Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

Functionnext_source_index_fills_missing_records_before_selecting_minimum

()

src/trgt/genotype_reader.rs:347

Functionnormalize_reads_keeps_dominant_ps

()

src/trgt/workflows/tr.rs:554

Functionnormalize_reads_no_ps_observed

()

src/trgt/workflows/tr.rs:592

Functionnormalize_reads_prefers_smaller_ps_on_ties

()

src/trgt/workflows/tr.rs:575

Functionoutput_suffix_matches_type_and_compression

()

src/utils/io_utils.rs:204

Functionparse_aga_repeat

()

src/hmm/builder.rs:253

Functionphase_by_hp_ps_counts_hp_reads_when_assigned

()

src/trgt/workflows/tr.rs:635

Functionphase_by_hp_ps_rejects_multiple_ps

()

src/trgt/workflows/tr.rs:610

Functionphase_by_hp_ps_requires_two_hps

()

src/trgt/workflows/tr.rs:623

Methodpreflight_ext

(&self)

src/utils/input_source.rs:338

Methodprocess_genotypes

( record: &Record, genotypes: &mut Vec<Vec<Vec<GenotypeAllele>>>, )

src/merge/vcf_processor.rs:1167

Methodquery_len

(&self)

src/trgt/reads/cigar.rs:40

Methodread_info_field

( record: &Record, descriptor: &FieldDescriptor<'static>, cache: &mut FieldIdCache,

src/merge/vcf_processor.rs:1028

Methodread_vcf_paths_from_file

(path: &Path)

src/cli.rs:563

Functionrecord_missing_required_info_field

()

src/merge/vcf_processor.rs:1351

Methodregion

(mut self, region: GenomicRegion)

src/utils/locus.rs:135

Functionrender_from_string

(svg_content: &str, path: &Path)

crates/pipeplot/src/pdf.rs:4

Functionrender_from_string

(svg_content: &str, path: &Path)

crates/pipeplot/src/png.rs:4

Methodright_flank

(mut self, flank: Vec<u8>)

src/utils/locus.rs:130

Functionsample_names_from_header

(header: &bam::Header)

src/utils/bam_utils.rs:161

Functionscoring_from_string

(s: &str)

src/cli.rs:786

Methodset_gt

This method encodes the genotype information and adds it to the VCF record. # Arguments `locus` - `Locus` struct containing information about the tan

src/trgt/writers/write_vcf.rs:251

Functionset_system_ca_bundle

()

src/utils/input_source.rs:304

Functionsilent_states_match_a_blank_character

()

src/hmm/events.rs:139

Methodsingle

(reader: bam::IndexedReader)

src/trgt/genotype_reader.rs:19

Functionsingle_source_reader_delegates_fetch_and_read

()

src/trgt/genotype_reader.rs:272

Functionsingle_source_sample_name_behavior_remains_backward_compatible

()

src/utils/bam_utils.rs:325

Functionsnv_at_tr_end_is_used

()

src/trgt/genotype/genotype_flank.rs:631

Functionsnv_at_tr_start_is_ignored

()

src/trgt/genotype/genotype_flank.rs:603

Functionstates_match_the_most_likely_base

()

src/hmm/events.rs:125

Functionstates_with_equal_emission_probs_match_n_base

()

src/hmm/events.rs:132

Functionstreaming_contig_order_mismatch_errors

()

src/merge/vcf_reader.rs:608

Functionstreaming_reader_accepts_unindexed_vcf

()

src/merge/vcf_reader.rs:562

Methodstruc

(mut self, struc: &str)

src/utils/locus.rs:115

Functionsummarize

(spans: &[Span])

src/hmm/builder.rs:191

Functionsupplemental_reference_dictionary_must_match_primary

()

src/utils/bam_utils.rs:229

Functiontest_add_extension

()

src/merge/vcf_reader.rs:550

Functiontest_add_locus_unchecked_extends_region

()

src/trgt/locus_group.rs:289

Functiontest_add_locus_unchecked_no_extension_needed

()

src/trgt/locus_group.rs:304

Functiontest_aligner_edit

()

src/wfaligner.rs:1153

Functiontest_aligner_ends_free_global

()

src/wfaligner.rs:1264

Functiontest_aligner_ends_free_left_extent

()

src/wfaligner.rs:1301

Functiontest_aligner_ends_free_right_extent

()

src/wfaligner.rs:1282

Functiontest_aligner_ends_free_right_overlap

()

src/wfaligner.rs:1319

Functiontest_aligner_gap_affine

()

src/wfaligner.rs:1185

Functiontest_aligner_gap_affine_2pieces

()

