@platforma-open/milaboratories.generation-probability.block 1.0.0 → 1.1.0

package/block-pack/CHANGELOG.md

@@ -1,5 +1,53 @@
 # @platforma-open/milaboratories.generation-probability.block
 
+## 1.1.0
+
+### Minor Changes
+
+- 5be7d5d: Score imported receptor sets, and fix swapped chain labels on single-cell TCR data
+
+  **Imported receptor sets.** A set from Import VDJ Data was offered nowhere and scored nothing.
+  Four separate things stopped it, each failing differently.
+
+  The dataset dropdown filtered on the presence of a per-record `pl7.app/vdj/chain` column, which
+  an imported set does not have — so it never appeared as an option at all. Its locus is a property
+  of the whole set, recorded on the key axis, and that is now accepted as an alternative.
+
+  The CDR3 alphabet was read from `pl7.app/alphabet` on the key axis or from a `<key>/structure`
+  domain key. An imported set states it in neither — the structure key belongs to the
+  `scClonotypeKey` vocabulary its axis does not use — so the run died on "Cannot determine CDR3
+  alphabet". Its sequence columns do carry the alphabet, so that is where it is now read from when
+  the axis says nothing. The axis stays authoritative when it does say something: a MiXCR set emits
+  both nucleotide and amino-acid CDR3 columns, and the axis is what says which of them defines the
+  clonotype.
+
+  Scoring needed a per-row locus column and quietly produced an empty result without one. The
+  scorer's input table is now assembled in a single pass that appends a constant locus column for a
+  unit whose locus is the same for every row, so the scoring script is unchanged and still simply
+  reads a locus per row.
+
+  Whether the two chains are scored separately followed the key axis being
+  `pl7.app/vdj/scClonotypeKey`. A paired imported set carries both chains in one frame under the
+  `pl7.app/vdj/scClonotypeChain` column domain on a `variantKey` axis, so it took the bulk path,
+  where the first CDR3 column found is scored and the other chain is silently dropped. That now
+  follows the column domain.
+
+  **A light chain from an imported set is reported as skipped, not scored.** OLGA needs IGK and IGL
+  as separate models and an imported set records only "IG Light", so the locus is genuinely unknown.
+  Rather than guess, the light unit keeps its chain name, gets no Pgen, and is named in the block's
+  existing skipped-chains banner. Heavy chains (IGH) and TCR alpha/beta (TRA, TRB) score normally.
+
+  **Swapped chain labels.** MiXCR fixes "A" as the more diverse chain — the one that recombines a D
+  segment — so a receptor's chain order is TCRBeta/TCRAlpha and TCRDelta/TCRGamma, not alphabetical.
+  The label table read A as Alpha and B as Beta, so on a single-cell TCR alpha/beta dataset the alpha
+  column was labelled "Generation probability (Beta)" and the beta column "(Alpha)". Gamma/delta was
+  swapped the same way. The Pgen values were always right — the locus came from the per-record chain
+  column, never from the A/B letter — but a mislabelled column reads as the wrong chain's result.
+  Labels are now derived from the chain that the A/B slot resolves to, through the single table that
+  also decides the locus, so a label cannot disagree with the model that produced the value beside it.
+
+  Bulk, single-cell IG, peptide and amplicon inputs are unaffected.
+
 ## 1.0.0
 
 ### Major Changes

package/block-pack/manifest.json

@@ -1 +1 @@
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