Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

↓ 1 callersFunctiontrvz

(args: PlotArgs)

src/commands/plot.rs:11

↓ 1 callersFunctionuniform_downsample

(spanning_reads: &mut Vec<SpanningRead>, output_len: usize)

src/trgt/workflows/tr.rs:180

↓ 1 callersMethodupdate_record_for_version

(&mut self)

src/merge/vcf_reader.rs:290

↓ 1 callersFunctionvalidate

(args: ValidateArgs)

src/commands/validate.rs:41

↓ 1 callersFunctionvalidate_indexed_vcf

(file: &Path)

src/merge/vcf_reader.rs:143

↓ 1 callersFunctionvalidate_reference_dictionary

( primary_source: &InputSource, source: &InputSource, primary_header: &bam::Header, header: &b

src/utils/bam_utils.rs:100

↓ 1 callersMethodverify_identical_contig_order

(&self)

src/merge/vcf_reader.rs:426

↓ 1 callersFunctionwfa_cigar_to_htslib

Convert the WFA Cigar strings to the ones from rust_htslib

src/commands/deepdive.rs:31

↓ 1 callersFunctionwith_analysis_thread_pool

( num_threads: usize, thread_context: ThreadContextParams, with_pool: F, )

src/commands/genotype.rs:434

↓ 1 callersMethodwith_trgt_format_values

(self)

src/utils/test_util.rs:261

↓ 1 callersMethodwith_trgt_merge_defaults

(self)

src/utils/test_util.rs:437

↓ 1 callersFunctionwith_username_only

(mut url: Url, user: &str)

src/utils/input_source.rs:373

↓ 1 callersMethodwrite_format_fields

(&mut self, out_gts: Vec<i32>)

src/merge/vcf_processor.rs:1179

↓ 1 callersFunctionwrite_test_bam

(path: &Path, contigs: &[(&str, u32)], samples: &[&str])

src/utils/test_util.rs:128

↓ 1 callersMethodwrite_to_record

( &self, writer: &mut VcfWriter, descriptor: &FieldDescriptor<'static>, )

src/merge/vcf_processor.rs:1259

Methodadd_allele_info

Adds allele information from genotyping results to a VCF record. # Arguments `locus` - `Locus` struct containing locus information. `results` - `Locu

src/trgt/writers/write_vcf.rs:210

Methodadd_locus_info

Adds basic locus information to a VCF record. # Arguments `locus` - `Locus` struct containing locus information. `record` - Mutable `Record` struct w

src/trgt/writers/write_vcf.rs:135

Methodadd_missing_allele_info

Adds allele information for missing genotypes to a VCF record. # Arguments `locus` - `Locus` struct containing locus information. `record` - Mutable

src/trgt/writers/write_vcf.rs:168

Methodadd_version_info

(out_header: &mut bcf::Header)

src/merge/vcf_processor.rs:226

Methodadvance_reader

(reader: &mut R, record: &mut bcf::Record)

src/merge/vcf_reader.rs:268

Functionalign

(backbone: &[u8], seqs: &[&[u8]])

src/utils/align.rs:14

Functionanalyze

(mut locus: Locus, params: &Params)

src/trgt/workflows/tr.rs:25

Functionannotate_imperfect_repeat_run

()

src/hmm/builder.rs:243

Functionannotate_motif_runs_separated_by_insertion

()

src/hmm/builder.rs:219

Functionannotate_two_perfect_motif_runs

()

src/hmm/builder.rs:209

Methodas_parts

(&self)

src/utils/region.rs:63

Methodassign_to_i32

(assign: AlleleAssign)

src/trgt/writers/write_bam.rs:72

Functionattach_to_writer_is_callable

()

src/merge/tpool.rs:251

Functionbam_sources_preserve_primary_and_supplemental_order

()

src/utils/input_source.rs:436

Methodbase

()

src/hmm/spans.rs:29

Functionbuffered_source_reader_caches_record_key_and_uses_caller_source_index

()

src/trgt/genotype_reader.rs:367

Functionbuild_read

(id: usize, hp: Option<u8>, ps: Option<u32>)

src/trgt/workflows/tr.rs:531

Methodbuilder

Create a builder for configuring a WFAligner

src/wfaligner.rs:393

Methodbuilder

()

src/utils/locus.rs:36

Methodbuiltin

( id: &'a [u8], category: FieldCategory, vcf_type: VcfType, number: FieldNumbe

src/merge/field_registry.rs:157

Methodbuiltin_with_aliases

( id: &'a [u8], category: FieldCategory, vcf_type: VcfType, number: FieldNumbe

src/merge/field_registry.rs:177

Functioncalculate_purity_of_empty_query

()

src/hmm/purity.rs:89

Functioncalculate_purity_of_imperfect_repeats

()

src/hmm/purity.rs:58

Functioncalculate_purity_of_perfect_repeats

()

src/hmm/purity.rs:49

Functioncalculate_purity_of_polyalanine_repeat

()

src/hmm/purity.rs:78

Functioncalculate_purity_of_repeats_with_skip_states

()

src/hmm/purity.rs:68

Functioncheck_file_exists

(s: &str)

src/cli.rs:755

Functioncheck_image_path

(s: &str)

