Functions — github.com/10XGenomics/rust-pseudoaligner

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Functions50 in github.com/10XGenomics/rust-pseudoaligner

⨍ Functions 50 ◇ Types & classes 8

↓ 6 callersFunctionread_obj

( filename: P, )

src/utils.rs:34

↓ 6 callersFunctionread_transcripts

( reader: fasta::Reader<BufReader<File>>, )

src/utils.rs:61

↓ 5 callersMethodmap_read

Pseudoalign the `read_seq` to the graph with # mismatches = 2. Returns a tuple of the eqivalence class and the number of bases aligned on success or N

src/pseudoaligner.rs:381

↓ 4 callersFunctionvalidate_dbg

(seqs: &[DnaString], al: &Pseudoaligner<K>)

src/build_index.rs:262

↓ 2 callersMethodflush_chunk

(&mut self, chunk: usize)

src/scatter.rs:75

↓ 2 callersFunctionintersect

Compute the intersection of v1 and v2 inplace on top of v1 v1 and v2 must be sorted and deduplicated.

src/pseudoaligner.rs:389

↓ 2 callersMethodmap_read_to_nodes

( &self, read_seq: &DnaString, nodes: &mut Vec<usize>, )

src/pseudoaligner.rs:54

↓ 2 callersMethodmap_read_to_nodes_with_mismatch

Pseudo-align `read_seq` and return a list of nodes that the read was aligned to, with configurable # of allowed mismatches

src/pseudoaligner.rs:64

↓ 2 callersFunctiontest_intersect

(v1: &[T], v2: &[T])

src/pseudoaligner.rs:526

↓ 2 callersMethodtotal_kmer_count

(&self)

src/mappability.rs:53

↓ 2 callersFunctionwrite_mappability_tsv

( records: Vec<MappabilityRecord>, outdir: P, )

src/mappability.rs:93

↓ 2 callersFunctionwrite_obj

( g: &T, filename: P, )

src/utils.rs:22

↓ 1 callersMethodadd_gene_count

(&mut self, count: usize, multiplicity: usize)

src/mappability.rs:65

↓ 1 callersMethodadd_tx_count

(&mut self, count: usize, multiplicity: usize)

src/mappability.rs:57

↓ 1 callersFunctiondetect_fasta_format

(record: &fasta::Record)

src/utils.rs:99

↓ 1 callersFunctionextract_tx_gene_id

( record: &'a fasta::Record, fasta_format: &FastaFormat, )

src/utils.rs:119

↓ 1 callersMethodget_eq_classes

(&self)

src/equiv_classes.rs:31

↓ 1 callersFunctionget_next_record

( reader: &Arc<Mutex<fastq::Records<R>>>, )

src/utils.rs:152

↓ 1 callersFunctiongroup_by_slices

Split the slice `data` into subslices of size at least `min_size`, while ensuring that consecutive runs of items with the same key as defined by the k

src/build_index.rs:227

↓ 1 callersMethodhandle

Create a writer handle. Each thread that produces values should give given it's own handle to write values with.

src/scatter.rs:40

↓ 1 callersFunctionmake_dbg_index

( dbg: &DebruijnGraph<K, EqClassIdType>, pool: &ThreadPool, num_threads: usize, )

src/build_index.rs:182

↓ 1 callersMethodmap_read_with_mismatch

Pseudoalign the `read_seq` to the graph. Returns a tuple of the eqivalence class, the number of bases aligned on success, and the number of mismatched

src/pseudoaligner.rs:361

↓ 1 callersFunctionmerge_shard_dbgs

( uncompressed_dbgs: Vec<BaseGraph<K, EqClassIdType>>, )

src/build_index.rs:174

↓ 1 callersMethodnodes_to_eq_class

Convert a list of nodes contacted by a read into an equivalence class. Supply node list in `nodes`. Equivalence class will be written to `eq_class`.

src/pseudoaligner.rs:323

↓ 1 callersFunctionopen_file

(filename: &str, outdir: P)

src/utils.rs:159

↓ 1 callersMethodwrite

Set data[index] = value in the data slice.

src/scatter.rs:64

Function_open_with_gz

Open a (possibly gzipped) file into a BufReader.

src/utils.rs:46

Functionanalyze_graph

( index: &Pseudoaligner<K>, )

src/mappability.rs:120

Functionassemble_shard

( shard_data: &[(u16, u32, DnaStringSlice, Exts)], summarizer: &Arc<CountFilterEqClass<u32>>, )

src/build_index.rs:153

Functionbuild_index

( seqs: &[DnaString], tx_names: &[String], tx_gene_map: &HashMap<String, String>, num_threads:

src/build_index.rs:27

Functioncount_a_t_bases

Count the number of A/T bases in a kmer

src/build_index.rs:116

Methoddrop

(&mut self)

src/scatter.rs:88

Methodfraction_unique_gene

(&self)

src/mappability.rs:77

Methodfraction_unique_tx

(&self)

src/mappability.rs:73

Methodget_number_of_eq_classes

(&self)

src/equiv_classes.rs:54

Functionintersect_test

()

src/pseudoaligner.rs:543

Functionmain

()

src/bin/pseudoaligner.rs:66

Methodnew

( dbg: DebruijnGraph<K, EqClassIdType>, eq_classes: Vec<Vec<u32>>, dbg_index: NoKeyBoo

src/pseudoaligner.rs:36

Methodnew

Create a new scatterer that permits efficiently writing (index, value) tuples into `data` from multiple threads.

src/scatter.rs:17

Methodnew

(tx_name: &'a str, gene_name: &'a str)

src/mappability.rs:42

Methodnew

(min_kmer_obs: usize)

src/equiv_classes.rs:23

Functionpartition_contigs

( contig: &DnaString, contig_id: u32, )

src/build_index.rs:127

Functionprocess_reads

( reader: fastq::Reader<io::BufReader<File>>, index: &Pseudoaligner<K>, outdir: P, num_threads

src/pseudoaligner.rs:420

Methodsummarize

( &self, items: F, )

src/equiv_classes.rs:62

Functiontest_alignment

()

src/build_index.rs:424

Functiontest_gencode_full_build_20

()

src/build_index.rs:414

Functiontest_gencode_full_build_64

()

src/build_index.rs:455

Functiontest_gencode_small_build_20

()

src/build_index.rs:395

Functiontest_gencode_small_build_64

()

src/build_index.rs:404

Methodto_tsv

(&self)

src/mappability.rs:81