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, invert=None)

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.

• invert (dict | bool | None (default: None)) -- Per-reference display-inversion flag(s). Either a single bool applied to every reference, a {ref: bool} mapping, or None (no inversion, the default). When a reference is inverted, its reindexed coordinate's sign is flipped (-(var_coords + offset) instead of var_coords + offset) so that "left of the anchor is negative, right of the anchor is positive" still holds after the reference is displayed in reverse column order. This never touches X/layers/var_names -- it is purely a reinterpretation of the reindexed coordinate value; callers that render columns are responsible for reordering them to match (see plotting.plotting_utils._ordered_columns).

Return type:

None

Notes

If offsets is None or missing a reference, the new column mirrors the existing var_names values (subject to the sign flip above).