├── .clang-format ├── .cmakelintrc ├── .drone.yml ├── .drone.yml.sig ├── .drone ├── build.sh ├── copy_build.sh └── test_quant.sh ├── .github └── ISSUE_TEMPLATE │ └── bug_report.md ├── .gitignore ├── .lgtm.yml ├── .travis.yml ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── cmake ├── Modules │ ├── FindJellyfish.cmake │ ├── FindJemalloc.cmake │ ├── FindTBB.cmake │ ├── FindTcmalloc.cmake │ ├── Findcereal.cmake │ ├── Findlibdivsufsort.cmake │ ├── Findlibgff.cmake │ └── Findlibstadenio.cmake ├── PostInstall.cmake ├── SimpleTest.cmake ├── TestSalmonFMD.cmake ├── TestSalmonQuasi.cmake └── UnitTests.cmake ├── current_version.txt ├── doc ├── FileFormats.md ├── Makefile ├── license-header.txt ├── logo.png ├── requirements.txt ├── salmon_logo.png ├── source │ ├── ReadLibraryIllustration.png │ ├── alevin.rst │ ├── building.rst │ ├── conf.py │ ├── file_formats.rst │ ├── index.rst │ ├── library_type.rst │ ├── license.rst │ └── salmon.rst └── steps_to_prepare_release.md ├── docker ├── Dockerfile └── build_test.sh ├── include ├── AlevinHash.hpp ├── AlevinOpts.hpp ├── AlevinTypes.hpp ├── AlevinUtils.hpp ├── AlignmentCommon.hpp ├── AlignmentGroup.hpp ├── AlignmentLibrary.hpp ├── AlignmentModel.hpp ├── AtomicMatrix.hpp ├── BAMQueue.hpp ├── BAMQueue.tpp ├── BAMUtils.hpp ├── BarcodeGroup.hpp ├── BarcodeModel.hpp ├── BiasParams.hpp ├── BinaryLiteral.hpp ├── BootstrapWriter.hpp ├── ClusterForest.hpp ├── CollapsedCellOptimizer.hpp ├── CollapsedEMOptimizer.hpp ├── CollapsedGibbsSampler.hpp ├── CommonTypes.hpp ├── DedupUMI.hpp ├── DistributionUtils.hpp ├── EMUtils.hpp ├── EffectiveLengthStats.hpp ├── EquivalenceClassBuilder.hpp ├── FASTAParser.hpp ├── FastxParser.hpp ├── FastxParserThreadUtils.hpp ├── ForgettingMassCalculator.hpp ├── FragmentLengthDistribution.hpp ├── FragmentList.hpp ├── FragmentStartPositionDistribution.hpp ├── GCFragModel.hpp ├── GZipWriter.hpp ├── GenomicFeature.hpp ├── Graph.hpp ├── IOUtils.hpp ├── IndexVersionInfo.hpp ├── KmerContext.hpp ├── LibraryFormat.hpp ├── LibraryTypeDetector.hpp ├── MappingStatistics.hpp ├── MicroOpts.hpp ├── MiniBatchInfo.hpp ├── MultinomialSampler.hpp ├── NullFragmentFilter.hpp ├── ONTAlignmentModel.hpp ├── OutputUnmappedFilter.hpp ├── PCA.hpp ├── ProgramOptionsGenerator.hpp ├── ReadExperiment.hpp ├── ReadKmerDist.hpp ├── ReadLibrary.hpp ├── ReadPair.hpp ├── ReadProducer.hpp ├── SBModel.hpp ├── SGSmooth.hpp ├── SalmonConfig.hpp ├── SalmonDefaults.hpp ├── SalmonExceptions.hpp ├── SalmonIndex.hpp ├── SalmonIndexVersionInfo.hpp ├── SalmonMappingUtils.hpp ├── SalmonMath.hpp ├── SalmonOpts.hpp ├── SalmonSpinLock.hpp ├── SalmonStringUtils.hpp ├── SalmonUtils.hpp ├── Sampler.hpp ├── SequenceBiasModel.hpp ├── SimplePosBias.hpp ├── SingleCellProtocols.hpp ├── StadenUtils.hpp ├── SufficientStatisticsQueue.hpp ├── TextBootstrapWriter.hpp ├── Transcript.hpp ├── TranscriptCluster.hpp ├── TranscriptGeneMap.hpp ├── TranscriptGroup.hpp ├── TryableSpinLock.hpp ├── UnpairedRead.hpp ├── UtilityFunctions.hpp ├── VersionChecker.hpp ├── WhiteList.hpp ├── atomicops.h ├── backtrace.hpp ├── blockingconcurrentqueue.h ├── bucket_container.hh ├── concurrentqueue.h ├── core │ ├── algorithm.hpp │ ├── any.hpp │ ├── array.hpp │ ├── deque.hpp │ ├── forward_list.hpp │ ├── functional.hpp │ ├── internal.hpp │ ├── iterator.hpp │ ├── list.hpp │ ├── map.hpp │ ├── memory.hpp │ ├── memory_resource.hpp │ ├── meta.hpp │ ├── numeric.hpp │ ├── optional.hpp │ ├── propagate_const.hpp │ ├── range.hpp │ ├── regex.hpp │ ├── set.hpp │ ├── string.hpp │ ├── string_view.hpp │ ├── type_traits.hpp │ ├── typeinfo.hpp │ ├── unordered_map.hpp │ ├── unordered_set.hpp │ ├── utility.hpp │ ├── variant.hpp │ └── vector.hpp ├── cuckoohash_config.hh ├── cuckoohash_map.hh ├── cuckoohash_util.hh ├── dbg.hpp ├── default_hasher.hh ├── edlib.h ├── eigen3 │ ├── Eigen │ │ ├── Cholesky │ │ ├── CholmodSupport │ │ ├── Core │ │ ├── Dense │ │ ├── Eigen │ │ ├── Eigenvalues │ │ ├── Geometry │ │ ├── Householder │ │ ├── IterativeLinearSolvers │ │ ├── Jacobi │ │ ├── LU │ │ ├── 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_LAPACKE.h │ │ │ ├── CholmodSupport │ │ │ └── CholmodSupport.h │ │ │ ├── Core │ │ │ ├── Array.h │ │ │ ├── ArrayBase.h │ │ │ ├── ArrayWrapper.h │ │ │ ├── Assign.h │ │ │ ├── AssignEvaluator.h │ │ │ ├── Assign_MKL.h │ │ │ ├── BandMatrix.h │ │ │ ├── Block.h │ │ │ ├── BooleanRedux.h │ │ │ ├── CommaInitializer.h │ │ │ ├── ConditionEstimator.h │ │ │ ├── CoreEvaluators.h │ │ │ ├── CoreIterators.h │ │ │ ├── CwiseBinaryOp.h │ │ │ ├── CwiseNullaryOp.h │ │ │ ├── CwiseTernaryOp.h │ │ │ ├── CwiseUnaryOp.h │ │ │ ├── CwiseUnaryView.h │ │ │ ├── DenseBase.h │ │ │ ├── DenseCoeffsBase.h │ │ │ ├── DenseStorage.h │ │ │ ├── Diagonal.h │ │ │ ├── DiagonalMatrix.h │ │ │ ├── DiagonalProduct.h │ │ │ ├── Dot.h │ │ │ ├── EigenBase.h │ │ │ ├── ForceAlignedAccess.h │ │ │ ├── Fuzzy.h │ │ │ ├── GeneralProduct.h │ │ │ ├── GenericPacketMath.h │ │ │ ├── GlobalFunctions.h │ │ │ ├── IO.h │ │ │ ├── Inverse.h │ │ │ ├── Map.h │ │ │ ├── MapBase.h │ │ │ ├── MathFunctions.h │ │ │ ├── MathFunctionsImpl.h │ │ │ ├── Matrix.h │ │ │ ├── MatrixBase.h │ │ │ ├── NestByValue.h │ │ │ ├── NoAlias.h │ │ │ ├── NumTraits.h │ │ │ ├── PermutationMatrix.h │ │ │ ├── PlainObjectBase.h │ │ │ ├── Product.h │ │ │ ├── ProductEvaluators.h │ │ │ ├── Random.h │ │ │ ├── Redux.h │ │ │ ├── Ref.h │ │ │ ├── Replicate.h │ │ │ ├── ReturnByValue.h │ │ │ ├── Reverse.h │ │ │ ├── Select.h │ │ │ ├── SelfAdjointView.h │ │ │ ├── SelfCwiseBinaryOp.h │ │ │ ├── Solve.h │ │ │ ├── SolveTriangular.h │ │ │ ├── SolverBase.h │ │ │ ├── StableNorm.h │ │ │ ├── Stride.h │ │ │ ├── Swap.h │ │ │ ├── Transpose.h │ │ │ ├── Transpositions.h │ │ │ ├── TriangularMatrix.h │ │ │ ├── VectorBlock.h │ │ │ ├── VectorwiseOp.h │ │ │ ├── Visitor.h │ │ │ ├── arch │ │ │ │ ├── AVX │ │ │ │ │ ├── Complex.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ └── TypeCasting.h │ │ │ │ ├── AVX512 │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ └── PacketMath.h │ │ │ │ ├── AltiVec │ │ │ │ │ ├── Complex.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ └── PacketMath.h │ │ │ │ ├── CUDA │ │ │ │ │ ├── Complex.h │ │ │ │ │ ├── Half.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ ├── PacketMathHalf.h │ │ │ │ │ └── TypeCasting.h │ │ │ │ ├── Default │ │ │ │ │ └── Settings.h │ │ │ │ ├── NEON │ │ │ │ │ ├── Complex.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ └── PacketMath.h │ │ │ │ ├── SSE │ │ │ │ │ ├── Complex.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ ├── PacketMath.h │ │ │ │ │ └── TypeCasting.h │ │ │ │ └── ZVector │ │ │ │ │ ├── Complex.h │ │ │ │ │ ├── MathFunctions.h │ │ │ │ │ └── PacketMath.h │ │ │ ├── functors │ │ │ │ ├── AssignmentFunctors.h │ │ │ │ ├── BinaryFunctors.h │ │ │ │ ├── NullaryFunctors.h │ │ │ │ ├── StlFunctors.h │ │ │ │ ├── TernaryFunctors.h │ │ │ │ └── UnaryFunctors.h │ │ │ ├── products │ │ │ │ ├── GeneralBlockPanelKernel.h │ │ │ │ ├── GeneralMatrixMatrix.h │ │ │ │ ├── GeneralMatrixMatrixTriangular.h │ │ │ │ ├── GeneralMatrixMatrixTriangular_BLAS.h │ │ │ │ ├── GeneralMatrixMatrix_BLAS.h │ │ │ │ ├── GeneralMatrixVector.h │ │ │ │ ├── GeneralMatrixVector_BLAS.h │ │ │ │ ├── Parallelizer.h │ │ │ │ ├── SelfadjointMatrixMatrix.h │ │ │ │ ├── SelfadjointMatrixMatrix_BLAS.h │ │ │ │ ├── SelfadjointMatrixVector.h │ │ │ │ ├── SelfadjointMatrixVector_BLAS.h │ │ │ │ ├── SelfadjointProduct.h │ │ │ │ ├── SelfadjointRank2Update.h │ │ │ │ ├── TriangularMatrixMatrix.h │ │ │ │ ├── TriangularMatrixMatrix_BLAS.h │ │ │ │ ├── TriangularMatrixVector.h │ │ │ │ ├── TriangularMatrixVector_BLAS.h │ │ │ │ ├── TriangularSolverMatrix.h │ │ │ │ ├── TriangularSolverMatrix_BLAS.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 │ │ │ ├── Eigenvalues │ │ │ ├── ComplexEigenSolver.h │ │ │ ├── ComplexSchur.h │ │ │ ├── ComplexSchur_LAPACKE.h │ │ │ ├── EigenSolver.h │ │ │ ├── GeneralizedEigenSolver.h │ │ │ ├── GeneralizedSelfAdjointEigenSolver.h │ │ │ ├── HessenbergDecomposition.h │ │ │ ├── MatrixBaseEigenvalues.h │ │ │ ├── RealQZ.h │ │ │ ├── RealSchur.h │ │ │ ├── RealSchur_LAPACKE.h │ │ │ ├── SelfAdjointEigenSolver.h │ │ │ ├── SelfAdjointEigenSolver_LAPACKE.