├── .gitignore ├── CMakeLists.txt ├── README.md ├── external ├── Eigen │ ├── Array │ ├── Cholesky │ ├── CholmodSupport │ ├── Core │ ├── Dense │ ├── Eigen │ ├── Eigen2Support │ ├── Eigenvalues │ ├── Geometry │ ├── Householder │ ├── IterativeLinearSolvers │ ├── Jacobi │ ├── LU │ ├── LeastSquares │ ├── MetisSupport │ ├── OrderingMethods │ ├── PaStiXSupport │ ├── PardisoSupport │ ├── QR │ ├── QtAlignedMalloc │ ├── SPQRSupport │ ├── SVD │ ├── Sparse │ ├── SparseCholesky │ ├── SparseCore │ ├── SparseLU │ ├── SparseQR │ ├── StdDeque │ ├── StdList │ ├── StdVector │ ├── SuperLUSupport │ ├── UmfPackSupport │ └── src │ │ ├── Cholesky │ │ ├── LDLT.h │ │ ├── LLT.h │ │ └── LLT_MKL.h │ │ ├── CholmodSupport │ │ └── CholmodSupport.h │ │ ├── Core │ │ ├── Array.h │ │ ├── ArrayBase.h │ │ ├── ArrayWrapper.h │ │ ├── Assign.h │ │ ├── Assign_MKL.h │ │ ├── BandMatrix.h │ │ ├── Block.h │ │ ├── BooleanRedux.h │ │ ├── CommaInitializer.h │ │ ├── CoreIterators.h │ │ ├── CwiseBinaryOp.h │ │ ├── CwiseNullaryOp.h │ │ ├── CwiseUnaryOp.h │ │ ├── CwiseUnaryView.h │ │ ├── DenseBase.h │ │ ├── DenseCoeffsBase.h │ │ ├── DenseStorage.h │ │ ├── Diagonal.h │ │ ├── DiagonalMatrix.h │ │ ├── DiagonalProduct.h │ │ ├── Dot.h │ │ ├── EigenBase.h │ │ ├── Flagged.h │ │ ├── ForceAlignedAccess.h │ │ ├── Functors.h │ │ ├── Fuzzy.h │ │ ├── GeneralProduct.h │ │ ├── GenericPacketMath.h │ │ ├── GlobalFunctions.h │ │ ├── IO.h │ │ ├── Map.h │ │ ├── MapBase.h │ │ ├── MathFunctions.h │ │ ├── Matrix.h │ │ ├── MatrixBase.h │ │ ├── NestByValue.h │ │ ├── NoAlias.h │ │ ├── NumTraits.h │ │ ├── PermutationMatrix.h │ │ ├── PlainObjectBase.h │ │ ├── ProductBase.h │ │ ├── Random.h │ │ ├── Redux.h │ │ ├── Ref.h │ │ ├── Replicate.h │ │ ├── ReturnByValue.h │ │ ├── Reverse.h │ │ ├── Select.h │ │ ├── SelfAdjointView.h │ │ ├── SelfCwiseBinaryOp.h │ │ ├── SolveTriangular.h │ │ ├── StableNorm.h │ │ ├── Stride.h │ │ ├── Swap.h │ │ ├── Transpose.h │ │ ├── Transpositions.h │ │ ├── TriangularMatrix.h │ │ ├── VectorBlock.h │ │ ├── VectorwiseOp.h │ │ ├── Visitor.h │ │ ├── arch │ │ │ ├── AltiVec │ │ │ │ ├── Complex.h │ │ │ │ └── PacketMath.h │ │ │ ├── Default │ │ │ │ └── Settings.h │ │ │ ├── NEON │ │ │ │ ├── Complex.h │ │ │ │ └── PacketMath.h │ │ │ └── SSE │ │ │ │ ├── Complex.h │ │ │ │ ├── MathFunctions.h │ │ │ │ └── PacketMath.h │ │ ├── products │ │ │ ├── CoeffBasedProduct.h │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ ├── GeneralMatrixMatrix.h │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ ├── GeneralMatrixMatrixTriangular_MKL.h │ │ │ ├── GeneralMatrixMatrix_MKL.h │ │ │ ├── GeneralMatrixVector.h │ │ │ ├── GeneralMatrixVector_MKL.h │ │ │ ├── Parallelizer.h │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ ├── SelfadjointMatrixMatrix_MKL.h │ │ │ ├── SelfadjointMatrixVector.h │ │ │ ├── SelfadjointMatrixVector_MKL.h │ │ │ ├── SelfadjointProduct.h │ │ │ ├── SelfadjointRank2Update.h │ │ │ ├── TriangularMatrixMatrix.h │ │ │ ├── TriangularMatrixMatrix_MKL.h │ │ │ ├── TriangularMatrixVector.h │ │ │ ├── TriangularMatrixVector_MKL.h │ │ │ ├── TriangularSolverMatrix.h │ │ │ ├── TriangularSolverMatrix_MKL.h │ │ │ └── TriangularSolverVector.h │ │ └── util │ │ │ ├── BlasUtil.h │ │ │ ├── Constants.h │ │ │ ├── DisableStupidWarnings.h │ │ │ ├── ForwardDeclarations.h │ │ │ ├── MKL_support.h │ │ │ ├── Macros.h │ │ │ ├── Memory.h │ │ │ ├── Meta.h │ │ │ ├── NonMPL2.h │ │ │ ├── ReenableStupidWarnings.h │ │ │ ├── StaticAssert.h │ │ │ └── XprHelper.h │ │ ├── Eigen2Support │ │ ├── Block.h │ │ ├── Cwise.h │ │ ├── CwiseOperators.h │ │ ├── Geometry │ │ │ ├── AlignedBox.h │ │ │ ├── All.h │ │ │ ├── AngleAxis.h │ │ │ ├── Hyperplane.h │ │ │ ├── ParametrizedLine.h │ │ │ ├── Quaternion.h │ │ │ ├── Rotation2D.h │ │ │ ├── RotationBase.h │ │ │ ├── Scaling.h │ │ │ ├── Transform.h │ │ │ └── Translation.h │ │ ├── LU.h │ │ ├── Lazy.h │ │ ├── LeastSquares.h │ │ ├── Macros.h │ │ ├── MathFunctions.h │ │ ├── Memory.h │ │ ├── Meta.h │ │ ├── Minor.h │ │ ├── QR.h │ │ ├── SVD.h │ │ ├── TriangularSolver.h │ │ └── VectorBlock.h │ │ ├── Eigenvalues │ │ ├── ComplexEigenSolver.h │ │ ├── ComplexSchur.h │ │ ├── ComplexSchur_MKL.h │ │ ├── EigenSolver.h │ │ ├── GeneralizedEigenSolver.h │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ ├── HessenbergDecomposition.h │ │ ├── MatrixBaseEigenvalues.h │ │ ├── RealQZ.h │ │ ├── RealSchur.h │ │ ├── RealSchur_MKL.h │ │ ├── SelfAdjointEigenSolver.h │ │ ├── SelfAdjointEigenSolver_MKL.h │ │ └── Tridiagonalization.h │ │ ├── Geometry │ │ ├── AlignedBox.h │ │ ├── AngleAxis.h │ │ ├── EulerAngles.h │ │ ├── Homogeneous.h │ │ ├── Hyperplane.h │ │ ├── OrthoMethods.h │ │ ├── ParametrizedLine.h │ │ ├── Quaternion.h │ │ ├── Rotation2D.h │ │ ├── RotationBase.h │ │ ├── Scaling.h │ │ ├── Transform.h │ │ ├── Translation.h │ │ ├── Umeyama.h │ │ └── arch │ │ │ └── Geometry_SSE.h │ │ ├── Householder │ │ ├── BlockHouseholder.h │ │ ├── Householder.h │ │ └── HouseholderSequence.h │ │ ├── IterativeLinearSolvers │ │ ├── BasicPreconditioners.h │ │ ├── BiCGSTAB.h │ │ ├── ConjugateGradient.h │ │ ├── IncompleteLUT.h │ │ └── IterativeSolverBase.h │ │ ├── Jacobi │ │ └── Jacobi.h │ │ ├── LU │ │ ├── Determinant.h │ │ ├── FullPivLU.h │ │ ├── Inverse.h │ │ ├── PartialPivLU.h │ │ ├── PartialPivLU_MKL.h │ │ └── arch │ │ │ └── Inverse_SSE.h │ │ ├── MetisSupport │ │ └── MetisSupport.h │ │ ├── OrderingMethods │ │ ├── Amd.h │ │ ├── Eigen_Colamd.h │ │ └── Ordering.h │ │ ├── PaStiXSupport │ │ └── PaStiXSupport.h │ │ ├── PardisoSupport │ │ └── PardisoSupport.h │ │ ├── QR │ │ ├── ColPivHouseholderQR.h │ │ ├── ColPivHouseholderQR_MKL.h │ │ ├── FullPivHouseholderQR.h │ │ ├── HouseholderQR.h │ │ └── HouseholderQR_MKL.h │ │ ├── SPQRSupport │ │ └── SuiteSparseQRSupport.h │ │ ├── SVD │ │ ├── JacobiSVD.h │ │ ├── JacobiSVD_MKL.h │ │ └── UpperBidiagonalization.h │ │ ├── SparseCholesky │ │ ├── SimplicialCholesky.h │ │ └── SimplicialCholesky_impl.h │ │ ├── SparseCore │ │ ├── AmbiVector.h │ │ ├── CompressedStorage.h │ │ ├── ConservativeSparseSparseProduct.h │ │ ├── MappedSparseMatrix.h │ │ ├── SparseBlock.h │ │ ├── SparseColEtree.h │ │ ├── SparseCwiseBinaryOp.h │ │ ├── SparseCwiseUnaryOp.h │ │ ├── SparseDenseProduct.h │ │ ├── SparseDiagonalProduct.h │ │ ├── SparseDot.h │ │ ├── SparseFuzzy.h │ │ ├── SparseMatrix.h │ │ ├── SparseMatrixBase.h │ │ ├── SparsePermutation.h │ │ ├── SparseProduct.h │ │ ├── SparseRedux.h │ │ ├── SparseSelfAdjointView.h │ │ ├── SparseSparseProductWithPruning.h │ │ ├── SparseTranspose.h │ │ ├── SparseTriangularView.h │ │ ├── SparseUtil.h │ │ ├── SparseVector.h │ │ ├── SparseView.h │ │ └── TriangularSolver.h │ │ ├── SparseLU │ │ ├── SparseLU.h │ │ ├── SparseLUImpl.h │ │ ├── SparseLU_Memory.h │ │ ├── SparseLU_Structs.h │ │ ├── SparseLU_SupernodalMatrix.h │ │ ├── SparseLU_Utils.h │ │ ├── SparseLU_column_bmod.h │ │ ├── SparseLU_column_dfs.h │ │ ├── SparseLU_copy_to_ucol.h │ │ ├── SparseLU_gemm_kernel.h │ │ ├── SparseLU_heap_relax_snode.h │ │ ├── SparseLU_kernel_bmod.h │ │ ├── SparseLU_panel_bmod.h │ │ ├── SparseLU_panel_dfs.h │ │ ├── SparseLU_pivotL.h │ │ ├── SparseLU_pruneL.h │ │ └── SparseLU_relax_snode.h │ │ ├── SparseQR │ │ └── SparseQR.h │ │ ├── StlSupport │ │ ├── StdDeque.h │ │ ├── StdList.h │ │ ├── StdVector.h │ │ └── details.h │ │ ├── SuperLUSupport │ │ └── SuperLUSupport.h │ │ ├── UmfPackSupport │ │ └── UmfPackSupport.h │ │ ├── misc │ │ ├── Image.h │ │ ├── Kernel.h │ │ ├── Solve.h │ │ ├── SparseSolve.h │ │ └── blas.h │ │ └── plugins │ │ ├── ArrayCwiseBinaryOps.h │ │ ├── ArrayCwiseUnaryOps.h │ │ ├── BlockMethods.h │ │ ├── CommonCwiseBinaryOps.h │ │ ├── CommonCwiseUnaryOps.h │ │ ├── MatrixCwiseBinaryOps.h │ │ └── MatrixCwiseUnaryOps.h ├── edlib │ ├── LICENSE │ ├── README.md │ ├── edlib.cpp │ └── edlib.h ├── kmc_api │ ├── CMakeLists.txt │ ├── kmc_file.cpp │ ├── kmc_file.h │ ├── kmer_api.cpp │ ├── kmer_api.h │ ├── kmer_defs.h │ ├── mmer.cpp │ ├── mmer.h │ └── stdafx.h └── ntHash │ ├── BloomFilter.hpp │ ├── LICENSE │ └── nthash.hpp ├── include ├── bayesTyper │ ├── BitsetCompare.hpp │ ├── ChromosomePloidy.hpp │ ├── Chromosomes.hpp │ ├── Combinator.hpp │ ├── CountAllocation.hpp │ ├── CountDistribution.hpp │ ├── DiscreteSampler.hpp │ ├── Filters.hpp │ ├── FrequencyDistribution.hpp │ ├── GenotypeWriter.hpp │ ├── Genotypes.hpp │ ├── HaplotypeFrequencyDistribution.hpp │ ├── HybridHash.hpp │ ├── HybridHash.tpp │ ├── InferenceEngine.hpp │ ├── InferenceUnit.hpp │ ├── Kmer.hpp │ ├── Kmer.tpp │ ├── KmerCounter.hpp │ ├── KmerCounts.hpp │ ├── KmerHash.hpp │ ├── KmerStats.hpp │ ├── LinearMap.hpp │ ├── LinearMap.tpp │ ├── NegativeBinomialDistribution.hpp │ ├── Nucleotide.hpp │ ├── OptionsContainer.hpp │ ├── OptionsContainer.tpp │ ├── ProducerConsumerQueue.hpp │ ├── ProducerConsumerQueue.tpp │ ├── Regions.hpp │ ├── Sample.hpp │ ├── SparsityEstimator.hpp │ ├── Utils.hpp │ ├── VariantCluster.hpp │ ├── VariantClusterGenotyper.hpp │ ├── VariantClusterGraph.hpp │ ├── VariantClusterGraphPath.hpp │ ├── VariantClusterGraphVertex.hpp │ ├── VariantClusterGroup.hpp │ ├── VariantClusterHaplotypes.hpp │ ├── VariantFileParser.hpp │ └── VariantInfo.hpp ├── bayesTyperTools │ ├── AddAttributes.hpp │ ├── Annotate.hpp │ ├── Combine.hpp │ ├── ConvertAllele.hpp │ ├── Filter.hpp │ ├── MakeBloom.hpp │ ├── ProducerConsumerQueue.hpp │ └── ProducerConsumerQueue.tpp ├── kmerBloom │ └── KmerBloom.hpp └── vcf++ │ ├── Allele.hpp │ ├── Attribute.hpp │ ├── AttributeFilter.hpp │ ├── AttributeSet.hpp │ ├── Auxiliaries.hpp │ ├── CompareOperators.hpp │ ├── Contig.hpp │ ├── FastaReader.hpp │ ├── FastaRecord.hpp │ ├── JoiningString.hpp │ ├── ReductionOperator.hpp │ ├── Regions.hpp │ ├── Sample.hpp │ ├── SampleAlleleAttributeFilter.hpp │ ├── Stats.hpp │ ├── Trio.hpp │ ├── Utils.hpp │ ├── Variant.hpp │ ├── VcfFile.hpp │ └── VcfMetaData.hpp ├── src ├── bayesTyper │ ├── CMakeLists.txt │ ├── ChromosomePloidy.cpp │ ├── Chromosomes.cpp │ ├── Combinator.cpp │ ├── CountAllocation.cpp │ ├── CountDistribution.cpp │ ├── DiscreteSampler.cpp │ ├── Filters.cpp │ ├── FrequencyDistribution.cpp │ ├── GenotypeWriter.cpp │ ├── HaplotypeFrequencyDistribution.cpp │ ├── InferenceEngine.cpp │ ├── KmerCounter.cpp │ ├── KmerCounts.cpp │ ├── KmerHash.cpp │ ├── KmerStats.cpp │ ├── NegativeBinomialDistribution.cpp │ ├── Regions.cpp │ ├── Sample.cpp │ ├── SparsityEstimator.cpp │ ├── VariantClusterGenotyper.cpp │ ├── VariantClusterGraph.cpp │ ├── VariantClusterGraphPath.cpp │ ├── VariantClusterGroup.cpp │ ├── VariantClusterHaplotypes.cpp │ ├── VariantFileParser.cpp │ └── main.cpp ├── bayesTyperTools │ ├── AddAttributes.cpp │ ├── Annotate.cpp │ ├── CMakeLists.txt │ ├── Combine.cpp │ ├── ConvertAllele.cpp │ ├── Filter.cpp │ ├── MakeBloom.cpp │ ├── main.cpp │ └── scripts │ │ ├── CMakeLists.txt │ │ ├── addEditDistanceAndCondordance.cpp │ │ ├── assessHaplotypeTransmissionSupport.cpp │ │ ├── collapseSummaryTable.cpp │ │ ├── convertNestedGenotypes.cpp │ │ ├── convertSeqToAlleleId.cpp │ │ ├── filterAlleleCallsetOrigin.cpp │ │ ├── filterStructuralVariants.cpp │ │ ├── generateDiplotypes.cpp │ │ ├── getGenomicIntervals.cpp │ │ ├── getKmerStats.cpp │ │ ├── getSummary.cpp │ │ └── writeIndels.cpp ├── kmerBloom │ ├── CMakeLists.txt │ └── KmerBloom.cpp └── vcf++ │ ├── Allele.cpp │ ├── Attribute.cpp │ ├── AttributeFilter.cpp │ ├── AttributeSet.cpp │ ├── Auxiliaries.cpp │ ├── CMakeLists.txt │ ├── Contig.cpp │ ├── FastaReader.cpp │ ├── FastaRecord.cpp │ ├── JoiningString.cpp │ ├── Regions.cpp │ ├── Sample.cpp │ ├── SampleAlleleAttributeFilter.cpp │ ├── Stats.cpp │ ├── Trio.cpp │ ├── Utils.cpp │ ├── Variant.cpp │ ├── VcfFile.cpp │ └── VcfMetaData.cpp └── workflows ├── call_candidates_and_genotype.smk ├── config.yaml ├── rules ├── call_candidates.smk └── estimate_genotypes.smk └── samples.tsv /.gitignore: -------------------------------------------------------------------------------- 1 | # Ignore Mac specific files 2 | .DS_Store 3 | -------------------------------------------------------------------------------- /CMakeLists.txt: -------------------------------------------------------------------------------- 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