Functions — github.com/10XGenomics/longranger

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Functions2,707 in github.com/10XGenomics/longranger

⨍ Functions 2,707◇ Types & classes 362

Returns chrom, start and stop from locus string. Enforces standardization of how locus is represented. chrom:start_stop (start and stop shoul

tenkit/lib/python/tenkit/bio_io.py:613

↓ 2 callersMethodget_overlaps_adaptive

ov_mat: sparse matrix window x window. ov_mat[i,j] is the number of BCs overlapping between the i-th window of the first chunk and th

lib/python/longranger/sv/overlap_detector.py:189

↓ 2 callersMethodget_pair_break_range

(read, other_read, max_ins)

lib/python/longranger/sv/readpairs.py:632

↓ 2 callersFunctionget_pos_confidence_intervals

(start, stop)

lib/python/longranger/sv/io.py:453

↓ 2 callersFunctionget_primary_contigs

(reference_path)

tenkit/lib/python/tenkit/reference.py:46

↓ 2 callersFunctionget_ranges

(poses1, poses2, max_dist = 1)

lib/python/longranger/sv/readpairs.py:395

↓ 2 callersFunctionget_read_group_endpoints

(reads)

mro/stages/structvars/call_structvars/__init__.py:335

↓ 2 callersMethodget_reads_iter_with_key

(self, key)

tenkit/lib/python/tenkit/bam.py:942

↓ 2 callersFunctionget_reads_section

Yield a Reads sample sheet section with the specified R1/R2 length. :rtype: SampleSheetSection

tenkit/lib/python/tenkit/samplesheet.py:379

↓ 2 callersFunctionget_record_genotype_phased

(record, sample_num=0)

tenkit/lib/python/tenkit/bio_io.py:372

↓ 2 callersFunctionget_record_max_length

(record)

tenkit/lib/python/tenkit/bio_io.py:151

↓ 2 callersFunctionget_region_overlaps

Finds overlaps between pairs of regions. regions1: Dictionary of NamedRegions objects as returned by loci_to_named_region_map. regions2: Simil

lib/python/longranger/sv/utils.py:222

↓ 2 callersFunctionget_run_data

Parse flowcell + lane from the first FASTQ record. NOTE: we don't check whether there are multiple FC / lanes in this file.

mro/stages/reads/setup_chunks/__init__.py:532

↓ 2 callersFunctionget_sex_chromosomes

(reference_path)

tenkit/lib/python/tenkit/reference.py:70

↓ 2 callersMethodget_summarizer

(self, summarizer_name)

tenkit/lib/python/tenkit/summary_manager.py:539

↓ 2 callersFunctionget_sv_type

(info_str)

lib/python/longranger/sv/io.py:120

↓ 2 callersFunctionget_variant_id

(variant,read)

mro/stages/reads/merge_pos_bam/__init__.py:456

↓ 2 callersFunctionget_variants

(read, tag)

mro/stages/reads/merge_pos_bam/__init__.py:437

↓ 2 callersFunctionget_variants_best

(read)

mro/stages/reads/merge_pos_bam/__init__.py:431

↓ 2 callersFunctionget_voffset

(bam, chrom, pos)

tenkit/lib/python/tenkit/chunk_utils.py:163

↓ 2 callersFunctiongo

(_args: &Args)

lib/pvc/src/detector.rs:50

↓ 2 callersFunctiongroup_bit_arr

(arr, start)

mro/stages/structvars/get_del_candidates/__init__.py:128

↓ 2 callersMethodhandle_bc_fragment_las

(&mut self, bam_writer: &mut bam::Writer, to_skip: bool)

lib/rust/report_single_partition/src/ec_las_fg.rs:236

↓ 2 callersMethodhas_ext

(&self, dir: Dir, base: u8)

lib/tada/src/kmer/exts.rs:66

↓ 2 callersMethodhas_item

(self, item)