src/cli.rs:735

Methodcheck_required_info_fields

( record: &Record, reader_file_path: &str, info_fields: &[FieldDescriptor<'static>],

src/merge/vcf_processor.rs:1003

Functioncheck_sample_name_nonempty

(s: &str)

src/cli.rs:764

Functioncigar_generated_even_if_clipped_alignment_has_no_query_len

()

src/trgt/reads/clip_bases.rs:213

Methodcigar_operations

src/wfaligner.rs:1002

Methodcigar_score_clipped

(&self, flank_len: usize)

src/wfaligner.rs:595

Methodcigar_score_edit_get_operations_score

(operation: char, op_length: i32)

src/wfaligner.rs:534

Methodcigar_score_gap_affine2p_get_operations_score

( operation: char, op_length: i32, penalties: &wfa2::affine2p_penalties_t, )

src/wfaligner.rs:578

Methodcigar_score_gap_affine_get_operations_score

( operation: char, op_length: i32, penalties: &wfa2::affine_penalties_t, )

src/wfaligner.rs:565

Methodcigar_score_gap_linear_get_operations_score

( operation: char, op_length: i32, penalties: &wfa2::linear_penalties_t, )

src/wfaligner.rs:552

Methodcigar_score_indel_get_operations_score

Note: Indel distance (LCS) is usually about maximizing matches, not minimizing penalties. For scoring purposes, we treat it like Edit distance in a co

src/wfaligner.rs:544

Methodcigar_string

(&self, flank_len: Option<usize>)

src/wfaligner.rs:1029

Functionclean_het_tr

()

src/trgt/genotype/diploid.rs:110

Functionclean_tr

()

src/trgt/genotype/haploid.rs:37

Functioncollect_qnames

(reader: &mut BamReader)

src/trgt/genotype_reader.rs:261

Functioncollect_records

(reader: &mut BamReader)

src/trgt/genotype_reader.rs:248

Functionconvert_am_field_converts_integer

()

src/merge/field_descriptors.rs:368

Methodcreate_header

(sample_name: &str, bam_header: &bam::Header)

src/trgt/writers/write_vcf.rs:80

Methodcreate_header

Creates a BAM header based on a template, including additional program information. # Arguments `template_header` - BAM header to be used as templat

src/trgt/writers/write_bam.rs:56

Methodcreate_output_header

(vcf_readers: &VcfReaders, args: &MergeArgs)

src/merge/vcf_processor.rs:206

Functioncreate_thread_local_ed

()

src/commands/genotype.rs:54

Functioncreate_thread_local_ga_aligner

()

src/commands/genotype.rs:48

Functioncreate_thread_local_ga_aligner_with_scoring

()

src/commands/genotype.rs:32

Functioncreate_unindexed_test_bam

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

src/utils/test_util.rs:114

Functiondecode_fields_accepts_unrecognized_catalog_info_fields

()

src/trgt/locus.rs:310

Methoddecode_sam_cigar

(sam_cigar_buffer: &[u32])

src/utils/io_utils.rs:27

Methoddefault

()

src/utils/locus.rs:154

Methoddefault

()

src/utils/readers/bam.rs:20

Methoddefault

()

crates/pipeplot/src/pipeplot.rs:53

Functiondefault_output_type_is_compressed_vcf

()

src/utils/io_utils.rs:127

Methoddefault_trgt

(trid: S, pos: i64, end: i32)

src/utils/test_util.rs:272

Functiondisplay_formats_as_region_label

()

src/utils/region.rs:86

src/merge/tpool.rs:177

Functiondummy_converter

(_record: &Record, _field_id: &[u8])

src/merge/field_registry.rs:886

Functiondummy_record_helpers_write_and_clear

()

src/merge/vcf_writer.rs:154

Functionduplicate_bam_sources_are_rejected_before_opening

()

src/utils/bam_utils.rs:195

Methodempty

(mode: VcfReadMode)

src/merge/vcf_reader.rs:516

Methodempty

()

src/trgt/workflows/locus_result.rs:38

Methodencode_al

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:323

Methodencode_allr

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:333

Methodencode_am

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:401

Methodencode_ap

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:391

Methodencode_hd

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:344

Methodencode_mc

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:354

Methodencode_ms

(genotype: &Genotype)

src/trgt/writers/write_vcf.rs:370

Functionensure_unit_float

(s: &str)

src/cli.rs:772

Methodeq

(&self, other: &Self)

src/merge/vcf_processor.rs:44

Functionexposes_region_parts

()

src/utils/region.rs:93

Methodextract_trid

(record: &Record, contig: &str, pos: i64)

src/merge/vcf_processor.rs:932

Methodfield_exists_in_header

( header: &bcf::header::HeaderView, descriptor: &FieldDescriptor<'static>, )

src/merge/vcf_processor.rs:410

Methodfirst_locus

(&self)

src/trgt/locus_group.rs:65

Methodflatten_genotypes

(out_gts: &[Vec<Vec<GenotypeAllele>>])

src/merge/vcf_processor.rs:1189

Methodfmt

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

src/wfaligner.rs:137

Methodfmt

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

src/merge/vcf_reader.rs:36

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