CMakeLists.txt
FindLAPACKE.cmake
FindLAPACKEXT.cmake
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
diamond4py/__init__.py
diamond4py.egg-info/PKG-INFO
diamond4py.egg-info/SOURCES.txt
diamond4py.egg-info/dependency_links.txt
diamond4py.egg-info/top_level.txt
src/align/align.cpp
src/align/align.h
src/align/alt_hsp.cpp
src/align/culling.cpp
src/align/extend.cpp
src/align/extend.h
src/align/full_db.cpp
src/align/gapped_filter.cpp
src/align/gapped_final.cpp
src/align/gapped_score.cpp
src/align/load_hits.h
src/align/memory.cpp
src/align/output.cpp
src/align/target.h
src/align/ungapped.cpp
src/align/global_ranking/extend.cpp
src/align/global_ranking/global_ranking.cpp
src/align/global_ranking/global_ranking.h
src/align/global_ranking/table.cpp
src/align/legacy/banded_swipe_pipeline.cpp
src/align/legacy/query_mapper.cpp
src/align/legacy/query_mapper.h
src/basic/basic.cpp
src/basic/config.cpp
src/basic/config.h
src/basic/const.h
src/basic/diagonal_segment.h
src/basic/hssp.cpp
src/basic/match.h
src/basic/packed_loc.h
src/basic/packed_sequence.h
src/basic/packed_transcript.h
src/basic/reduction.h
src/basic/seed.h
src/basic/seed_iterator.h
src/basic/sequence.h
src/basic/shape.h
src/basic/shape_config.h
src/basic/statistics.h
src/basic/translate.h
src/basic/translated_position.h
src/basic/value.cpp
src/basic/value.h
src/chaining/chaining.h
src/chaining/greedy_align.cpp
src/chaining/smith_waterman.cpp
src/cluster/cluster.h
src/cluster/cluster_registry.cpp
src/cluster/cluster_registry.h
src/cluster/disjoint_set.h
src/cluster/mcl.cpp
src/cluster/mcl.h
src/cluster/medoid.cpp
src/cluster/multi_step_cluster.cpp
src/cluster/multi_step_cluster.h
src/cluster/sparse_matrix_stream.h
src/data/block.cpp
src/data/block.h
src/data/enum_seeds.h
src/data/flags.h
src/data/frequent_seeds.cpp
src/data/frequent_seeds.h
src/data/index.cpp
src/data/index.h
src/data/load_seqs.h
src/data/queries.cpp
src/data/queries.h
src/data/reference.cpp
src/data/reference.h
src/data/seed_array.cpp
src/data/seed_array.h
src/data/seed_histogram.cpp
src/data/seed_histogram.h
src/data/seed_set.cpp
src/data/seed_set.h
src/data/sequence_file.cpp
src/data/sequence_file.h
src/data/sequence_set.cpp
src/data/sequence_set.h
src/data/string_set.h
src/data/taxon_list.cpp
src/data/taxon_list.h
src/data/taxonomy.cpp
src/data/taxonomy.h
src/data/taxonomy_nodes.cpp
src/data/taxonomy_nodes.h
src/data/blastdb/blastdb.cpp
src/data/blastdb/blastdb.h
src/data/dmnd/dmnd.cpp
src/data/dmnd/dmnd.h
src/dp/dp.h
src/dp/flags.h
src/dp/hsp_traits.h
src/dp/scan_diags.cpp
src/dp/scan_diags.h
src/dp/score_profile.h
src/dp/score_vector.h
src/dp/score_vector_int16.h
src/dp/score_vector_int8.h
src/dp/ungapped.h
src/dp/ungapped_align.cpp
src/dp/ungapped_simd.cpp
src/dp/ungapped_simd.h
src/dp/swipe/banded_3frame_swipe.cpp
src/dp/swipe/banded_matrix.h
src/dp/swipe/banded_swipe.h
src/dp/swipe/cell_update.h
src/dp/swipe/full_matrix.h
src/dp/swipe/full_swipe.h
src/dp/swipe/stat_cell.h
src/dp/swipe/swipe.h
src/dp/swipe/swipe_wrapper.cpp
src/dp/swipe/target_iterator.h
