[med-svn] [Git][med-team/diamond-aligner][master] 11 commits: d/watch: consolidate Github template

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / diamond-aligner


Commits:
634fbdda by Andreas Tille at 2026-08-13T16:23:40+02:00
d/watch: consolidate Github template

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4169b325 by Andreas Tille at 2026-08-13T16:24:19+02:00
New upstream version

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428607d0 by Andreas Tille at 2026-08-13T16:24:21+02:00
New upstream version 2.2.5
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3c9809a4 by Andreas Tille at 2026-08-13T16:25:18+02:00
Update upstream source from tag 'upstream/2.2.5'

Update to upstream version '2.2.5'
with Debian dir 43c1fec5d9a5a959bf2ebc5691e01f751789e215
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b4a8d1de by Andreas Tille at 2026-08-13T16:25:19+02:00
Standards-Version: 4.7.4 (routine-update)

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4b448733 by Andreas Tille at 2026-08-13T16:25:21+02:00
Changes made by cme

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bd6e3fc9 by Andreas Tille at 2026-08-13T16:25:22+02:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)

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4962db09 by Andreas Tille at 2026-08-13T15:25:30+01:00
Set upstream metadata fields: Bug-Database, Repository-Browse.

Changes-By: lintian-brush

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ab8875e4 by Andreas Tille at 2026-08-13T16:29:08+02:00
Build-Depends: libsqlite3-dev

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f4335b89 by Andreas Tille at 2026-08-13T16:32:20+02:00
Upload to unstable

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82c8b501 by Andreas Tille at 2026-08-13T16:36:51+02:00
Drop src/lib/Eigen from d/copyright since upstream stopped shipping this

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838 changed files:

