Functions — github.com/COMBINE-lab/alevin-fry

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Functions221 in github.com/COMBINE-lab/alevin-fry

⨍ Functions 221◇ Types & classes 43

↓ 1 callersFunctionem_update_long_read

em tailored for long read dataset

src/em.rs:716

↓ 1 callersFunctionem_update_subset

( alphas_in: &[f32], alphas_out: &mut [f32], eqclasses: &IndexedEqList, cell_data: &[(u32, u32

src/em.rs:116

↓ 1 callersFunctionem_update_subset_usa

( alphas_in: &[f32], alphas_out: &mut [f32], eqclasses: &IndexedEqList, cell_data: &[(u32, u32

src/em.rs:146

↓ 1 callersMethodeq_classes_containing

(&self, r: u32)

src/eq_class.rs:1061

↓ 1 callersFunctionextract_counts_mm_uniform

Extracts UMI counts from the `gene_eqc` HashMap. This function is to be used when we are counting UMIs in USA mode. Multimappers will be uniformly al

src/utils.rs:745

↓ 1 callersFunctionextract_graph

Extracts the parsimonious UMI graphs (PUGs) from the equivalence class map for a given cell. The returned graph is a directed graph (potentially with

src/pugutils.rs:65

↓ 1 callersFunctiongenerate_permit_list

(gpl_opts: GenPermitListOpts)

src/atac/cellfilter.rs:358

↓ 1 callersFunctiongenerate_whitelist_set

( whitelist_bcs: &[u64], bc_length: usize, )

src/utils.rs:999

↓ 1 callersFunctionget_bc_string

(kmerseq: &BitKmerSeq, reverse_barcode: bool, bc_len: u8)

src/atac/utils.rs:9

↓ 1 callersFunctionget_bin_id

(pos: u32, ref_id: usize, size_range: u32, blens: &[u64])

src/atac/utils.rs:3

↓ 1 callersFunctionget_filter_type

(mdata: &serde_json::Value, log: &slog::Logger)

src/collate.rs:217

↓ 1 callersFunctionget_map

()

src/pugutils.rs:290

↓ 1 callersFunctionget_most_ambiguous_record

(mdata: &serde_json::Value, log: &slog::Logger)

src/collate.rs:233

↓ 1 callersFunctionget_num_molecules_cell_ranger_like

( eq_map: &EqMap, tid_to_gid: &[u32], _num_genes: usize, gene_eqclass_hash: &mut HashMap<Vec<u

src/pugutils.rs:799

↓ 1 callersFunctionget_num_molecules_cell_ranger_like_small

( cell_chunk: &mut chunk::Chunk<R>, tid_to_gid: &[u32], _num_genes: usize, gene_eqclass_hash:

src/pugutils.rs:751

↓ 1 callersFunctionget_num_molecules_large_component

given the connected component (subgraph) of `g` defined by the vertices in `vertex_ids`, apply the cell-ranger-like algorithm within this subgraph.

src/pugutils.rs:916

↓ 1 callersFunctionget_num_molecules_trivial_discard_all_ambig

( eq_map: &EqMap, tid_to_gid: &[u32], num_genes: usize, _log: &slog::Logger, )

src/pugutils.rs:852

↓ 1 callersFunctionget_sample_names

Get sample names for canonical barcodes. Uses names from the barcode file, falling back to hex-encoded canonical barcode.

src/cellfilter.rs:1267

↓ 1 callersFunctioninfer

( //num_bootstraps, //init_uniform, //summary_stat, count_mat_file: &PathBuf, eq_label_fil

src/infer.rs:31

↓ 1 callersMethodinit_from_chunk_gene_level

( &mut self, cell_chunk: &mut chunk::Chunk<R>, tid_to_gid: &[u32], )

src/eq_class.rs:723

↓ 1 callersFunctioninitialize_rec_list

Initialize the index map with key being references and position Take the largest reference length (from chromosome) For each chromosome divide into ra

src/atac/cellfilter.rs:38

↓ 1 callersFunctionis_velo_mode

(input_dir: &PathBuf)

src/utils.rs:1080

↓ 1 callersFunctionload_sample_barcode_list

Load sample barcodes from a file. Supports two formats: 1. Simple: one barcode per line (each line is a separate sample) 2. TSV with rotation mapping

src/cellfilter.rs:1085

↓ 1 callersFunctionload_unfiltered_barcodes

Load and validate unfiltered barcode list if provided

src/cellfilter.rs:1505

↓ 1 callersFunctionlog_parsing_stats

Log parsing statistics

src/cellfilter.rs:1898

↓ 1 callersFunctionlog_rad_header_info

Log information about the RAD file header

src/cellfilter.rs:1561

↓ 1 callersFunctionmake_multi_bc_prelude

Build a multi-barcode RadPrelude and TagMap for test RAD files.