src/lib/Eigen/CMakeLists.txt
src/lib/Eigen/Cholesky
src/lib/Eigen/CholmodSupport
src/lib/Eigen/Core
src/lib/Eigen/Dense
src/lib/Eigen/Eigen
src/lib/Eigen/Eigenvalues
src/lib/Eigen/Geometry
src/lib/Eigen/Householder
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src/lib/Eigen/Jacobi
src/lib/Eigen/LU
src/lib/Eigen/MetisSupport
src/lib/Eigen/OrderingMethods
src/lib/Eigen/PaStiXSupport
src/lib/Eigen/PardisoSupport
src/lib/Eigen/QR
src/lib/Eigen/QtAlignedMalloc
src/lib/Eigen/SPQRSupport
src/lib/Eigen/SVD
src/lib/Eigen/Sparse
src/lib/Eigen/SparseCholesky
src/lib/Eigen/SparseCore
src/lib/Eigen/SparseLU
src/lib/Eigen/SparseQR
src/lib/Eigen/StdDeque
src/lib/Eigen/StdList
src/lib/Eigen/StdVector
src/lib/Eigen/SuperLUSupport
src/lib/Eigen/UmfPackSupport
src/lib/Eigen/src/Cholesky/LDLT.h
src/lib/Eigen/src/Cholesky/LLT.h
src/lib/Eigen/src/Cholesky/LLT_LAPACKE.h
src/lib/Eigen/src/CholmodSupport/CholmodSupport.h
src/lib/Eigen/src/Core/Array.h
src/lib/Eigen/src/Core/ArrayBase.h
src/lib/Eigen/src/Core/ArrayWrapper.h
src/lib/Eigen/src/Core/Assign.h
src/lib/Eigen/src/Core/AssignEvaluator.h
src/lib/Eigen/src/Core/Assign_MKL.h
src/lib/Eigen/src/Core/BandMatrix.h
src/lib/Eigen/src/Core/Block.h
src/lib/Eigen/src/Core/BooleanRedux.h
src/lib/Eigen/src/Core/CommaInitializer.h
src/lib/Eigen/src/Core/ConditionEstimator.h
src/lib/Eigen/src/Core/CoreEvaluators.h
src/lib/Eigen/src/Core/CoreIterators.h
src/lib/Eigen/src/Core/CwiseBinaryOp.h
src/lib/Eigen/src/Core/CwiseNullaryOp.h
src/lib/Eigen/src/Core/CwiseTernaryOp.h
src/lib/Eigen/src/Core/CwiseUnaryOp.h
src/lib/Eigen/src/Core/CwiseUnaryView.h
src/lib/Eigen/src/Core/DenseBase.h
src/lib/Eigen/src/Core/DenseCoeffsBase.h
src/lib/Eigen/src/Core/DenseStorage.h
src/lib/Eigen/src/Core/Diagonal.h
src/lib/Eigen/src/Core/DiagonalMatrix.h
src/lib/Eigen/src/Core/DiagonalProduct.h
src/lib/Eigen/src/Core/Dot.h
src/lib/Eigen/src/Core/EigenBase.h
src/lib/Eigen/src/Core/ForceAlignedAccess.h
src/lib/Eigen/src/Core/Fuzzy.h
src/lib/Eigen/src/Core/GeneralProduct.h
src/lib/Eigen/src/Core/GenericPacketMath.h
src/lib/Eigen/src/Core/GlobalFunctions.h
src/lib/Eigen/src/Core/IO.h
src/lib/Eigen/src/Core/Inverse.h
src/lib/Eigen/src/Core/Map.h
src/lib/Eigen/src/Core/MapBase.h
src/lib/Eigen/src/Core/MathFunctions.h
src/lib/Eigen/src/Core/MathFunctionsImpl.h
src/lib/Eigen/src/Core/Matrix.h
src/lib/Eigen/src/Core/MatrixBase.h
src/lib/Eigen/src/Core/NestByValue.h
src/lib/Eigen/src/Core/NoAlias.h
src/lib/Eigen/src/Core/NumTraits.h
src/lib/Eigen/src/Core/PermutationMatrix.h
src/lib/Eigen/src/Core/PlainObjectBase.h
src/lib/Eigen/src/Core/Product.h
src/lib/Eigen/src/Core/ProductEvaluators.h
src/lib/Eigen/src/Core/Random.h
src/lib/Eigen/src/Core/Redux.h
src/lib/Eigen/src/Core/Ref.h
src/lib/Eigen/src/Core/Replicate.h
src/lib/Eigen/src/Core/ReturnByValue.h
src/lib/Eigen/src/Core/Reverse.h
src/lib/Eigen/src/Core/Select.h
src/lib/Eigen/src/Core/SelfAdjointView.h
src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h
src/lib/Eigen/src/Core/Solve.h
src/lib/Eigen/src/Core/SolveTriangular.h
