Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

↓ 5 callersFunctionwrite_vcf_with_gt

( trid: &[u8], alleles: &[&[u8]], genotype: &[GenotypeAllele], )

src/utils/test_util.rs:444

↓ 4 callersFunctionadd_extension

(path: &Path, ext: &str)

src/merge/vcf_reader.rs:58

↓ 4 callersFunctionalign

(locus: &InputLocus, longest_read: usize, read: &Read)

src/trvz/waterfall_plot.rs:36

↓ 4 callersFunctioncreate_chrom_lookup

(reader: &faidx::Reader)

src/trgt/locus.rs:100

↓ 4 callersMethodget_by_index_mut

(&mut self, index: usize)

src/merge/field_registry.rs:404

↓ 4 callersFunctionget_dist

(seq1: &[u8], seq2: &[u8], aligner: &mut WFAligner)

src/trgt/genotype/genotype_cluster.rs:234

↓ 4 callersMethodget_or_lookup

( &mut self, header: &rust_htslib::bcf::header::HeaderView, field_id: &[u8], )

src/merge/field_registry.rs:55

↓ 4 callersFunctionmerge_exact

( vcf_gts: Vec<Vec<Vec<GenotypeAllele>>>, sample_alleles: &'a [Vec<&'a [u8]>], )

src/merge/strategy/exact.rs:6

↓ 4 callersMethodname

(&self)

src/cli.rs:71

↓ 4 callersFunctionnormalize_by_phase_set

(reads: &mut [SpanningRead])

src/trgt/workflows/tr.rs:427

↓ 4 callersFunctionopen_catalog_reader

(src: &InputSource)

src/utils/readers/catalog.rs:8

↓ 4 callersFunctionremap_genotype

(g: &mut [GenotypeAllele], mapping: &[Option<i32>])

src/merge/genotype_types.rs:5

↓ 4 callersFunctionremove_imperfect_motifs

Replace imperfect STR motif copies with Skip states

src/hmm/operations.rs:6

↓ 4 callersFunctionreplace_invalid_bases

(seq: &[u8], allowed: &[u8])

src/hmm/utils.rs:44

↓ 4 callersFunctionsend_locus_group_result

( sender: &Sender<Result<LocusGroup>>, result: Result<LocusGroup>, )

src/trgt/locus.rs:196

↓ 4 callersFunctionspawn_scoped_stage

( scope: &'scope thread::Scope<'scope, 'env>, thread_name: &str, f: F, )

src/commands/genotype.rs:406

↓ 4 callersFunctionsummarize_vcf

(path: &Path)

src/merge/vcf_processor.rs:1461

↓ 4 callersFunctionwith_basic_auth

(mut url: Url, user: &str, pass: &str)

src/utils/input_source.rs:368

↓ 4 callersMethodwriter_options

(&self)

src/utils/io_utils.rs:61

↓ 3 callersMethodadd_rect

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

crates/pipeplot/src/svg.rs:142

↓ 3 callersMethodadvance

(&mut self)

src/merge/vcf_reader.rs:255

↓ 3 callersMethodappend_record

( &mut self, record: &Record, descriptors: &[FieldDescriptor<'static>], cache:

src/merge/field_registry.rs:422

↓ 3 callersMethodattach_to_hts_file

( &self, hts_file_ptr: *mut htslib::htsFile, target: &str, )

src/merge/tpool.rs:147

↓ 3 callersMethodattach_to_indexed_reader

(&self, reader: &mut bcf::IndexedReader)

src/merge/tpool.rs:42

↓ 3 callersMethodattach_to_reader

(&self, reader: &mut bcf::Reader)

src/merge/tpool.rs:93

↓ 3 callersMethodattach_to_writer

(&self, writer: &mut bcf::Writer)

src/merge/tpool.rs:117

↓ 3 callersMethodborrowed_id

(&self)

src/merge/field_registry.rs:286

↓ 3 callersFunctioncall_snvs

( reads: &[&LocusRead], region: &GenomicRegion, min_freq: f64, analysis_region: (i64, i64), )

src/trgt/genotype/genotype_flank.rs:297

↓ 3 callersMethodcan_add_locus

(&self, locus: &Locus, max_span: u32)

src/trgt/locus_group.rs:33

↓ 3 callersFunctionconvert_am_field

(record: &Record, field_id: &[u8])

src/merge/field_descriptors.rs:126

↓ 3 callersFunctioncreate_bam_reader_with_options

( reads_src: &InputSource, opts: &BamOpenOptions<'_>, )

src/utils/readers/bam.rs:44

↓ 3 callersMethodcreate_empty_value

(&self)

src/merge/field_registry.rs:213

↓ 3 callersMethodcreate_mapping

(&self, allele_list: &[&'a [u8]])

