Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

↓ 280 callersMethoditer

(&self)

src/merge/field_registry.rs:408

↓ 145 callersMethodlen

(&self)

src/trgt/locus_group.rs:75

↓ 84 callersMethodlen

(&self)

src/hmm/spans.rs:9

↓ 65 callersMethodpath

(&self)

src/utils/test_util.rs:57

↓ 48 callersMethodget

(&self, field_id: &[u8])

src/merge/field_registry.rs:388

↓ 47 callersMethodpos

(mut self, pos: i64)

src/utils/test_util.rs:187

↓ 40 callersMethodsample

(mut self, name: S)

src/utils/test_util.rs:290

↓ 39 callersMethodcontig

(mut self, name: S, length: u64)

src/utils/test_util.rs:285

↓ 37 callersMethodempty_record

(&self)

src/merge/vcf_reader.rs:50

↓ 35 callersMethodbuild

Build the WFAligner with the configured settings

src/wfaligner.rs:360

↓ 33 callersMethodalleles

(mut self, alleles: &[T])

src/utils/test_util.rs:207

↓ 33 callersMethodread

(&mut self, record: &mut Record)

src/trgt/genotype_reader.rs:35

↓ 31 callersMethodfilter

(mut self, filter: S)

src/utils/test_util.rs:202

↓ 28 callersMethodrecord

(mut self, record: TestVcfRecord)

src/utils/test_util.rs:295

↓ 27 callersFunctionmake_cigar

(ref_pos: i64, encoding: &str)

src/trgt/reads/test_utils.rs:22

↓ 27 callersFunctionmake_read

(bases: &str, meths: Vec<u8>, cigar: Cigar)

src/trgt/reads/test_utils.rs:4

↓ 25 callersMethodinfo_string

(mut self, key: K, value: V)

src/utils/test_util.rs:217

↓ 25 callersMethodis_empty

(&self)

src/hmm/spans.rs:13

↓ 25 callersMethodlen

(&self)

src/merge/vcf_reader.rs:507

↓ 22 callersMethodadd_info

(mut self, id: S, num: &str, type_: &str, desc: &str)

src/utils/test_util.rs:305

↓ 22 callersFunctioncreate_test_locus

(id: &str, contig: &str, start: u32, end: u32)

src/trgt/locus_group.rs:214

↓ 21 callersMethodadd_format

(mut self, id: S, num: &str, type_: &str, desc: &str)

src/utils/test_util.rs:316

↓ 21 callersMethodaffine

Configure for gap-affine penalties (Smith-Waterman-Gotoh) with match_ = 0

src/wfaligner.rs:292

↓ 21 callersMethodalign_end_to_end

(&mut self, pattern: &[u8], text: &[u8])

src/wfaligner.rs:489

↓ 20 callersMethodas_slice

(&self)

src/utils/input_source.rs:106

↓ 18 callersMethodgenotype

(mut self, genotypes: &[GenotypeAllele])

src/utils/test_util.rs:212

↓ 16 callersMethodadd_line

(&mut self, line: &str)

crates/pipeplot/src/svg.rs:59

↓ 16 callersFunctioncreate_indexed_bam

(records: &[(&str, &str, i64)])

src/utils/test_util.rs:66

↓ 16 callersMethodfetch

(&mut self, region: (&str, u32, u32))

src/trgt/genotype_reader.rs:31

↓ 16 callersMethodis_empty

(&self)

src/trgt/locus_group.rs:81

↓ 16 callersMethodset_trans

(&mut self, target_state: usize, in_states: Vec<usize>, in_probs: Vec<f64>)

src/hmm/hmm_model.rs:44

↓ 15 callersMethodcmp

(&self, other: &Self)

src/merge/vcf_processor.rs:58

↓ 15 callersMethodset_ems

(&mut self, target_state: usize, ems: Vec<f64>)

src/hmm/hmm_model.rs:49

↓ 14 callersFunctionbuild_hmm

(motifs: &[Vec<u8>])

src/hmm/builder.rs:4

↓ 14 callersMethodclear

(&mut self)

src/merge/field_registry.rs:92

↓ 14 callersFunctionvalidate

(sources: &BamSources, sample_name: Option<&str>)