src/lib/Eigen/src/Core/SolverBase.h
src/lib/Eigen/src/Core/StableNorm.h
src/lib/Eigen/src/Core/Stride.h
src/lib/Eigen/src/Core/Swap.h
src/lib/Eigen/src/Core/Transpose.h
src/lib/Eigen/src/Core/Transpositions.h
src/lib/Eigen/src/Core/TriangularMatrix.h
src/lib/Eigen/src/Core/VectorBlock.h
src/lib/Eigen/src/Core/VectorwiseOp.h
src/lib/Eigen/src/Core/Visitor.h
src/lib/Eigen/src/Core/arch/AVX/Complex.h
src/lib/Eigen/src/Core/arch/AVX/MathFunctions.h
src/lib/Eigen/src/Core/arch/AVX/PacketMath.h
src/lib/Eigen/src/Core/arch/AVX/TypeCasting.h
src/lib/Eigen/src/Core/arch/AVX512/MathFunctions.h
src/lib/Eigen/src/Core/arch/AVX512/PacketMath.h
src/lib/Eigen/src/Core/arch/AltiVec/Complex.h
src/lib/Eigen/src/Core/arch/AltiVec/MathFunctions.h
src/lib/Eigen/src/Core/arch/AltiVec/PacketMath.h
src/lib/Eigen/src/Core/arch/CUDA/Complex.h
src/lib/Eigen/src/Core/arch/CUDA/Half.h
src/lib/Eigen/src/Core/arch/CUDA/MathFunctions.h
src/lib/Eigen/src/Core/arch/CUDA/PacketMath.h
src/lib/Eigen/src/Core/arch/CUDA/PacketMathHalf.h
src/lib/Eigen/src/Core/arch/CUDA/TypeCasting.h
src/lib/Eigen/src/Core/arch/Default/ConjHelper.h
src/lib/Eigen/src/Core/arch/Default/Settings.h
src/lib/Eigen/src/Core/arch/NEON/Complex.h
src/lib/Eigen/src/Core/arch/NEON/MathFunctions.h
src/lib/Eigen/src/Core/arch/NEON/PacketMath.h
src/lib/Eigen/src/Core/arch/SSE/Complex.h
src/lib/Eigen/src/Core/arch/SSE/MathFunctions.h
src/lib/Eigen/src/Core/arch/SSE/PacketMath.h
src/lib/Eigen/src/Core/arch/SSE/TypeCasting.h
src/lib/Eigen/src/Core/arch/ZVector/Complex.h
src/lib/Eigen/src/Core/arch/ZVector/MathFunctions.h
src/lib/Eigen/src/Core/arch/ZVector/PacketMath.h
src/lib/Eigen/src/Core/functors/AssignmentFunctors.h
src/lib/Eigen/src/Core/functors/BinaryFunctors.h
src/lib/Eigen/src/Core/functors/NullaryFunctors.h
src/lib/Eigen/src/Core/functors/StlFunctors.h
src/lib/Eigen/src/Core/functors/TernaryFunctors.h
src/lib/Eigen/src/Core/functors/UnaryFunctors.h
src/lib/Eigen/src/Core/products/GeneralBlockPanelKernel.h
src/lib/Eigen/src/Core/products/GeneralMatrixMatrix.h
src/lib/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
src/lib/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h
src/lib/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h
src/lib/Eigen/src/Core/products/GeneralMatrixVector.h
src/lib/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h
src/lib/Eigen/src/Core/products/Parallelizer.h
src/lib/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
src/lib/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h
src/lib/Eigen/src/Core/products/SelfadjointMatrixVector.h
src/lib/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
src/lib/Eigen/src/Core/products/SelfadjointProduct.h
src/lib/Eigen/src/Core/products/SelfadjointRank2Update.h
src/lib/Eigen/src/Core/products/TriangularMatrixMatrix.h
src/lib/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h
src/lib/Eigen/src/Core/products/TriangularMatrixVector.h
src/lib/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
src/lib/Eigen/src/Core/products/TriangularSolverMatrix.h