mro/stages/reporter/filter_barcodes/union_find.py:51

↓ 2 callersFunctionhas_too_many_clipped

(in_bam, chrom, start, stop, min_mapq = 30, max_clipped_frac = 0.1)

mro/stages/structvars/filter_pileups/__init__.py:41

↓ 2 callersFunctioninfile

(path)

mro/stages/snpindels/populate_info/test/test_populate_info_fields.py:15

↓ 2 callersFunctioninit_threads

(num_threads: usize)

lib/tada/src/cmd_sort_fastq.rs:301

↓ 2 callersFunctionisZero

(o bgzf.Offset)

lib/go/src/code.google.com/p/biogo.bam/index.go:28

↓ 2 callersFunctionis_int

(s)

tenkit/lib/python/tenkit/preflight.py:18

↓ 2 callersMethodis_overlap

(&self, c: &Chrom, s: i32, e: i32)

lib/rust/report_single_partition/src/bed.rs:116

↓ 2 callersMethodlast_kmer

Get the last kmer in the sequence

lib/tada/src/kmer/mod.rs:106

↓ 2 callersMethodlength

()

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:87

↓ 2 callersFunctionlengthCode

(len uint32)

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:89

↓ 2 callersMethodliteral

Returns the literal of a literal token

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:82

↓ 2 callersFunctionliteralToken

Convert a literal into a literal token.

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:71

↓ 2 callersFunctionload_alerts

()

tenkit/lib/python/tenkit/supernova.py:30

↓ 2 callersFunctionload_barcode_whitelist2

(filename: P)

lib/tada/src/utils.rs:161

↓ 2 callersMethodload_key_index

(self)

tenkit/lib/python/tenkit/bam.py:927

↓ 2 callersFunctionload_sex_chromosomes

(reference_path, chr_type)

tenkit/lib/python/tenkit/reference.py:76

↓ 2 callersMethodlock_gem_estimate

Cache the GEM estimate and do not allow any more barcode updates.

tenkit/mro/stages/make_fastqs/make_qc_summary/__init__.py:145

↓ 2 callersFunctionlockstep_variant_iterator

Traverse two copies of the same variants in lockstep, making sure we never get out of sync.

mro/stages/snpindels/phase_snpindels/stitcher.py:48

↓ 2 callersFunctionlog_sum_exp

(p: &Vec<f64>)

lib/rust/hmm-bc-cnv/src/hmm.rs:7

↓ 2 callersFunctionmain_msp

(trim_min_qual: u8, bc_wl: &Path, fastq: Vec<PathBuf>, permutation: &Path, out_path: &Path)

lib/tada/src/cmd_msp.rs:76

↓ 2 callersFunctionmain_shard_asm

(min_kmer_obs: usize, chunk_id: usize, total_chunks: usize, shard_chunks: Vec<PathBuf>, sedge_asm_out: &Path,

lib/tada/src/cmd_shard_asm.rs:52

↓ 2 callersFunctionmain_sort_variants

(args, outs)

mro/stages/snpindels/sort_snpindels/__init__.py:24

↓ 2 callersFunctionmakeReader

(r io.Reader)

lib/go/src/code.google.com/p/biogo.bam/bgzf/reader.go:28

↓ 2 callersFunctionmakeReader

(r io.Reader)

lib/go/src/code.google.com/p/biogo.bam/bgzf/gzip/gunzip.go:30

↓ 2 callersFunctionmake_df_chunk

(fragments, bcs)

mro/stages/reporter/report_single_partition/__init__.py:582

↓ 2 callersFunctionmake_index_array

(uniques, values, dtype=np.uint16)

tenkit/lib/python/tenkit/hdf5.py:20

↓ 2 callersFunctionmake_index_array_dict

(idx_dict, values, dtype=np.uint16)

tenkit/lib/python/tenkit/hdf5.py:28

↓ 2 callersFunctionmapq_changed

(read)

mro/stages/structvars/filter_low_mapq/__init__.py:30

↓ 2 callersFunctionmatchToken

Convert a < xlength, xoffset > pair into a match token.