- .dockerignore
- .github/workflows/cmake.yml
- .gitignore
- CITATION.cff
- CMakeLists.txt
- Dockerfile
- README.md
- + TRADEMARKS
- debian/changelog
- debian/control
- debian/copyright
- debian/upstream/metadata
- debian/watch
- src/ChangeLog
- src/align/align.cpp
- src/align/align.h
- src/align/alt_hsp.cpp
- src/align/culling.cpp
- src/align/culling.h
- src/align/def.h
- 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/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/pipeline.h
- src/align/legacy/query_mapper.cpp
- src/align/legacy/query_mapper.h
- src/align/load_hits.h
- src/align/output.cpp
- + src/align/reseek.cpp
- src/cluster/cluster_registry.cpp → src/align/reseek.h
- src/align/target.h
- src/align/ungapped.cpp
- src/basic/basic.cpp
- src/basic/config.cpp
- src/basic/config.h
- src/basic/const.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/sequence.h
- src/basic/shape.h
- src/basic/shape_config.h
- src/basic/statistics.h
- src/basic/translated_position.h
- src/basic/value.cpp
- src/basic/value.h
- src/chaining/aligner.h
- src/chaining/backtrace.cpp
- src/chaining/chaining.h
- src/chaining/diag_graph.h
- src/chaining/greedy_align.cpp
- src/chaining/hamming_ext.cpp
- src/chaining/smith_waterman.cpp
- − src/cluster/cascaded/cascaded.cpp
- − src/cluster/cascaded/cascaded.h
- − src/cluster/cascaded/helpers.cpp
- − src/cluster/cascaded/wrapper.cpp
- src/cluster/cluster.h
- − src/cluster/cluster_registry.h
- + src/cluster/data.cpp
- − src/cluster/external/align.cpp
- − src/cluster/external/build_pair_table.h
- − src/cluster/external/cluster.cpp
- − src/cluster/external/external.cpp
- − src/cluster/external/external.h
- − src/cluster/external/output.cpp
- − src/cluster/external/radix_sort.h
- + src/cluster/file_array.h
- src/cluster/helpers.cpp
- + src/cluster/input_buffer.h
- + src/cluster/len_sort.cpp
- + src/cluster/lin_index.cpp
- + src/cluster/make_blocks.cpp
- src/util/io/output_stream_buffer.h → src/cluster/merge.cpp
- + src/cluster/multinode.cpp
- + src/cluster/multinode.h
- src/cluster/output.cpp
- + src/cluster/radixed_table.h
- src/cluster/realign.cpp
- src/cluster/reassign.cpp
- src/cluster/cascaded/recluster.cpp → src/cluster/recluster.cpp
- + src/cluster/search.cpp
- + src/cluster/volume.h
- src/compile-osx.sh
- src/contrib/dna/build_score.cpp
- src/contrib/dna/chain.h
- src/contrib/mcl/clustering_format.cpp
- src/contrib/mcl/clustering_variables.cpp
- src/contrib/mcl/clustering_variables.h
- src/contrib/mcl/dense.h
- src/contrib/mcl/lazy_disjoint_set.h
- src/contrib/mcl/mcl.cpp
- src/contrib/mcl/mcl.h
- src/contrib/mcl/recursive_parser.h
- src/contrib/mcl/sparse.h
- src/contrib/mcl/sparse_matrix_stream.h
- + src/data/blastdb/asn1.cpp
- src/util/io/compressed_stream.h → src/data/blastdb/asn1.h
- src/util/io/input_file.h → src/data/blastdb/ber.h
- src/data/blastdb/blastdb.cpp
- src/data/blastdb/blastdb.h
- + src/data/blastdb/pal.cpp
- src/util/io/output_file.h → src/data/blastdb/pal.h
- + src/data/blastdb/phr.cpp
- + src/data/blastdb/pin.cpp
- + src/data/blastdb/psq.cpp
- src/util/io/file_sink.h → src/data/blastdb/taxdmp.h
- + src/data/blastdb/volume.h
- src/data/block/block.cpp
- src/data/block/block.h
- src/data/block/block_wrapper.cpp
- src/data/block/block_wrapper.h
- src/data/fasta/fasta_file.cpp
- src/data/fasta/fasta_file.h
- src/util/string/tokenizer_dyn.h → src/data/fasta/parser.h
- src/data/frequent_seeds.cpp
- src/data/frequent_seeds.h
- src/data/index.cpp
- src/data/queries.cpp
- src/data/queries.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/dp/dp.h
- src/dp/flags.h
- src/dp/scalar/double_buffer.h
- src/dp/scalar/needleman_wunsch.h
- src/dp/scalar/scalar.h
- src/dp/scalar/smith_waterman.cpp
- src/dp/scalar/traceback.h
- src/dp/scan_diags.cpp
- src/dp/scan_diags.h
- src/dp/score_profile.cpp
- src/dp/score_profile.h
- src/dp/score_vector.h
- src/dp/score_vector_int16.h
- src/dp/score_vector_int8.h
- src/dp/swipe/anchored.h
