Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | Z A adapter_max_edits (smftools.informatics.bam_functions.UMIKitConfig attribute) adapter_pad (smftools.informatics.bam_functions.FlankingConfig attribute) adapter_side (smftools.informatics.bam_functions.FlankingConfig attribute) add_demux_type_annotation() (in module smftools.informatics.h5ad_functions) add_demux_type_from_bm_tag() (in module smftools.informatics.h5ad_functions) add_ep_obs_columns() (in module smftools.analysis.compute.ep_classification) add_read_length_and_mapping_qc() (in module smftools.informatics.h5ad_functions) add_read_tag_annotations() (in module smftools.informatics.h5ad_functions) add_secondary_supplementary_alignment_flags() (in module smftools.informatics.h5ad_functions) align_and_sort_BAM() (in module smftools.informatics.bam_functions) align_sequences_with_mismatches() (in module smftools.tools.sequence_alignment) aligned_BAM_to_bed() (in module smftools.informatics.bed_functions) alignment_to_ragged_record() (in module smftools.informatics.ragged_store) AlignmentMismatch (class in smftools.tools.sequence_alignment) amplicon_max_edits (smftools.informatics.bam_functions.UMIKitConfig attribute) amplicon_pad (smftools.informatics.bam_functions.FlankingConfig attribute) amplicon_side (smftools.informatics.bam_functions.FlankingConfig attribute) analysis_mode (smftools.informatics.storage_planner.ReferencePlan attribute) analyze_autocorr_matrix() (in module smftools.tools.spatial_autocorrelation) analyze_fft_periodicity() (in module smftools.analysis.compute.ls_periodicity) analyze_ls_periodicity() (in module smftools.analysis.compute.ls_periodicity) analyze_ls_periodicity_direct() (in module smftools.analysis.compute.ls_periodicity) analyze_umi_bipartite_graph() (in module smftools.preprocessing.umi_bipartite_analysis) annotate_demux_type_from_bi_tag() (in module smftools.informatics.bam_functions) annotate_pod5_origin() (in module smftools.informatics.h5ad_functions) annotate_umi_tags_in_bam() (in module smftools.informatics.bam_functions) annotate_zero_hamming_segments() (in module smftools.tools.rolling_nn_distance) append_base_context() (in module smftools.preprocessing) append_binary_layer_by_base_context() (in module smftools.preprocessing) append_mismatch_frequency_sites() (in module smftools.preprocessing) append_modification_qc_mask() (in module smftools.preprocessing.partitioned_executor) append_reference_strand_quality_stats() (in module smftools.informatics.h5ad_functions) append_sequence_mismatch_annotations() (in module smftools.preprocessing) append_variant_call_layer() (in module smftools.preprocessing) assign_per_read_segments_layer() (in module smftools.tools.rolling_nn_distance) assign_rolling_nn_results() (in module smftools.tools.rolling_nn_distance) AttentionPooling1d (class in smftools.analysis.compute.ml_cnn) B bam_qc() (in module smftools.informatics.bam_functions) barcode_amplicon_gap_tolerance (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_composite_max_edits (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_ends (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_length (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_max_edit_distance (smftools.informatics.bam_functions.BarcodeKitConfig attribute) barcode_min_separation (smftools.informatics.bam_functions.BarcodeKitConfig attribute) BarcodeKitConfig (class in smftools.informatics.bam_functions) barcodes (smftools.informatics.bam_functions.BarcodeKitConfig attribute) base_signal_features() (in module smftools.informatics.signal_features) base_signal_trace() (in module smftools.informatics.signal_features) basecall_pod5s() (in module smftools.informatics.pod5_functions) baseline_mode (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) binarize_adata() (in module smftools.preprocessing.binarize) binarize_converted_base_identities() (in module smftools.informatics.binarize_converted_base_identities) binarize_on_Youden() (in module smftools.preprocessing) binary_autocorrelation_with_spacing() (in module smftools.analysis.compute.autocorrelation) (in module smftools.tools.read_stats) (in module smftools.tools.spatial_autocorrelation) binary_layers_to_ohe() (in module smftools.preprocessing.binary_layers_to_ohe) block_channels (smftools.analysis.compute.ml_cnn.CNNConfig attribute) bootstrap_periodicity() (in module smftools.tools.spatial_autocorrelation) build_barcode_index() (in module