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Functions640 in github.com/BoevaLab/FREEC

⨍ Functions 640◇ Types & classes 40

↓ 2 callersFunctionrmatrixlq

LQ decomposition of a rectangular matrix of size MxN Input parameters: A - matrix A whose indexes range within [0..M-1, 0..N-1]. M -

src/ortfac.cpp:245

↓ 2 callersFunctionrmatrixqr

QR decomposition of a rectangular matrix of size MxN Input parameters: A - matrix A whose indexes range within [0..M-1, 0..N-1]. M -

src/ortfac.cpp:102

↓ 2 callersFunctionrunWithDefinedPloidy

src/main.cpp:1224

↓ 2 callersMethodsetChrLength

src/ChrCopyNumber.cpp:393

↓ 2 callersMethodsetCopyNumberFromPileup

src/SNPinGenome.cpp:205

↓ 2 callersMethodsetIfLogged

src/GenomeCopyNumber.cpp:4319

↓ 2 callersMethodsetIsSmoothed

src/ChrCopyNumber.cpp:1060

↓ 2 callersMethodsetPloidy

src/ChrCopyNumber.cpp:365

↓ 2 callersMethodsetReference

src/GenomeCopyNumber.cpp:4300

↓ 2 callersMethodsetSNPChr

src/SNPinGenome.cpp:31

↓ 2 callersMethodsetSambamba

src/GenomeCopyNumber.cpp:4304

↓ 2 callersMethodsetSamtools

src/GenomeCopyNumber.cpp:4295

↓ 2 callersMethodsetSeekSubclones

src/GenomeCopyNumber.cpp:4329

↓ 2 callersMethodsetSex

src/GenomeCopyNumber.cpp:97

↓ 2 callersMethodsetStep

src/GenomeCopyNumber.cpp:82

↓ 2 callersMethodsetValueAt

src/SNPatChr.cpp:59

↓ 2 callersMethodsetVectorLength

src/ChrCopyNumber.cpp:378

↓ 2 callersMethodsetWindowSize

src/ChrCopyNumber.cpp:361

↓ 2 callersMethodsetmakingPileup

src/GenomeCopyNumber.cpp:4323

↓ 2 callersFunctionsvd2x2

src/bdsvd.cpp:1042

↓ 2 callersFunctionsymmetricmatrixvectormultiply

src/sblas.cpp:30

↓ 2 callersFunctionsymmetricrank2update

src/sblas.cpp:128

↓ 1 callersMethodPercentage_GenomeExplained

src/GenomeCopyNumber.cpp:4355

↓ 1 callersFunction_vadd

↓ 1 callersMethodaddBAFinfo

src/ChrCopyNumber.cpp:1631

↓ 1 callersMethodaddToCGcontent

src/ChrCopyNumber.cpp:1391

↓ 1 callersMethodaddToGenes_name

src/ChrCopyNumber.cpp:1402

↓ 1 callersMethodaddToMappabilityProfile

src/ChrCopyNumber.cpp:1398

↓ 1 callersMethodaddToNonNpercent

src/ChrCopyNumber.cpp:1394

↓ 1 callersFunctionargmin

Calculate argmin for a vector for the first smallest value in a range ---------------------------------------------------------------------------

src/myFunc.cpp:166

↓ 1 callersMethodcalculateBreakpoints

src/GenomeCopyNumber.cpp:223

↓ 1 callersFunctioncalculateBreakpoints_perform

src/myFunc.cpp:684

↓ 1 callersMethodcalculateCopyNumberMedian

src/ChrCopyNumber.cpp:711

↓ 1 callersFunctioncalculateLogLikelyHoodNormalMixtureForBAFs

src/myFunc.cpp:2151

↓ 1 callersMethodcalculateMedianReadCountPerWindow

src/GenomeCopyNumber.cpp:1004

↓ 1 callersMethodcalculateRSS

src/GenomeCopyNumber.cpp:1138

↓ 1 callersMethodcalculateReadCountQuartiles

src/GenomeCopyNumber.cpp:1604

↓ 1 callersMethodcalculateSDReadCountPerWindow

src/GenomeCopyNumber.cpp:981

↓ 1 callersMethodcalculateSomaticCNVs

src/GenomeCopyNumber.cpp:2946

↓ 1 callersFunctioncalculateTotalLength

src/myFunc.cpp:2601

↓ 1 callersFunctioncheckChrLen

src/myFunc.cpp:74

↓ 1 callersMethodcheckOrCreateNotNprofileWithZeros

src/ChrCopyNumber.cpp:1412

↓ 1 callersFunctionchomp

src/myFunc.cpp:1826

↓ 1 callersMethodclearCGcontent

src/ChrCopyNumber.cpp:1380

↓ 1 callersMethodclearMappabilityProfile

src/ChrCopyNumber.cpp:1387

↓ 1 callersMethodclearNonNpercent

src/ChrCopyNumber.cpp:1383

↓ 1 callersFunctioncmatrixgemmf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:354

↓ 1 callersFunctioncmatrixgemmk

GEMM kernel -- ALGLIB routine -- 16.12.2009 Bochkanov Sergey *************************************************************************/

src/ablas.cpp:2686

↓ 1 callersFunctioncmatrixlefttrsm2

Level-2 subroutine *************************************************************************/

src/ablas.cpp:1889

↓ 1 callersFunctioncmatrixlefttrsmf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:167

