Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

↓ 2 callersFunctionprepare_svg_tree

(svg_data: &[u8])

crates/pipeplot/src/common.rs:3

↓ 2 callersMethodprocess_grouped_records

( &mut self, grouped: TridGroups, contig: &str, pos: i64, sample_recor

src/merge/vcf_processor.rs:607

↓ 2 callersMethodpush_missing_for_n

(&mut self, n: usize)

src/merge/field_registry.rs:124

↓ 2 callersMethodqual

(mut self, qual: f32)

src/utils/test_util.rs:197

↓ 2 callersMethodread_next_stream_record

( &mut self, reader_idx: usize, last_rid_per_reader: &mut [Option<u32>], last_

src/merge/vcf_processor.rs:721

↓ 2 callersFunctionreference_dictionary

(header: &bam::Header)

src/utils/bam_utils.rs:114

↓ 2 callersMethodreturn_record

(&mut self, record: bcf::Record)

src/merge/vcf_reader.rs:285

↓ 2 callersFunctionrun_fetcher_thread

( mut bam_reader: R, locus_group_rx: Receiver<Result<LocusGroup>>, populated_locus_tx: Sender<Resu

src/commands/genotype.rs:240

↓ 2 callersMethodscheme_str

(&self)

src/utils/input_source.rs:42

↓ 2 callersFunctionselect_inplace

Iterative Quickselect algorithm using median-of-three to avoid worst case quadratic runtime

src/utils/math.rs:42

↓ 2 callersMethodsource

(&self)

src/utils/test_util.rs:61

↓ 2 callersFunctionsource_reader

(label: &str, bam_file: &NamedTempFile)

src/trgt/genotype_reader.rs:234

↓ 2 callersMethodtr_slice

(&self)

src/trgt/reads/read.rs:28

↓ 2 callersFunctionvalidate_bam_sources

( bam_sources: &BamSources, sample_name_override: Option<&str>, )

src/utils/bam_utils.rs:47

↓ 2 callersFunctionvalidate_bgzip_vcf

(file: &Path)

src/merge/vcf_reader.rs:102

↓ 2 callersMethodwith_converter

(mut self, converter: FieldConverter)

src/merge/field_registry.rs:203

↓ 2 callersFunctionwith_fragment

(mut url: Url, frag: &str)

src/utils/input_source.rs:381

↓ 2 callersMethodwith_special_handling

(mut self)

src/merge/field_registry.rs:208

↓ 2 callersMethodwrite

Writes a VCF record for a given locus and its genotyping results. # Arguments `locus` - `Locus` struct containing locus information. `results` - `Loc

src/trgt/writers/write_vcf.rs:119

↓ 2 callersFunctionwrite_trgt_vcf

( path: &Path, sample: &str, trid: &str, pos: i64, )

src/utils/test_util.rs:462

↓ 1 callersMethodadd_background

(&mut self)

crates/pipeplot/src/svg.rs:298

↓ 1 callersMethodadd_double_arrow

( &mut self, pos: (f64, f64), dims: (f64, f64), color: &Color, stroke:

crates/pipeplot/src/svg.rs:193

↓ 1 callersMethodadd_filter

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

src/utils/test_util.rs:327

↓ 1 callersMethodadd_hline

(&mut self, pos: (f64, f64), dims: (f64, f64), color: &Color, stroke: f64)

crates/pipeplot/src/svg.rs:162

↓ 1 callersMethodadd_missing_values_for_field_idx

(&mut self, descriptor_idx: usize, n: usize)

src/merge/field_registry.rs:520

↓ 1 callersMethodadd_padding_base

(&mut self, sample_records: &mut [Option<Record>], contig: &str, pos: i64)

src/merge/vcf_processor.rs:817

↓ 1 callersMethodadd_tick

( &mut self, pos: (f64, f64), dims: (f64, f64), color: &Color, label:

crates/pipeplot/src/svg.rs:238

↓ 1 callersMethodadd_vline

(&mut self, pos: (f64, f64), dims: (f64, f64), color: &Color)

crates/pipeplot/src/svg.rs:177

↓ 1 callersMethodaffine2p_penalties

( mut self, match_: i32, mismatch: i32, gap_opening1: i32, gap_extensi

src/wfaligner.rs:226

↓ 1 callersMethodaffine2p_with_match

( mut self, match_: i32, mismatch: i32, gap_opening1: i32, gap_extensi

src/wfaligner.rs:332

↓ 1 callersMethodaffine_penalties

( mut self, match_: i32, mismatch: i32, gap_opening: i32, gap_extensio

src/wfaligner.rs:211

↓ 1 callersFunctionalign_consensus

Aligns a given allele to a perfect repeat as specified by the locus definition

src/trvz/align_consensus.rs:9

↓ 1 callersFunctionalign_reads

Align reads to the consensus sequence

src/trvz/align_reads.rs:7

↓ 1 callersMethodalignment_scope

(mut self, alignment_scope: AlignmentScope)

