Preprocessing: pp

Preprocessing module diagram

smftools.preprocessing.append_base_context(adata)	Append base context annotations to adata.
smftools.preprocessing.append_binary_layer_by_base_context(...)	Build per-reference masked layers for base-context sites.
smftools.preprocessing.append_mismatch_frequency_sites(adata)	Append mismatch frequency metadata and variable-site flags per reference.
smftools.preprocessing.append_sequence_mismatch_annotations(...)	Append mismatch annotations by aligning full reference sequences.
smftools.preprocessing.append_variant_call_layer(...)	Append a layer recording per-read, per-position variant calls at reference mismatch sites.
smftools.preprocessing.binarize
smftools.preprocessing.binarize_on_Youden(adata)	Binarize SMF values using thresholds from calculate_position_Youden.
smftools.preprocessing.binary_layers_to_ohe
smftools.preprocessing.calculate_complexity_II(adata)	Estimate and optionally plot library complexity.
smftools.preprocessing.calculate_consensus
smftools.preprocessing.calculate_coverage(adata)	Append position-level coverage metadata per reference category.
smftools.preprocessing.calculate_pairwise_differences
smftools.preprocessing.calculate_pairwise_hamming_distances
smftools.preprocessing.calculate_position_Youden(adata)	Add position-level Youden thresholds and optional ROC plots.
smftools.preprocessing.calculate_read_length_stats(adata)	Calculate per-read length statistics and store them in adata.obs.
smftools.preprocessing.calculate_read_modification_stats(...)	Add methylation/deamination statistics for each read.
smftools.preprocessing.clean_NaN(adata[, ...])	Append layers to adata that contain NaN-cleaning strategies.
smftools.preprocessing.filter_adata_by_nan_proportion(...)	Filter an AnnData object on NaN proportion in a matrix axis.
smftools.preprocessing.filter_reads_on_cigar_indels(adata)	Filter reads whose longest internal indel exceeds a threshold.
smftools.preprocessing.filter_reads_on_length_quality_mapping(adata)	Filter AnnData by coordinates, read length, quality, and mapping metrics.
smftools.preprocessing.filter_reads_on_modification_thresholds(...)	Filter reads based on per-read modification thresholds.
smftools.preprocessing.flag_duplicate_reads(...)	Flag duplicate reads with demux-aware keeper preference.
smftools.preprocessing.invert_adata(adata[, ...])	Invert the AnnData object along the column axis in-place.
smftools.preprocessing.label_deaminase_pcr_chimeras(adata)	Flag deaminase PCR-chimeric reads from per-read strand-switch metrics.
smftools.preprocessing.load_sample_sheet(...)	Load a sample sheet CSV and map metadata into adata.obs.
smftools.preprocessing.make_dirs
smftools.preprocessing.min_non_diagonal
smftools.preprocessing.partitioned_executor	Execute bounded preprocessing work units into derived partition stores.
smftools.preprocessing.preprocess_umi_annotations(adata)	Preprocess UMI annotations: validate, filter, and cluster UMIs.
smftools.preprocessing.recipes
smftools.preprocessing.reindex_references_adata(adata)	Reindex genomic coordinates by adding per-reference offsets.
smftools.preprocessing.subsample_adata(adata)	Subsample an AnnData object by observation categories.
smftools.preprocessing.umi_bipartite_analysis	Bipartite graph analysis for U1×U2 UMI cluster pairing QC.

partitioned_executor implements the bounded-task partitioned preprocessing pipeline used when a partitioned raw/spatial spine is available (see the smftools preprocess CLI tutorial); the other newly listed modules back the CIGAR-indel filter, deaminase PCR-chimera labeling, variant/mismatch annotation, and UMI preprocessing features described there.