Functions — github.com/PacificBiosciences/trgt

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Functions837 in github.com/PacificBiosciences/trgt

⨍ Functions 837◇ Types & classes 113

↓ 1 callersFunctionget_len_hist

(seqs: &[&[u8]])

src/trgt/genotype/genotype_size.rs:66

↓ 1 callersFunctionget_loci

( catalog_reader: R, genome_reader: faidx::Reader, karyotype: Karyotype, flank_len: usize,

src/commands/validate.rs:10

↓ 1 callersFunctionget_locus

( catalog_reader: R, genome_reader: faidx::Reader, tr_id: &str, flank_len: usize, )

src/utils/input.rs:51

↓ 1 callersFunctionget_loglik

(gt: &(Vec<bool>, Vec<bool>), profiles: &[Profile])

src/trgt/genotype/genotype_flank.rs:183

↓ 1 callersFunctionget_longest_pipe

(plot: &PipePlot)

crates/pipeplot/src/svg.rs:21

↓ 1 callersFunctionget_match_emissions

(base: u8)

src/hmm/builder.rs:175

↓ 1 callersFunctionget_meth_by_hap

(gt: &Gt, spanning_reads: &[SpanningRead])

src/trgt/workflows/tr.rs:199

↓ 1 callersFunctionget_mm_tag

Given a DNA sequence, make the MM tag for CpGs

src/commands/deepdive.rs:40

↓ 1 callersMethodget_padding_base

(&self, contig: &str, pos: i64)

src/merge/vcf_processor.rs:806

↓ 1 callersFunctionget_pipe

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

src/trvz/waterfall_plot.rs:234

↓ 1 callersMethodget_ploidy

(&self, chrom: &str)

src/utils/karyotype.rs:94

↓ 1 callersFunctionget_ps_tag

Retrieves the PS (phase set) tag from a BAM record. # Arguments `rec` - A reference to the BAM record. # Returns Returns an `Option<u32>` which is `

src/trgt/reads/read.rs:215

↓ 1 callersFunctionget_reference_end

Calculates the end position of the reference sequence based on the CIGAR operations. # Arguments `cigar` - A reference to the `Cigar` struct represen

src/trgt/reads/clip_region.rs:59

↓ 1 callersFunctionget_sample_name

(reads_src: &InputSource, bam_header: &bam::Header)

src/utils/bam_utils.rs:14

↓ 1 callersFunctionget_seq_hist

(mut seqs: Vec<&[u8]>)

src/trgt/genotype/genotype_size.rs:77

↓ 1 callersFunctionget_spanning_reads

(locus: &mut Locus, params: &Params)

src/trgt/workflows/tr.rs:158

↓ 1 callersFunctionget_tr_meth

(sr: &SpanningRead)

src/trgt/workflows/tr.rs:260

↓ 1 callersFunctionget_trgt_version

(vcf_header: &HeaderView, file: &Path)

src/merge/vcf_reader.rs:307

↓ 1 callersFunctionget_trs_with_clustering

( reads: &[&LocusRead], tr_seqs: &[&'a [u8]], region: &GenomicRegion, )

src/trgt/genotype/genotype_flank.rs:85

↓ 1 callersFunctionget_trs_with_hp

( reads: &[&LocusRead], tr_seqs: &[&'a [u8]], )

src/trgt/genotype/genotype_flank.rs:49

↓ 1 callersFunctionhas_ext

(p: &Path, ext: &str)

src/utils/readers/bam.rs:37

↓ 1 callersFunctionhas_gzip_magic

(path: &Path)

src/merge/vcf_reader.rs:77

↓ 1 callersFunctionhas_reference_targets

(bam_header: &bam::Header)

src/utils/bam_utils.rs:10

↓ 1 callersMethodid

(mut self, id: &str)

src/utils/locus.rs:110

↓ 1 callersMethodindel_penalties

(mut self)

src/wfaligner.rs:193

↓ 1 callersFunctionindex_to_base

(index: usize)

src/trgt/genotype/consensus.rs:81

↓ 1 callersMethodindexed_reader_mut

(&mut self)

src/merge/vcf_reader.rs:248

↓ 1 callersMethodinfo_flag

(mut self, key: K)

src/utils/test_util.rs:229

↓ 1 callersMethodinit_heap

(&mut self, contig: &str)

src/merge/vcf_processor.rs:681

↓ 1 callersMethodinit_streaming_heap

( &mut self, last_rid_per_reader: &mut [Option<u32>], last_pos_per_reader: &mut [Optio

src/merge/vcf_processor.rs:705

↓ 1 callersFunctioninit_verbose

(args: &Cli)

src/cli.rs:691

↓ 1 callersMethodinto_parts

(self)

