BayesTyper
A method for variant graph genotyping based on exact alignment of k-mers
파일 탐색기
최종 버전 다운로드 (.zip)- edlib.cpp
- edlib.h
- LICENSE
- README.md
- LDLT.h
- LLT.h
- LLT_MKL.h
- CholmodSupport.h
- Complex.h
- PacketMath.h
- Settings.h
- Complex.h
- PacketMath.h
- Complex.h
- MathFunctions.h
- PacketMath.h
- CoeffBasedProduct.h
- GeneralBlockPanelKernel.h
- GeneralMatrixMatrix.h
- GeneralMatrixMatrix_MKL.h
- GeneralMatrixMatrixTriangular.h
- GeneralMatrixMatrixTriangular_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
- BlasUtil.h
- Constants.h
- DisableStupidWarnings.h
- ForwardDeclarations.h
- Macros.h
- Memory.h
- Meta.h
- MKL_support.h
- NonMPL2.h
- ReenableStupidWarnings.h
- StaticAssert.h
- XprHelper.h
- 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
- AlignedBox.h
- All.h
- AngleAxis.h
- Hyperplane.h
- ParametrizedLine.h
- Quaternion.h
- Rotation2D.h
- RotationBase.h
- Scaling.h
- Transform.h
- Translation.h
- Block.h
- Cwise.h
- CwiseOperators.h
- Lazy.h
- LeastSquares.h
- LU.h
- Macros.h
- MathFunctions.h
- Memory.h
- Meta.h
- Minor.h
- QR.h
- SVD.h
- TriangularSolver.h
- VectorBlock.h
- 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_SSE.h
- 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
- BlockHouseholder.h
- Householder.h
- HouseholderSequence.h
- BasicPreconditioners.h
- BiCGSTAB.h
- ConjugateGradient.h
- IncompleteLUT.h
- IterativeSolverBase.h
- Jacobi.h
- Inverse_SSE.h
- Determinant.h
- FullPivLU.h
- Inverse.h
- PartialPivLU.h
- PartialPivLU_MKL.h
- MetisSupport.h
- blas.h
- Image.h
- Kernel.h
- Solve.h
- SparseSolve.h
- Amd.h
- Eigen_Colamd.h
- Ordering.h
- PardisoSupport.h
- PaStiXSupport.h
- ArrayCwiseBinaryOps.h
- ArrayCwiseUnaryOps.h
- BlockMethods.h
- CommonCwiseBinaryOps.h
- CommonCwiseUnaryOps.h
- MatrixCwiseBinaryOps.h
- MatrixCwiseUnaryOps.h
- ColPivHouseholderQR.h
- ColPivHouseholderQR_MKL.h
- FullPivHouseholderQR.h
- HouseholderQR.h
- HouseholderQR_MKL.h
- SimplicialCholesky.h
- SimplicialCholesky_impl.h
- 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.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_Memory.h
- SparseLU_panel_bmod.h
- SparseLU_panel_dfs.h
- SparseLU_pivotL.h
- SparseLU_pruneL.h
- SparseLU_relax_snode.h
- SparseLU_Structs.h
- SparseLU_SupernodalMatrix.h
- SparseLU_Utils.h
- SparseLUImpl.h
- SparseQR.h
- SuiteSparseQRSupport.h
- details.h
- StdDeque.h
- StdList.h
- StdVector.h
- SuperLUSupport.h
- JacobiSVD.h
- JacobiSVD_MKL.h
- UpperBidiagonalization.h
- UmfPackSupport.h
- Array
- Cholesky
- CholmodSupport
- Core
- Dense
- Eigen
- Eigen2Support
- Eigenvalues
- Geometry
- Householder
- IterativeLinearSolvers
- Jacobi
- LeastSquares
- LU
- MetisSupport
- OrderingMethods
- PardisoSupport
- PaStiXSupport
- QR
- QtAlignedMalloc
- Sparse
- SparseCholesky
- SparseCore
- SparseLU
- SparseQR
- SPQRSupport
- StdDeque
- StdList
- StdVector
- SuperLUSupport
- SVD
- UmfPackSupport
- CMakeLists.txt
- kmc_file.cpp
- kmc_file.h
- kmer_api.cpp
- kmer_api.h
- kmer_defs.h
- mmer.cpp
- mmer.h
- stdafx.h
- BloomFilter.hpp
- LICENSE
- nthash.hpp
- BitsetCompare.hpp
- ChromosomePloidy.hpp
- Chromosomes.hpp
- Combinator.hpp
- CountAllocation.hpp
- CountDistribution.hpp
- DiscreteSampler.hpp
- Filters.hpp
- FrequencyDistribution.hpp
- Genotypes.hpp
- GenotypeWriter.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
- AddAttributes.hpp
- Annotate.hpp
- Combine.hpp
- ConvertAllele.hpp
- Filter.hpp
- MakeBloom.hpp
- ProducerConsumerQueue.hpp
- ProducerConsumerQueue.tpp
- KmerBloom.hpp
- 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
- ChromosomePloidy.cpp
- Chromosomes.cpp
- CMakeLists.txt
- 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
- main.cpp
- NegativeBinomialDistribution.cpp
- Regions.cpp
- Sample.cpp
- SparsityEstimator.cpp
- VariantClusterGenotyper.cpp
- VariantClusterGraph.cpp
- VariantClusterGraphPath.cpp
- VariantClusterGroup.cpp
- VariantClusterHaplotypes.cpp
- VariantFileParser.cpp
- addEditDistanceAndCondordance.cpp
- assessHaplotypeTransmissionSupport.cpp
- CMakeLists.txt
- collapseSummaryTable.cpp
- convertNestedGenotypes.cpp
- convertSeqToAlleleId.cpp
- filterAlleleCallsetOrigin.cpp
- filterStructuralVariants.cpp
- generateDiplotypes.cpp
- getGenomicIntervals.cpp
- getKmerStats.cpp
- getSummary.cpp
- writeIndels.cpp
- AddAttributes.cpp
- Annotate.cpp
- CMakeLists.txt
- Combine.cpp
- ConvertAllele.cpp
- Filter.cpp
- main.cpp
- MakeBloom.cpp
- CMakeLists.txt
- KmerBloom.cpp
- 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
- call_candidates.smk
- estimate_genotypes.smk
- call_candidates_and_genotype.smk
- config.yaml
- samples.tsv
- .gitignore
- CMakeLists.txt
- README.md
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/bioinformatics-centre/BayesTyper
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd BayesTyper
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. CMake
보통 추천사전 준비물
mkdir build && cd build
빌드 결과물을 담을 폴더를 만들고 그 안으로 이동합니다.
cmake ..
소스코드를 분석해 빌드 설정 파일을 생성합니다 (build 폴더 안에서 실행해야 함).
make
생성된 빌드 설정을 바탕으로 실제 컴파일을 진행해 실행 파일을 만듭니다.
build 폴더 안에 실행 파일이 생성됐는지 확인하고, 직접 실행해보세요 (예: ./build/앱이름).
// repository documentation
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