- src/dp/swipe/anchored_wrapper.cpp
- 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/config.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/dp/ungapped.h
- src/dp/ungapped_align.cpp
- src/dp/ungapped_simd.cpp
- src/dp/ungapped_simd.h
- src/output/daa/daa_file.h → src/legacy/daa/daa_file.h
- src/output/daa/daa_record.cpp → src/legacy/daa/daa_record.cpp
- src/output/daa/daa_record.h → src/legacy/daa/daa_record.h
- src/output/daa/daa_write.cpp → src/legacy/daa/daa_write.cpp
- src/output/daa/daa_write.h → src/legacy/daa/daa_write.h
- src/output/daa/merge.cpp → src/legacy/daa/merge.cpp
- src/output/daa/view.cpp → src/legacy/daa/view.cpp
- src/legacy/dmnd/compact_array.h
- src/data/dmnd/dmnd.cpp → src/legacy/dmnd/dmnd.cpp
- src/data/dmnd/dmnd.h → src/legacy/dmnd/dmnd.h
- src/legacy/dmnd/io.h
- src/legacy/dmnd/record_reader.h
- src/legacy/util/task_queue.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
- − src/lib/Eigen/IterativeLinearSolvers
- − 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
- − src/lib/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
- − src/lib/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
- − src/lib/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
- − src/lib/Eigen/src/SparseLU/SparseLU_panel_bmod.h
- − 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
- − src/lib/Eigen/src/StlSupport/StdList.h
- − 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/alp/njn_function.hpp
- src/lib/alp/njn_localmaxstat.cpp
- src/lib/alp/njn_localmaxstatutil.cpp
- src/lib/alp/sls_alignment_evaluer.hpp
- src/lib/alp/sls_alp.cpp
- src/lib/alp/sls_alp_data.cpp
- src/lib/alp/sls_alp_sim.cpp
- src/lib/alp/sls_basic.cpp
- src/lib/alp/sls_pvalues.cpp
- src/lib/alp/sls_pvalues.hpp
- src/lib/blast/blast_seg.cpp
- src/lib/blast/blastn_score.cpp
- src/lib/gsl/gsl.h
- src/lib/ips4o/buffers.hpp
- src/lib/ips4o/classifier.hpp
- src/lib/ips4o/config.hpp
- − src/lib/ksw2/ksw2.h
- − src/lib/ksw2/ksw2_extz.c
- − src/lib/ksw2/ksw2_extz2_sse.c
- src/lib/mio/detail/mmap.ipp
- src/lib/tantan/COPYING.txt
- src/lib/tantan/LambdaCalculator.cc
- src/lib/tantan/LambdaCalculator.hh
- src/masking/def.h
- + src/masking/lambda.cpp
- src/masking/masking.cpp
- src/masking/masking.h
- src/masking/motifs.cpp
- src/masking/tantan.cpp
- src/masking/tantan.h
- src/output/blast_pairwise_format.cpp
- src/output/blast_tab_format.cpp
- src/output/def.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/sam_format.cpp
- src/output/target_culling.cpp
- src/output/target_culling.h
- src/output/taxon_format.cpp
- src/output/xml_format.cpp
- src/run/config.cpp
- src/run/config.h
- src/run/double_indexed.cpp
- src/run/main.cpp
- src/run/tools.cpp
- src/run/workflow.h
- − src/search/finger_print.h
- + src/search/hamming/finger_print.h
- + src/search/hamming/hit_field.h
- + src/search/hamming/kernel.h
- + src/search/hamming/kernel_lin.h
- + src/search/hamming/kernel_mutual_cov.h
- + src/search/hamming/kernel_self.h
- + src/search/hamming/stage1_2.cpp
- src/search/hit.h
- src/search/hit_buffer.cpp
- src/search/hit_buffer.h
- src/search/kmer_ranking.cpp
- src/search/kmer_ranking.h
- src/search/left_most.h
- + src/search/lin_index/lin_index.cpp
- + src/search/lin_index/lin_index.h
- + src/search/lin_index/scan.cpp
- src/search/search.h
- src/data/enum_seeds.h → src/search/seed_array/enum_seeds.h
- src/data/flags.h → src/search/seed_array/flags.h
- src/search/stage1_2.cpp → src/search/seed_array/seed_array.cpp
- src/data/seed_array.h → src/search/seed_array/seed_array.h
- src/data/seed_array.cpp → src/search/seed_array/seed_array_extra.cpp
- + src/search/seed_array/seed_array_impl.h
- src/data/seed_histogram.cpp → src/search/seed_array/seed_histogram.cpp
- src/data/seed_histogram.h → src/search/seed_array/seed_histogram.h
- src/basic/seed_iterator.h → src/search/seed_array/seed_iterator.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/stage1.h
- src/search/stage2.h
- − src/stats/blast/linear_algebra.h
