Functions — github.com/Illumina/paragraph

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Functions1,164 in github.com/Illumina/paragraph

⨍ Functions 1,164◇ Types & classes 218

external/jsoncpp/jsoncpp.cpp:2726

MethodCandidate

src/c++/lib/grm/KmerAligner.cpp:49

MethodCandidate

src/c++/lib/grm/KlibAligner.cpp:50

MethodCharReaderBuilder

external/jsoncpp/jsoncpp.cpp:2159

MethodCigarCoder

src/c++/include/common/Alignment.hh:238

MethodCommentInfo

external/jsoncpp/jsoncpp.cpp:2694

MethodCompositeAligner

src/c++/lib/grm/CompositeAligner.cpp:38

MethodException

external/jsoncpp/jsoncpp.cpp:2662

src/c++/include/common/Threads.hh:114

MethodFastWriter

external/jsoncpp/jsoncpp.cpp:4480

MethodFastaFileImpl

src/c++/lib/common/Fasta.cpp:376

external/jsoncpp/jsoncpp.cpp:280

FunctionFlagsForFile

( filename, **kwargs )

.ycm_extra_conf.py:143

src/c++/include/common/Fragment.hh:35

MethodFuncExecutor

src/c++/include/common/Threads.hh:214

src/c++/lib/genotyping/CombinedGenotype.cpp:117

MethodGTestEnvironment

src/c++/test-blackbox/common.hh:40

MethodGTestEnvironment

src/c++/test/common.hh:49

src/c++/include/genotyping/Genotype.hh:46

MethodGenotypingParameters

src/c++/lib/genotyping/GenotypingParameters.cpp:37

MethodGraphAligner

src/c++/lib/grm/GraphAligner.cpp:259

MethodGraphAlignerImpl

src/c++/lib/grm/GraphAligner.cpp:70

MethodGraphBreakpointGenotyper

src/c++/include/genotyping/GraphBreakpointGenotyper.hh:42

MethodGraphGenotyper

src/c++/lib/genotyping/GraphGenotyper.cpp:56

MethodGraphGenotyper

src/c++/include/genotyping/GraphGenotyper.hh:50

src/c++/lib/paragraph/readfilters/KmerFilter.cpp:54

src/c++/include/paragraph/Workflow.hh:43

MethodInterleavedKmerGenerator

src/c++/include/oligo/KmerGenerator.hh:274

MethodInterleavedKmerGeneratorImpl

src/c++/include/oligo/KmerGenerator.hh:174

MethodInterleavedKmerGeneratorImpl

src/c++/include/oligo/KmerGenerator.hh:250

MethodKlibAligner

src/c++/lib/grm/KlibAligner.cpp:444

MethodKlibAlignment

src/c++/lib/common/Klib.cpp:35

MethodKlibAlignment

src/c++/include/common/Klib.hh:42

MethodKlibAlignmentImpl

src/c++/lib/common/KlibImpl.hh:107

MethodKmerAligner

src/c++/lib/grm/KmerAligner.cpp:541

MethodKmerFilter

src/c++/lib/paragraph/readfilters/KmerFilter.cpp:65

MethodKmerGenerator

** \build a KmerGenerator for the given sequence. ** ** \param begin the beginning of the sequence ** ** \param end the end of the

src/c++/include/oligo/KmerGenerator.hh:56

MethodKmerPosition

src/c++/lib/grm/KmerAligner.cpp:94

MethodLogicError

external/jsoncpp/jsoncpp.cpp:2674

MethodMMappedFastaFile

src/c++/lib/common/Fasta.cpp:64

MethodMinCovDetGaussian

* Minimum Covariance Determinant fit constructor using default * raw support fraction (0.5) */