src/merge/genotype_types.rs:94

↓ 3 callersFunctiondecode_fields

(info_fields: &str)

src/trgt/locus.rs:246

↓ 3 callersFunctionget_analysis_region

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

src/trgt/genotype/genotype_flank.rs:240

↓ 3 callersMethodget_contig_order

(&self)

src/merge/vcf_reader.rs:388

↓ 3 callersFunctionget_meth

(rec: &bam::Record, bases: &[u8])

src/trgt/reads/read.rs:89

↓ 3 callersMethodgroup_records_by_trid

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

src/merge/vcf_processor.rs:871

↓ 3 callersMethodindel

Configure for indel penalties (Longest Common Subsequence - LCS)

src/wfaligner.rs:266

↓ 3 callersMethodindex_of

(&self, field_id: &[u8])

src/merge/field_registry.rs:384

↓ 3 callersMethodis_empty

(&self)

src/merge/vcf_reader.rs:511

↓ 3 callersMethodmerged_alleles

(&self)

src/merge/genotype_types.rs:87

↓ 3 callersFunctionopen_bam_reader

(reads_src: &InputSource, threads: usize)

src/utils/readers/bam.rs:122

↓ 3 callersFunctionpopulate_dummy_record

(writer: &mut VcfWriter)

src/merge/vcf_writer.rs:133

↓ 3 callersFunctionproject_betas

Convert betas from read coordinates to allele coordinates according to the provided alignment between the read and the allele consensus sequence

src/utils/read.rs:24

↓ 3 callersMethodrecord_ptr

(&self)

src/trgt/writers/write_vcf.rs:412

↓ 3 callersFunctionrender_from_string

(svg_content: &str, path: &Path)

crates/pipeplot/src/svg.rs:17

↓ 3 callersMethodset_info_field_from_all_records

( &mut self, sample_records: &[Option<Record>], descriptor: &FieldDescriptor<'static>,

src/merge/vcf_processor.rs:1112

↓ 3 callersMethodtake_current_record

(&mut self)

src/merge/vcf_reader.rs:275

↓ 3 callersMethodtr_len

(&self)

src/trgt/reads/read.rs:32

↓ 3 callersMethodtry_read_field_id

Try to find the field ID in the record using a cache to avoid repeated FFI lookups. Returns the primary field ID if present, otherwise checks aliases

src/merge/field_registry.rs:235

↓ 3 callersFunctionwith_query

(mut url: Url, k: &str, v: &str)

src/utils/input_source.rs:377

↓ 3 callersMethodwith_trgt_format_defaults

(self)

src/utils/test_util.rs:427

↓ 3 callersMethodwrite_index

(self)

src/merge/vcf_writer.rs:88

↓ 2 callersMethodaffine_with_match

Configure for gap-affine penalties (Smith-Waterman-Gotoh) with explicit match score

src/wfaligner.rs:297

↓ 2 callersFunctionalign_motifs

Aligns the given sequence to a perfect repeat composed of the given set of motifs

src/trvz/align_consensus.rs:29

↓ 2 callersFunctioncalculate_stats

(data: &[usize])

src/commands/validate.rs:106

↓ 2 callersFunctioncheck_missing_faidx

(fasta: &Path)

src/utils/readers/genome.rs:19

↓ 2 callersFunctioncheck_region_bounds

( region: &GenomicRegion, flank_len: usize, chrom_lookup: &HashMap<String, u32>, )

src/trgt/locus.rs:267

↓ 2 callersMethodclear_dummy_record

(&mut self)

src/merge/vcf_writer.rs:74

↓ 2 callersMethodcollect_variant_data

( &mut self, sample_records: &'a [Option<Record>], )

src/merge/vcf_processor.rs:949

↓ 2 callersFunctionconvert

Convert a rust-wfa alignment into an internal alignments

src/trvz/waterfall_plot.rs:123

↓ 2 callersFunctioncreate_test_bam

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

src/utils/test_util.rs:118

↓ 2 callersFunctioncreate_writer

(output_prefix: &Path, output_suffix: &str, f: F)

src/utils/io_utils.rs:5

↓ 2 callersMethoddiscover_custom_fields

( &self, category: FieldCategory, predefined_descriptors: &'static [FieldDescriptor<'s

src/merge/vcf_processor.rs:344

↓ 2 callersMethoddiscover_predefined_fields

( &self, descriptors: &'static [FieldDescriptor<'static>], category: FieldCategory,

src/merge/vcf_processor.rs:257

↓ 2 callersMethoddummy_record

(&self)

src/merge/vcf_writer.rs:60

↓ 2 callersFunctionempty_record

()