src/wfaligner.rs:184

↓ 1 callersMethodappend_field

( &mut self, record: &Record, descriptor: &FieldDescriptor<'static>, descripto

src/merge/field_registry.rs:471

↓ 1 callersFunctionappend_ins_consensus

(consensus: &mut Vec<u8>, bucket: &mut Vec<&[u8]>, n_reads: usize)

src/trgt/genotype/consensus.rs:90

↓ 1 callersMethodapply

(self)

src/cli.rs:682

↓ 1 callersFunctionassign_read

(gt: &Gt, tr_len: usize)

src/trgt/workflows/tr.rs:231

↓ 1 callersFunctionbam_source_identity

(source: &InputSource)

src/utils/bam_utils.rs:90

↓ 1 callersFunctionbase_to_index

(base: u8)

src/trgt/genotype/consensus.rs:71

↓ 1 callersFunctionbuild_predefined_field_ids

( descriptors: &'static [FieldDescriptor<'static>], )

src/merge/field_registry.rs:342

↓ 1 callersFunctioncalc_gt_penalty

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

src/trgt/genotype/haploid.rs:17

↓ 1 callersFunctioncalc_gt_penalty

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

src/trgt/genotype/diploid.rs:51

↓ 1 callersMethodcalc_viterbi_score

( &self, query: &[u8], scores: &MatF64, state: usize, index: usize,

src/hmm/hmm_model.rs:54

↓ 1 callersFunctioncentral_read

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

src/trgt/genotype/genotype_cluster.rs:12

↓ 1 callersFunctioncheck_prefix_path

(s: &str)

src/cli.rs:725

↓ 1 callersMethodclip_bases

(&self, left_len: usize, right_len: usize)

src/trgt/reads/clip_bases.rs:9

↓ 1 callersFunctionclip_cigar

Clips CIGAR by a specified number of bases on left and right

src/trgt/reads/clip_bases.rs:78

↓ 1 callersFunctionclip_cigar

Clips an alignment to a given reference region

src/trgt/reads/clip_region.rs:68

↓ 1 callersFunctioncluster

(num_seqs: usize, dists: &mut [f64])

src/trgt/genotype/genotype_cluster.rs:150

↓ 1 callersFunctioncollapse_labels

(spans: Vec<Span>)

src/hmm/utils.rs:11

↓ 1 callersMethodcollect_contig_union

(&self)

src/merge/vcf_reader.rs:395

↓ 1 callersMethodcontig_tid

(&self, contig: &str)

src/trgt/writers/write_bam.rs:82

↓ 1 callersFunctioncontigs_in_header_order

( header: &HeaderView, file_path: &str, )

src/merge/vcf_reader.rs:525

↓ 1 callersFunctionconvert

Convert a WFA alignment into an internal alignment

src/trvz/align_reads.rs:31

↓ 1 callersMethodcount_matches

Counts the number of match ('M') operations in the CIGAR string. TODO: Possibly remove safety checks?

src/wfaligner.rs:988

↓ 1 callersFunctioncount_motifs

(motifs: &[Vec<u8>], labels: &Vec<Span>)

src/hmm/utils.rs:3

↓ 1 callersFunctioncreate_indexed_bam_from_records

(records: I)

src/utils/test_util.rs:74

↓ 1 callersFunctioncreate_indexed_test_bam

(name: &str, contigs: &[(&str, u32)], samples: &[&str])

src/utils/test_util.rs:107

↓ 1 callersMethodcreate_missing_values

(&self, n_samples: usize)

src/merge/field_registry.rs:223

↓ 1 callersMethodcurrent_sort_key

(&self, source_index: usize)

src/trgt/genotype_reader.rs:221

↓ 1 callersFunctiondecode_info_field

(encoding: &str)

src/trgt/locus.rs:257

↓ 1 callersFunctiondeepdive

Align .spanning.bam reads to their consensus and produce outputs meant to be used on downstream tools, using the consensus sequences as the reference

src/commands/deepdive.rs:73

↓ 1 callersFunctiondefine_motif_block

(hmm: &mut Hmm, ms: usize, motif: &[u8])

src/hmm/builder.rs:80

↓ 1 callersMethoddescribe

(&self)

src/merge/vcf_processor.rs:1244

↓ 1 callersFunctiondeterministic_shuffle

(reads: &mut [SpanningRead], locus_id: &str)

src/trgt/workflows/tr.rs:419

↓ 1 callersFunctiondisable_htslib_logging

()