- − src/stats/blast/math.h
- − src/stats/blast/matrix_adjust.cpp
- − src/stats/blast/matrix_adjust.h
- 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/matrices/blosum45.h
- src/stats/matrices/blosum50.h
- src/stats/matrices/blosum62.h
- src/stats/matrices/blosum80.h
- src/stats/matrices/blosum90.h
- src/stats/matrices/pam250.h
- src/stats/matrices/pam30.h
- src/stats/matrices/pam70.h
- + src/stats/matrix_adjust/kernel_arm64.h
- + src/stats/matrix_adjust/kernel_avx2.h
- + src/stats/matrix_adjust/kernel_sse41.h
- src/stats/blast/linear_algebra_ncbi.h → src/stats/matrix_adjust/linear_algebra_ncbi.h
- src/util/io/temp_file.h → src/stats/matrix_adjust/matrix_adjust.cpp
- + src/stats/matrix_adjust/matrix_adjust_scalar.cpp
- src/stats/matrix_adjust.cpp → src/stats/matrix_adjust/matrix_adjust_wrapper.cpp
- src/stats/blast/ncbi.cpp → src/stats/matrix_adjust/ncbi.cpp
- src/stats/score_matrix.cpp
- src/stats/score_matrix.h
- src/stats/standard_matrix.h
- src/stats/stats.cpp
- src/stats/stats.h
- + src/test/5.faa
- + src/test/SRR14011045_1.fastq
- + src/test/SRR14011045_1.fna.gz
- + src/test/blast/nr_10k.pdb
- + src/test/blast/nr_10k.phr
- + src/test/blast/nr_10k.pin
- + src/test/blast/nr_10k.pjs
- + src/test/blast/nr_10k.pog
- + src/test/blast/nr_10k.pos
- + src/test/blast/nr_10k.pot
- + src/test/blast/nr_10k.psq
- + src/test/blast/nr_10k.ptf
- + src/test/blast/nr_10k.pto
- + src/test/blast/nr_10k_filtered.pal
- + src/test/blast/seqidlist.txt
- + src/test/blastp-blocked.out
- + src/test/blastp-cbs6.out
- + src/test/blastp-daa.out
- + src/test/blastp-global-ranking.out
- + src/test/blastp_blastaliasdb_seqidlist.out
- + src/test/blastp_blastdb.out
- + src/test/blastp_nr10k.out
- + src/test/blastx-nanopore-fna.out
- + src/test/blastx-nanopore.out
- − src/test/data.cpp
- + src/test/data.dmnd
- + src/test/data.faa
- + src/test/deepclust-multiblock.out
- + src/test/deepclust.out
- + src/test/diamond-test-blastp-blocked.out
- + src/test/diamond-test-blastp-blosum50.out
- + src/test/diamond-test-blastp-comp-based-stats-0.out
- + src/test/diamond-test-blastp-comp-based-stats-2.out
- + src/test/diamond-test-blastp-comp-based-stats-3.out
- + src/test/diamond-test-blastp-comp-based-stats-4.out
- + src/test/diamond-test-blastp-default.out
- + src/test/diamond-test-blastp-evalue.out
- + src/test/diamond-test-blastp-max-hsps.out
- + src/test/diamond-test-blastp-more-sensitive.out
- + src/test/diamond-test-blastp-multithreaded.out
- + src/test/diamond-test-blastp-paf-format.out
- + src/test/diamond-test-blastp-pairwise-format.out
- + src/test/diamond-test-blastp-query-indexed.out
- + src/test/diamond-test-blastp-target-parallel.out
- + src/test/diamond-test-blastp-target-seqs.out
- + src/test/diamond-test-blastp-top.out
- + src/test/diamond-test-blastp-ultra-sensitive.out
- + src/test/diamond-test-blastp-very-sensitive.out
- + src/test/galaxy/db.dmnd
- + src/test/galaxy/nucleotide.fasta
- + src/test/galaxy_7.out
- + src/test/galaxy_9.out
- + src/test/greedy_vertex_cover_numeric.out
- + src/test/greedy_vertex_cover_numeric.tsv
- + src/test/hit_buffer_stress.cpp
- + src/test/linclust.out
- + src/test/mini_names.dmp
- + src/test/mini_nodes.dmp
- + src/test/nr_10k.faa
- + src/test/nr_10k.taxids.tsv
- + src/test/nr_300.faa
- + src/test/queue.cpp
- + src/test/realign.out
- src/test/test.cmake
- src/test/test.cpp
- + src/test/test.daa
- + src/test/test.ps1
- − src/test/test_cases.cpp
- + src/test/test_exit_code.cmake
- + src/test/view.out
- src/tools/benchmark.cpp
- − src/tools/benchmark_io.cpp
- src/tools/benchmark_swipe.cpp
- + src/tools/composition_matrix.cpp
- − src/tools/find_shapes.cpp
- src/tools/greedy_vertex_cover.cpp
- − src/tools/roc.cpp
- − src/tools/rocid.cpp
- src/tools/tools.cpp
- src/run/tools.h → src/tools/tools.h
- − src/tools/tsv.cpp
- + src/util/algo/aho_corasick.h
- src/util/algo/algo.h
- src/util/algo/binary_search.h
- + src/util/algo/degree_partition.h
- src/util/algo/external_sort.h