smftools.analysis.compute.read_cache) build_barcode_sidecar_from_split_bams() (in module smftools.informatics.bam_functions) build_binary_classifier() (in module smftools.analysis.compute.ml_metrics) build_classified_read_set() (in module smftools.informatics.bam_functions) build_cnn_baseline() (in module smftools.analysis.compute.ml_cnn) build_cnn_input() (in module smftools.analysis.compute.ml_cnn) build_cnn_model() (in module smftools.analysis.compute.ml_cnn) build_leave_one_group_out_splits() (in module smftools.analysis.compute.ml_splits) build_obs_mask() (in module smftools.analysis.filters.obs_filters) build_position_mask() (in module smftools.analysis.filters.position_filters) build_sequence_one_hot_and_mask() (in module smftools.tools.tensor_factorization) build_spine() (in module smftools.informatics.partition_store) C cache_dir() (in module smftools.analysis.compute.read_cache) cache_key() (in module smftools.analysis.compute.read_cache) cache_mode (smftools.informatics.storage_planner.ReferencePlan attribute) calculate_complexity_II() (in module smftools.preprocessing) calculate_consensus() (in module smftools.preprocessing.calculate_consensus) calculate_coverage() (in module smftools.preprocessing) calculate_knn() (in module smftools.tools) calculate_leiden() (in module smftools.tools) calculate_nmf() (in module smftools.tools) calculate_pairwise_differences() (in module smftools.preprocessing.calculate_pairwise_differences) calculate_pairwise_hamming_distances() (in module smftools.preprocessing.calculate_pairwise_hamming_distances) calculate_pca() (in module smftools.tools) calculate_position_Youden() (in module smftools.preprocessing) calculate_read_length_stats() (in module smftools.preprocessing) calculate_read_modification_stats() (in module smftools.preprocessing) calculate_relative_risk_on_activity() (in module smftools.tools.position_stats) calculate_row_entropy() (in module smftools.tools.read_stats) calculate_sequence_cp_decomposition() (in module smftools.tools.tensor_factorization) calculate_umap() (in module smftools.tools) canoncall() (in module smftools.informatics.basecalling) cigar_max_indel_runs() (in module smftools.informatics.ragged_store) cigar_query_length() (in module smftools.informatics.ragged_store) cigar_reference_length() (in module smftools.informatics.ragged_store) classify_position() (in module smftools.analysis.compute.ep_classification) clean_barplot() (in module smftools.plotting.plotting_utils) clean_NaN() (in module smftools.preprocessing) cluster_adata_on_methylation() (in module smftools.tools) cluster_from_pca() (in module smftools.analysis.compute.dimensionality_reduction) cnn_config_from_dict() (in module smftools.analysis.compute.ml_cnn) cnn_config_to_dict() (in module smftools.analysis.compute.ml_cnn) CNNConfig (class in smftools.analysis.compute.ml_cnn) combine_layers() (in module smftools.tools.general_tools) combined_hmm_length_clustermap() (in module smftools.plotting.general_plotting) (in module smftools.plotting.hmm_plotting) combined_hmm_raw_clustermap() (in module smftools.plotting.general_plotting) (in module smftools.plotting.hmm_plotting) combined_raw_clustermap() (in module smftools.plotting.general_plotting) (in module smftools.plotting.spatial_plotting) complement_base_list() (in module smftools.informatics.complement_base_list) compute_positionwise_statistics() (in module smftools.tools.position_stats) compute_replicate_curve() (in module smftools.analysis.compute.autocorrelation) compute_single_molecule_periodicity() (in module smftools.analysis.compute.autocorrelation) compute_single_molecule_periodicity_direct() (in module smftools.analysis.compute.autocorrelation) concatenate_fastqs_to_bam() (in module smftools.informatics.bam_functions) config (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) consolidate() (in module smftools.analysis.compute.metrics_store) converted_BAM_to_adata() (in module smftools.informatics) count_aligned_reads() (in module smftools.informatics.bam_functions) coverage_filter() (in module smftools.analysis.compute.dimensionality_reduction) create_nan_mask_from_X() (in module smftools.tools.general_tools) create_nan_or_non_gpc_mask() (in module smftools.tools.general_tools) D dCas9_kinetics() (in module smftools.datasets.datasets) decode_int_sequence() (in module smftools.informatics.sequence_encoding) default_cnn_config() (in module smftools.analysis.compute.ml_cnn) demux_and_index_BAM() (in module