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

hub / github.com/COMBINE-lab/alevin-fry / functions

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

⨍ Functions 221◇ Types & classes 43

↓ 224 callersMethodlen

(&self)

src/eq_class.rs:545

↓ 178 callersMethodpush

(&mut self, eq_id: u32, probs: &[T])

src/eq_class.rs:539

↓ 40 callersMethodclear

(&mut self)

src/eq_class.rs:207

↓ 25 callersMethodis_empty

(&self)

src/eq_class.rs:392

↓ 22 callersMethodinc

(&mut self)

src/utils.rs:102

↓ 19 callersMethodrefs_for_eqc

Returns a slice of gene IDs corresponding to the label for equivalence class `idx`.

src/eq_class.rs:302

↓ 18 callersMethodnext

(&mut self)

src/eq_class.rs:463

↓ 15 callersFunctionis_spliced

(gid: u32)

src/utils.rs:402

↓ 12 callersMethodcount

(&self)

src/utils.rs:97

↓ 8 callersMethodcmp

(&self, other: &Self)

src/atac/sort.rs:46

↓ 8 callersMethodmark_umi_end

(&mut self)

src/eq_class.rs:396

↓ 8 callersFunctionsame_gene

(g1: u32, g2: u32, with_unspliced: bool)

src/utils.rs:397

↓ 7 callersMethodprobs_for_eq_id_umi_rank

(&self, eq_id: usize, umi_rank: usize)

src/eq_class.rs:414

↓ 6 callersFunctionget_bit_mask

(nt_index: usize, fill_with: u64)

src/utils.rs:911

↓ 5 callersFunctiongenerate_permit_list

Given the input RAD file `input_file`, compute and output (in `output_dir`) the list of valid (i.e. "permitted") barcode values, as well as a map from

src/cellfilter.rs:487

↓ 5 callersMethodnum_eq_classes

returns the number of equivalence classes represented in this `IndexedEqList`

src/eq_class.rs:181

↓ 5 callersFunctionwrite_permit_list_freq

Write the permit_freq.bin and all_freq.bin files

src/utils.rs:414

↓ 4 callersMethodadd_probs

(&mut self, _p: &[f64])

src/utils.rs:117

↓ 4 callersFunctioncollate

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

src/collate.rs:50

↓ 4 callersFunctionem_optimize_subset

( eqclasses: &IndexedEqList, cell_data: &[(u32, u32)], // indices into eqclasses relevant for this cel

src/em.rs:178

↓ 4 callersFunctiongenerate_permitlist_map

* generates a map that contains all one edit distance neighbors * of the permitted barcodes. The key is the neighbor and the value * is the origina

src/utils.rs:1026

↓ 4 callersFunctionmake_test_logger

()

tests/multi_barcode_integration.rs:236

↓ 4 callersMethodmark_eq_class_end

(&mut self)

src/eq_class.rs:400

↓ 4 callersFunctionquantify

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

src/quant.rs:358

↓ 3 callersFunctioncreate_synthetic_multi_bc_rad_with_shared_cells

Create a synthetic multi-barcode RAD file with optional shared cell barcodes across samples.

tests/multi_barcode_integration.rs:141

↓ 3 callersFunctionextract_counts

Extracts UMI counts from the `gene_eqc` HashMap. This function is to be used when we are counting UMIs in USA mode, and when we do not wish to conside

src/utils.rs:656

↓ 3 callersMethodfill_label_sizes

(&mut self)

src/eq_class.rs:648

↓ 3 callersMethodfill_ref_offsets

(&mut self)

src/eq_class.rs:636

↓ 3 callersFunctionget_all_one_edit_neighbors

( bc: u64, bc_length: usize, neighbors: &mut HashSet<u64>, )

src/utils.rs:983

↓ 3 callersFunctionget_orientation

(mdata: &serde_json::Value)

src/collate.rs:198

↓ 3 callersFunctionget_record_type_from_prelude

( prelude: &RadPrelude, file_tag_map: &TagMap, )

src/utils.rs:296

↓ 3 callersMethodis_compatible_with

(&self, other: &InternalVersionInfo)

src/utils.rs:1103

↓ 3 callersFunctionmake_packed_bc

Simple deterministic barcode generator from an index.

tests/multi_barcode_integration.rs:35

↓ 3 callersMethodorder_by_eq_id

Reorder this probability map's entries by the equivalence class IDs of the underlying map

src/eq_class.rs:555

↓ 3 callersFunctionpermit_list_from_threshold

( hist: &HashMap<u64, u64, ahash::RandomState>, min_freq: u64, )

src/cellfilter.rs:1420

↓ 3 callersMethodprobs_for_eq_umi_tx

Returns the probability row (length = label_len) for a specific graph node (eqid, umi_idx).