src/lib/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
src/lib/Eigen/src/Core/products/TriangularSolverVector.h
src/lib/Eigen/src/Core/util/BlasUtil.h
src/lib/Eigen/src/Core/util/Constants.h
src/lib/Eigen/src/Core/util/DisableStupidWarnings.h
src/lib/Eigen/src/Core/util/ForwardDeclarations.h
src/lib/Eigen/src/Core/util/MKL_support.h
src/lib/Eigen/src/Core/util/Macros.h
src/lib/Eigen/src/Core/util/Memory.h
src/lib/Eigen/src/Core/util/Meta.h
src/lib/Eigen/src/Core/util/NonMPL2.h
src/lib/Eigen/src/Core/util/ReenableStupidWarnings.h
src/lib/Eigen/src/Core/util/StaticAssert.h
src/lib/Eigen/src/Core/util/XprHelper.h
src/lib/Eigen/src/Eigenvalues/ComplexEigenSolver.h
src/lib/Eigen/src/Eigenvalues/ComplexSchur.h
src/lib/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h
src/lib/Eigen/src/Eigenvalues/EigenSolver.h
src/lib/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
src/lib/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
src/lib/Eigen/src/Eigenvalues/HessenbergDecomposition.h
src/lib/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
src/lib/Eigen/src/Eigenvalues/RealQZ.h
src/lib/Eigen/src/Eigenvalues/RealSchur.h
src/lib/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h
src/lib/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
src/lib/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h
src/lib/Eigen/src/Eigenvalues/Tridiagonalization.h
src/lib/Eigen/src/Geometry/AlignedBox.h
src/lib/Eigen/src/Geometry/AngleAxis.h
src/lib/Eigen/src/Geometry/EulerAngles.h
src/lib/Eigen/src/Geometry/Homogeneous.h
src/lib/Eigen/src/Geometry/Hyperplane.h
src/lib/Eigen/src/Geometry/OrthoMethods.h
src/lib/Eigen/src/Geometry/ParametrizedLine.h
src/lib/Eigen/src/Geometry/Quaternion.h
src/lib/Eigen/src/Geometry/Rotation2D.h
src/lib/Eigen/src/Geometry/RotationBase.h
src/lib/Eigen/src/Geometry/Scaling.h
src/lib/Eigen/src/Geometry/Transform.h
src/lib/Eigen/src/Geometry/Translation.h
src/lib/Eigen/src/Geometry/Umeyama.h
src/lib/Eigen/src/Geometry/arch/Geometry_SSE.h
src/lib/Eigen/src/Householder/BlockHouseholder.h
src/lib/Eigen/src/Householder/Householder.h
src/lib/Eigen/src/Householder/HouseholderSequence.h
src/lib/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
src/lib/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
src/lib/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
src/lib/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h
src/lib/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
src/lib/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
src/lib/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h
src/lib/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h
src/lib/Eigen/src/Jacobi/Jacobi.h
src/lib/Eigen/src/LU/Determinant.h
src/lib/Eigen/src/LU/FullPivLU.h
src/lib/Eigen/src/LU/InverseImpl.h
src/lib/Eigen/src/LU/PartialPivLU.h
src/lib/Eigen/src/LU/PartialPivLU_LAPACKE.h
src/lib/Eigen/src/LU/arch/Inverse_SSE.h
src/lib/Eigen/src/MetisSupport/MetisSupport.h
src/lib/Eigen/src/OrderingMethods/Amd.h