src/utils/bam_utils.rs:190

↓ 14 callersMethodwrite

(&mut self)

src/merge/vcf_writer.rs:68

↓ 13 callersMethodbuild

(allele_lists: &[Vec<&'a [u8]>])

src/merge/genotype_types.rs:36

↓ 13 callersMethodmatching

( &self, pattern: &[u8], text: &[u8], flank_len: Option<usize>, )

src/wfaligner.rs:1064

↓ 13 callersMethodset_heuristic

(&mut self, heuristic: Heuristic)

src/wfaligner.rs:707

↓ 12 callersMethoddummy_record_mut

(&mut self)

src/merge/vcf_writer.rs:64

↓ 12 callersMethodlabel

(&self, query: &[u8])

src/hmm/hmm_model.rs:144

↓ 12 callersMethodrequired

(mut self)

src/merge/field_registry.rs:198

↓ 12 callersMethodto_x

(&self, x: u32)

crates/pipeplot/src/svg.rs:302

↓ 12 callersMethodurl

(&self)

src/utils/input_source.rs:36

↓ 11 callersFunctionbam_sources

(primary: &TestBam, supplemental: Option<&TestBam>)

src/utils/bam_utils.rs:186

↓ 11 callersMethodbuild

(self)

src/utils/locus.rs:140

↓ 11 callersMethodbuild

(self)

src/utils/test_util.rs:357

↓ 11 callersMethodbuild_header

(&self)

src/utils/test_util.rs:336

↓ 11 callersMethodget_query_len

(&self)

src/trgt/reads/cigar.rs:20

↓ 10 callersFunctionparse_cigar_string

(cigar_string: &str)

src/trgt/reads/snp.rs:162

↓ 10 callersFunctionredact_url

(u: &Url)

src/utils/input_source.rs:13

↓ 9 callersMethodclip_to_region

Clips the `HiFiRead` to the specified reference region. # Arguments `region` - A tuple `(i64, i64)` representing the start and end positions of the r

src/trgt/reads/clip_region.rs:20

↓ 9 callersMethodformat_integer

(mut self, key: K, values: &[i32])

src/utils/test_util.rs:234

↓ 9 callersMethodget_ref_len

(&self)

src/trgt/reads/cigar.rs:9

↓ 9 callersMethodinfo_integer

(mut self, key: K, values: &[i32])

src/utils/test_util.rs:223

↓ 8 callersMethodaffine2p

Configure for gap-affine dual-cost penalties (concave 2-pieces) with match_ = 0

src/wfaligner.rs:312

↓ 8 callersMethodalign_ends_free

( &mut self, pattern: &[u8], pattern_begin_free: i32, pattern_end_free: i32,

src/wfaligner.rs:503

↓ 8 callersMethodformat_float

(mut self, key: K, values: &[f32])

src/utils/test_util.rs:240

↓ 7 callersFunctionclip_meth

( bases: &[u8], meth_profile: Option<&[u8]>, left_len: usize, right_len: usize, )

src/trgt/reads/clip_bases.rs:38

↓ 7 callersMethodformat_error

Use this when wrapping errors from htslib that might leak URLs

src/utils/input_source.rs:194

↓ 7 callersMethodget_alignment

TODO: Refactor TODO: THIS DOES NOT WORK WITH BIWFA

src/wfaligner.rs:784

↓ 7 callersMethodmerge_variants

(&mut self)

src/merge/vcf_processor.rs:451

↓ 7 callersMethodto_y

(&self, y: u32)

crates/pipeplot/src/svg.rs:306

↓ 6 callersMethodadd_locus_unchecked

(&mut self, locus: Locus)

src/trgt/locus_group.rs:59

↓ 6 callersMethodbuild_with_compression

(self, compress: bool)

src/utils/test_util.rs:361

↓ 6 callersFunctioncalc_purity

(query: &[u8], hmm: &Hmm, motifs: &[Vec<u8>], states: &[usize])

src/hmm/purity.rs:6

↓ 6 callersMethodformat_string

(mut self, key: K, values: &[V])

src/utils/test_util.rs:246

↓ 6 callersFunctiongenotype

(sizes: &[usize], counts: &[usize])

src/trgt/genotype/haploid.rs:3

↓ 6 callersFunctionget_alleles

(vcf_src: &InputSource, locus: &InputLocus)