↓ 1 callersFunctioncmatrixlqbasecase

Base case for complex LQ -- LAPACK routine (version 3.0) -- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., Courant Institute

src/ortfac.cpp:3022

↓ 1 callersFunctioncmatrixmvf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:87

↓ 1 callersFunctioncmatrixqrbasecase

Base case for complex QR -- LAPACK routine (version 3.0) -- Univ. of Tennessee, Univ. of California Berkeley, NAG Ltd., Courant Institute

src/ortfac.cpp:2965

↓ 1 callersFunctioncmatrixrank1f

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:31

↓ 1 callersFunctioncmatrixrighttrsm2

Level 2 variant of CMatrixRightTRSM *************************************************************************/

src/ablas.cpp:1676

↓ 1 callersFunctioncmatrixrighttrsmf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:137

↓ 1 callersFunctioncmatrixsyrk2

Level 2 subroutine *************************************************************************/

src/ablas.cpp:2412

↓ 1 callersFunctioncmatrixsyrkf

Fast kernel -- ALGLIB routine -- 19.01.2010 Bochkanov Sergey *************************************************************************/

src/ablasf.cpp:257

↓ 1 callersMethodcoveragePlusOneAtI

src/ChrDensity.cpp:55

↓ 1 callersMethodcreateMappabilityProfile

src/ChrCopyNumber.cpp:1407

↓ 1 callersMethoddeleteArg

src/ThreadPool.h:133

↓ 1 callersMethoddeleteFlanks

src/ChrCopyNumber.cpp:1239

↓ 1 callersMethodduration

src/ThreadPool.h:125

↓ 1 callersFunctionerfc

Complementary error function 1 - erf(x) = inf. - 2 | | 2

src/normaldistr.cpp:123

↓ 1 callersMethodevaluateContamination

src/GenomeCopyNumber.cpp:3395

↓ 1 callersMethodevaluateContaminationwithLR

src/GenomeCopyNumber.cpp:3452

↓ 1 callersMethodfillInRatio

src/ChrCopyNumber.cpp:424

↓ 1 callersFunctionfilterWithQualities

src/myFunc.cpp:1837

↓ 1 callersFunctionfindSmallestSuffix

src/myFunc.cpp:2397

↓ 1 callersMethodfinishCopyNumber

src/GenomeCopyNumber.cpp:213

↓ 1 callersMethodfinished

src/ThreadPool.h:94

↓ 1 callersMethodgetBAFat

src/ChrCopyNumber.cpp:1555

↓ 1 callersFunctiongetBAFinfo

src/myFunc.cpp:1868

↓ 1 callersMethodgetBin

src/SNPposition.cpp:102

↓ 1 callersMethodgetBinAt

src/SNPatChr.cpp:82

↓ 1 callersMethodgetCNVs

src/GenomeCopyNumber.cpp:2937

↓ 1 callersMethodgetCN_subc

src/ChrCopyNumber.cpp:292

↓ 1 callersFunctiongetControlNameFromCommandLine

src/main.cpp:126

↓ 1 callersFunctiongetCopyNumbers

src/myFunc.cpp:2070

↓ 1 callersFunctiongetELANDinfo

src/myFunc.cpp:2478

↓ 1 callersMethodgetFittedBAFProfileAt

src/ChrCopyNumber.cpp:1563

↓ 1 callersMethodgetFragmentLengths_notNA_At

src/ChrCopyNumber.cpp:1119

↓ 1 callersFunctiongetLineNumber

src/myFunc.cpp:355

↓ 1 callersMethodgetMedianCopyNumber

src/GenomeCopyNumber.cpp:1650

↓ 1 callersMethodgetNucleotide

src/SNPposition.cpp:79

↓ 1 callersMethodgetNumber

src/ThreadPool.h:122

↓ 1 callersMethodgetNumberOfChromosomes

src/GenomeCopyNumber.cpp:1129

↓ 1 callersMethodgetNumberOfFragments

src/ChrCopyNumber.cpp:1127

↓ 1 callersMethodgetNumberOfGoodFragments

src/ChrCopyNumber.cpp:1156

↓ 1 callersMethodgetPloidy

src/GenomeCopyNumber.cpp:2941

↓ 1 callersMethodgetPopulation_subc

src/ChrCopyNumber.cpp:303

↓ 1 callersMethodgetPosition

src/SNPposition.cpp:75

↓ 1 callersMethodgetRadius

src/KernelVector.cpp:53

↓ 1 callersFunctiongetReadNumberFromPileup

src/myFunc.cpp:468

↓ 1 callersFunctiongetSampleNameFromCommandLine

src/main.cpp:93

↓ 1 callersMethodgetSmoothedForInterval

src/ChrCopyNumber.cpp:1583

↓ 1 callersMethodgetStatus

src/SNPposition.cpp:95

↓ 1 callersMethodgetSum

src/KernelVector.cpp:49

↓ 1 callersMethodgetThreadSelf

src/ThreadPool.h:123

↓ 1 callersMethodgetValue

src/SNPposition.cpp:91

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