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Types & classes237 in github.com/Illumina/hap.py

⨍ Functions 854◇ Types & classes 237

↓ 32 callersClassValue

external/jsoncpp/json/json.h:240

↓ 12 callersClassimportexception

when things go wrong, this gets thrown */

src/c++/include/helpers/BCFHelpers.hh:67

↓ 11 callersClassivcount

src/c++/test/test_intervallist.cpp:87

↓ 9 callersClassVariants

* @brief Stores multiple VCF/BCF Variant records * @details Performs basic validation * */

src/c++/include/Variant.hh:163

↓ 8 callersClassivlist

src/c++/test/test_intervallist.cpp:158

↓ 7 callersClassCall

* @brief Variant call for a given location */

src/c++/include/Variant.hh:74

↓ 6 callersClassPathArgument

external/jsoncpp/json/json.h:239

↓ 5 callersClassCallInfo

src/c++/lib/variant/VariantAlleleSplitter.cpp:135

↓ 5 callersClassVariantStatistics

src/c++/include/variant/VariantStatistics.hh:54

↓ 5 callersClassbcf_get_info

src/c++/lib/tools/BCFHelpers.cpp:205

↓ 4 callersClassLoggingWriter

Helper class to write tracebacks to log file

src/python/Tools/__init__.py:105

↓ 2 callersClassAlignmentResult

Alignment result storage */

src/c++/include/Alignment.hh:136

↓ 2 callersClassFastaFile

src/c++/include/Fasta.hh:45

↓ 2 callersClassFeatures

external/jsoncpp/json/json.h:233

↓ 2 callersClassHaplotypeDiff

src/c++/include/HaploCompare.hh:52

↓ 2 callersClassRoc

src/c++/include/helpers/Roc.hh:194

↓ 2 callersClassStaticString

external/jsoncpp/json/json.h:237

↓ 2 callersClassValueIteratorBase

external/jsoncpp/json/json.h:241

↓ 2 callersClassinterval

interval interface */

src/c++/include/helpers/IntervalList.hh:53

↓ 1 callersClassAlignmentParameters

src/c++/include/Alignment.hh:45

↓ 1 callersClassBedIntervalTree

src/python/Tools/bedintervaltree.py:17

↓ 1 callersClassCallerInfo

Class for collecting caller info and version

src/python/Tools/vcfcallerinfo.py:20

↓ 1 callersClassFastWriter

external/jsoncpp/json/json.h:226

↓ 1 callersClassHCall_less

src/c++/lib/variant/VariantAlleleSplitter.cpp:244

↓ 1 callersClassHaplotype

src/c++/include/Haplotype.hh:52

↓ 1 callersClassIteratorState

external/jsoncpp/json/json.h:1011

↓ 1 callersClassMaxEnumException

src/c++/lib/scmp/HapSetMatcher.cpp:119

↓ 1 callersClassPath

external/jsoncpp/json/json.h:238

↓ 1 callersClassReader

external/jsoncpp/json/json.h:230

↓ 1 callersClassReferenceEdge

src/c++/include/GraphReference.hh:50

↓ 1 callersClassStyledWriter

external/jsoncpp/json/json.h:227

↓ 1 callersClassUpdates

src/c++/lib/scmp/BlockAlleleCompare.cpp:239

↓ 1 callersClassValueConstIterator

external/jsoncpp/json/json.h:243

↓ 1 callersClassValueInternalArray

external/jsoncpp/json/json.h:247

↓ 1 callersClassValueInternalLink

external/jsoncpp/json/json.h:246

↓ 1 callersClassValueInternalMap

external/jsoncpp/json/json.h:248

↓ 1 callersClassValueIterator

external/jsoncpp/json/json.h:242

↓ 1 callersClassValueMapAllocator

external/jsoncpp/json/json.h:245

↓ 1 callersClassiv_less

src/c++/test/test_intervalbuffer.cpp:113

↓ 1 callersClassstat

src/c++/lib/tools/Fasta.cpp:77

ClassAbstractVariantProcessingStep

src/c++/include/Variant.hh:379

EnumAggregationType

src/c++/include/variant/VariantLocationAggregator.hh:53

* @brief Sequence alignment class interface */

src/c++/include/Alignment.hh:85

ClassAlignmentTimer

src/c++/test/test_align.cpp:303

ClassAlleleMatcher

* Exact matcher for sets of variants assigned to haplotypes * * Exponential time with cutoff */