src/wfaligner.rs:1214

Functiontest_aligner_gap_linear

()

src/wfaligner.rs:1169

Functiontest_aligner_indel

()

src/wfaligner.rs:1137

Functiontest_aligner_score_only

()

src/wfaligner.rs:1201

Functiontest_aligner_span_1

()

src/wfaligner.rs:1230

Functiontest_aligner_span_2

()

src/wfaligner.rs:1246

Functiontest_allele_registry_basic

()

src/merge/genotype_types.rs:128

Functiontest_allele_registry_empty_list

()

src/merge/genotype_types.rs:187

Functiontest_allele_registry_mapping

()

src/merge/genotype_types.rs:153

Functiontest_allele_registry_ref_mismatch

()

src/merge/genotype_types.rs:175

Functiontest_allr_has_alci_alias

()

src/merge/field_descriptors.rs:219

Functiontest_am_has_converter

()

src/merge/field_descriptors.rs:230

Functiontest_append_record_missing_optional_field

()

src/merge/field_registry.rs:789

Functiontest_attach_to_all

()

src/merge/tpool.rs:291

Functiontest_attach_to_reader_is_callable

()

src/merge/tpool.rs:199

src/trgt/workflows/locus_result.rs:17

Functiontest_basemods_error

()

src/trgt/reads/read.rs:247

Functiontest_build_header_only

()

src/utils/test_util.rs:695

Functiontest_builder_pattern

()

src/wfaligner.rs:1525

Functiontest_cached_record_reuse

()

src/trgt/writers/write_vcf.rs:498

Functiontest_can_add_locus_different_contig

()

src/trgt/locus_group.rs:261

Functiontest_can_add_locus_exceeds_max_span

()

src/trgt/locus_group.rs:270

Functiontest_can_add_locus_same_contig

()

src/trgt/locus_group.rs:248

Functiontest_can_add_locus_unsorted_warning

()

src/trgt/locus_group.rs:280

Functiontest_cigar_conversion

()

src/trgt/reads/snp.rs:196

Functiontest_clip_edge_cases

()

src/trgt/reads/clip_bases.rs:146

Functiontest_clip_from_both_sides

()

src/trgt/reads/clip_bases.rs:199

Functiontest_clip_from_left

()

src/trgt/reads/clip_bases.rs:163

Functiontest_clip_from_right

()

src/trgt/reads/clip_bases.rs:181

Functiontest_clipping_score

()

src/wfaligner.rs:1337

Functiontest_consecutive_mismatches

()

src/trgt/reads/snp.rs:530

Functiontest_convert_am_field

()

src/merge/field_descriptors.rs:312

Functiontest_convert_am_field_multisample

()

src/merge/field_descriptors.rs:338

Functiontest_custom_info_field_optional_across_vcfs

()

src/merge/vcf_processor.rs:1855

Functiontest_duplicate_records_within_reader

()

src/merge/vcf_processor.rs:1613

Functiontest_emits_trailing_insertion_with_majority

()

src/trgt/genotype/consensus.rs:193

Functiontest_exact_max_span_boundary

()

src/trgt/locus_group.rs:350

Functiontest_extract_mismatch_positions_full_cigar

()

src/trgt/reads/snp.rs:618

Functiontest_extract_mismatch_positions_multiple_mismatches

()

src/trgt/reads/snp.rs:598

Functiontest_extract_mismatch_positions_no_mismatches

()

src/trgt/reads/snp.rs:588

Functiontest_extract_mismatch_positions_simple

()

src/trgt/reads/snp.rs:578

Functiontest_extract_mismatch_positions_with_del_and_skip

()

src/trgt/reads/snp.rs:608

Functiontest_field_data_registry

()

src/merge/field_registry.rs:696

Functiontest_field_data_registry_iter_mut

()

src/merge/field_registry.rs:737

Functiontest_field_descriptor

()

src/merge/field_registry.rs:672

Functiontest_field_descriptor_builder_helpers

()

src/merge/field_registry.rs:885

Functiontest_field_id_cache

()

src/merge/field_registry.rs:934

Functiontest_field_value_all_types

()

src/merge/field_registry.rs:625

Functiontest_format_error_local_unchanged

()

src/utils/input_source.rs:467

Functiontest_format_error_redacts_url

()

src/utils/input_source.rs:454

Functiontest_format_error_with_query

()

src/utils/input_source.rs:481

Functiontest_format_fields_defined

()

src/merge/field_descriptors.rs:195

Functiontest_format_number_with_commas_i16

()

src/utils/util.rs:58

Functiontest_format_number_with_commas_i32

()

src/utils/util.rs:74

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