smftools.informatics.bam_functions) derive_bm_from_bi_to_sidecar() (in module smftools.informatics.bam_functions) derive_umi_orientation_tags_from_aligned_bam() (in module smftools.informatics.bam_functions) detect_torch_device() (in module smftools.analysis.compute.ml_cnn) device (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) dilations (smftools.analysis.compute.ml_cnn.CNNConfig attribute) dropout (smftools.analysis.compute.ml_cnn.CNNConfig attribute) E encode_sequence_to_int() (in module smftools.informatics.sequence_encoding) estimate_snr() (in module smftools.tools.spatial_autocorrelation) estimated_dense_bytes (smftools.informatics.storage_planner.ReferencePlan attribute) evaluate_binary_classifier() (in module smftools.analysis.compute.ml_metrics) event (smftools.tools.sequence_alignment.AlignmentMismatch attribute) execute_hmm_task() (in module smftools.tools.partitioned_hmm) execute_partitioned_hmm() (in module smftools.tools.partitioned_hmm) execute_partitioned_preprocessing() (in module smftools.preprocessing.partitioned_executor) execute_partitioned_spatial() (in module smftools.tools.partitioned_spatial) execute_preprocess_task() (in module smftools.preprocessing.partitioned_executor) execute_spatial_task() (in module smftools.tools.partitioned_spatial) expand_bi_tag_columns() (in module smftools.informatics.h5ad_functions) extract_and_assign_barcodes_in_bam() (in module smftools.informatics.bam_functions) extract_base_identities() (in module smftools.informatics.bam_functions) extract_intervals_from_row() (in module smftools.analysis.compute.hmm_features) extract_mods() (in module smftools.informatics.modkit_functions) extract_pod5_read_metadata() (in module smftools.informatics.pod5_functions) extract_read_features_from_bam() (in module smftools.informatics.bam_functions) extract_read_lengths_from_bed() (in module smftools.informatics.bed_functions) extract_read_relative_base_identities() (in module smftools.informatics.bam_functions) extract_read_tags_from_bam() (in module smftools.informatics.bam_functions) extract_readnames_from_bam() (in module smftools.informatics.bam_functions) extract_secondary_supplementary_alignment_spans() (in module smftools.informatics.bam_functions) F fast5_to_pod5() (in module smftools.informatics.pod5_functions) filter_adata_by_nan_proportion() (in module smftools.preprocessing) filter_reads_on_cigar_indels() (in module smftools.preprocessing) filter_reads_on_length_quality_mapping() (in module smftools.preprocessing) filter_reads_on_modification_thresholds() (in module smftools.preprocessing) find_conversion_sites() (in module smftools.informatics.fasta_functions) find_peak_in_nrl_band() (in module smftools.tools.spatial_autocorrelation) find_peak_ls() (in module smftools.analysis.compute.ls_periodicity) find_secondary_supplementary_read_names() (in module smftools.informatics.bam_functions) fit_classifier() (in module smftools.analysis.compute.ml_metrics) fit_direct_modality_youden_thresholds() (in module smftools.preprocessing.partitioned_executor) fit_exponential_envelope() (in module smftools.tools.spatial_autocorrelation) fit_simple_cnn() (in module smftools.analysis.compute.ml_cnn) flag_duplicate_reads() (in module smftools.preprocessing) flank_seq (smftools.informatics.bam_functions.UMIExtractionResult attribute) flanking (smftools.informatics.bam_functions.BarcodeKitConfig attribute) (smftools.informatics.bam_functions.UMIKitConfig attribute) FlankingConfig (class in smftools.informatics.bam_functions) forward() (smftools.analysis.compute.ml_cnn.AttentionPooling1d method) (smftools.analysis.compute.ml_cnn.ResidualDilatedBlock1d method) (smftools.analysis.compute.ml_cnn.ResidualDilatedCNN1d method) (smftools.analysis.compute.ml_cnn.SqueezeExcite1d method) forward_features() (smftools.analysis.compute.ml_cnn.ResidualDilatedCNN1d method) fwhm_freq_to_bp() (in module smftools.tools.spatial_autocorrelation) fwhm_ls() (in module smftools.analysis.compute.ls_periodicity) G gaussian_fit_plot() (in module smftools.analysis.plot.histograms) generate_converted_FASTA() (in module smftools.informatics.fasta_functions) get_chromosome_lengths() (in module smftools.informatics.fasta_functions) get_native_references() (in module smftools.informatics.fasta_functions) group_path (smftools.informatics.partition_store.PartitionInfo attribute) H hidden_dim (smftools.analysis.compute.ml_cnn.CNNConfig attribute) I import_HERE() (in module smftools.datasets.datasets) in_channels (smftools.analysis.compute.ml_cnn.CNNConfig attribute) include_design_mask (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) include_positional (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) include_spacing (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) index_fasta() (in module smftools.informatics.fasta_functions) invert_adata() (in module smftools.preprocessing) is_cached() (in module smftools.analysis.compute.read_cache) iter_cigar_aligned_pairs() (in module smftools.informatics.ragged_store) iter_pod5_signals() (in module smftools.informatics.pod5_functions) iter_reference_tiles() (in module smftools.informatics.storage_planner) K kernel_size (smftools.analysis.compute.ml_cnn.CNNConfig attribute) Kissiov_and_McKenna_2025() (in module smftools.datasets.datasets) L label_deaminase_pcr_chimeras() (in module smftools.preprocessing) left_ref_end (smftools.informatics.bam_functions.PerEndFlankingConfig attribute) length (smftools.informatics.bam_functions.UMIKitConfig attribute) load_barcode_index() (in module smftools.analysis.compute.read_cache) load_barcode_references_from_yaml() (in module smftools.informatics.bam_functions) load_layer() (in module smftools.analysis.compute.read_cache) load_obs_metadata() (in module smftools.analysis.compute.read_cache) load_sample_sheet() (in module smftools.preprocessing) load_spine() (in module smftools.informatics.partition_read) load_umi_config_from_yaml() (in module smftools.informatics.bam_functions) load_var_info() (in module smftools.analysis.compute.read_cache) load_zarr_layer() (in module smftools.analysis.compute.read_cache) load_zarr_obs() (in module smftools.analysis.compute.read_cache) load_zarr_var() (in module smftools.analysis.compute.read_cache) load_zarr_var_fast() (in module smftools.analysis.compute.read_cache) ls_periodogram_from_autocorr() (in module smftools.analysis.compute.ls_periodicity) ls_periodogram_from_signal() (in module smftools.analysis.compute.ls_periodicity) M make_dirs() (in module smftools.preprocessing.make_dirs) make_features_acf() (in module smftools.analysis.compute.dimensionality_reduction) make_features_raw() (in module smftools.analysis.compute.dimensionality_reduction) make_metrics_row() (in module smftools.analysis.compute.ml_metrics) make_modbed() (in module smftools.informatics.modkit_functions) make_row_colors() (in module smftools.plotting.plotting_utils) make_ticks() (in module smftools.analysis.compute.pearson) materialize() (in module smftools.informatics.partition_read) materialize_ragged() (in module smftools.informatics.ragged_store) max_cigar_deletion() (in module smftools.analysis.filters.obs_filters) methylation_fraction() (in module smftools.plotting.plotting_utils) min_non_diagonal() (in module smftools.preprocessing.min_non_diagonal) modcall() (in module smftools.informatics.basecalling) model (smftools.analysis.compute.ml_cnn.TrainedCNNModel attribute) modkit_extract_to_adata() (in module smftools.informatics) modQC() (in module smftools.informatics.modkit_functions) module smftools.analysis.compute.autocorrelation smftools.analysis.compute.dimensionality_reduction smftools.analysis.compute.ep_classification smftools.analysis.compute.hmm_features smftools.analysis.compute.ls_periodicity smftools.analysis.compute.metrics_store smftools.analysis.compute.ml_cnn smftools.analysis.compute.ml_metrics smftools.analysis.compute.ml_splits smftools.analysis.compute.pearson smftools.analysis.compute.read_cache smftools.analysis.config.hmm_histogram smftools.analysis.filters.obs_filters smftools.analysis.filters.position_filters smftools.analysis.plot.autocorr smftools.analysis.plot.embeddings smftools.analysis.plot.heatmaps smftools.analysis.plot.histograms smftools.analysis.plot.locus smftools.analysis.plot.ml smftools.datasets smftools.datasets.datasets smftools.informatics smftools.informatics.bam_functions smftools.informatics.basecalling smftools.informatics.bed_functions smftools.informatics.binarize_converted_base_identities smftools.informatics.complement_base_list smftools.informatics.fasta_functions smftools.informatics.fastq_export smftools.informatics.h5ad_functions smftools.informatics.modkit_functions smftools.informatics.ohe smftools.informatics.partition_read smftools.informatics.partition_store smftools.informatics.pod5_functions smftools.informatics.ragged_store smftools.informatics.raw_store smftools.informatics.reference_identity smftools.informatics.sequence_encoding