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Changes In Branch master Excluding Merge-Ins

This is equivalent to a diff from a0360ebe1c to d8b5eeb514

2025-03-01
16:14		Bingwa: work toward supporting multiple variants (i.e. hptest support) check-in: 8bbdb57401 user: gav tags: gb:bingwa-multivariant
2025-02-28
09:02		Create new branch named "gb:bingwa-multivariant" check-in: d3e3909166 user: gav tags: gb:bingwa-multivariant
2024-08-18
11:05		Doc: fix qctool download links Leaf check-in: d8b5eeb514 user: gav tags: master, trunk
2024-08-14
12:40		selfmap: remove more unwanted debug check-in: ac5365a023 user: gav tags: master, trunk
2020-06-30
09:08		Bump to v2.0.8-beta; allow VCF GP field without GT field fixing ticket 4d88dff8cc check-in: 1757d58665 user: gav tags: 4d88dff8cc-fix
2020-06-27
11:16		Whoops, merge boost files change into release branch check-in: a1361a4ee4 user: gav tags: release
11:11		Removed unneeded boost files Leaf check-in: a0360ebe1c user: gav
2020-01-15
21:17		Bump to 2.0.7 check-in: 41a178a395 user: gavin.band@well.ox.ac.uk tags: v2.0.7

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Deleted .hgignore.

Deleted .hgrc.

Deleted 3rd_party/boost_1_55_0/libs/filesystem/tools/backup.bat.

Deleted 3rd_party/boost_1_55_0/libs/filesystem/tools/exclude.txt.

Deleted 3rd_party/boost_1_55_0/libs/regex/tools/generate/tables.cpp.

Deleted 3rd_party/boost_1_55_0/libs/test/Jamfile.v2.

Deleted 3rd_party/boost_1_55_0/libs/test/tools/console_test_runner/Jamfile.v2.

Deleted 3rd_party/boost_1_55_0/libs/test/tools/console_test_runner/src/console_test_runner.cpp.

Deleted 3rd_party/boost_1_55_0/libs/test/tools/console_test_runner/test/test_runner_test.cpp.

Changes to 3rd_party/boost_1_55_0/wscript.

Added 3rd_party/catch/catch.hpp.

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Changes to 3rd_party/eigen/Eigen/Cholesky.

Changes to 3rd_party/eigen/Eigen/CholmodSupport.

Changes to 3rd_party/eigen/Eigen/Core.

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Deleted 3rd_party/eigen/Eigen/Eigen2Support.

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Changes to 3rd_party/eigen/Eigen/IterativeLinearSolvers.

Changes to 3rd_party/eigen/Eigen/Jacobi.

Changes to 3rd_party/eigen/Eigen/LU.

Deleted 3rd_party/eigen/Eigen/LeastSquares.

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Changes to 3rd_party/eigen/Eigen/QtAlignedMalloc.

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Added 3rd_party/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h.

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Deleted 3rd_party/eigen/Eigen/src/CholmodSupport/CMakeLists.txt.

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Deleted 3rd_party/eigen/Eigen/src/Core/CMakeLists.txt.

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Added 3rd_party/eigen/Eigen/src/Core/ConditionEstimator.h.

Added 3rd_party/eigen/Eigen/src/Core/CoreEvaluators.h.

Changes to 3rd_party/eigen/Eigen/src/Core/CoreIterators.h.

Changes to 3rd_party/eigen/Eigen/src/Core/CwiseBinaryOp.h.

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Changes to 3rd_party/eigen/Eigen/src/Core/PlainObjectBase.h.

Added 3rd_party/eigen/Eigen/src/Core/Product.h.

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Changes to 3rd_party/eigen/Eigen/src/Core/arch/AltiVec/PacketMath.h.

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Added 3rd_party/eigen/Eigen/src/Core/arch/CUDA/Half.h.

Added 3rd_party/eigen/Eigen/src/Core/arch/CUDA/MathFunctions.h.

Added 3rd_party/eigen/Eigen/src/Core/arch/CUDA/PacketMath.h.

Added 3rd_party/eigen/Eigen/src/Core/arch/CUDA/PacketMathHalf.h.

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Added 3rd_party/eigen/Eigen/src/Core/arch/SSE/TypeCasting.h.

Added 3rd_party/eigen/Eigen/src/Core/arch/ZVector/Complex.h.

Added 3rd_party/eigen/Eigen/src/Core/arch/ZVector/MathFunctions.h.

