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Fix issue #635 in reindexing annotated features #636

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Fix issue #635 in reindexing annotated features #636

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4 changes: 4 additions & 0 deletions src/pyscenic/transform.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,10 @@ def module2features_auc1st_impl(
annotated_features = annotated_features[
~annotated_features.index.duplicated(keep="last")
]

# BUG FIX #635: Reindex back to original enriched feature order so the boolean mask
# aligns with the rccs/rankings numpy arrays (which are in original feature order).
annotated_features = annotated_features.reindex(enriched_features.index)
annotated_features_idx = (
pd.notnull(annotated_features[COLUMN_NAME_ANNOTATION])
if filter_for_annotation
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