smftools.informatics.sidecar_manifest smftools.informatics.signal_features smftools.informatics.storage_planner smftools.plotting smftools.plotting.autocorrelation_plotting smftools.plotting.chimeric_plotting smftools.plotting.classifiers smftools.plotting.general_plotting smftools.plotting.hmm_plotting smftools.plotting.latent_plotting smftools.plotting.plotting_utils smftools.plotting.pod5_plotting smftools.plotting.position_stats smftools.plotting.preprocess_plotting smftools.plotting.qc_plotting smftools.plotting.spatial_plotting smftools.plotting.umi_plotting smftools.plotting.variant_plotting smftools.preprocessing smftools.preprocessing.binarize smftools.preprocessing.binary_layers_to_ohe smftools.preprocessing.calculate_consensus smftools.preprocessing.calculate_pairwise_differences smftools.preprocessing.calculate_pairwise_hamming_distances smftools.preprocessing.make_dirs smftools.preprocessing.min_non_diagonal smftools.preprocessing.partitioned_executor smftools.preprocessing.recipes smftools.preprocessing.umi_bipartite_analysis smftools.tools smftools.tools.general_tools smftools.tools.partitioned_hmm smftools.tools.partitioned_spatial smftools.tools.position_stats smftools.tools.read_stats smftools.tools.rolling_nn_distance smftools.tools.sequence_alignment smftools.tools.spatial_autocorrelation smftools.tools.tensor_factorization move_table_to_base_ranges() (in module smftools.informatics.signal_features) N n_positions (smftools.informatics.partition_store.PartitionInfo attribute) n_reads (smftools.informatics.partition_store.PartitionInfo attribute) (smftools.informatics.storage_planner.ReferencePlan attribute) name (smftools.informatics.bam_functions.BarcodeKitConfig attribute) nan_pearson_matrix() (in module smftools.analysis.compute.pearson) normalize_pr_auc() (in module smftools.analysis.compute.ml_metrics) normalized_mean() (in module smftools.plotting.plotting_utils) O ohe_batching() (in module smftools.informatics.ohe) ohe_layers_decode() (in module smftools.informatics.ohe) one_hot_decode() (in module smftools.informatics.ohe) one_hot_encode() (in module smftools.informatics.ohe) open_metrics_store() (in module smftools.analysis.compute.metrics_store) open_or_create() (in module smftools.analysis.compute.metrics_store) open_zarr_cache() (in module smftools.analysis.compute.read_cache) P parse_cigar() (in module smftools.informatics.ragged_store) partition_id (smftools.informatics.partition_store.PartitionInfo attribute) PartitionInfo (class in smftools.informatics.partition_store) PerEndFlankingConfig (class in smftools.informatics.bam_functions) phred_to_fastq_quality_string() (in module smftools.informatics.sequence_encoding) plan_references() (in module smftools.informatics.storage_planner) plot_autocorr_overlay() (in module smftools.analysis.plot.autocorr) plot_bar_relative_risk() (in module smftools.plotting.position_stats) plot_cluster_composition_barplot() (in module smftools.analysis.plot.embeddings) plot_cluster_proportion_grouped_barplot() (in module smftools.analysis.plot.embeddings) plot_cp_sequence_components() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_delta_hamming_summary() (in module smftools.plotting.chimeric_plotting) plot_embedding() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_embedding_density_grid() (in module smftools.analysis.plot.embeddings) plot_embedding_grid() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_embedding_scatter() (in module smftools.analysis.plot.embeddings) plot_explained_variance() (in module smftools.analysis.plot.embeddings) plot_feature_importances_or_saliency() (in module smftools.plotting.classifiers) plot_hamming_span_trio() (in module smftools.plotting.chimeric_plotting) plot_hmm_layers_rolling_by_sample_ref() (in module smftools.plotting.general_plotting) (in module smftools.plotting.hmm_plotting) plot_hmm_size_contours() (in module smftools.plotting.hmm_plotting) plot_interval_histogram() (in module smftools.analysis.plot.histograms) plot_ls_overlay() (in module smftools.analysis.plot.autocorr) plot_metric_barplot() (in module smftools.analysis.plot.ml) plot_metric_barplot_paired() (in module smftools.analysis.plot.autocorr) plot_metric_histogram() (in module smftools.analysis.plot.autocorr) plot_mismatch_base_frequency_by_position() (in module smftools.plotting.variant_plotting) plot_model_curves_from_adata() (in module smftools.plotting.classifiers) plot_model_curves_from_adata_with_frequency_grid() (in