Added 3rd_party/eigen/Eigen/src/Core/arch/ZVector/PacketMath.h.

Added 3rd_party/eigen/Eigen/src/Core/functors/AssignmentFunctors.h.

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Added 3rd_party/eigen/Eigen/src/Core/functors/NullaryFunctors.h.

Added 3rd_party/eigen/Eigen/src/Core/functors/StlFunctors.h.

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Deleted 3rd_party/eigen/Eigen/src/Core/products/CMakeLists.txt.

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Changes to 3rd_party/eigen/Eigen/src/Core/products/GeneralMatrixMatrix.h.

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Added 3rd_party/eigen/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h.

Deleted 3rd_party/eigen/Eigen/src/Core/products/GeneralMatrixMatrix_MKL.h.

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Added 3rd_party/eigen/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h.

Deleted 3rd_party/eigen/Eigen/src/Core/products/GeneralMatrixVector_MKL.h.

Changes to 3rd_party/eigen/Eigen/src/Core/products/Parallelizer.h.

Changes to 3rd_party/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix.h.

Added 3rd_party/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h.

Deleted 3rd_party/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix_MKL.h.

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Deleted 3rd_party/eigen/Eigen/src/Core/products/TriangularMatrixMatrix_MKL.h.

Changes to 3rd_party/eigen/Eigen/src/Core/products/TriangularMatrixVector.h.

Added 3rd_party/eigen/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h.

Deleted 3rd_party/eigen/Eigen/src/Core/products/TriangularMatrixVector_MKL.h.

Changes to 3rd_party/eigen/Eigen/src/Core/products/TriangularSolverMatrix.h.

Added 3rd_party/eigen/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h.

Deleted 3rd_party/eigen/Eigen/src/Core/products/TriangularSolverMatrix_MKL.h.

Changes to 3rd_party/eigen/Eigen/src/Core/products/TriangularSolverVector.h.

Changes to 3rd_party/eigen/Eigen/src/Core/util/BlasUtil.h.

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Deleted 3rd_party/eigen/Eigen/src/Eigen2Support/LeastSquares.h.

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Changes to 3rd_party/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h.

Changes to 3rd_party/eigen/Eigen/src/Eigenvalues/ComplexSchur.h.

Added 3rd_party/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h.

Deleted 3rd_party/eigen/Eigen/src/Eigenvalues/ComplexSchur_MKL.h.

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Deleted 3rd_party/eigen/Eigen/src/Eigenvalues/RealSchur_MKL.h.

Changes to 3rd_party/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h.

Added 3rd_party/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h.

Deleted 3rd_party/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_MKL.h.

Changes to 3rd_party/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/AlignedBox.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/AngleAxis.h.

Deleted 3rd_party/eigen/Eigen/src/Geometry/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/Geometry/EulerAngles.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Homogeneous.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Hyperplane.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/OrthoMethods.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/ParametrizedLine.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Quaternion.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Rotation2D.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/RotationBase.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Scaling.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Transform.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Translation.h.

Changes to 3rd_party/eigen/Eigen/src/Geometry/Umeyama.h.

Deleted 3rd_party/eigen/Eigen/src/Geometry/arch/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/Geometry/arch/Geometry_SSE.h.

Changes to 3rd_party/eigen/Eigen/src/Householder/BlockHouseholder.h.

Deleted 3rd_party/eigen/Eigen/src/Householder/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/Householder/Householder.h.

Changes to 3rd_party/eigen/Eigen/src/Householder/HouseholderSequence.h.

Changes to 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h.

Changes to 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h.

Deleted 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h.

Added 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h.

Changes to 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h.

Changes to 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h.

Added 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h.

Added 3rd_party/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h.

Deleted 3rd_party/eigen/Eigen/src/Jacobi/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/Jacobi/Jacobi.h.

Deleted 3rd_party/eigen/Eigen/src/LU/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/LU/Determinant.h.

Changes to 3rd_party/eigen/Eigen/src/LU/FullPivLU.h.

Deleted 3rd_party/eigen/Eigen/src/LU/Inverse.h.

Added 3rd_party/eigen/Eigen/src/LU/InverseImpl.h.

Changes to 3rd_party/eigen/Eigen/src/LU/PartialPivLU.h.

Added 3rd_party/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h.

Deleted 3rd_party/eigen/Eigen/src/LU/PartialPivLU_MKL.h.

Deleted 3rd_party/eigen/Eigen/src/LU/arch/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/LU/arch/Inverse_SSE.h.

