smftools.preprocessing.reindex_references_adata

smftools.preprocessing.reindex_references_adata(adata, reference_col='Reference_strand', offsets=None, new_col='reindexed', uns_flag='reindex_references_adata_performed', force_redo=False)

Reindex genomic coordinates by adding per-reference offsets.

Parameters:

• adata (AnnData) -- AnnData object.

• reference_col (str (default: 'Reference_strand')) -- Obs column containing reference identifiers.

• offsets (dict | None (default: None)) -- Mapping of reference to integer offset.

• new_col (str (default: 'reindexed')) -- Suffix for generated reindexed columns.

• uns_flag (str (default: 'reindex_references_adata_performed')) -- Flag in adata.uns indicating prior completion.

• force_redo (bool (default: False)) -- Whether to rerun even if uns_flag is set.

Return type:

None

Notes

If offsets is None or missing a reference, the new column mirrors the existing var_names values.