smftools.preprocessing.append_mismatch_frequency_sites

smftools.preprocessing.append_mismatch_frequency_sites#

smftools.preprocessing.append_mismatch_frequency_sites(adata, ref_column='Reference_strand', mismatch_layer='mismatch_integer_encoding', read_span_layer='read_span_mask', quality_layer=None, mismatch_frequency_range=(0.05, 0.95), uns_flag='append_mismatch_frequency_sites_performed', force_redo=False, bypass=False)#

Append mismatch frequency metadata and variable-site flags per reference.

Parameters:

  • adata (AnnData) -- AnnData object.

  • ref_column (str (default: 'Reference_strand')) -- Obs column defining reference categories.

  • mismatch_layer (str (default: 'mismatch_integer_encoding')) -- Layer containing mismatch integer encodings.

  • read_span_layer (str (default: 'read_span_mask')) -- Layer containing read span masks (1=covered, 0=not covered).

  • quality_layer (str | None (default: None)) -- Layer containing base quality scores for Q-value based error rates.

  • mismatch_frequency_range (Optional[Sequence[float]] (default: (0.05, 0.95))) -- Lower/upper bounds (inclusive) for variable site flagging.

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

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

  • bypass (bool (default: False)) -- Whether to skip running this step.

Return type:

None