src/eq_class.rs:1039

↓ 3 callersFunctionremove_file_if_exists

(fname: &Path)

src/utils.rs:362

↓ 3 callersFunctionreorder_in_place

Reorder a vector in-place using the given permutation indices. This is more memory-efficient but modifies the original vector. Time: O(n), Space: O(n)

src/eq_class.rs:107

↓ 3 callersFunctionresolve_num_molecules_crlike_from_vec

( umi_gene_count_vec: &mut [(u64, u32, u32)], gene_eqclass_hash: &mut HashMap<Vec<u32>, P, ahash::Rand

src/pugutils.rs:644

↓ 3 callersFunctionwrite_bed_string

( writer: &mut W, hit_info_vec: &[HitInfo], ref_names: &[String], bc_len: u16, rev: bool,

src/atac/sort.rs:64

↓ 2 callersFunctioncb_string_to_u64

replace first occurance of 'N' if there are more than one 'N', ignore the string non-random replacement to avoid stochasticity https://github.com/k3ya

src/convert.rs:75

↓ 2 callersFunctioncollate_with_temp

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

src/collate.rs:942

↓ 2 callersFunctioncorrect_unmapped_counts

( correct_map: &Arc<HashMap<u64, u64>>, unmapped_file: &std::path::Path, parent: &std::path::Path,

src/atac/collate.rs:224

↓ 2 callersFunctioncreate_progress_callback

Create callback for progress bar updates

src/cellfilter.rs:1891

↓ 2 callersFunctioncreate_synthetic_multi_bc_rad

Create a synthetic multi-barcode RAD file. Creates `num_samples` samples, each with `cells_per_sample` cells, each with `reads_per_cell` reads. All r

tests/multi_barcode_integration.rs:123

↓ 2 callersFunctiondo_deduplicate

(mut br: T, dedup_opts: DeduplicateOpts)

src/atac/deduplicate.rs:89

↓ 2 callersFunctiondo_quantify_dispatch

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

src/quant.rs:1894

↓ 2 callersFunctionem_optimize

( eqclasses: &HashMap<Vec<u32>, P, ahash::RandomState>, unique_evidence: &mut [bool], no_ambiguity

src/em.rs:330

↓ 2 callersFunctionend_probabilities

(ends: &[u32], tlens: &[u32])

src/eq_class.rs:40

↓ 2 callersMethodeq_class_aln_view_iter

Get an iterator over the alignments for each equivalence class

src/eq_class.rs:582

↓ 2 callersFunctionextract_usa_eqmap

Extracts an `IndexedEqList` and equivalence class ID / count vector from the `gene_eqc` HashMap. This function is used in USA-mode when we wish to res

src/utils.rs:825

↓ 2 callersFunctionget_abundance_for

(idx: u32, alphas_in: &[f32], usa_offset: (usize, usize))

src/em.rs:94

↓ 2 callersFunctionget_all_indels

(bc: u64, bc_length: usize)

src/utils.rs:945

↓ 2 callersFunctionget_all_snps

(bc: u64, bc_length: usize)

src/utils.rs:917

↓ 2 callersFunctionget_filter_type

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

src/atac/collate.rs:181

↓ 2 callersFunctionget_knee

Get the knee of the cure using the `distance` method as described in the [UMI-tools documentation](https://github.com/CGATOxford/UMI-tools). This meth

src/knee_finding.rs:99

↓ 2 callersFunctionget_max_distance_index

This method is a implementation of the distance method used in umi_tools : Smith, Tom, Andreas Heger, and Ian Sudbery. "UMI-tools: modeling sequencing

src/knee_finding.rs:43

↓ 2 callersFunctionget_mode_num_genes

(frydir, quiet=True)

scripts/testing/compare_counts.py:7

↓ 2 callersFunctionget_most_ambiguous_record

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

src/atac/collate.rs:197

↓ 2 callersFunctionget_num_chunks

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

src/atac/collate.rs:212

↓ 2 callersMethodget_probs_for_read_rank

get the probabilities for the read of the associated rank within this equivalence class

src/eq_class.rs:437

↓ 2 callersFunctionget_score

( as_val: Option<Result<noodles::sam::alignment::record::data::field::Value<'_>, std::io::Error>>, )

src/convert.rs:146

↓ 2 callersMethodinit_from_chunk

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

src/eq_class.rs:823

↓ 2 callersFunctionlikely_valid_permit_list

( num_unmatched: usize, total_mapped: usize, thresh: f64, )

src/diagnostics.rs:3

↓ 2 callersMethodnum_reads

the number of reads in this eq class for which we have information

src/eq_class.rs:431

↓ 2 callersFunctionpacked_to_nuc

Convert a 2-bit packed barcode to a nucleotide string.