Deleted 3rd_party/eigen/Eigen/src/MetisSupport/CMakeLists.txt.

Changes to 3rd_party/eigen/Eigen/src/MetisSupport/MetisSupport.h.

Changes to 3rd_party/eigen/Eigen/src/OrderingMethods/Amd.h.

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Changes to 3rd_party/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h.

Changes to 3rd_party/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h.

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Changes to 3rd_party/eigen/Eigen/src/StlSupport/StdList.h.

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Changes to 3rd_party/eigen/Eigen/src/StlSupport/details.h.

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Changes to 3rd_party/eigen/Eigen/src/misc/Image.h.

Changes to 3rd_party/eigen/Eigen/src/misc/Kernel.h.

Added 3rd_party/eigen/Eigen/src/misc/RealSvd2x2.h.

Deleted 3rd_party/eigen/Eigen/src/misc/Solve.h.

Deleted 3rd_party/eigen/Eigen/src/misc/SparseSolve.h.

Changes to 3rd_party/eigen/Eigen/src/misc/blas.h.

Added 3rd_party/eigen/Eigen/src/misc/lapack.h.

Added 3rd_party/eigen/Eigen/src/misc/lapacke.h.

Added 3rd_party/eigen/Eigen/src/misc/lapacke_mangling.h.

Changes to 3rd_party/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h.

Changes to 3rd_party/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h.

Changes to 3rd_party/eigen/Eigen/src/plugins/BlockMethods.h.

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Changes to 3rd_party/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h.

Changes to 3rd_party/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h.

Changes to 3rd_party/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h.

Changes to 3rd_party/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h.

Added 3rd_party/eigen/README.md.

Changes to 3rd_party/eigen/bench/BenchTimer.h.

Added 3rd_party/eigen/bench/analyze-blocking-sizes.cpp.

Changes to 3rd_party/eigen/bench/benchCholesky.cpp.

Changes to 3rd_party/eigen/bench/bench_gemm.cpp.

Changes to 3rd_party/eigen/bench/bench_norm.cpp.

Added 3rd_party/eigen/bench/benchmark-blocking-sizes.cpp.

Changes to 3rd_party/eigen/bench/btl/CMakeLists.txt.

Changes to 3rd_party/eigen/bench/btl/actions/action_axpby.hh.

Changes to 3rd_party/eigen/bench/btl/actions/action_axpy.hh.

Changes to 3rd_party/eigen/bench/btl/cmake/FindACML.cmake.

Changes to 3rd_party/eigen/bench/btl/cmake/FindATLAS.cmake.

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Changes to 3rd_party/eigen/bench/btl/cmake/FindCBLAS.cmake.

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Added 3rd_party/eigen/bench/btl/cmake/FindOPENBLAS.cmake.

Changes to 3rd_party/eigen/bench/btl/data/action_settings.txt.

Changes to 3rd_party/eigen/bench/btl/data/perlib_plot_settings.txt.

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Changes to 3rd_party/eigen/bench/btl/generic_bench/timers/portable_perf_analyzer.hh.

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Changes to 3rd_party/eigen/bench/btl/generic_bench/utils/size_lin_log.hh.

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Changes to 3rd_party/eigen/bench/btl/libs/BLAS/main.cpp.

Changes to 3rd_party/eigen/bench/btl/libs/STL/STL_interface.hh.

Added 3rd_party/eigen/bench/btl/libs/blaze/CMakeLists.txt.

Added 3rd_party/eigen/bench/btl/libs/blaze/blaze_interface.hh.

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Changes to 3rd_party/eigen/bench/btl/libs/eigen2/eigen2_interface.hh.

Changes to 3rd_party/eigen/bench/btl/libs/eigen3/eigen3_interface.hh.

Changes to 3rd_party/eigen/bench/btl/libs/eigen3/main_adv.cpp.

Added 3rd_party/eigen/bench/btl/libs/tensors/CMakeLists.txt.

Added 3rd_party/eigen/bench/btl/libs/tensors/main_linear.cpp.

Added 3rd_party/eigen/bench/btl/libs/tensors/main_matmat.cpp.

Added 3rd_party/eigen/bench/btl/libs/tensors/main_vecmat.cpp.

Added 3rd_party/eigen/bench/btl/libs/tensors/tensor_interface.hh.

Added 3rd_party/eigen/bench/dense_solvers.cpp.

