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Types & classes362 in github.com/10XGenomics/longranger

⨍ Functions 2,707◇ Types & classes 362

↓ 191 callersTypeAliasset

lib/go/src/code.google.com/p/biogo.bam/header.go:85

↓ 21 callersClassBedpeInfoField

A BEDPE INFO field

lib/python/longranger/sv/io.py:305

↓ 15 callersClassLocus

lib/pvc/src/locus.rs:13

↓ 12 callersClassBedpeFilterField

A BEDPE filter field

lib/python/longranger/sv/io.py:323

↓ 11 callersClassRegions

Defines a set of regions and allows for determining whether a point is in ths sets or another region overlaps those sets.

tenkit/lib/python/tenkit/regions.py:29

↓ 10 callersTypeAliasCorruptInputError

A CorruptInputError reports the presence of corrupt input at a given offset.

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

↓ 9 callersClassSampleSheetSection

A named section with rows of text.

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

↓ 9 callersTypeAliasbyBeginOffset

lib/go/src/code.google.com/p/biogo.bam/index.go:46

↓ 8 callersClassNotSupportedException

For when a specified method isn't supported yet- e.g. when a distribution is specified that hasn't been built yet for the given code.

tenkit/lib/python/tenkit/exceptions.py:8

↓ 7 callersClassDupSummary

mro/stages/reads/mark_duplicates/__init__.py:194

↓ 6 callersTypeAliasAux

An Aux represents an auxilliary tag data field from a SAM alignment record.

lib/go/src/code.google.com/p/biogo.bam/auxtags.go:17

↓ 6 callersClassOverlapDetector

lib/python/longranger/sv/overlap_detector.py:36

↓ 5 callersClassFastqParser

tenkit/mro/stages/bcl_processor/demultiplex/__init__.py:123

↓ 4 callersClassBreakpointAnalyzer

Class for finding barcode and read overlaps around given SVs

lib/python/longranger/sv/breakpoint_analyzer.py:23

↓ 4 callersClassIlmnFastqFile

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

↓ 4 callersClassReadPair

Class representing a junction-supporting pair of reads (i.e. improperly mapped or split).

lib/python/longranger/sv/readpairs.py:561

↓ 3 callersTypeAliasCigarOp

lib/go/src/code.google.com/p/biogo.bam/cigar.go:40

↓ 3 callersTypeAliasHeader

lib/go/src/code.google.com/p/biogo.bam/bgzf/reader.go:156

↓ 3 callersTypeAliasInternalError

An InternalError reports an error in the flate code itself.

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/inflate.go:35

↓ 3 callersClassMergedQuantileEstimator

tenkit/lib/python/tenkit/summary_manager.py:206

↓ 3 callersClassPhaser

Constructs and outputs inferred haplotypes.

mro/stages/snpindels/phase_snpindels/phaser.py:30

↓ 3 callersClassVariantFileReader

tenkit/lib/python/tenkit/bio_io.py:21

↓ 3 callersTypeAliasbyBinNumber

lib/go/src/code.google.com/p/biogo.bam/index.go:40

↓ 3 callersTypeAliasbyVirtOffset

lib/go/src/code.google.com/p/biogo.bam/index.go:52

↓ 2 callersClassAmbiguousValueError

Special value error signaling that the arguments need to be more specific.

tenkit/lib/python/tenkit/fasta.py:282

↓ 2 callersClassEvent

lib/python/longranger/cnv/event_bed.py:4

↓ 2 callersClassHomoEvent

lib/python/longranger/cnv/event_bed.py:199

↓ 2 callersClassLaneLayout

Extents of a particular flowcell, lane combination

tenkit/lib/python/tenkit/lane.py:86

↓ 2 callersClassReadInfo

lib/python/longranger/sv/read_model.py:15

↓ 2 callersClassTrioRow

mro/stages/snpindels/analyze_trio_variants/trio.py:20

↓ 2 callersClassTruthStatus

lib/python/longranger/cnv/compare_utils.py:10

↓ 2 callersClassTruthStatus

lib/python/longranger/cnv/analysis.py:11

↓ 2 callersTypeAliasfailure

lib/go/src/code.google.com/p/biogo.bam/bam_test.go:29

↓ 2 callersTypeAliastoken

lib/go/src/code.google.com/p/biogo.bam/bgzf/flate/token.go:68

↓ 1 callersClassAligner

@class SSWAligner @brief Wrapper for SSW align library

tenkit/lib/python/striped_smith_waterman/ssw_wrap.py:40

↓ 1 callersClassBasicSummary

tenkit/lib/python/tenkit/summary_manager.py:432

↓ 1 callersClassBcSimilarity

mro/stages/reporter/filter_barcodes/coalescence.py:19

↓ 1 callersClassBclProcessorFastqFile

Parse the FASTQ name from the demux stage output, to get the read name, lane, sample index, and chunk.