src/c++/include/AlleleMatcher.hh:57

src/c++/include/helpers/BCFHelpers.hh:176

ClassAnnotatedRefVar

src/c++/include/DiploidComparisonResult.hh:101

BGZip file helper

src/python/Tools/__init__.py:175

ClassBatchAllocator

external/jsoncpp/jsoncpp.cpp:1074

external/jsoncpp/jsoncpp.cpp:1133

ClassBlockAlleleCompare

src/c++/include/BlockAlleleCompare.hh:50

ClassBlockAlleleCompare::BlockAlleleCompareImpl

src/c++/lib/scmp/BlockAlleleCompare.cpp:45

ClassBlockAlleleCompareImpl

src/c++/include/BlockAlleleCompare.hh:115

ClassBlockQuantify

src/c++/include/BlockQuantify.hh:50

ClassBlockQuantify::BlockQuantifyImpl

src/c++/lib/quantify/BlockQuantifyImpl.hh:57

ClassBlockQuantifyImpl

src/c++/include/BlockQuantify.hh:112

ClassBreakpoint

src/c++/main/blocksplit.cpp:298

src/c++/include/helpers/Timing.hh:42

external/jsoncpp/json/json.h:501

ClassCommentInfo

external/jsoncpp/json/json.h:796

EnumCommentPlacement

external/jsoncpp/json/json.h:386

EnumComparisonMode

src/c++/include/BlockAlleleCompare.hh:77

EnumDecisionType

* Decision types: * * on a ROC, we change variants depending if their level is above (PASS) or below (FAIL) the current threshold *

src/c++/include/helpers/Roc.hh:63

ClassDiploidCompare

src/c++/include/DiploidCompare.hh:54

ClassDiploidCompareImpl

src/c++/lib/diploidgraphs/DiploidCompare.cpp:56

ClassDiploidCompareImpl

* @brief Diploid Haplotype comparison * @details Compare Variants assuming * */

src/c++/include/DiploidCompare.hh:53

ClassDiploidComparisonResult

src/c++/include/DiploidComparisonResult.hh:108

ClassDiploidRef

Diploid (modified) reference sequence */

src/c++/include/DiploidReference.hh:48

ClassDiploidReference

src/c++/include/DiploidReference.hh:60

ClassDiploidReferenceImpl

src/c++/lib/diploidgraphs/DiploidReference.cpp:82

ClassDiploidReferenceImpl

src/c++/include/DiploidReference.hh:59

ClassDiploidReferenceTester

src/c++/test/test_diploidreference.cpp:58

ClassDistanceBasedMatcher

* Exact matcher for sets of variants assigned to haplotypes * * Exponential time with cutoff */

src/c++/include/DistanceBasedMatcher.hh:57

EnumDuplicationPolicy

external/jsoncpp/json/json.h:503

external/jsoncpp/json/json.h:1592

ClassFastWriter

external/jsoncpp/json/json-forwards.h:227

ClassFastaFileCache

src/c++/lib/tools/Fasta.cpp:335

ClassFastaFileImpl

src/c++/lib/tools/Fasta.cpp:367

ClassFastaFileImpl

src/c++/include/Fasta.hh:44

ClassFeatureSet

VCF paired Feature set for somatic comparison

src/python/Somatic/__init__.py:23

external/jsoncpp/json/json-forwards.h:234

ClassGA4GHQuantify

src/c++/lib/quantify/GA4GHQuantify.hh:47

ClassGenericFeatures

Collect generic variant features

src/python/Somatic/__init__.py:52

ClassGraphReference

src/c++/include/GraphReference.hh:53

ClassGraphReferenceImpl

src/c++/lib/diploidgraphs/GraphReference.cpp:73

ClassGraphReferenceImpl

src/c++/include/GraphReference.hh:52

ClassGraphReferenceTester

src/c++/test/test_graphreference.cpp:58

"half-call" -- one allele of a call

src/c++/lib/variant/VariantAlleleSplitter.cpp:158

ClassHapAssignment

src/c++/include/HapSetMatcher.hh:54

ClassHapSetMatcher

* Exact matcher for sets of variants assigned to haplotypes * * Exponential time with cutoff */

src/c++/include/HapSetMatcher.hh:83

ClassHapSetMatcher::HapSetMatcherImpl

src/c++/lib/scmp/HapSetMatcherImpl.hh:53

ClassHapSetMatcherImpl

src/c++/include/HapSetMatcher.hh:126

ClassHaploCompare

src/c++/include/HaploCompare.hh:81

ClassHaploCompareImpl

src/c++/lib/diploidgraphs/HaploCompare.cpp:86

ClassHaploCompareImpl

* @brief Two-Haplotype Comparison */

src/c++/include/HaploCompare.hh:80

ClassHaplotypeData

Haplotype implementation data storage */

src/c++/lib/diploidgraphs/Haplotype.cpp:64

ClassHaplotypeData

* @brief Class to collect reference sequence modifications */

src/c++/include/Haplotype.hh:51

EnumInternalFlags

sizeof(ValueInternalLink) = 128 on 32 bits architecture.

external/jsoncpp/json/json.h:970

ClassIntervalBuffer

src/c++/include/helpers/IntervalBuffer.hh:49

ClassIntervalBuffer::IntervalBufferImpl

src/c++/lib/tools/IntervalBuffer.cpp:53

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