src/c++/lib/statistics/MinCovDetGaussian.cpp:87

MethodMinCovDetGaussian

src/c++/include/statistics/MinCovDetGaussian.hh:49

MethodMinCovDetGaussianImpl

src/c++/lib/statistics/MinCovDetGaussian.cpp:69

MethodNaiveGaussian

src/c++/include/statistics/NaiveGaussian.hh:41

src/c++/lib/common/Program.cpp:47

src/c++/main/grmpy.cpp:86

src/c++/main/paragraph.cpp:83

MethodOurCharReader

external/jsoncpp/jsoncpp.cpp:2142

MethodOurReader

external/jsoncpp/jsoncpp.cpp:1262

MethodParameters

src/c++/include/idxdepth/Parameters.hh:30

MethodParameters

src/c++/include/paragraph/Parameters.hh:47

MethodParameters

src/c++/include/pam/Parameters.hh:42

MethodParameters

src/c++/include/grmpy/Parameters.hh:33

external/jsoncpp/jsoncpp.cpp:4002

MethodPathAligner

src/c++/lib/grm/PathAligner.cpp:61

MethodPathArgument

external/jsoncpp/jsoncpp.cpp:3988

MethodPopulationStatistics

src/c++/lib/genotyping/PopulationStatistics.cpp:38

src/c++/include/common/Read.hh:50

MethodReadPairs

src/c++/include/common/ReadPairs.hh:47

MethodReadPileup

src/c++/lib/common/ReadPileup.cpp:55

MethodReadPileup

src/c++/include/common/ReadPileup.hh:64

external/jsoncpp/jsoncpp.cpp:308

src/c++/include/common/Region.hh:32

MethodReverseBases

src/c++/include/oligo/Nucleotides.hh:479

MethodRuntimeError

external/jsoncpp/jsoncpp.cpp:2671

MethodSampleInfo

src/c++/include/genotyping/SampleInfo.hh:46

MethodScopeEndCall

src/c++/include/common/Threads.hh:63

src/c++/test/test_statistics_basics.cpp:47

src/c++/test/test_disambiguation.cpp:50

src/c++/test/test_readpair.cpp:36

src/c++/test/test_kmeraligner.cpp:51

src/c++/test/test_paragraph_parts.cpp:53

src/c++/test/test_readextraction.cpp:50

src/c++/test/test_readextraction.cpp:75

src/c++/test/test_readpairs.cpp:38

src/c++/test/test_klibaligner.cpp:51

MethodSimpleRead

src/c++/include/common/ReadPileup.hh:40

MethodSinglePosition

src/c++/lib/common/ReadPileup.cpp:38

MethodSkipToNextGoodAlign

src/c++/lib/common/BamReader.cpp:307

MethodStreamWriter

external/jsoncpp/jsoncpp.cpp:5272

MethodStreamWriterBuilder

external/jsoncpp/jsoncpp.cpp:5281

MethodStyledStreamWriter

external/jsoncpp/jsoncpp.cpp:4768

MethodStyledWriter

external/jsoncpp/jsoncpp.cpp:4555

src/c++/test-blackbox/test_pathaligner_blackbox.cpp:45

src/c++/test-blackbox/test_paragraph.cpp:60

src/c++/test-blackbox/test_multithreading.cpp:51

src/c++/test-blackbox/test_grm.cpp:33

src/c++/test/test_graph_input.cpp:46

src/c++/test/test_readfilter.cpp:32

src/c++/test/test_jsonhelpers.cpp:37

src/c++/test/test_align.cpp:38

src/c++/test/test_combined_genotype.cpp:34

src/c++/test/test_genotype.cpp:27

src/c++/test/test_error.cpp:78

src/c++/test/test_phred.cpp:36

src/c++/test/test_breakpoint_genotyper.cpp:31

src/c++/test/test_statistics_min_cov_det_gaussian.cpp:38

src/c++/test/test_breakpointstatistics.cpp:30

src/c++/test/test_statistics_naive_gaussian.cpp:38

src/c++/test/test_genotyping_parameter.cpp:25

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