Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

Methodfmt

(&self, f: &mut fmt::Formatter<'_>)

src/utils/input_source.rs:52

Methodfmt

(&self, f: &mut std::fmt::Formatter<'_>)

src/utils/io_utils.rs:97

Methodfmt

(&self, f: &mut fmt::Formatter<'_>)

src/utils/region.rs:69

Methodfmt

(&self, f: &mut std::fmt::Formatter<'_>)

src/trgt/reads/read.rs:73

Methodfmt

(&self, formatter: &mut fmt::Formatter)

src/trvz/params.rs:89

Functionformat_log

(buf: &mut env_logger::fmt::Formatter, record: &log::Record)

src/cli.rs:718

Functionformat_number_with_commas

src/merge/vcf_reader.rs:26

Methodfrom

(tr_size: TrSize)

src/trgt/genotype/gt.rs:18

Methodfrom_bed_fields

(fields: &[&str])

src/utils/region.rs:35

Methodfrom_descriptors

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

src/merge/field_registry.rs:365

Methodfrom_extension

(extension: &str)

crates/pipeplot/src/image.rs:26

Methodfrom_header_values

( id: &str, type_str: &str, number_str: &str, description: &str, categ

src/merge/field_registry.rs:293

Methodfrom_hts_rec

Creates a `HiFiRead` from an HTSlib record. # Arguments `rec` - A BAM record from HTSlib. # Returns Returns a `HiFiRead` populated with data extract

src/trgt/reads/read.rs:135

Methodfrom_reader

(reader: R)

src/utils/karyotype.rs:47

Methodfrom_str

(s: &str)

src/utils/ploidy.rs:13

Methodfrom_str

(s: &str)

src/utils/input_source.rs:118

Methodfrom_str

(preset: &str)

src/utils/presets.rs:11

Methodfrom_str

(genotyper: &str)

src/utils/genotyper.rs:11

Methodfrom_string

(encoding: &str)

src/utils/region.rs:24

(plot: &PipePlot, path: &Path)

crates/pipeplot/src/image.rs:4

Functiongenotype

(ploidy: Ploidy, seqs: &[&[u8]])

src/trgt/genotype/genotype_size.rs:6

Functiongenotype

(ploidy: Ploidy, trs: &[&[u8]])

src/trgt/genotype/genotype_cluster.rs:55

Functionget_cigar_string

(cigar: &Vec<CigarOp>)

src/trgt/reads/snp.rs:145

Functionget_gradient

(value: f64)

src/trvz/params.rs:110

(&mut self, field_id: &[u8])

src/merge/field_registry.rs:392

Methodget_penalties

(&self)

src/wfaligner.rs:397

Methodget_template_record

(sample_records: &[Option<Record>])

src/merge/vcf_processor.rs:1104

Functionheaders_without_reference_records_are_rejected

()

src/utils/bam_utils.rs:218

Functionif_alignment_contained_inside_region_then_original_read

()

src/trgt/reads/clip_region.rs:183

Functionif_alignment_overlaps_left_flank_then_clipped_read

()

src/trgt/reads/clip_region.rs:200

Functionif_alignment_starts_inside_region_then_clipped_read

()

src/trgt/reads/clip_region.rs:242

Functionif_het_snvs_then_genotype

()

src/trgt/genotype/genotype_flank.rs:374

Functionif_hom_snvs_then_none

()

src/trgt/genotype/genotype_flank.rs:432

Functionif_hp_tags_insufficient_then_cluster

()

src/trgt/genotype/genotype_flank.rs:545

Functionif_hp_tags_then_genotype

()

src/trgt/genotype/genotype_flank.rs:495

Functionif_no_overlap_then_none

()

src/trgt/reads/clip_region.rs:166

Functionif_no_snvs_then_none

()

src/trgt/genotype/genotype_flank.rs:471

Functionif_op_overlaps_flanks_then_clipped_read

()

src/trgt/reads/clip_region.rs:214

Functionif_op_spans_entire_region_then_clipped_read

()

src/trgt/reads/clip_region.rs:228

Functionindexed_contig_order_allows_union

()

src/merge/vcf_reader.rs:647

Functionindexed_reader_requires_index

()

src/merge/vcf_reader.rs:586

Methodinfer_from_path

(path: &Path)

src/utils/io_utils.rs:36

Functioninfer_from_path_recognizes_known_extensions

()

src/utils/io_utils.rs:138

Functioninit_region_from_bed_fields_invalid_start

()

src/utils/region.rs:150

Functioninit_region_from_bed_fields_padding_valid

()

src/utils/region.rs:141

Functioninit_region_from_bed_fields_too_few_fields

()

src/utils/region.rs:156

Functioninit_region_from_bed_fields_valid

()

src/utils/region.rs:132

Functioninit_region_from_invalid_interval_err

()

src/utils/region.rs:116

Functioninit_region_from_invalid_interval_new

()

src/utils/region.rs:124

Functioninit_region_from_invalid_start_err

()