- − src/util/algo/greedy_vertex_cover.cpp
- src/util/tsv/helpers.h → src/util/algo/hash.h
- src/util/algo/hash_join.h
- src/util/algo/hyperloglog.h
- src/util/algo/join_result.h
- − src/util/algo/mcl.cpp
- src/util/algo/merge_files.h
- src/util/algo/merge_sort.h
- − src/util/algo/pagerank.cpp
- 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/io/output_stream_buffer.cpp → src/util/algo/sort.h
- src/util/algo/sort_helper.h
- src/util/algo/transform_iterator.h
- src/util/algo/varint.h
- src/util/binary_buffer.h
- src/util/command_line_parser.cpp
- src/util/command_line_parser.h
- src/util/data_structures/array.h
- src/util/data_structures/bit_vector.h
- src/util/data_structures/deque.h
- src/util/data_structures/disjoint_set.h
- src/util/data_structures/double_array.h
- src/util/data_structures/flat_array.h
- + src/util/data_structures/growable_buffer.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/queue.h
- src/util/data_structures/range_partition.h
- src/util/data_structures/reorder_queue.h
- src/util/data_structures/sparse_flat_array.h
- src/util/enum.h
- src/util/escape_sequences.h
- src/util/geo/diagonal_segment.h
- src/util/geo/geo.h
- src/util/geo/hit.h
- src/util/geo/interval.h
- src/util/geo/interval_partition.h
- src/util/geo/interval_tree.h
- src/util/hash_function.h
- src/util/io/input_stream_buffer.h → src/util/heartbeat.h
- src/util/hsp/approx_hsp.h
- src/util/intrin.h
- + src/util/io/compressed_buffer.cpp
- src/util/io/compressed_buffer.h
- − src/util/io/compressed_stream.cpp
- + src/util/io/compressor.h
- − src/util/io/consumer.h
- + src/util/io/decompressor.h
- − src/util/io/deserializer.cpp
- − src/util/io/deserializer.h
- − src/util/io/exceptions.h
- + src/util/io/file.cpp
- + src/util/io/file.h
- − src/util/io/file_sink.cpp
- − src/util/io/file_source.cpp
- − src/util/io/file_source.h
- − src/util/io/input_file.cpp
- − src/util/io/input_stream_buffer.cpp
- − src/util/io/mmap.h
- − src/util/io/output_file.cpp
- src/util/tsv/read_tsv.cpp → src/util/io/read_text_mt.cpp
- − 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/text_input_file.cpp
- − src/util/io/text_input_file.h
- + src/util/io/zlib_bridge.cpp
- + src/util/io/zstd_bridge.cpp
- − src/util/io/zstd_stream.cpp
- − src/util/io/zstd_stream.h
- src/util/kmer/kmer.h
- src/util/log_stream.h
- src/util/math/integer.h
- src/util/math/log2_fast.h
- + src/util/math/math.h
- src/util/memory/alignment.h
- + src/util/memory/memory_resource.h
- + src/util/memory/vmbuffer.h
- − src/util/memory_resource.h
- + src/util/optional.h
- src/util/options/option.h
- src/util/parallel/atomic.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/semaphore.h
- + src/util/parallel/simple_thread_pool.h
- src/util/parallel/thread_pool.h
- − src/util/profiler.h
- src/util/ptr_vector.h
- src/util/range.h
- src/util/scores/cutoff_table.h
- src/util/search/seed_table.cpp
- src/util/search/seed_table.h
- + src/util/sequence/seqindex.cpp
- src/test/test.h → src/util/sequence/seqindex.h
- src/util/sequence/sequence.cpp
- src/util/sequence/sequence.h
- src/util/sequence/translate.h
- src/util/simd.cpp
- src/util/simd.h
- src/util/simd/dispatch.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_avx512.h
- src/util/simd/vector8_neon.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/system.h
- src/util/system/endianness.h
- src/util/system/getRSS.cpp
- src/util/system/system.cpp
- src/util/system/system.h
- src/util/table.h
- src/util/text_buffer.h
- − src/util/tsv/build_helper.h
- − src/util/tsv/construct.h
- − src/util/tsv/def.h
- − src/util/tsv/file.cpp
- − src/util/tsv/file.h
- − src/util/tsv/file_read.h
- − src/util/tsv/join.cpp
- − src/util/tsv/merge.cpp
- − src/util/tsv/merge_mt.cpp
- − src/util/tsv/record.cpp
- − src/util/tsv/record.h
- − src/util/tsv/table.cpp
- − src/util/tsv/table.h
- − src/util/tsv/tsv.cpp
- − src/util/tsv/tsv.h
- src/util/util.cpp
- src/util/util.h


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