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:74

↓ 2 callersMethodmerge

(&mut self, other: &Fragment)

lib/rust/report_single_partition/src/fragment.rs:34

↓ 2 callersFunctionmerge_freq_bins

Merges bins of a histogram with similar frequency. Args: - frag_sizes: Ends of bins. - frag_counts: counts in bins. - merge_thresh: ma

lib/python/longranger/sv/stats.py:21

↓ 2 callersFunctionmerge_loci

(loci, start_idx = 0, merge = True)

mro/stages/structvars/detect_overlaps/__init__.py:237

↓ 2 callersFunctionnegative_binomial_loglikelihood

(mu: f64, alpha: f64, obs: i32)

lib/rust/hmm-bc-cnv/src/math.rs:27

↓ 2 callersFunctionoff_target_amp_corr_factor

Correction factor for amp rate (alpha) in off target regions. Args: - target_regions: region map with target regions per chrom. - prob_off

lib/python/longranger/sv/stats.py:96

↓ 2 callersFunctionoffsetCode

Returns the offset code corresponding to a specific offset

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:92

↓ 2 callersFunctionoutfile

(path)

mro/stages/structvars/analyze_sv_calls/test/test_analyze_sv_calls.py:21

↓ 2 callersFunctionoutfile

(path)

mro/stages/snpindels/analyze_snpindel_calls/test/test_analyze_snpindel_calls.py:22

↓ 2 callersFunctionoutfile

(path)

mro/stages/snpindels/populate_info/test/test_populate_info_fields.py:18

↓ 2 callersFunctionoutfile

(path)

tenkit/mro/stages/bcl_processor/demultiplex/test/test_demultiplex.py:32

↓ 2 callersFunctionoverlap

(s1, e1, s2, e2)

mro/stages/structvars/call_hmm_bc_cnv/__init__.py:177

↓ 2 callersMethodoverlapping_region_names

Returns a set of names of regions overlapping the given interval.

tenkit/lib/python/tenkit/regions.py:295

↓ 2 callersFunctionp_base_del_coverage

Model for P(Base Deletion | Coverage) Exponential with probability of 0.99 at 0 coverage and 0.02 at mean coverage

lib/pvc/src/validate.rs:397

↓ 2 callersMethodparseHeader

(text []byte)

lib/go/src/code.google.com/p/biogo.bam/parse_header.go:134

↓ 2 callersFunctionparse_gzip_sz

(fn)

mro/stages/reads/setup_chunks/__init__.py:438

↓ 2 callersFunctionpath_hap_summary

(path: &Vec<(usize, Dir)>, graph: &DebruijnGraph<Kmer1, PhasedReads>)

lib/pvc/src/asm_caller.rs:282

↓ 2 callersFunctionpick_files

(pathglob)

tenkit/mro/stages/bcl_processor/demultiplex/test/test_demultiplex.py:19

↓ 2 callersFunctionpostP

(n,m,l)

mro/stages/cnv/call_cnv/rPM_test.py:55

↓ 2 callersMethodprecompute_bc_overlaps

(frags, method, step=1000, max_frag_size=MAX_FRAG_SIZE, genome_size=3e9)

lib/python/longranger/sv/overlap_detector.py:69

↓ 2 callersFunctionprepare_loci

Merge and sort input lists of candidate loci.