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

↓ 1 callersTypeAliasBucketChunk

filetype for sorting

lib/go/src/reads/sort_fastq_by_bc/main.go:147

↓ 1 callersClassCall

mro/stages/snpindels/analyze_trio_variants/trio.py:220

↓ 1 callersTypeAliasCigarOpType

A CigarOpType represents the type of operation described by a CigarOp.

lib/go/src/code.google.com/p/biogo.bam/cigar.go:57

↓ 1 callersClassDictionaryDistribution

tenkit/lib/python/tenkit/summary_manager.py:391

↓ 1 callersClassDiscreteDistribution

tenkit/lib/python/tenkit/summary_manager.py:284

↓ 1 callersClassEvent

lib/python/longranger/cnv/compare_utils.py:142

↓ 1 callersClassFakeNamedTuple

tenkit/lib/python/tenkit/bio_io.py:520

↓ 1 callersClassFastqRow

tenkit/mro/stages/bcl_processor/demultiplex/__init__.py:111

↓ 1 callersClassFindCommonBarcodes

tenkit/mro/stages/bcl_processor/demultiplex/__init__.py:149

↓ 1 callersTypeAliasFlags

A Flags represents a BAM record's alignment FLAG field.

lib/go/src/code.google.com/p/biogo.bam/flag.go:8

↓ 1 callersClassLaneCoordinateSystem

tenkit/lib/python/tenkit/lane.py:122

↓ 1 callersClassPyAlignRes

@class PyAlignRes @brief Extract and verify result from a CAlignRes structure. A comprehensive python object is created according to us

tenkit/lib/python/striped_smith_waterman/ssw_wrap.py:267

↓ 1 callersClassQuantileEstimator

tenkit/lib/python/tenkit/summary_manager.py:36

↓ 1 callersTypeAliasRawGeneArray

lib/go/src/loupe/formats/bed.go:69

↓ 1 callersClassRevTuple

tenkit/lib/python/tenkit/bam.py:603

↓ 1 callersClassSimpleEvent

lib/python/longranger/cnv/event_bed.py:295

↓ 1 callersClassStatus

lib/python/longranger/cnv/compare_utils.py:16

↓ 1 callersClassStatus

lib/python/longranger/cnv/analysis.py:17

↓ 1 callersClassSummaryManager

tenkit/lib/python/tenkit/summary_manager.py:534

↓ 1 callersTypeAliasTrackDataSorter

lib/go/src/loupe/formats/bed.go:351

↓ 1 callersTypeAliasVCFArray

lib/go/src/loupe/formats/vcf.go:74

↓ 1 callersClassVariantFileWriter

tenkit/lib/python/tenkit/bio_io.py:159

↓ 1 callersTypeAliasnybblePairs

lib/go/src/code.google.com/p/biogo.bam/record.go:225

↓ 1 callersClassrPMRecord

lib/python/longranger/cnv/rpm_utils.py:15

ClassAlertLogger

tenkit/lib/python/tenkit/supernova.py:60

ClassAlignedSegment

lib/pvc/src/detector.rs:89

Class for taking in a fastq file and running an aligner on it.

tenkit/lib/python/tenkit/align.py:15

tenkit/lib/python/striped_smith_waterman/ssw_cpp.h:69

tenkit/lib/python/striped_smith_waterman/ssw_cpp.h:10

lib/pvc/src/event.rs:16

lib/tada/src/main.rs:97

lib/pvc/src/main.rs:73

lib/rust/report_single_partition/src/main.rs:59

lib/rust/hmm-bc-cnv/src/main.rs:60

* * This structure represents the entire contents of a BED file. */

lib/go/src/loupe/formats/bed.go:35

lib/rust/report_single_partition/src/ec_las_fg.rs:77

lib/rust/hmm-bc-cnv/src/bed.rs:12

ClassBamBCIndex

tenkit/lib/python/tenkit/bam.py:1047

tenkit/lib/python/tenkit/bam.py:891

ClassBamQnameIndex

tenkit/lib/python/tenkit/bam.py:1021

ClassBarcodeCount

lib/rust/report_single_partition/src/bc_correction.rs:12

StructBarcodeCounter

tenkit/lib/go/src/tenkit/barcode/barcode.go:15

StructBarcodeCounts

tenkit/lib/go/src/tenkit/barcode/barcode.go:247

StructBarcodeInfo

tenkit/lib/go/src/barcodeqc/main.go:14

ClassBarcodeState

lib/rust/report_single_partition/src/fragment.rs:47

ClassBarcodeValidator

lib/rust/report_single_partition/src/bc_correction.rs:18

StructBarcodeValidator

tenkit/lib/go/src/tenkit/barcode/barcode.go:173

lib/rust/report_single_partition/src/ec_las_fg.rs:637

lib/tada/src/utils.rs:95

lib/rust/report_single_partition/src/bed.rs:84

lib/rust/hmm-bc-cnv/src/bed.rs:6

lib/go/src/cnv/molecular_count/bed.go:24

lib/pvc/src/event.rs:202

lib/go/src/code.google.com/p/biogo.bam/index.go:71

lib/tada/src/bitenc.rs:23

ClassBitEncIter

Iterator over values of a bitencoded sequence (values will be unpacked into bytes).

lib/tada/src/bitenc.rs:364

ClassBitEncSlice

lib/tada/src/bitenc.rs:381

StructBlockIndexBuilder

* * This object contains all of the intermediate data we need to build up the index * and data segments of the blocked index. */

lib/go/src/loupe/formats/blocked_index.go:91

StructBlockedIndex

* * This forms the entirety of the "index" section of a blocked annotation * data structure. */

lib/go/src/loupe/formats/blocked_index.go:78

StructBlockedJSONIndex

* This holds all of the data we require to build (and store) a blocked index. TODO: Right now this holds both the "internal" state as well as any ex

lib/go/src/loupe/formats/blocked_json_index.go:44

StructBlockedJSONIndexEntry

* This associates a particular region with an array of GenericTrackData objects (for teh actual intervals within that region) located at a particula

lib/go/src/loupe/formats/blocked_json_index.go:32

StructBreakpointDetails

* * Holds data related to structural variant phasing */

lib/go/src/loupe/formats/sv.go:27

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