tests/multi_barcode_integration.rs:245

↓ 2 callersFunctionpermit_list_from_file

(ifile: P, bclen: u16)

src/cellfilter.rs:1431

↓ 2 callersFunctionpopulate_unfiltered_barcode_map

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

src/cellfilter.rs:73

↓ 2 callersFunctionread_filter_list

Reads the contents of the file `flist`, which should contain a single barcode per-line, and returns a Result that is either a HashSet containing the k

src/utils.rs:1057

↓ 2 callersFunctionresolve_num_molecules_crlike_from_vec_prefer_ambig

( umi_gene_count_vec: &mut [(u64, u32, u32)], gene_eqclass_hash: &mut HashMap<Vec<u32>, P, ahash::Rand

src/pugutils.rs:505

↓ 2 callersFunctionscore_probabilities

(scores: &[i32])

src/eq_class.rs:20

↓ 2 callersFunctionspliced_id

(gid: u32)

src/utils.rs:392

↓ 2 callersFunctionwrite_barcode

(barcode_t: &RadType, barcode: u64, w: &mut W)

src/convert.rs:92

↓ 2 callersFunctionwrite_list

( tid_list: &[u32], bct: &RadType, bc: u64, umit: &RadType, umi: u64, w: &mut W, )

src/convert.rs:124

↓ 2 callersFunctionwrite_named_sample_bc_list

( path: &Path, entries: &[(&str, u64)], bc_len: u16, )

tests/multi_barcode_integration.rs:215

↓ 2 callersFunctionwrite_tg_map

(path: &Path)

tests/multi_barcode_integration.rs:228

↓ 1 callersMethodadd_label_vec

(&mut self, lab: &[u32])

src/eq_class.rs:195

↓ 1 callersMethodadd_single_label

(&mut self, lab: u32)

src/eq_class.rs:189

↓ 1 callersFunctionargsort

Modified from https://stackoverflow.com/questions/69764050/how-to-get-the-indices-that-would-sort-a-vec kmdreko

src/eq_class.rs:89

↓ 1 callersFunctionargsort_by

initially suggested by Claude

src/eq_class.rs:95

↓ 1 callersFunctionatac_sub_commands

()

src/main.rs:680

↓ 1 callersFunctionbam2rad

( input_file: P1, rad_file: P2, num_threads: u32, filter_best: bool, log: &slog::Logger, )

src/convert.rs:167

↓ 1 callersFunctionbuild_sample_permit_map

Build the sample barcode permit map (observed -> canonical). Returns (permit_map, bc_to_idx) where: - permit_map maps every observed rotation barcode

src/cellfilter.rs:1202

↓ 1 callersFunctioncheck_permit_list_validity

Check if permit list appears valid

src/cellfilter.rs:1916

↓ 1 callersFunctioncollapse_vertices

Find the largest monochromatic spanning arboresence in the graph `g` starting at vertex `v`. The arboresence is monochromatic if every vertex can be

src/pugutils.rs:308

↓ 1 callersFunctioncollapse_vertices_weighted

Find the largest monochromatic spanning arboresence in the graph `g` starting at vertex `v`. The arboresence is monochromatic if every vertex can be

src/pugutils.rs:398

↓ 1 callersFunctioncollate

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

src/atac/collate.rs:40

↓ 1 callersFunctioncollate_with_temp

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

src/atac/collate.rs:263

↓ 1 callersFunctioncompare_quants

(args)

scripts/testing/compare_counts.py:38

↓ 1 callersFunctioncorrect_unmapped_counts

Correct unmapped barcode counts for single-barcode data. Reads unmapped_bc_count.bin (self-describing format), applies cell BC correction, writes unm

src/collate.rs:344

↓ 1 callersFunctioncorrect_unmapped_counts_multi_bc

Correct unmapped barcode counts for multi-barcode (Flex) data. Reads the raw unmapped_bc_count.bin (self-describing format with per-field barcodes),

src/collate.rs:253

↓ 1 callersFunctioncount_diff_2_bit_packed

FROM https://github.com/10XGenomics/rust-debruijn/blob/master/src/dna_string.rs count Hamming distance between 2 2-bit DNA packed u64s

src/utils.rs:372

↓ 1 callersFunctioncreate_progress_bar

Create progress bar for chunk processing

src/cellfilter.rs:1629

↓ 1 callersFunctiondeduplicate

(dedup_opts: DeduplicateOpts)

src/atac/deduplicate.rs:48

↓ 1 callersFunctiondistance_to_line

compute the distance between the query point `Q` and the line defined by points `P1` and `P2`. The formula used here is taken from : https://en.wikip

src/knee_finding.rs:12

↓ 1 callersFunctiondo_collate_multi_bc_fast

( input_dir: P1, rad_dir: P2, rec_context: MultiBarcodeRecordContext, cell_bc_len: u32, pr

src/collate.rs:1160

↓ 1 callersFunctiondo_collate_multi_bc_two_round

( input_dir: P1, rad_dir: P2, rec_context: MultiBarcodeRecordContext, prelude: RadPrelude,

src/collate.rs:1977

↓ 1 callersFunctiondo_generate_permit_list_multi_bc

Multi-barcode generate-permit-list implementation. For protocols like 10x Flex with multiple barcodes per read (e.g., sample + cell): 1. Reads all re

src/cellfilter.rs:563

↓ 1 callersFunctionem_optimize_long_read

( eqclasses_prob: &HashMap<Vec<u32>, P, ahash::RandomState>, unique_evidence: &mut [bool], no_ambi

src/em.rs:750

↓ 1 callersFunctionem_update

( alphas_in: &[f32], alphas_out: &mut [f32], eqclasses: &HashMap<Vec<u32>, P, ahash::RandomState>,

src/em.rs:301

next →1–100 of 221, ranked by callers