mro/stages/structvars/call_structvars/__init__.py:79

↓ 2 callersMethodprior

(&self, _: usize)

lib/rust/hmm-bc-cnv/src/hmm.rs:233

↓ 2 callersFunctionprobability

(qual:u8)

lib/rust/report_single_partition/src/ec_las_fg.rs:626

↓ 2 callersFunctionprobability

(qual byte)

tenkit/lib/go/src/tenkit/barcode/barcode.go:322

↓ 2 callersFunctionpval_to_qual

(log10_pval)

lib/python/longranger/sv/utils.py:82

↓ 2 callersFunctionqP_byte

Generate query profile rearrange query sequence & calculate the weight of match/mismatch. */

tenkit/lib/python/striped_smith_waterman/ssw.c:89

↓ 2 callersFunctionqP_word

tenkit/lib/python/striped_smith_waterman/ssw.c:347

↓ 2 callersMethodquantile

(self, q)

tenkit/lib/python/tenkit/summary_manager.py:176

↓ 2 callersFunctionrand_set

(n: usize, m: usize)

lib/tada/src/min_hash/mod.rs:205

↓ 2 callersMethodraw_bc_qual

Raw barcode QVs

lib/tada/src/cmd_sort_fastq.rs:109

↓ 2 callersMethodread

(r io.Reader)

lib/go/src/code.google.com/p/biogo.bam/parse_header.go:59

↓ 2 callersMethodread2

()

lib/go/src/code.google.com/p/biogo.bam/bgzf/gzip/gunzip.go:158

↓ 2 callersMethodreadUint8

()

lib/go/src/code.google.com/p/biogo.bam/reader.go:270

↓ 2 callersFunctionread_bedpes

(args)

mro/stages/structvars/get_joint_read_lr/__init__.py:44

↓ 2 callersFunctionread_generation_pmf

Computes the log-probability of generating n reads from a region of length high_len + low_len, of which high_len have an amp rate of high_alpha

lib/python/longranger/sv/stats.py:212

↓ 2 callersFunctionread_locus

(fa: &mut fasta::IndexedReader<File>, loc: &Locus, pad_left: u32,

lib/pvc/src/call.rs:46

↓ 2 callersFunctionread_tabix_index

(h5_group)

tenkit/lib/python/tenkit/hdf5.py:829

↓ 2 callersFunctionread_table

(filename: P, has_headers: bool, delim: u8)

lib/rust/hmm-bc-cnv/src/support.rs:44

↓ 2 callersFunctionreal_file

(f)

mro/stages/snpindels/populate_info/__init__.py:56

↓ 2 callersFunctionreassemble_contigs

Take some input contig, which likely form a complicated graph, and test the kmer, bsp, sedge and edge construction machinery

lib/tada/src/sim_tests.rs:227

↓ 2 callersFunctionrefine_breaks

(read_groups, s1, e1, s2, e2, grid_len=1000, max_cand_breaks=100)

mro/stages/structvars/call_structvars/__init__.py:346

↓ 2 callersFunctionremove_commas

(s: &str)

lib/pvc/src/locus.rs:36

↓ 2 callersFunctionremove_deprecated_args

Given the argstr to pass into bcl2fastq, parse out any deprecated arguments and return the tokenized list.

tenkit/mro/stages/make_fastqs/bcl2fastq_with_samplesheet/__init__.py:44

↓ 2 callersFunctionrender

Render a variable, recursively.

tenkit/lib/go/src/tenkit/tenkit_py/export.py:133

↓ 2 callersFunctionrow_get_section_name

Return the name of the section contained in the row, if the row is a section header. :type row: list[string] :rtype: string

tenkit/lib/python/tenkit/samplesheet.py:303

↓ 2 callersFunctionrow_is_section_header

Return whether or not the specified row marks a new section in the sample sheet (e.g., [Header] in first cell) :type row: list[string]

tenkit/lib/python/tenkit/samplesheet.py:292

↓ 2 callersFunctionrow_is_simple_data

Return whether row appears to match lane-sample-index criteria, and why not if there is not a match. :type row: list[string] :rtype:

tenkit/lib/python/tenkit/samplesheet.py:165

↓ 2 callersFunctionrow_is_simple_header

Determine whether the row is a header row. The three cols must be "lane","sample" and "index", in order :type row: list[string] :rt

tenkit/lib/python/tenkit/samplesheet.py:108

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