src/merge/vcf_writer.rs:78

↓ 1 callersFunctionis_cram_source

(src: &InputSource)

src/utils/readers/bam.rs:30

↓ 1 callersFunctionis_indexed_local

(file: &Path)

src/merge/vcf_reader.rs:73

↓ 1 callersFunctionis_path_like

(encoding: &str)

src/utils/karyotype.rs:118

↓ 1 callersMethoditer_mut_with_id

(&mut self)

src/merge/field_registry.rs:415

↓ 1 callersFunctionlabel_with_hmm

(locus: &Locus, seqs: &[Vec<u8>])

src/trgt/workflows/tr.rs:370

↓ 1 callersMethodlast_locus

(&self)

src/trgt/locus_group.rs:70

↓ 1 callersFunctionlevel_style

(level: Level)

src/cli.rs:708

↓ 1 callersMethodlinear_penalties

(mut self, match_: i32, mismatch: i32, indel: i32)

src/wfaligner.rs:203

↓ 1 callersFunctionln_sum_exp

(term1: f64, term2: f64)

src/trgt/genotype/genotype_flank.rs:210

↓ 1 callersFunctionlocus_search_start

(locus: &Locus, flank_len: u32)

src/trgt/locus_group.rs:87

↓ 1 callersMethodlog_discovery_summary

(&self)

src/merge/vcf_processor.rs:395

↓ 1 callersFunctionlooks_like_bcf

(p: &[u8])

src/merge/vcf_reader.rs:86

↓ 1 callersFunctionlooks_like_vcf

(p: &[u8])

src/merge/vcf_reader.rs:90

↓ 1 callersFunctionlookup_idx

(idx: i32, mapping: &[Option<i32>])

src/merge/genotype_types.rs:18

↓ 1 callersFunctionmedian

(data: &[i32])

src/utils/math.rs:73

↓ 1 callersFunctionmedian_of_three_index

(data: &[i32], low: usize, mid: usize, high: usize)

src/utils/math.rs:4

↓ 1 callersMethodmemory_model

(mut self, memory_model: MemoryModel)

src/wfaligner.rs:173

↓ 1 callersFunctionmerge

(args: MergeArgs)

src/commands/merge.rs:5

↓ 1 callersMethodmerge_headers

(&self, dst_header: &mut Header)

src/merge/vcf_reader.rs:475

↓ 1 callersMethodmerge_variant

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

src/merge/vcf_processor.rs:854

↓ 1 callersMethodmerge_variants_indexed

(&mut self)

src/merge/vcf_processor.rs:459

↓ 1 callersMethodmerge_variants_streaming

(&mut self)

src/merge/vcf_processor.rs:526

↓ 1 callersFunctionmissing_required_format_field_error

(processor: &VcfProcessor)

src/merge/vcf_processor.rs:1423

↓ 1 callersFunctionmissing_required_info_field_error

(processor: &mut VcfProcessor)

src/merge/vcf_processor.rs:1433

↓ 1 callersFunctionop_to_cigar

Convert individual WFA ops to rust htslib

src/commands/deepdive.rs:21

↓ 1 callersFunctionopen_genotyper_bam_reader

( reads_src: &InputSource, genome_src: &InputSource, decompression_threads: usize, )

src/utils/readers/bam.rs:94

↓ 1 callersFunctionopen_genotyper_bam_reader_with_thread_pool

( reads_src: &InputSource, genome_src: &InputSource, thread_pool: &ThreadPool, )

src/utils/readers/bam.rs:108

↓ 1 callersFunctionopen_multi_fetcher_bam_reader

( bam_sources: &BamSources, genome_src: &InputSource, decompression_threads: usize, )

src/commands/genotype.rs:364

↓ 1 callersFunctionopen_single_fetcher_bam_reader

( reads_src: &InputSource, genome_src: &InputSource, decompression_threads: usize, )

src/commands/genotype.rs:355

↓ 1 callersFunctionopen_vcf_reader

(bcf_src: &InputSource)

src/utils/readers/vcf.rs:4

↓ 1 callersMethodorder_states

(&self)

src/hmm/hmm_model.rs:206

↓ 1 callersMethodoutput_suffix

(&self)

src/utils/io_utils.rs:72

↓ 1 callersFunctionparse_meth

(read: &bam::Record, seq: &[u8])

src/utils/input.rs:233

↓ 1 callersFunctionpartition_inplace

Partition data in-place using Lomuto scheme

src/utils/math.rs:18

↓ 1 callersFunctionpick_colors

(motifs: &[Vec<u8>])

src/trvz/params.rs:30

↓ 1 callersFunctionpick_params

(motifs: &[Vec<u8>], is_squished: bool)