tests/multi_barcode_integration.rs:43

↓ 1 callersFunctionmean

(data: &[f64])

src/em.rs:44

↓ 1 callersFunctionparse_chunks_filtered

Parse chunks with filtered barcode tracking

src/cellfilter.rs:1833

↓ 1 callersFunctionparse_chunks_unfiltered

Parse chunks with unfiltered barcode tracking

src/cellfilter.rs:1762

↓ 1 callersFunctionparse_tg_map

( tg_map: &PathBuf, ref_count: usize, rname_to_id: &HashMap<String, u32, ahash::RandomState>,

src/utils.rs:603

↓ 1 callersFunctionparse_tg_spliced

( rdr: &mut csv::Reader<File>, ref_count: usize, rname_to_id: &HashMap<String, u32, ahash::RandomS

src/utils.rs:539

↓ 1 callersFunctionparse_tg_spliced_unspliced

Parse a 3 column tsv of the format transcript_name gene_name status where status is one of S or U each gene will be allocated both a spliced and uns

src/utils.rs:470

↓ 1 callersFunctionpopulate_unfiltered_barcode_map

( br: BufReader<T>, first_bclen: &mut usize, rev_bc: bool, )

src/atac/cellfilter.rs:104

↓ 1 callersMethodprobs

(&self)

src/utils.rs:107

↓ 1 callersFunctionprocess_filtered

( hm: DashMap<u64, u64, ahash::RandomState>, file_tag_map: &rad_types::TagMap, filter_meth: &CellF

src/cellfilter.rs:336

↓ 1 callersFunctionprocess_filtered_workflow

Process filtered barcode workflow

src/cellfilter.rs:1706

↓ 1 callersFunctionprocess_unfiltered

( hm: DashMap<u64, u64, ahash::RandomState>, mut unmatched_bc: Vec<u64>, file_tag_map: &rad_types:

src/cellfilter.rs:105

↓ 1 callersFunctionprocess_unfiltered

( hm: ParBCMap, mut unmatched_bc: Vec<u64>, file_tag_map: &rad_types::TagMap, filter_meth: &Ce

src/atac/cellfilter.rs:142

↓ 1 callersFunctionprocess_unfiltered_workflow

Process unfiltered barcode workflow

src/cellfilter.rs:1643

↓ 1 callersMethodrecord_cell

Record bootstrap results for one cell. Computes mean and variance across replicates and stores nonzero entries as sparse triplets.

src/quant.rs:158

↓ 1 callersMethodrecord_cell_from_replicates

Compute mean and variance from full bootstrap replicates for one cell.

src/quant.rs:184

↓ 1 callersFunctionrun

(opts: &ArgMatches, version: &str, cmdline: &str, log: &Logger)

src/atac/run.rs:12

↓ 1 callersFunctionrun_bootstrap

( eqclasses: &HashMap<Vec<u32>, P, ahash::RandomState>, num_bootstraps: u32, gene_alpha: &[f32],

src/em.rs:523

↓ 1 callersFunctionrun_bootstrap_subset

( eqclasses: &IndexedEqList, cell_data: &[(u32, u32)], // (eq_id, count) vec for classes relevant for

src/em.rs:427

↓ 1 callersMethodsample_u32

(&mut self, rnd: &mut R)

src/multinomial.rs:41

↓ 1 callersFunctionsort

( input_dir: P1, rad_dir: P2, num_threads: u32, max_records: u32, compress_out: bool,

src/atac/sort.rs:169

↓ 1 callersFunctionsort_temp_bucket

( reader: &mut BufReader<T>, bct: &rad_types::RadIntId, barcode_len: u16, rc: bool, ref_na

src/atac/sort.rs:101

↓ 1 callersFunctionsort_with_temp

( input_dir: P1, rad_dir: P2, num_threads: u32, max_records: u32, bin_recs: Vec<u64>,

src/atac/sort.rs:286

↓ 1 callersFunctionspliced_of

(gid: u32)

src/utils.rs:385

↓ 1 callersFunctionunspliced_of

(gid: u32)

src/utils.rs:379

↓ 1 callersFunctionupdate_barcode_hist

( hist: &DashMap<u64, u64, ahash::RandomState>, max_ambiguity_read: &mut usize, chunk: &chunk::Chu

src/cellfilter.rs:1372

↓ 1 callersFunctionupdate_barcode_hist_unfiltered

update teh counts in the barcode histogram for those reads matching the prescribed orientation.