Changes to 3rd_party/eigen/bench/eig33.cpp.

Added 3rd_party/eigen/bench/perf_monitoring/gemm/changesets.txt.

Added 3rd_party/eigen/bench/perf_monitoring/gemm/gemm.cpp.

Added 3rd_party/eigen/bench/perf_monitoring/gemm/gemm_settings.txt.

Added 3rd_party/eigen/bench/perf_monitoring/gemm/lazy_gemm.cpp.

Added 3rd_party/eigen/bench/perf_monitoring/gemm/lazy_gemm_settings.txt.

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Added 3rd_party/eigen/blas/f2c/lsame.c.

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Changes to 3rd_party/eigen/cmake/FindEigen3.cmake.

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Changes to 3rd_party/eigen/cmake/FindMetis.cmake.

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Changes to 3rd_party/eigen/cmake/FindUmfpack.cmake.

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Changes to 3rd_party/eigen/cmake/language_support.cmake.

Changes to 3rd_party/eigen/debug/gdb/printers.py.

Changes to 3rd_party/eigen/demos/opengl/quaternion_demo.cpp.

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Changes to 3rd_party/eigen/doc/TutorialReductionsVisitorsBroadcasting.dox.

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Changes to 3rd_party/eigen/doc/TutorialSparse.dox.

Changes to 3rd_party/eigen/doc/UnalignedArrayAssert.dox.

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Changes to 3rd_party/eigen/doc/examples/CMakeLists.txt.

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Added 3rd_party/eigen/doc/examples/Cwise_erf.cpp.

Added 3rd_party/eigen/doc/examples/Cwise_erfc.cpp.

Added 3rd_party/eigen/doc/examples/Cwise_lgamma.cpp.

Deleted 3rd_party/eigen/doc/examples/MatrixBase_cwise_const.cpp.

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Changes to 3rd_party/eigen/doc/examples/TutorialLinAlgInverseDeterminant.cpp.

Added 3rd_party/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_reductions_operatornorm.cpp.

Added 3rd_party/eigen/doc/examples/make_circulant.cpp.

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Added 3rd_party/eigen/doc/examples/make_circulant.cpp.evaluator.

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Added 3rd_party/eigen/doc/examples/make_circulant2.cpp.

Added 3rd_party/eigen/doc/examples/matrixfree_cg.cpp.

Added 3rd_party/eigen/doc/examples/nullary_indexing.cpp.

Added 3rd_party/eigen/doc/ftv2node.png.

Added 3rd_party/eigen/doc/ftv2pnode.png.

Added 3rd_party/eigen/doc/snippets/BiCGSTAB_simple.cpp.

Added 3rd_party/eigen/doc/snippets/BiCGSTAB_step_by_step.cpp.

Changes to 3rd_party/eigen/doc/snippets/CMakeLists.txt.

Added 3rd_party/eigen/doc/snippets/Cwise_arg.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_array_power_array.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_atan.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_boolean_not.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_boolean_xor.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_ceil.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_cosh.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_floor.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_isFinite.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_isInf.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_isNaN.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_log10.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_round.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_scalar_power_array.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_sign.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_sinh.cpp.

Added 3rd_party/eigen/doc/snippets/Cwise_tanh.cpp.

Added 3rd_party/eigen/doc/snippets/DenseBase_LinSpacedInt.cpp.

Added 3rd_party/eigen/doc/snippets/DirectionWise_hnormalized.cpp.

Changes to 3rd_party/eigen/doc/snippets/EigenSolver_eigenvectors.cpp.

Added 3rd_party/eigen/doc/snippets/LeastSquaresNormalEquations.cpp.

Added 3rd_party/eigen/doc/snippets/LeastSquaresQR.cpp.

Added 3rd_party/eigen/doc/snippets/MatrixBase_cwiseSign.cpp.

Deleted 3rd_party/eigen/doc/snippets/MatrixBase_extract.cpp.

Added 3rd_party/eigen/doc/snippets/MatrixBase_hnormalized.cpp.

Added 3rd_party/eigen/doc/snippets/MatrixBase_homogeneous.cpp.

Deleted 3rd_party/eigen/doc/snippets/MatrixBase_marked.cpp.

Deleted 3rd_party/eigen/doc/snippets/MatrixBase_part.cpp.

Added 3rd_party/eigen/doc/snippets/MatrixBase_selfadjointView.cpp.

Added 3rd_party/eigen/doc/snippets/MatrixBase_triangularView.cpp.