module smftools.plotting.classifiers) plot_model_performance() (in module smftools.plotting.classifiers) plot_nmf_components() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_pca() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_pca_components() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_pca_explained_variance() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_pca_grid() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_pearson_heatmap() (in module smftools.analysis.plot.heatmaps) plot_positionwise_matrices() (in module smftools.tools.position_stats) plot_positionwise_matrix() (in module smftools.plotting.position_stats) plot_positionwise_matrix_grid() (in module smftools.plotting.position_stats) plot_pr_curve() (in module smftools.analysis.plot.ml) plot_read_current_traces() (in module smftools.plotting.pod5_plotting) plot_read_qc_histograms() (in module smftools.plotting.qc_plotting) plot_read_span_quality_clustermaps() (in module smftools.plotting.general_plotting) (in module smftools.plotting.preprocess_plotting) plot_reference_barcode_chimera_rate() (in module smftools.plotting.qc_plotting) plot_roc_curve() (in module smftools.analysis.plot.ml) plot_roc_pr_pair() (in module smftools.analysis.plot.ml) plot_rolling_grid() (in module smftools.plotting.autocorrelation_plotting) plot_rolling_metrics() (in module smftools.plotting.autocorrelation_plotting) plot_rolling_nn_and_layer() (in module smftools.plotting.chimeric_plotting) (in module smftools.plotting.general_plotting) (in module smftools.plotting.spatial_plotting) plot_rolling_nn_and_two_layers() (in module smftools.plotting.chimeric_plotting) (in module smftools.plotting.general_plotting) plot_segment_length_histogram() (in module smftools.plotting.chimeric_plotting) (in module smftools.plotting.general_plotting) plot_sequence_integer_encoding_clustermaps() (in module smftools.plotting.general_plotting) (in module smftools.plotting.variant_plotting) plot_sm_periodogram_overlay() (in module smftools.analysis.plot.autocorr) plot_span_length_distributions() (in module smftools.plotting.chimeric_plotting) plot_spatial_autocorr_grid() (in module smftools.plotting.autocorrelation_plotting) plot_umap() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_umap_grid() (in module smftools.plotting.general_plotting) (in module smftools.plotting.latent_plotting) plot_umi_bipartite_summary() (in module smftools.plotting.umi_plotting) plot_variant_segment_clustermaps() (in module smftools.plotting.variant_plotting) plot_variant_segment_clustermaps_multi_obs() (in module smftools.plotting.variant_plotting) plot_volcano_relative_risk() (in module smftools.plotting.position_stats) plot_zero_hamming_pair_counts() (in module smftools.plotting.chimeric_plotting) (in module smftools.plotting.general_plotting) (in module smftools.plotting.spatial_plotting) plot_zero_hamming_span_and_layer() (in module smftools.plotting.chimeric_plotting) (in module smftools.plotting.general_plotting) (in module smftools.plotting.spatial_plotting) predict_binary_scores() (in module smftools.analysis.compute.ml_metrics) predict_cnn_scores() (in module smftools.analysis.compute.ml_cnn) preprocess_umi_annotations() (in module smftools.preprocessing) psd_from_autocorr() (in module smftools.analysis.compute.ls_periodicity) (in module smftools.tools.spatial_autocorrelation) R random_fill_nans() (in module smftools.tools.position_stats) (in module smftools.tools.read_stats) (in module smftools.tools.spatial_autocorrelation) read_catalog() (in module smftools.informatics.partition_read) read_ids (smftools.informatics.partition_store.PartitionInfo attribute) read_ragged_parquet() (in module smftools.informatics.ragged_store) read_signal_features() (in module smftools.informatics.signal_features) read_signal_trace() (in module smftools.informatics.signal_features) recipe_1_Kissiov_and_McKenna_2025() (in module smftools.preprocessing.recipes) recipe_2_Kissiov_and_McKenna_2025() (in module smftools.preprocessing.recipes) reduce_duplicate_reads() (in module smftools.preprocessing.partitioned_executor) reduce_partial_coverage() (in module smftools.preprocessing.partitioned_executor) reduce_read_modification_stats() (in module smftools.preprocessing.partitioned_executor) reference (smftools.informatics.partition_store.PartitionInfo attribute) (smftools.informatics.storage_planner.ReferencePlan attribute) reference_length (smftools.informatics.storage_planner.ReferencePlan