src/lib/Eigen/src/OrderingMethods/Eigen_Colamd.h
src/lib/Eigen/src/OrderingMethods/Ordering.h
src/lib/Eigen/src/PaStiXSupport/PaStiXSupport.h
src/lib/Eigen/src/PardisoSupport/PardisoSupport.h
src/lib/Eigen/src/QR/ColPivHouseholderQR.h
src/lib/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h
src/lib/Eigen/src/QR/CompleteOrthogonalDecomposition.h
src/lib/Eigen/src/QR/FullPivHouseholderQR.h
src/lib/Eigen/src/QR/HouseholderQR.h
src/lib/Eigen/src/QR/HouseholderQR_LAPACKE.h
src/lib/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
src/lib/Eigen/src/SVD/BDCSVD.h
src/lib/Eigen/src/SVD/JacobiSVD.h
src/lib/Eigen/src/SVD/JacobiSVD_LAPACKE.h
src/lib/Eigen/src/SVD/SVDBase.h
src/lib/Eigen/src/SVD/UpperBidiagonalization.h
src/lib/Eigen/src/SparseCholesky/SimplicialCholesky.h
src/lib/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
src/lib/Eigen/src/SparseCore/AmbiVector.h
src/lib/Eigen/src/SparseCore/CompressedStorage.h
src/lib/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
src/lib/Eigen/src/SparseCore/MappedSparseMatrix.h
src/lib/Eigen/src/SparseCore/SparseAssign.h
src/lib/Eigen/src/SparseCore/SparseBlock.h
src/lib/Eigen/src/SparseCore/SparseColEtree.h
src/lib/Eigen/src/SparseCore/SparseCompressedBase.h
src/lib/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
src/lib/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
src/lib/Eigen/src/SparseCore/SparseDenseProduct.h
src/lib/Eigen/src/SparseCore/SparseDiagonalProduct.h
src/lib/Eigen/src/SparseCore/SparseDot.h
src/lib/Eigen/src/SparseCore/SparseFuzzy.h
src/lib/Eigen/src/SparseCore/SparseMap.h
src/lib/Eigen/src/SparseCore/SparseMatrix.h
src/lib/Eigen/src/SparseCore/SparseMatrixBase.h
src/lib/Eigen/src/SparseCore/SparsePermutation.h
src/lib/Eigen/src/SparseCore/SparseProduct.h
src/lib/Eigen/src/SparseCore/SparseRedux.h
src/lib/Eigen/src/SparseCore/SparseRef.h
src/lib/Eigen/src/SparseCore/SparseSelfAdjointView.h
src/lib/Eigen/src/SparseCore/SparseSolverBase.h
src/lib/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
src/lib/Eigen/src/SparseCore/SparseTranspose.h
src/lib/Eigen/src/SparseCore/SparseTriangularView.h
src/lib/Eigen/src/SparseCore/SparseUtil.h
src/lib/Eigen/src/SparseCore/SparseVector.h
src/lib/Eigen/src/SparseCore/SparseView.h
src/lib/Eigen/src/SparseCore/TriangularSolver.h
src/lib/Eigen/src/SparseLU/SparseLU.h
src/lib/Eigen/src/SparseLU/SparseLUImpl.h
src/lib/Eigen/src/SparseLU/SparseLU_Memory.h
src/lib/Eigen/src/SparseLU/SparseLU_Structs.h
src/lib/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
src/lib/Eigen/src/SparseLU/SparseLU_Utils.h
src/lib/Eigen/src/SparseLU/SparseLU_column_bmod.h
src/lib/Eigen/src/SparseLU/SparseLU_column_dfs.h
src/lib/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
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src/lib/Eigen/src/SparseLU/SparseLU_panel_dfs.h
src/lib/Eigen/src/SparseLU/SparseLU_pivotL.h
src/lib/Eigen/src/SparseLU/SparseLU_pruneL.h
src/lib/Eigen/src/SparseLU/SparseLU_relax_snode.h
src/lib/Eigen/src/SparseQR/SparseQR.h
src/lib/Eigen/src/StlSupport/StdDeque.h