src/utils/input.rs:21

↓ 6 callersFunctionget_field

(fields: &HashMap<&str, &str>, key: &str)

src/trgt/locus.rs:239

↓ 6 callersMethodheader_line

(mut self, line: S)

src/utils/test_util.rs:300

↓ 6 callersMethodlabel_motifs

(&self, states: &[usize])

src/hmm/hmm_model.rs:158

↓ 6 callersFunctionmerge_args_for_test

(vcfs: Vec<PathBuf>, output: PathBuf, no_index: bool)

src/merge/vcf_processor.rs:1441

↓ 6 callersMethodpreflight_checks

(&self)

src/utils/input_source.rs:282

↓ 6 callersFunctionrepair_consensus

(reference: &[u8], seqs: &[&[u8]], aligns: &[Vec<CigarOp>])

src/trgt/genotype/consensus.rs:5

↓ 6 callersFunctionrun_repair

(reference: &str, reads: &[&str], cigars: &[Vec<CigarOp>])

src/trgt/genotype/consensus.rs:178

↓ 6 callersMethodwith_heuristic

Set a heuristic for the aligner

src/wfaligner.rs:354

↓ 6 callersMethodwith_trgt_defaults

(self)

src/utils/test_util.rs:420

↓ 6 callersFunctionwrite_trgt_vcf_with_records

( records: Vec<TestVcfRecord>, path: &Path, sample: &str, )

src/utils/test_util.rs:475

↓ 5 callersFunctioncreate_mock_processor

()

src/merge/vcf_processor.rs:1382

↓ 5 callersFunctioncreate_record

(bases: &[u8], mm: &str, ml: &[u8], reverse: bool)

src/trgt/reads/read.rs:234

↓ 5 callersMethodedit

Configure for edit penalties (Levenshtein)

src/wfaligner.rs:273

↓ 5 callersMethodemits_base

(&self, state: usize)

src/hmm/hmm_model.rs:202

↓ 5 callersFunctionextract_mismatch_positions

Collect all mismatch positions from a CIGAR alignment. # Arguments `cigar` - The CIGAR object of the read alignment. # Returns Returns a `Vec<u32>`

src/trgt/reads/snp.rs:13

↓ 5 callersFunctionextract_snps

(cigar: &Cigar, region: &GenomicRegion)

src/trgt/reads/snp.rs:75

↓ 5 callersFunctiongenotype

( reads: &[&LocusRead], tr_seqs: &[&[u8]], region: &GenomicRegion, )

src/trgt/genotype/genotype_flank.rs:9

↓ 5 callersMethodget_alignment_span

TODO: Deprecate and use get_alignment? TODO: THIS DOES NOT WORK WITH BIWFA

src/wfaligner.rs:864

↓ 5 callersFunctionget_profiles

(reads: &[&LocusRead], snvs: &[u32], region: &GenomicRegion)

src/trgt/genotype/genotype_flank.rs:262

↓ 5 callersFunctionget_record_from_builder

(builder: TestVcfBuilder)

src/merge/field_registry.rs:618

↓ 5 callersMethodget_sam_cigar

TODO: Possibly remove safety checks?

src/wfaligner.rs:932

↓ 5 callersFunctionhandle_error_and_exit

src/merge/field_registry.rs:463

↓ 5 callersFunctionmake_consensus

( num_seqs: usize, trs: &[&[u8]], dists: &[f64], group: &[usize], )

src/trgt/genotype/genotype_cluster.rs:41

↓ 5 callersFunctionmake_reads

(specs: &[TestRead])

src/trgt/genotype/genotype_flank.rs:369

↓ 5 callersFunctionmulti_reader

(sources: &[(&str, &NamedTempFile)])

src/trgt/genotype_reader.rs:239

↓ 5 callersFunctionopen_genome_reader

(genome_src: &InputSource)

src/utils/readers/genome.rs:5

↓ 5 callersMethodpartial_cmp

(&self, other: &Self)

src/merge/vcf_processor.rs:52

↓ 5 callersMethodpreflight

(&self)

src/cli.rs:339

↓ 5 callersMethodpush_missing_and_end

(&mut self)

src/merge/field_registry.rs:102

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