src/trgt/writers/write_vcf.rs:430

↓ 2 callersFunctioneval_profile_given_hap

(profile: &Profile, hap: &[bool])

src/trgt/genotype/genotype_flank.rs:194

↓ 2 callersFunctionexpected_index_path

(output_path: &Path, suffix: &str)

src/merge/vcf_writer.rs:146

↓ 2 callersFunctionextract_mismatch_offsets

( mismatch_positions: &[u32], region_start: u32, region_end: u32, )

src/trgt/reads/snp.rs:34

↓ 2 callersMethodfield_exists

(&self, record: &Record, field_id: &[u8], cache: &mut FieldIdCache)

src/merge/field_registry.rs:248

↓ 2 callersMethodfill_current_record

(&mut self)

src/trgt/genotype_reader.rs:200

↓ 2 callersFunctionfind_spans

(piece: &[u8], seqs: &[&[u8]], min_n_matches: f64)

src/trgt/genotype/span_locater.rs:8

↓ 2 callersFunctionget_closest_size

(seqs: &[&[u8]], allele: usize)

src/trgt/genotype/consensus.rs:146

↓ 2 callersFunctionget_dist

(read: &[Option<bool>], allele: &[bool])

src/trgt/genotype/genotype_flank.rs:149

↓ 2 callersFunctionget_dist_matrix

(trs: &[&[u8]])

src/trgt/genotype/genotype_cluster.rs:246

↓ 2 callersFunctionget_events

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

src/hmm/events.rs:17

↓ 2 callersFunctionget_flank_align

(ref_seq: &[u8], read_seq: &[u8])

src/trvz/waterfall_plot.rs:114

↓ 2 callersFunctionget_meth_colors

(motifs: &[Vec<u8>])

src/trvz/params.rs:57

↓ 2 callersFunctionget_most_frequent_seq

(seqs: &[&[u8]], counts: &[usize], length: usize)

src/trgt/genotype/consensus.rs:164

↓ 2 callersFunctionget_pipe

( xpos: u32, ypos: u32, height: u32, align: &Align, betas: &Betas, colors: &ColorMap,

src/trvz/allele_plot.rs:105

↓ 2 callersFunctionget_reads

( reads_src: &InputSource, locus: &InputLocus, max_allele_reads: Option<usize>, )

src/utils/input.rs:74

↓ 2 callersFunctionget_rq_tag

Retrieves the RQ (read quality) tag from a BAM record. # Arguments `rec` - A reference to the BAM record. # Returns Returns an `Option<f32>` which i

src/trgt/reads/read.rs:187

↓ 2 callersFunctionget_scale

(mut xpos: u32, ypos: u32, height: u32, align: &Align)

src/trvz/scale.rs:5

↓ 2 callersFunctionget_tr_and_flanks

( genome: &faidx::Reader, region: &GenomicRegion, flank_len: usize, )

src/trgt/locus.rs:209

↓ 2 callersMethodid

(mut self, id: T)

src/utils/test_util.rs:192

↓ 2 callersMethodintersect_position

(&self, position: u32)

src/utils/region.rs:59

↓ 2 callersMethoditer_labeled

(&self)

src/utils/input_source.rs:110

↓ 2 callersMethodlinear

Configure for gap-linear penalties (Needleman-Wunsch) with match_ = 0

src/wfaligner.rs:280

↓ 2 callersMethodlinear_with_match

Configure for gap-linear penalties (Needleman-Wunsch) with explicit match score

src/wfaligner.rs:285

↓ 2 callersMethodload_group_into_sample_records

( &self, sample_records: &mut [Option<Record>], mut group_records: Vec<(usize, Record)

src/merge/vcf_processor.rs:887

↓ 2 callersFunctionlocus_search_end

(locus: &Locus, flank_len: u32)

src/trgt/locus_group.rs:92

↓ 2 callersMethodlog_merge_summary

(&self, progress: &MergeProgress)

src/merge/vcf_processor.rs:667

↓ 2 callersFunctionmake_test_records

(trids: &[&str])

src/merge/vcf_processor.rs:1492

↓ 2 callersFunctionmapped_bam_record

(name: &str, tid: i32, pos: i64)

src/utils/test_util.rs:160

↓ 2 callersMethodmerge_and_write

( &mut self, collected: CollectedVariantData, sample_records: &[Option<Record>], )

src/merge/vcf_processor.rs:1064

↓ 2 callersMethodnext_source_index

(&mut self)

src/trgt/genotype_reader.rs:148

↓ 2 callersFunctionphase_by_hp_ps

(reads: &[SpanningRead])

src/trgt/workflows/tr.rs:454

↓ 2 callersMethodpreflight_key

(&self)

src/utils/input_source.rs:206

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