQQQQQQQQ` agreed with nothing on every locus and was still handed TRA; over the 461 real keys the winning locus clears it on every one. scripts/audit_cdr3fix.py kept blank-side keys out. It required both a V and a J to be named, so the A/B instrument was blind to exactly the rows 2.34.0 and this release change. Corpus 189,596 -> 192,726 keys, digest rebases to 0df8541ed1060fe1; on the 189,596 the old filter kept, the digest is unchanged at 2b75491b380310aa, so nothing that already worked moved. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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2.34.0 proposed a missing V or J from the junction, but only within the locus the other side named. A record naming neither came back refused — no locus, no boundary, nothing for a nucleotide stage to work on.
There is no new rule here. Every locus the organism ships now competes, scored by the same
anchor_depthfrom each germline's own anchor, and a locus only wins by explaining residues at both ends — which is what keeps a TRA junction out of TRD, where the V genes are shared and the J genes are not.Measured
522 of VDJdb's curated
chunksrecords name neither side (461 distinct keys). All 461 now get a locus and 459 come backgood, against none before.The check is VDJdb's own filing: the proposed locus agrees with the
cdr3.alpha/cdr3.betacolumn the record was filed under on 457 of 461 (99.13 %) — 318 TRB, 139 TRA. All four disagreements areCACD…DKLIF, which is TRDV2's own anchor and TRDJ1's own ending, in a schema with no δ column.The floor is measured too
Each end must explain its own anchor residue or no locus is named. Without it a junction agreeing with nothing (
QQQQQQQQQQQQ) reached depth 0 on both ends of every locus and was still handed TRA. Over the 461 real keys the winning locus clears the floor on every one — 16 at depth 1, 200 at 4, 156 at 5.The audit instrument was blind to this
scripts/audit_cdr3fix.pyrequired both a V and a J to be named, so the A/B could not see the rows 2.34.0 and this release change. Widened:0df8541ed1060fe12b75491b380310aa— nothing that already worked movedWhy now
vdjtools4.8.0's junction pipeline pinsarda-mapper>=2.36.0: those 461 keys are the last of VDJdb's corpus that answered nothing.Gate: 1,339 passed / 9 skipped.
ruff check src/clean. Docs build with-W, zero warnings.🤖 Generated with Claude Code