src/main.rs:9

↓ 1 callersMethoddiscover_fields

(&mut self)

src/merge/vcf_processor.rs:242

↓ 1 callersMethodedit_penalties

(mut self)

src/wfaligner.rs:198

↓ 1 callersFunctionencode_base

(base: u8)

src/hmm/hmm_model.rs:243

↓ 1 callersMethodend_svg

(&mut self)

crates/pipeplot/src/svg.rs:294

↓ 1 callersMethodequals

(&self, other: &Self)

src/merge/vcf_processor.rs:1229

↓ 1 callersFunctionextend_character_field

(record: &Record, field_id: &[u8], out: &mut Vec<u8>)

src/merge/field_registry.rs:601

↓ 1 callersFunctionextend_float_field

(record: &Record, field_id: &[u8], out: &mut Vec<f32>)

src/merge/field_registry.rs:579

↓ 1 callersFunctionextend_integer_field

(record: &Record, field_id: &[u8], out: &mut Vec<i32>)

src/merge/field_registry.rs:565

↓ 1 callersFunctionextend_string_field

(record: &Record, field_id: &[u8], out: &mut Vec<Vec<u8>>)

src/merge/field_registry.rs:590

↓ 1 callersFunctionextract_reads_for_group

( reader: &mut R, mut group: LocusGroup, params: &Arc<Params>, )

src/trgt/locus_group.rs:96

↓ 1 callersFunctionextract_snps_offset

(cigar: &Cigar, region: &GenomicRegion)

src/trgt/reads/snp.rs:108

↓ 1 callersMethodfile_stem

(&self)

src/utils/input_source.rs:178

↓ 1 callersFunctionfilter_impure_trs

( locus: &Locus, spanning_reads: Vec<SpanningRead>, rq_cutoff: f32, )

src/trgt/workflows/tr.rs:294

↓ 1 callersFunctionfind_locus_line

Get the relevant info for a locus to avoid re-opening the caller

src/commands/deepdive.rs:59

↓ 1 callersFunctionfind_tr_spans

( lf: &[u8], rf: &[u8], reads: &[LocusRead], params: &Params, )

src/trgt/genotype/span_locater.rs:33

↓ 1 callersFunctionfnv1a64

(bytes: &[u8])

src/trgt/workflows/tr.rs:410

↓ 1 callersMethodgenerate

(&mut self, pipe_plot: &PipePlot)

crates/pipeplot/src/svg.rs:44

↓ 1 callersMethodgenerate_mats

(&self, query: &[u8])

src/hmm/hmm_model.rs:99

↓ 1 callersFunctiongenerate_random_dna

(rng: &mut impl Rng, min_len: usize, max_len: usize)

src/trgt/genotype/genotype_cluster.rs:291

↓ 1 callersFunctiongenerate_string

(plot: &PipePlot)

crates/pipeplot/src/svg.rs:8

↓ 1 callersFunctiongenotype

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

src/trgt/genotype/diploid.rs:5

↓ 1 callersFunctionget_allele_align

(locus: &InputLocus, consensus: &[u8], reads: &[&Read])

src/trvz/align_allele.rs:6

↓ 1 callersFunctionget_allele_seqs

(locus: &InputLocus, record: &bcf::Record)

src/utils/input.rs:200

↓ 1 callersFunctionget_bam_header

(reads_src: &InputSource)

src/utils/bam_utils.rs:5

↓ 1 callersFunctionget_base_match

(hmm: &Hmm, state: usize)

src/hmm/events.rs:88

↓ 1 callersMethodget_by_index

(&self, index: usize)

src/merge/field_registry.rs:400

↓ 1 callersFunctionget_candidate_gts

(profiles: &[Profile])

src/trgt/genotype/genotype_flank.rs:215

↓ 1 callersFunctionget_ci

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

src/trgt/genotype/diploid.rs:86

↓ 1 callersFunctionget_ci

(seqs: &[&[u8]])

src/trgt/genotype/genotype_cluster.rs:225

↓ 1 callersFunctionget_consensus

(sizes: &ArrayVec<usize, 2>, seqs: &[&[u8]], counts: &[usize])

src/trgt/genotype/consensus.rs:130

↓ 1 callersMethodget_dimensions

(&self, pipe_plot: &PipePlot)

crates/pipeplot/src/svg.rs:271

↓ 1 callersFunctionget_dist_matrix_simple

(trs: &[&[u8]])

src/trgt/genotype/genotype_cluster.rs:305

↓ 1 callersFunctionget_hp_tag

Retrieves the HP (haplotype) tag from a BAM record. # Arguments `rec` - A reference to the BAM record. # Returns Returns an `Option<u8>` which is `S

src/trgt/reads/read.rs:201

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