src/utils/region.rs:108

Functioninit_region_from_invalid_string_err

()

src/utils/region.rs:100

Functioninit_region_from_valid_string_ok

()

src/utils/region.rs:78

Methodis_empty

(&self)

src/merge/field_registry.rs:467

Methodleft_flank

(mut self, flank: Vec<u8>)

src/utils/locus.rs:125

src/trgt/genotype/genotype_flank.rs:334

Functionmean

(xs: &[f64])

src/trgt/workflows/tr.rs:195

Methodmode

(&self)

src/merge/vcf_reader.rs:244

Functionmosaic_tr

()

src/trgt/genotype/haploid.rs:46

Methodmotifs

(mut self, motifs: Vec<Vec<u8>>)

src/utils/locus.rs:120

Methodmulti

(sources: Vec<BamSourceReader>)

src/trgt/genotype_reader.rs:23

Functionmulti_source_allows_missing_sample_metadata_when_another_source_has_sample_name

()

src/utils/bam_utils.rs:300

Functionmulti_source_conflicting_sample_metadata_is_rejected_even_with_override

()

src/utils/bam_utils.rs:287

Functionmulti_source_equal_coordinate_records_are_deterministic

()

src/trgt/genotype_reader.rs:379

Functionmulti_source_fetch_errors_report_source_and_queried_region

()

src/trgt/genotype_reader.rs:410

Functionmulti_source_fetch_reads_the_interval_from_every_source

()

src/trgt/genotype_reader.rs:306

Functionmulti_source_records_are_emitted_in_virtual_coordinate_order

()

src/trgt/genotype_reader.rs:320

Functionmulti_source_records_do_not_receive_source_metadata

()

src/trgt/genotype_reader.rs:422

Functionmulti_source_requires_explicit_sample_name_when_all_metadata_is_missing

()

src/utils/bam_utils.rs:311

Functionmulti_source_sample_name_override_is_output_label_only

()

src/utils/bam_utils.rs:276

Functionmulti_source_sample_names_resolve_when_metadata_agrees

()

src/utils/bam_utils.rs:251

Methodmulti_with_tpool

(sources: Vec<BamSourceReader>, thread_pool: ThreadPool)

src/trgt/genotype_reader.rs:27

Functionnaive_median

(data: &[i32])

src/utils/math.rs:104

Methodnew

(alignment_scope: AlignmentScope, memory_model: MemoryModel)

src/wfaligner.rs:254

Methodnew

(args: &MergeArgs, vcfs: Vec<PathBuf>)

src/merge/vcf_processor.rs:119

Methodnew

( header: &bcf::Header, output_type: Option<&OutputType>, output: Option<&PathBuf>,

src/merge/vcf_writer.rs:16

Methodnew

(file: PathBuf, index: usize, mode: VcfReadMode)

src/merge/vcf_reader.rs:168

Methodnew

(n_threads: i32)

src/merge/tpool.rs:24

Methodnew

()

src/merge/field_registry.rs:47

Methodnew

(primary: InputSource, supplemental: Option<InputSource>)

src/utils/input_source.rs:83

Methodnew

(encoding: &str)

src/utils/karyotype.rs:17

Methodnew

( genome_reader: &faidx::Reader, chrom_lookup: &HashMap<String, u32>, line: &str,

src/utils/locus.rs:40

Methodnew

()

src/utils/test_util.rs:179

Methodnew

(contig: impl Into<String>, start: u32, end: u32)

src/utils/region.rs:12

Methodnew

(num_states: usize)

src/hmm/hmm_model.rs:29

Methodnew

(source_label: impl Into<Arc<str>>, reader: bam::IndexedReader)

src/trgt/genotype_reader.rs:62

Methodnew

( genome_reader: &faidx::Reader, chrom_lookup: &HashMap<String, u32>, line: &str,

src/trgt/locus.rs:25

Methodnew

Creates a new group with the first locus.

src/trgt/locus_group.rs:23

Methodnew

Constructs a new `VcfWriter` instance. # Arguments `output_path` - Path of the output VCF file. `sample_name` - The name of the sample to be written

src/trgt/writers/write_vcf.rs:61

Methodnew

Constructs a new `BamWriter` instance. # Arguments `output_bam_path` - Path of the output BAM file. `template_header` - The BAM header to use as a te

src/trgt/writers/write_bam.rs:33

Methodnew

(size: usize, ci: (usize, usize))

src/trgt/genotype/gt.rs:10

Methodnew

(scale: (f64, f64), pad: f64)

crates/pipeplot/src/svg.rs:36

Methodnew_for_test

(ploidies: HashMap<String, Ploidy>)

src/utils/karyotype.rs:41

Methodnew_inner

(sources: Vec<BamSourceReader>, tpool: Option<ThreadPool>)

src/trgt/genotype_reader.rs:107

Methodnew_with_thread_pool

( file: PathBuf, index: usize, mode: VcfReadMode, thread_pool: Option<Arc<HtsT

src/merge/vcf_reader.rs:172

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