attribute) reference_uid() (in module smftools.informatics.reference_identity) ReferencePlan (class in smftools.informatics.storage_planner) register_sidecar() (in module smftools.informatics.sidecar_manifest) reindex_references_adata() (in module smftools.preprocessing) relative_uns_path() (in module smftools.informatics.partition_read) ResidualDilatedBlock1d (class in smftools.analysis.compute.ml_cnn) ResidualDilatedCNN1d (class in smftools.analysis.compute.ml_cnn) resolve_barcode_config() (in module smftools.informatics.bam_functions) resolve_barcode_str() (in module smftools.analysis.compute.read_cache) resolve_relative_path() (in module smftools.informatics.partition_read) resolve_sidecar() (in module smftools.informatics.sidecar_manifest) resolve_umi_config() (in module smftools.informatics.bam_functions) right_ref_end (smftools.informatics.bam_functions.PerEndFlankingConfig attribute) rolling_autocorr_metrics() (in module smftools.tools.spatial_autocorrelation) rolling_mean_nan() (in module smftools.analysis.compute.ls_periodicity) rolling_smooth() (in module smftools.analysis.plot.autocorr) rolling_window_nn_distance() (in module smftools.tools.rolling_nn_distance) run_multiqc() (in module smftools.informatics) run_pipeline() (in module smftools.analysis.compute.dimensionality_reduction) S same_orientation (smftools.informatics.bam_functions.PerEndFlankingConfig attribute) (smftools.informatics.bam_functions.UMIKitConfig attribute) sample (smftools.informatics.partition_store.PartitionInfo attribute) sample_autocorr_at_harmonics() (in module smftools.tools.spatial_autocorrelation) segments_to_per_read_dataframe() (in module smftools.tools.rolling_nn_distance) select_top_segments_per_read() (in module smftools.tools.rolling_nn_distance) separate_bam_by_bc() (in module smftools.informatics.bam_functions) seq1_base (smftools.tools.sequence_alignment.AlignmentMismatch attribute) seq1_pos (smftools.tools.sequence_alignment.AlignmentMismatch attribute) seq2_base (smftools.tools.sequence_alignment.AlignmentMismatch attribute) seq2_pos (smftools.tools.sequence_alignment.AlignmentMismatch attribute) sidecar_manifest_path() (in module smftools.informatics.sidecar_manifest) slot (smftools.informatics.bam_functions.UMIExtractionResult attribute) smftools.analysis.compute.autocorrelation module smftools.analysis.compute.dimensionality_reduction module smftools.analysis.compute.ep_classification module smftools.analysis.compute.hmm_features module smftools.analysis.compute.ls_periodicity module smftools.analysis.compute.metrics_store module smftools.analysis.compute.ml_cnn module smftools.analysis.compute.ml_metrics module smftools.analysis.compute.ml_splits module smftools.analysis.compute.pearson module smftools.analysis.compute.read_cache module smftools.analysis.config.hmm_histogram module smftools.analysis.filters.obs_filters module smftools.analysis.filters.position_filters module smftools.analysis.plot.autocorr module smftools.analysis.plot.embeddings module smftools.analysis.plot.heatmaps module smftools.analysis.plot.histograms module smftools.analysis.plot.locus module smftools.analysis.plot.ml module smftools.datasets module smftools.datasets.datasets module smftools.informatics module smftools.informatics.bam_functions module smftools.informatics.basecalling module smftools.informatics.bed_functions module smftools.informatics.binarize_converted_base_identities module smftools.informatics.complement_base_list module smftools.informatics.fasta_functions module smftools.informatics.fastq_export module smftools.informatics.h5ad_functions module smftools.informatics.modkit_functions module smftools.informatics.ohe module smftools.informatics.partition_read module smftools.informatics.partition_store module smftools.informatics.pod5_functions module smftools.informatics.ragged_store module smftools.informatics.raw_store module smftools.informatics.reference_identity module smftools.informatics.sequence_encoding module smftools.informatics.sidecar_manifest module smftools.informatics.signal_features module smftools.informatics.storage_planner module smftools.plotting module smftools.plotting.autocorrelation_plotting module smftools.plotting.chimeric_plotting module smftools.plotting.classifiers module smftools.plotting.general_plotting module smftools.plotting.hmm_plotting module smftools.plotting.latent_plotting module smftools.plotting.plotting_utils module smftools.plotting.pod5_plotting