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src/lib/Eigen/src/StlSupport/StdVector.h
src/lib/Eigen/src/StlSupport/details.h
src/lib/Eigen/src/SuperLUSupport/SuperLUSupport.h
src/lib/Eigen/src/UmfPackSupport/UmfPackSupport.h
src/lib/Eigen/src/misc/Image.h
src/lib/Eigen/src/misc/Kernel.h
src/lib/Eigen/src/misc/RealSvd2x2.h
src/lib/Eigen/src/misc/blas.h
src/lib/Eigen/src/misc/lapack.h
src/lib/Eigen/src/misc/lapacke.h
src/lib/Eigen/src/misc/lapacke_mangling.h
src/lib/Eigen/src/plugins/ArrayCwiseBinaryOps.h
src/lib/Eigen/src/plugins/ArrayCwiseUnaryOps.h
src/lib/Eigen/src/plugins/BlockMethods.h
src/lib/Eigen/src/plugins/CommonCwiseBinaryOps.h
src/lib/Eigen/src/plugins/CommonCwiseUnaryOps.h
src/lib/Eigen/src/plugins/MatrixCwiseBinaryOps.h
src/lib/Eigen/src/plugins/MatrixCwiseUnaryOps.h
src/lib/MemoryPool/MemoryPool.h
src/lib/MemoryPool/MemoryPool.tcc
src/lib/alp/njn_approx.hpp
src/lib/alp/njn_doubletype.hpp
src/lib/alp/njn_dynprogprob.cpp
src/lib/alp/njn_dynprogprob.hpp
src/lib/alp/njn_dynprogproblim.cpp
src/lib/alp/njn_dynprogproblim.hpp
src/lib/alp/njn_dynprogprobproto.cpp
src/lib/alp/njn_dynprogprobproto.hpp
src/lib/alp/njn_function.hpp
src/lib/alp/njn_integer.hpp
src/lib/alp/njn_ioutil.cpp
src/lib/alp/njn_ioutil.hpp
src/lib/alp/njn_localmaxstat.cpp
src/lib/alp/njn_localmaxstat.hpp
src/lib/alp/njn_localmaxstatmatrix.cpp
src/lib/alp/njn_localmaxstatmatrix.hpp
src/lib/alp/njn_localmaxstatutil.cpp
src/lib/alp/njn_localmaxstatutil.hpp
src/lib/alp/njn_matrix.hpp
src/lib/alp/njn_memutil.hpp
src/lib/alp/njn_random.cpp
src/lib/alp/njn_random.hpp
src/lib/alp/njn_root.hpp
src/lib/alp/njn_uniform.hpp
src/lib/alp/njn_vector.hpp
src/lib/alp/sls_alignment_evaluer.cpp
src/lib/alp/sls_alignment_evaluer.hpp
src/lib/alp/sls_alp.cpp
src/lib/alp/sls_alp.hpp
src/lib/alp/sls_alp_data.cpp
src/lib/alp/sls_alp_data.hpp
src/lib/alp/sls_alp_regression.cpp
src/lib/alp/sls_alp_regression.hpp
src/lib/alp/sls_alp_sim.cpp
src/lib/alp/sls_alp_sim.hpp
src/lib/alp/sls_basic.cpp
src/lib/alp/sls_basic.hpp
src/lib/alp/sls_normal_distr_array.hpp
src/lib/alp/sls_pvalues.cpp
src/lib/alp/sls_pvalues.hpp
src/lib/blast/blast_def.h
src/lib/blast/blast_encoding.h
src/lib/blast/blast_filter.cpp
src/lib/blast/blast_filter.h
src/lib/blast/blast_message.h
src/lib/blast/blast_program.h
src/lib/blast/blast_query_info.h
src/lib/blast/blast_seg.cpp
src/lib/blast/blast_seg.h
src/lib/blast/blast_stat.h
src/lib/blast/ncbi_math.h
src/lib/blast/ncbi_std.h
src/lib/blast/ncbitype.h
src/lib/blast/nlm_linear_algebra.cpp
src/lib/blast/nlm_linear_algebra.h
src/lib/blast/raw_scoremat.h
src/lib/blast/sm_blosum45.c
src/lib/blast/sm_blosum50.c
src/lib/blast/sm_blosum62.c
src/lib/blast/sm_blosum80.c
src/lib/blast/sm_blosum90.c
src/lib/blast/sm_pam250.c
src/lib/blast/sm_pam30.c
src/lib/blast/sm_pam70.c
src/lib/ips4o/base_case.hpp
src/lib/ips4o/block_permutation.hpp
src/lib/ips4o/bucket_pointers.hpp
src/lib/ips4o/buffers.hpp
src/lib/ips4o/classifier.hpp
src/lib/ips4o/cleanup_margins.hpp
src/lib/ips4o/config.hpp