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 │ │ │ ├── IncompleteCholesky.h │ │ │ ├── IncompleteLUT.h │ │ │ ├── IterativeSolverBase.h │ │ │ ├── LeastSquareConjugateGradient.h │ │ │ └── SolveWithGuess.h │ │ │ ├── Jacobi │ │ │ └── Jacobi.h │ │ │ ├── LU │ │ │ ├── Determinant.h │ │ │ ├── FullPivLU.h │ │ │ ├── InverseImpl.h │ │ │ ├── PartialPivLU.h │ │ │ ├── PartialPivLU_LAPACKE.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_LAPACKE.h │ │ │ ├── CompleteOrthogonalDecomposition.h │ │ │ ├── FullPivHouseholderQR.h │ │ │ ├── HouseholderQR.h │ │ │ └── HouseholderQR_LAPACKE.h │ │ │ ├── SPQRSupport │ │ │ └── SuiteSparseQRSupport.h │ │ │ ├── SVD │ │ │ ├── BDCSVD.h │ │ │ ├── JacobiSVD.h │ │ │ ├── JacobiSVD_LAPACKE.h │ │ │ ├── SVDBase.h │ │ │ └── UpperBidiagonalization.h │ │ │ ├── SparseCholesky │ │ │ ├── SimplicialCholesky.h │ │ │ └── SimplicialCholesky_impl.h │ │ │ ├── SparseCore │ │ │ ├── AmbiVector.h │ │ │ ├── CompressedStorage.h │ │ │ ├── ConservativeSparseSparseProduct.h │ │ │ ├── MappedSparseMatrix.h │ │ │ ├── SparseAssign.h │ │ │ ├── SparseBlock.h │ │ │ ├── SparseColEtree.h │ │ │ ├── SparseCompressedBase.h │ │ │ ├── SparseCwiseBinaryOp.h │ │ │ ├── SparseCwiseUnaryOp.h │ │ │ ├── SparseDenseProduct.h │ │ │ ├── SparseDiagonalProduct.h │ │ │ ├── SparseDot.h │ │ │ ├── SparseFuzzy.h │ │ │ ├── SparseMap.h │ │ │ ├── SparseMatrix.h │ │ │ ├── SparseMatrixBase.h │ │ │ ├── SparsePermutation.h │ │ │ ├── SparseProduct.h │ │ │ ├── SparseRedux.h │ │ │ ├── SparseRef.h │ │ │ ├── SparseSelfAdjointView.h │ │ │ ├── SparseSolverBase.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 │ │ │ ├── RealSvd2x2.h │ │ │ ├── blas.h │ │ │ ├── lapack.h │ │ │ ├── lapacke.h │ │ │ └── lapacke_mangling.h │ │ │ └── plugins │ │ │ ├── ArrayCwiseBinaryOps.h │ │ │ ├── ArrayCwiseUnaryOps.h │ │ │ ├── BlockMethods.h │ │ │ ├── CommonCwiseBinaryOps.h │ │ │ ├── CommonCwiseUnaryOps.h │ │ │ ├── MatrixCwiseBinaryOps.h │ │ │ └── MatrixCwiseUnaryOps.h │ ├── signature_of_eigen3_matrix_library │ └── unsupported │ │ └── Eigen │ │ ├── AdolcForward │ │ ├── AlignedVector3 │ │ ├── ArpackSupport │ │ ├── AutoDiff │ │ ├── BVH │ │ ├── CXX11 │ │ ├── Tensor │ │ ├── TensorSymmetry │ │ ├── ThreadPool │ │ └── src │ │ │ ├── Tensor │ │ │ ├── Tensor.h │ │ │ ├── TensorArgMax.h │ │ │ ├── TensorAssign.h │ │ │ ├── TensorBase.h │ │ │ ├── TensorBroadcasting.h │ │ │ ├── TensorChipping.h │ │ │ ├── TensorConcatenation.h │ │ │ ├── TensorContraction.h │ │ │ ├── TensorContractionBlocking.h │ │ │ ├── TensorContractionCuda.h │ │ │ ├── TensorContractionMapper.h │ │ │ ├── TensorContractionThreadPool.h │ │ │ ├── TensorConversion.h │ │ │ ├── TensorConvolution.h │ │ │ ├── TensorCostModel.h │ │ │ ├── TensorCustomOp.h │ │ │ ├── TensorDevice.h │ │ │ ├── TensorDeviceCuda.h │ │ │ ├── TensorDeviceDefault.h │ │ │ ├── TensorDeviceSycl.h │ │ │ ├── TensorDeviceThreadPool.h │ │ │ ├── TensorDimensionList.h │ │ │ ├── TensorDimensions.h │ │ │ ├── TensorEvalTo.h │ │ │ ├── TensorEvaluator.h │ │ │ ├── TensorExecutor.h │ │ │ ├── TensorExpr.h │ │ │ ├── TensorFFT.h │ │ │ ├── TensorFixedSize.h │ │ │ ├── TensorForcedEval.h │ │ │ ├── TensorForwardDeclarations.h │ │ │ ├── TensorFunctors.h │ │ │ ├── TensorGenerator.h │ │ │ ├── TensorGlobalFunctions.h │ │ │ ├── TensorIO.h │ │ │ ├── TensorImagePatch.h │ │ │ ├── TensorIndexList.h │ │ │ ├── TensorInflation.h │ │ │ ├── TensorInitializer.h │ │ │ ├── TensorIntDiv.h │ │ │ ├── TensorLayoutSwap.h │ │ │ ├── TensorMacros.h │ │ │ ├── TensorMap.h │ │ │ ├── TensorMeta.h │ │ │ ├── TensorMorphing.h │ │ │ ├── TensorPadding.h │ │ │ ├── TensorPatch.h │ │ │ ├── TensorRandom.h │ │ │ ├── TensorReduction.h │ │ │ ├── TensorReductionCuda.h │ │ │ ├── TensorReductionSycl.h │ │ │ ├── TensorRef.h │ │ │ ├── TensorReverse.h │ │ │ ├── TensorScan.h │ │ │ ├── TensorShuffling.h │ │ │ ├── TensorStorage.h │ │ │ ├── TensorStriding.h │ │ │ ├── TensorSycl.h │ │ │ ├── TensorSyclConvertToDeviceExpression.h │ │ │ ├── TensorSyclExprConstructor.h │ │ │ ├── TensorSyclExtractAccessor.h │ │ │ ├── TensorSyclExtractFunctors.h │ │ │ ├── TensorSyclLeafCount.h │ │ │ ├── TensorSyclPlaceHolderExpr.h │ │ │ ├── TensorSyclRun.h │ │ │ ├── TensorSyclTuple.h │ │ │ ├── TensorTraits.h │ │ │ ├── TensorUInt128.h │ │ │ └── TensorVolumePatch.h │ │ │ ├── TensorSymmetry │ │ │ ├── DynamicSymmetry.h │ │ │ ├── StaticSymmetry.h │ │ │ ├── Symmetry.h │ │ │ └── util │ │ │ │ └── TemplateGroupTheory.h │ │ │ ├── ThreadPool │ │ │ ├── EventCount.h │ │ │ ├── NonBlockingThreadPool.h │ │ │ ├── RunQueue.h │ │ │ ├── SimpleThreadPool.h │ │ │ ├── ThreadEnvironment.h │ │ │ ├── ThreadLocal.h │ │ │ ├── ThreadPoolInterface.h │ │ │ └── ThreadYield.h │ │ │ └── util │ │ │ ├── CXX11Meta.h │ │ │ ├── CXX11Workarounds.h │ │ │ ├── EmulateArray.h │ │ │ ├── EmulateCXX11Meta.h │ │ │ └── MaxSizeVector.h │ │ ├── EulerAngles │ │ ├── FFT │ │ ├── IterativeSolvers │ │ ├── KroneckerProduct │ │ ├── LevenbergMarquardt │ │ ├── MPRealSupport │ │ ├── MatrixFunctions │ │ ├── MoreVectorization │ │ ├── NonLinearOptimization │ │ ├── NumericalDiff │ │ ├── OpenGLSupport │ │ ├── Polynomials │ │ ├── Skyline │ │ ├── SparseExtra │ │ ├── SpecialFunctions │ │ ├── Splines │ │ └── src │ │ ├── AutoDiff │ │ ├── AutoDiffJacobian.h │ │ ├── AutoDiffScalar.h │ │ └── AutoDiffVector.h │ │ ├── BVH │ │ ├── BVAlgorithms.h │ │ └── KdBVH.h │ │ ├── Eigenvalues │ │ └── ArpackSelfAdjointEigenSolver.h │ │ ├── EulerAngles │ │ ├── EulerAngles.h │ │ └── EulerSystem.h │ │ ├── FFT │ │ ├── ei_fftw_impl.h │ │ └── ei_kissfft_impl.h │ │ ├── IterativeSolvers │ │ ├── ConstrainedConjGrad.h │ │ ├── DGMRES.h │ │ ├── GMRES.h │ │ ├── IncompleteLU.h │ │ ├── IterationController.h │ │ ├── MINRES.h │ │ └── Scaling.h │ │ ├── KroneckerProduct │ │ └── KroneckerTensorProduct.h │ │ ├── LevenbergMarquardt │ │ ├── LMcovar.h │ │ ├── LMonestep.h │ │ ├── LMpar.h │ │ ├── LMqrsolv.h │ │ └── LevenbergMarquardt.h │ │ ├── MatrixFunctions │ │ ├── MatrixExponential.h │ │ ├── MatrixFunction.h │ │ ├── MatrixLogarithm.h │ │ ├── MatrixPower.h │ │ ├── MatrixSquareRoot.h │ │ └── StemFunction.h │ │ ├── MoreVectorization │ │ └── MathFunctions.h │ │ ├── NonLinearOptimization │ │ ├── HybridNonLinearSolver.h │ │ ├── LevenbergMarquardt.h │ │ ├── chkder.h │ │ ├── covar.h │ │ ├── dogleg.h │ │ ├── fdjac1.h │ │ ├── lmpar.h │ │ ├── qrsolv.h │ │ ├── r1mpyq.h │ │ ├── r1updt.h │ │ └── rwupdt.h │ │ ├── NumericalDiff │ │ └── NumericalDiff.h │ │ ├── Polynomials │ │ ├── Companion.h │ │ ├── PolynomialSolver.h │ │ └── PolynomialUtils.h │ │ ├── Skyline │ │ ├── SkylineInplaceLU.h │ │ ├── SkylineMatrix.h │ │ ├── SkylineMatrixBase.h │ │ ├── SkylineProduct.h │ │ ├── SkylineStorage.h │ │ └── SkylineUtil.h │ │ ├── SparseExtra │ │ ├── BlockOfDynamicSparseMatrix.h │ │ ├── BlockSparseMatrix.h │ │ ├── DynamicSparseMatrix.h │ │ ├── MarketIO.h │ │ ├── MatrixMarketIterator.h │ │ └── RandomSetter.h │ │ ├── SpecialFunctions │ │ ├── SpecialFunctionsArrayAPI.h │ │ ├── SpecialFunctionsFunctors.h │ │ ├── SpecialFunctionsHalf.h │ │ ├── SpecialFunctionsImpl.h │ │ ├── SpecialFunctionsPacketMath.h │ │ └── arch │ │ │ └── CUDA │ │ │ └── CudaSpecialFunctions.h │ │ └── Splines │ │ ├── Spline.h │ │ ├── SplineFitting.h │ │ └── SplineFwd.h ├── ezETAProgressBar.hpp ├── fastapprox.h ├── format.h ├── httplib.hpp ├── jellyfish │ ├── int128.hpp │ ├── mer_dna.hpp │ └── misc.hpp ├── json.hpp ├── kseq++.hpp ├── kseq.h ├── lightweightsemaphore.h ├── make_unique.hpp ├── nonstd │ ├── optional.hpp │ └── string_view.hpp ├── parallel_hashmap │ ├── btree.h │ ├── conanfile.py │ ├── meminfo.h │ ├── phmap.h │ ├── phmap_base.h │ ├── phmap_bits.h │ ├── phmap_config.h │ ├── phmap_dump.h │ ├── phmap_fwd_decl.h │ └── phmap_utils.h ├── pcg_extras.hpp ├── pcg_random.hpp ├── peglib.h ├── posix.h ├── radicl │ ├── BasicBinWriter.hpp │ └── RADHeader.hpp ├── readerwriterqueue.h ├── spdlog │ ├── async_logger.h │ ├── common.h │ ├── details │ │ ├── async_log_helper.h │ │ ├── async_logger_impl.h │ │ ├── file_helper.h │ │ ├── log_msg.h │ │ ├── logger_impl.h │ │ ├── mpmc_bounded_q.h │ │ ├── null_mutex.h │ │ ├── os.h │ │ ├── pattern_formatter_impl.h │ │ ├── registry.h │ │ └── spdlog_impl.h │ ├── fmt │ │ ├── bundled │ │ │ ├── container.h │ │ │ ├── format.cc │ │ │ ├── format.h │ │ │ ├── ostream.cc │ │ │ ├── ostream.h │ │ │ ├── posix.cc │ │ │ ├── posix.h │ │ │ ├── printf.cc │ │ │ ├── printf.h │ │ │ ├── string.h │ │ │ └── time.h │ │ ├── fmt.h │ │ └── ostr.h │ ├── formatter.h │ ├── logger.h │ ├── sinks │ │ ├── android_sink.h │ │ ├── ansicolor_sink.h │ │ ├── base_sink.h │ │ ├── dist_sink.h │ │ ├── file_sinks.h │ │ ├── msvc_sink.h │ │ ├── null_sink.h │ │ ├── ostream_sink.h │ │ ├── sink.h │ │ ├── stdout_sinks.h │ │ ├── syslog_sink.h │ │ ├── wincolor_sink.h │ │ └── windebug_sink.h │ ├── spdlog.h │ └── tweakme.h ├── spline.h ├── strict_fstream.hpp ├── stx │ ├── any.hpp │ ├── optional.hpp │ ├── string_view.hpp │ └── variant.hpp ├── xxhash.h └── zstr.hpp ├── sample_data.tgz ├── scripts ├── AddHeaders.sh ├── ComputeMutationRate.py ├── ConvertBootstrapsToTSV.py ├── Dockerfile ├── MutateReference.py ├── build_docker_binary.sh ├── bump_version.sh ├── check_shasum.sh ├── compile.sh ├── cpld.bash ├── fetchPufferfish.sh ├── fetchRapMap.sh ├── lint.sh ├── make-release.sh ├── merge_into_develop.sh ├── merge_into_master.sh ├── push-binary.sh ├── runner.sh ├── test_sim_corr.py └── v1_10x │ ├── run.sh │ └── wrapper.cpp ├── src ├── Alevin.cpp ├── AlevinHash.cpp ├── AlevinUtils.cpp ├── AlignmentCommon.cpp ├── AlignmentModel.cpp ├── BAMUtils.cpp ├── BuildSalmonIndex.cpp ├── CMakeLists.txt ├── CollapsedCellOptimizer.cpp ├── CollapsedEMOptimizer.cpp ├── CollapsedGibbsSampler.cpp ├── DedupUMI.cpp ├── DistributionUtils.cpp ├── EMUtils.cpp ├── EffectiveLengthStats.cpp ├── FASTAParser.cpp ├── FastxParser.cpp ├── FragmentLengthDistribution.cpp ├── FragmentList.cpp ├── FragmentStartPositionDistribution.cpp ├── GZipWriter.cpp ├── GenomicFeature.cpp ├── Graph.cpp ├── LibraryFormat.cpp ├── ONTAlignmentModel.cpp ├── PCA.cpp ├── PCAUtils.cpp ├── ProgramOptionsGenerator.cpp ├── SBModel.cpp ├── SGSmooth.cpp ├── Salmon.cpp ├── SalmonAlevin.cpp ├── SalmonExceptions.cpp ├── SalmonQuantMerge.cpp ├── SalmonQuantify.cpp ├── SalmonQuantifyAlignments.cpp ├── SalmonStringUtils.cpp ├── SalmonUtils.cpp ├── SequenceBiasModel.cpp ├── SimplePosBias.cpp ├── SingleCellProtocols.cpp ├── StadenUtils.cpp ├── TestUtils.cpp ├── TranscriptGroup.cpp 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