src/trvz/params.rs:12

↓ 1 callersFunctionplot

( locus: &InputLocus, what_to_show: &str, reads: &[(Align, Vec<Beta>)], params: &PlotParams, )

src/trvz/waterfall_plot.rs:182

↓ 1 callersFunctionplot_alleles

( locus: &InputLocus, what_to_show: &str, allele_seqs: &[Vec<u8>], reads: &[Read], params:

src/trvz/allele_plot.rs:10

↓ 1 callersMethodplot_legend

(&mut self, legend: &Legend, font: &FontConfig)

crates/pipeplot/src/svg.rs:65

↓ 1 callersMethodplot_outline

(&mut self, pipe: &Pipe)

crates/pipeplot/src/svg.rs:128

↓ 1 callersMethodplot_pipe

(&mut self, pipe: &Pipe, font: &FontConfig)

crates/pipeplot/src/svg.rs:84

↓ 1 callersFunctionplot_waterfall

( locus: &InputLocus, what_to_show: &str, reads: &[Read], params: &PlotParams, )

src/trvz/waterfall_plot.rs:16

↓ 1 callersMethodpreflight_checks_inner

(&self)

src/utils/input_source.rs:223

↓ 1 callersMethodprimary

(&self)

src/utils/input_source.rs:100

↓ 1 callersFunctionprocess_locus

( locus: Locus, workflow_params: &Params, sender_result: &Sender<(Locus, LocusResult)>, )

src/commands/genotype.rs:386

↓ 1 callersMethodprocess_vcf_paths

(&self)

src/cli.rs:555

↓ 1 callersMethodpush_missing_for_all_fields

(&mut self, n: usize)

src/merge/field_registry.rs:444

↓ 1 callersMethodread_sources

(&self)

src/cli.rs:335

↓ 1 callersFunctionrecord_missing_required_format_field

()

src/merge/vcf_processor.rs:1312

↓ 1 callersFunctionreject_duplicate_bam_sources

(bam_sources: &[InputSource])

src/utils/bam_utils.rs:80

↓ 1 callersFunctionreplace_invalid_bases_inplace

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

src/hmm/utils.rs:30

↓ 1 callersMethodreset

(&mut self)

src/trgt/genotype_reader.rs:194

↓ 1 callersFunctionresolve_sample_name

( bam_sources: &[InputSource], headers: &[bam::Header], sample_name_override: Option<&str>, )

src/utils/bam_utils.rs:128

↓ 1 callersMethodreturn_records

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

src/merge/vcf_processor.rs:924

↓ 1 callersFunctionrunner

()

src/main.rs:22

↓ 1 callersMethodscore

(&self)

src/wfaligner.rs:530

↓ 1 callersMethodset_alignment_end_to_end

(&mut self)

src/wfaligner.rs:465

↓ 1 callersMethodset_alignment_ends_free

( &mut self, pattern_begin_free: i32, pattern_end_free: i32, text_begin_free:

src/wfaligner.rs:471

↓ 1 callersMethodset_font_family

(&mut self, font_family: &str)

crates/pipeplot/src/pipeplot.rs:70

↓ 1 callersFunctionsimple_consensus

Determine consensus for the input sequences Return the most frequent sequence and its relative frequency. If multiple sequences have the same frequen

src/trgt/genotype/genotype_flank.rs:162

↓ 1 callersFunctionsmall_group_is_outlier

GS: this should be handled better, but for now we just check for small differences in size and large differences in cov

src/trgt/genotype/genotype_cluster.rs:83

↓ 1 callersFunctionspawn_fetcher_threads

( scope: &'scope thread::Scope<'scope, '_>, bam_sources: &BamSources, genome_src: &InputSource,

src/commands/genotype.rs:275

↓ 1 callersFunctionsplit

( allele_lens: ArrayVec<usize, 2>, seqs: &'a [&'a [u8]], counts: &'a [usize], )

src/trgt/genotype/genotype_size.rs:89

↓ 1 callersMethodstart_svg

(&mut self, width: f64, height: f64)

crates/pipeplot/src/svg.rs:285

↓ 1 callersFunctionstream_locus_groups_into_channel

( repeats_src: &InputSource, genome_src: &InputSource, flank_len: usize, genotyper: Genotyper,

src/trgt/locus.rs:118

↓ 1 callersFunctiontest_bam_contig_tid

(contig: &str)

src/utils/test_util.rs:152

↓ 1 callersMethodtraceback

(&self, query: &[u8], states: &[Vec<Option<usize>>])

src/hmm/hmm_model.rs:125

↓ 1 callersFunctiontrgt

(args: GenotypeArgs)

src/commands/genotype.rs:69

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