src/lib/ips4o/empty_block_movement.hpp
src/lib/ips4o/ips4o.hpp
src/lib/ips4o/ips4o_fwd.hpp
src/lib/ips4o/local_classification.hpp
src/lib/ips4o/memory.hpp
src/lib/ips4o/parallel.hpp
src/lib/ips4o/partitioning.hpp
src/lib/ips4o/sampling.hpp
src/lib/ips4o/sequential.hpp
src/lib/ips4o/synchronization.hpp
src/lib/ips4o/thread_pool.hpp
src/lib/ips4o/utils.hpp
src/lib/mio/mmap.hpp
src/lib/mio/page.hpp
src/lib/mio/shared_mmap.hpp
src/lib/mio/detail/mmap.ipp
src/lib/mio/detail/string_util.hpp
src/lib/psnip/builtin.h
src/lib/psnip/endian.h
src/lib/tantan/LambdaCalculator.cc
src/lib/tantan/LambdaCalculator.hh
src/masking/def.h
src/masking/masking.cpp
src/masking/masking.h
src/masking/motifs.cpp
src/output/blast_pairwise_format.cpp
src/output/blast_tab_format.cpp
src/output/clustering_format.cpp
src/output/clustering_variables.cpp
src/output/clustering_variables.h
src/output/join_blocks.cpp
src/output/output.h
src/output/output_format.cpp
src/output/output_format.h
src/output/output_sink.cpp
src/output/paf_format.cpp
src/output/recursive_parser.h
src/output/sam_format.cpp
src/output/target_culling.cpp
src/output/target_culling.h
src/output/taxon_format.cpp
src/output/xml_format.cpp
src/output/daa/daa_file.h
src/output/daa/daa_record.cpp
src/output/daa/daa_record.h
src/output/daa/daa_write.cpp
src/output/daa/daa_write.h
src/output/daa/merge.cpp
src/output/daa/view.cpp
src/python/libdiamond.cpp
src/run/config.cpp
src/run/config.h
src/run/double_indexed.cpp
src/run/main.cpp
src/run/main.h
src/run/tools.cpp
src/run/tools.h
src/run/workflow.h
src/search/finger_print.h
src/search/hit.h
src/search/left_most.h
src/search/search.h
src/search/seed_complexity.cpp
src/search/seed_complexity.h
src/search/setup.cpp
src/search/sse_dist.h
src/search/stage0.cpp
src/search/stage2.cpp
src/stats/cbs.cpp
src/stats/cbs.h
src/stats/comp_based_stats.cpp
src/stats/hauser_correction.cpp
src/stats/hauser_correction.h
src/stats/matrix_adjust.cpp
src/stats/matrix_adjust_eigen.cpp
src/stats/score_matrix.cpp
src/stats/score_matrix.h
src/stats/standard_matrix.h
src/stats/stats.cpp
src/stats/matrices/blosum45.cpp
src/stats/matrices/blosum50.cpp
src/stats/matrices/blosum62.cpp
src/stats/matrices/blosum80.cpp
src/stats/matrices/blosum90.cpp
src/stats/matrices/pam250.cpp
src/stats/matrices/pam30.cpp
src/stats/matrices/pam70.cpp
src/test/data.cpp
src/test/simulate.cpp
src/test/test.cpp
src/test/test.h
src/test/test_cases.cpp
src/tools/benchmark.cpp
src/tools/benchmark_io.cpp
src/tools/benchmark_swipe.cpp
src/tools/find_shapes.cpp
src/tools/join.cpp
src/tools/merge_tsv.cpp
src/tools/roc.cpp
src/tools/rocid.cpp
src/tools/tools.cpp
src/tools/tsv_record.cpp
src/tools/tsv_record.h
src/tools/view.cpp
src/util/async_buffer.h
src/util/binary_buffer.h
src/util/command_line_parser.cpp
src/util/command_line_parser.h
src/util/double_buffer.h
src/util/dynamic_iterator.h
src/util/enum.h
src/util/escape_sequences.h
src/util/hash_function.h
src/util/hash_table.h
src/util/interval.h
src/util/interval_partition.h
src/util/intrin.h