src/cellfilter.rs:1283

↓ 1 callersFunctionupdate_barcode_hist_unfiltered

( hist: &ParBCMap, unmatched_bc: &mut Vec<u64>, max_ambiguity_read: &mut usize, chunk: &chunk:

src/atac/cellfilter.rs:67

↓ 1 callersFunctionvalidate_chunks

Validate that chunks are present in the RAD file

src/cellfilter.rs:1620

↓ 1 callersFunctionvalidate_tag_types

Validate that barcode and UMI tags are present and of correct type

src/cellfilter.rs:1587

↓ 1 callersFunctionvelo_quantify

TODO: see if we'd rather pass an structure with these options

src/quant.rs:1972

↓ 1 callersFunctionview

(rad_file: P, print_header: bool, log: &slog::Logger)

src/convert.rs:596

↓ 1 callersFunctionview2

(rad_file: P, print_header: bool, log: &slog::Logger)

src/convert.rs:602

↓ 1 callersFunctionweakly_connected_components

Extract the weakly connected components from the directed graph G. Interestingly, `petgraph` has a builtin algorithm for returning the strongly-conne

src/pugutils.rs:278

↓ 1 callersFunctionwrite_bed

( bd_writer_lock: &Arc<Mutex<File>>, hit_info_vec: &[HitInfo], ref_names: &[String], rev: bool

src/atac/deduplicate.rs:17

↓ 1 callersFunctionwrite_eqc_counts

( eqid_map_lock: &Arc<Mutex<EqcMap>>, num_genes: usize, usa_mode: bool, output_path: &std::pat

src/quant.rs:228

↓ 1 callersFunctionwrite_sample_bc_list

Write a sample barcode list file (one nucleotide sequence per line).

tests/multi_barcode_integration.rs:205

Methoddefault

()

src/eq_class.rs:309

Functiondo_collate_with_temp

( input_dir: P1, rad_dir: P2, rec_context: <R as MappedRecord>::ParsingContext, prelude: RadPr

src/collate.rs:396

Functiondo_generate_permit_list

Main entry point - now much cleaner

src/cellfilter.rs:1454

Functiondo_quantify

( mut br: T, quant_opts: QuantOpts, prelude: RadPrelude, file_tag_map: TagMap, sample_bc_e

src/quant.rs:1287

Methodfmt

(&self, f: &mut fmt::Formatter<'_>)

src/utils.rs:1117

Methodfmt

(&self, f: &mut fmt::Formatter<'_>)

Functiongen_random_kmer

(k: usize)

src/main.rs:35

Functionget_bed_string

( hit_info_vec: &[HitInfo], ref_names: &[String], bc_len: u16, rev: bool, )

Functionget_num_molecules

Given the digraph `g` representing the PUGs within the current cell, the EqMap `eqmap` to decode all equivalence classes and the transcript-to-gene ma

src/pugutils.rs:989

Functionget_random_nucl

Methodinit_from_eqc_file

Loads the `IndexedEqList` from a gzip compressed file

src/eq_class.rs:249

Methodinit_from_hash

Creates an `IndexedEqList` from a HashMap of eq labels to counts

src/eq_class.rs:215

Methodinit_from_small_chunk

(&mut self, cell_chunk: &mut chunk::Chunk<R>)

( _output_path: &std::path::Path, num_bootstraps: u32, summary_stat: bool, )

src/quant.rs:136

Methodnew

(w: I, n: usize)

src/multinomial.rs:16

Methodnew_from_count

(_eqc_len: usize, ct: u32)

src/utils.rs:88

Methodnew_from_count_and_probs

(_eqc_len: usize, _ct: u32, _probs: &[f64])

Methodnum_umis_for_eq

(&self, eq_id: usize)

src/eq_class.rs:404

Methodpartial_cmp

(&self, other: &Self)

src/atac/sort.rs:59

Functionpathbuf_directory_exists_validator

Checks if the path pointed to by v exists and is a valid directory on disk. If there is any issue with permissions or failure to properly resolve sym

src/cmd_parse_utils.rs:73

Functionpathbuf_file_exists_validator

Checks if the path pointed to by v exists. It can be any valid entity (e.g. disk file, FIFO, directory, etc.). If there is any issue with permissions

src/cmd_parse_utils.rs:57

Functionprob_map_access

()

src/eq_class.rs:1126

Functionprob_map_oob_panics

()

src/utils.rs:1243

Functionprob_map_works

Functionquantify_small_cell_sparse

Sparse fast path for quantifying small cells without any HashMap or dense vector overhead. Implements the same cr-like (winner-take-all) UMI resoluti

src/quant.rs:453

Functionrun_worker_thread

( _worker_num: usize, config: WorkerConfig, shared: WorkerSharedState<R>, log: slog::Logger,

src/quant.rs:643

Methodsample_u64

(&mut self, rnd: &mut R)

src/multinomial.rs:32

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