module smftools.plotting.position_stats module smftools.plotting.preprocess_plotting module smftools.plotting.qc_plotting module smftools.plotting.spatial_plotting module smftools.plotting.umi_plotting module smftools.plotting.variant_plotting module smftools.preprocessing module smftools.preprocessing.binarize module smftools.preprocessing.binary_layers_to_ohe module smftools.preprocessing.calculate_consensus module smftools.preprocessing.calculate_pairwise_differences module smftools.preprocessing.calculate_pairwise_hamming_distances module smftools.preprocessing.make_dirs module smftools.preprocessing.min_non_diagonal module smftools.preprocessing.partitioned_executor module smftools.preprocessing.recipes module smftools.preprocessing.umi_bipartite_analysis module smftools.tools module smftools.tools.general_tools module smftools.tools.partitioned_hmm module smftools.tools.partitioned_spatial module smftools.tools.position_stats module smftools.tools.read_stats module smftools.tools.rolling_nn_distance module smftools.tools.sequence_alignment module smftools.tools.spatial_autocorrelation module smftools.tools.tensor_factorization module snr_ls() (in module smftools.analysis.compute.ls_periodicity) split_and_index_BAM() (in module smftools.informatics.bam_functions) split_train_validation() (in module smftools.analysis.compute.ml_cnn) SqueezeExcite1d (class in smftools.analysis.compute.ml_cnn) stem_channels (smftools.analysis.compute.ml_cnn.CNNConfig attribute) stem_kernel_size (smftools.analysis.compute.ml_cnn.CNNConfig attribute) strand_switch_metrics() (in module smftools.informatics.ragged_store) subsample_adata() (in module smftools.preprocessing) subsample_fasta_from_bed() (in module smftools.informatics.fasta_functions) subsample_pod5() (in module smftools.informatics.pod5_functions) subsample_pod5_for_basecalling() (in module smftools.informatics.pod5_functions) subsample_split_bams() (in module smftools.informatics.bam_functions) subset_adata() (in module smftools.tools) summarize_split() (in module smftools.analysis.compute.ml_splits) T tile_halo (smftools.informatics.storage_planner.ReferencePlan attribute) tile_size (smftools.informatics.storage_planner.ReferencePlan attribute) to_dict() (smftools.informatics.storage_planner.ReferencePlan method) tqdm_joblib() (in module smftools.tools.position_stats) TrainedCNNModel (class in smftools.analysis.compute.ml_cnn) U umap_from_pca() (in module smftools.analysis.compute.dimensionality_reduction) umi_ends (smftools.informatics.bam_functions.UMIKitConfig attribute) umi_flank_mode (smftools.informatics.bam_functions.UMIKitConfig attribute) umi_seq (smftools.informatics.bam_functions.UMIExtractionResult attribute) UMIExtractionResult (class in smftools.informatics.bam_functions) UMIKitConfig (class in smftools.informatics.bam_functions) use_attention_pool (smftools.analysis.compute.ml_cnn.CNNConfig attribute) use_se (smftools.analysis.compute.ml_cnn.CNNConfig attribute) V validate_disjoint_groups() (in module smftools.analysis.compute.ml_splits) validate_ragged_frame() (in module smftools.informatics.ragged_store) W weighted_mean_autocorr() (in module smftools.analysis.compute.autocorrelation) (in module smftools.tools.spatial_autocorrelation) write_catalog() (in module smftools.informatics.partition_store) write_dense_cache_from_spine() (in module smftools.informatics.partition_store) write_experiment_store() (in module smftools.informatics.partition_store) write_fastq_manifest() (in module smftools.informatics.fastq_export) write_fastq_per_barcode() (in module smftools.informatics.fastq_export) write_obs_array() (in module smftools.analysis.compute.metrics_store) write_obsm_array() (in module smftools.analysis.compute.metrics_store) write_partitioned_store() (in module smftools.informatics.partition_store) write_ragged_parquet() (in module smftools.informatics.ragged_store) write_raw_store() (in module smftools.informatics.raw_store) write_raw_store_streaming() (in module smftools.informatics.raw_store) write_read_qc_sidecar() (in module smftools.preprocessing.partitioned_executor) write_zarr_cache() (in module smftools.analysis.compute.read_cache) Z zarr_cache_exists() (in module smftools.analysis.compute.read_cache) zarr_index_path() (in module smftools.analysis.compute.read_cache) zero_hamming_segments_to_dataframe() (in module smftools.tools.rolling_nn_distance) zero_pairs_to_dataframe() (in module smftools.tools.rolling_nn_distance)