src/util/log_stream.h
src/util/profiler.h
src/util/ptr_vector.h
src/util/queue.h
src/util/range.h
src/util/seq_file_format.cpp
src/util/seq_file_format.h
src/util/simd.cpp
src/util/simd.h
src/util/system.h
src/util/system_c.h
src/util/table.h
src/util/tantan.cpp
src/util/tantan.h
src/util/task_queue.h
src/util/text_buffer.h
src/util/util.cpp
src/util/util.h
src/util/algo/MurmurHash3.cpp
src/util/algo/MurmurHash3.h
src/util/algo/algo.h
src/util/algo/binary_search.h
src/util/algo/edge_vec.cpp
src/util/algo/edge_vec.h
src/util/algo/external_sort.h
src/util/algo/greedy_vertex_cover.cpp
src/util/algo/hash_join.h
src/util/algo/join_result.h
src/util/algo/merge_sort.h
src/util/algo/partition.h
src/util/algo/pattern_matcher.h
src/util/algo/radix_cluster.h
src/util/algo/radix_sort.h
src/util/algo/sort_helper.h
src/util/algo/upgma.cpp
src/util/algo/upgma_mc.cpp
src/util/algo/varint.h
src/util/data_structures/bit_vector.h
src/util/data_structures/compact_array.h
src/util/data_structures/deque.h
src/util/data_structures/double_array.h
src/util/data_structures/flat_array.h
src/util/data_structures/hash_set.h
src/util/data_structures/hash_table.h
src/util/data_structures/mem_buffer.h
src/util/data_structures/range_partition.h
src/util/data_structures/writer.h
src/util/io/async_file.h
src/util/io/compressed_stream.cpp
src/util/io/compressed_stream.h
src/util/io/consumer.h
src/util/io/deserializer.cpp
src/util/io/deserializer.h
src/util/io/exceptions.h
src/util/io/file_sink.cpp
src/util/io/file_sink.h
src/util/io/file_source.cpp
src/util/io/file_source.h
src/util/io/input_file.cpp
src/util/io/input_file.h
src/util/io/input_stream_buffer.cpp
src/util/io/input_stream_buffer.h
src/util/io/output_file.cpp
src/util/io/output_file.h
src/util/io/output_stream_buffer.cpp
src/util/io/output_stream_buffer.h
src/util/io/record_reader.h
src/util/io/serialize.h
src/util/io/serializer.cpp
src/util/io/serializer.h
src/util/io/stream_entity.h
src/util/io/temp_file.cpp
src/util/io/temp_file.h
src/util/io/text_input_file.cpp
src/util/io/text_input_file.h
src/util/io/zstd_stream.cpp
src/util/io/zstd_stream.h
src/util/math/integer.h
src/util/memory/alignment.h
src/util/options/option.h
src/util/parallel/filestack.cpp
src/util/parallel/filestack.h
src/util/parallel/multiprocessing.cpp
src/util/parallel/multiprocessing.h
src/util/parallel/mutex.h
src/util/parallel/parallelizer.cpp
src/util/parallel/parallelizer.h
src/util/parallel/thread_pool.h
src/util/scores/cutoff_table.h
src/util/search/seed_table.cpp
src/util/search/seed_table.h
src/util/sequence/sequence.cpp
src/util/sequence/sequence.h
src/util/simd/transpose.h
src/util/simd/transpose16x16.h
src/util/simd/transpose32x32.h
src/util/simd/vector.h
src/util/simd/vector8_avx2.h
src/util/simd/vector8_sse.h
src/util/simd/vector_generic.h
src/util/string/string.cpp
src/util/string/string.h
src/util/string/tokenizer.h
src/util/string/tsv.cpp
src/util/string/tsv.h
src/util/system/endianness.h
src/util/system/getRSS.cpp
src/util/system/system.cpp
src/util/system/system.h