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README.md

@@ -1,6 +1,6 @@
 ---
 pretty_name: "GAMBA Functional Regions: Feature vs Category-Matched Random"
-license: mit
+license: other
 tags:
 - biology
 - genomics
@@ -103,7 +103,8 @@ For the paper protocol:
 | `split`, `sequence`, `label`, `pair_id` | Chromosome partition, exact input, `feature`/`random` class, and matched pair. |
 | `category`, `repeat_class`, `scope` | Source category, nullable repeat class, and `full` scope. |
 | `context_policy` | `causal` or `symmetric`. |
-| `chrom`, `start`, `end`, `strand` | Zero-based, half-open hg38 coordinates. |
+| `chrom`, `start`, `end`, `source_strand` | Zero-based, half-open hg38 coordinates and biological strand (`.` means unknown). |
+| `sequence_orientation` | Explicit `+`/`-` orientation used for sequence geometry and reverse complementation. |
 | `context_start`, `context_end` | Forward-genome sequence context coordinates. |
 | `roi_start`, `roi_end` | Feature/control offsets inside oriented `sequence`. |
 | `pool_start_in_window`, `pool_end_in_window` | Evaluation pooling offsets. |
@@ -113,17 +114,21 @@ For the paper protocol:
 ## Corrected repeat processing
 
 RepeatMasker genomic strand and repeat class are separate fields. The release
-uses UCSC `rmsk` field 9 as `strand`, field 11 as `repeat_class`, and rebuilds
-repeat-derived controls and sequence orientation. Labels remain unchanged.
+uses UCSC `rmsk` field 9 as `source_strand`, field 11 as `repeat_class`, and
+rebuilds repeat-derived controls and sequence orientation. Labels remain
+unchanged.
 
 Published pair identities and deterministic 100 bp selections for unaffected
 features are preserved.
+Release `repeat-strand-v2` restores the pinned paper control coordinates for
+every unaffected category; only repeat controls are regenerated with keyed
+RNG.
 
 ## Processing and citation
 
 Processing and verification:
 
-https://github.com/TaykhoomDalal/Gamba-Processing/tree/main/Functional-Regions
+https://github.com/TaykhoomDalal/Gamba-Processing/commit/549985683a1c52014a64c5781937dd25360f1553
 
 Consens, M. E. et al. *Predicting evolutionary rate as a pretraining task
 improves genome language model representations*. bioRxiv (2026).
@@ -131,5 +136,7 @@ https://doi.org/10.64898/2026.02.02.703275
 
 ## License
 
-GAMBA benchmark code/data are MIT licensed. Upstream resources retain their
-own terms.
+The processing code derived from GAMBA is MIT licensed under the processing
+repository's `LICENSE`. This generated dataset is marked `other`: incorporated
+reference sequence, annotations, and phyloP-derived values retain their
+upstream terms, so no blanket MIT license is asserted for the Parquets.

functional-random-gamba-bidi.parquet

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functional-random-gamba-causal.parquet

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