## Preprocessing: `pp`

## Preprocessing module diagram
```{image} ../_static/smftools_preprocessing_diagram.png
:width: 1000px
```

```{eval-rst}
.. autosummary::
   :toctree: generated/preprocessing
   
   smftools.preprocessing.append_base_context
   smftools.preprocessing.append_binary_layer_by_base_context
   smftools.preprocessing.binarize
   smftools.preprocessing.binarize_on_Youden
   smftools.preprocessing.binary_layers_to_ohe
   smftools.preprocessing.calculate_complexity_II
   smftools.preprocessing.calculate_consensus
   smftools.preprocessing.calculate_coverage
   smftools.preprocessing.calculate_pairwise_differences
   smftools.preprocessing.calculate_pairwise_hamming_distances
   smftools.preprocessing.calculate_position_Youden
   smftools.preprocessing.calculate_read_length_stats
   smftools.preprocessing.calculate_read_modification_stats
   smftools.preprocessing.clean_NaN
   smftools.preprocessing.filter_adata_by_nan_proportion
   smftools.preprocessing.filter_reads_on_length_quality_mapping
   smftools.preprocessing.filter_reads_on_modification_thresholds
   smftools.preprocessing.flag_duplicate_reads
   smftools.preprocessing.invert_adata
   smftools.preprocessing.load_sample_sheet
   smftools.preprocessing.make_dirs
   smftools.preprocessing.min_non_diagonal
   smftools.preprocessing.recipes
   smftools.preprocessing.reindex_references_adata
   smftools.preprocessing.subsample_adata
```

```{eval-rst}
.. automodule:: smftools.preprocessing
   :no-members:
   :show-inheritance:
```