Changes to 3rd_party/eigen/doc/snippets/PartialRedux_count.cpp.

Added 3rd_party/eigen/doc/snippets/SparseMatrix_coeffs.cpp.

Added 3rd_party/eigen/doc/snippets/TopicAliasing_mult4.cpp.

Added 3rd_party/eigen/doc/snippets/TopicAliasing_mult5.cpp.

Added 3rd_party/eigen/doc/snippets/Triangular_solve.cpp.

Changes to 3rd_party/eigen/doc/snippets/Tutorial_AdvancedInitialization_Join.cpp.

Added 3rd_party/eigen/doc/snippets/Tutorial_ReshapeMat2Mat.cpp.

Added 3rd_party/eigen/doc/snippets/Tutorial_ReshapeMat2Vec.cpp.

Added 3rd_party/eigen/doc/snippets/Tutorial_SlicingCol.cpp.

Added 3rd_party/eigen/doc/snippets/Tutorial_SlicingVec.cpp.

Added 3rd_party/eigen/doc/snippets/VectorwiseOp_homogeneous.cpp.

Changes to 3rd_party/eigen/doc/snippets/compile_snippet.cpp.in.

Changes to 3rd_party/eigen/doc/special_examples/CMakeLists.txt.

Changes to 3rd_party/eigen/doc/special_examples/Tutorial_sparse_example.cpp.

Changes to 3rd_party/eigen/doc/special_examples/Tutorial_sparse_example_details.cpp.

Added 3rd_party/eigen/doc/special_examples/random_cpp11.cpp.

Changes to 3rd_party/eigen/eigen3.pc.in.

Changes to 3rd_party/eigen/failtest/CMakeLists.txt.

Added 3rd_party/eigen/failtest/bdcsvd_int.cpp.

Added 3rd_party/eigen/failtest/colpivqr_int.cpp.

Added 3rd_party/eigen/failtest/cwiseunaryview_nonconst_ctor_on_const_xpr.cpp.

Added 3rd_party/eigen/failtest/cwiseunaryview_on_const_type_actually_const.cpp.

Added 3rd_party/eigen/failtest/eigensolver_cplx.cpp.

Added 3rd_party/eigen/failtest/eigensolver_int.cpp.

Added 3rd_party/eigen/failtest/fullpivlu_int.cpp.

Added 3rd_party/eigen/failtest/fullpivqr_int.cpp.

Added 3rd_party/eigen/failtest/jacobisvd_int.cpp.

Added 3rd_party/eigen/failtest/ldlt_int.cpp.

Added 3rd_party/eigen/failtest/llt_int.cpp.

Added 3rd_party/eigen/failtest/partialpivlu_int.cpp.

Added 3rd_party/eigen/failtest/qr_int.cpp.

Added 3rd_party/eigen/failtest/selfadjointview_nonconst_ctor_on_const_xpr.cpp.

Added 3rd_party/eigen/failtest/selfadjointview_on_const_type_actually_const.cpp.

Added 3rd_party/eigen/failtest/sparse_ref_1.cpp.

Added 3rd_party/eigen/failtest/sparse_ref_2.cpp.

Added 3rd_party/eigen/failtest/sparse_ref_3.cpp.

Added 3rd_party/eigen/failtest/sparse_ref_4.cpp.

Added 3rd_party/eigen/failtest/sparse_ref_5.cpp.

Added 3rd_party/eigen/failtest/sparse_storage_mismatch.cpp.

Added 3rd_party/eigen/failtest/swap_1.cpp.

Added 3rd_party/eigen/failtest/swap_2.cpp.

Added 3rd_party/eigen/failtest/ternary_1.cpp.

Added 3rd_party/eigen/failtest/ternary_2.cpp.

Added 3rd_party/eigen/failtest/triangularview_nonconst_ctor_on_const_xpr.cpp.

Added 3rd_party/eigen/failtest/triangularview_on_const_type_actually_const.cpp.

Changes to 3rd_party/eigen/lapack/complex_double.cpp.

Changes to 3rd_party/eigen/lapack/complex_single.cpp.

Changes to 3rd_party/eigen/lapack/double.cpp.

Changes to 3rd_party/eigen/lapack/eigenvalues.cpp.

Changes to 3rd_party/eigen/lapack/lapack_common.h.

Changes to 3rd_party/eigen/lapack/single.cpp.

Added 3rd_party/eigen/lapack/svd.cpp.

Changes to 3rd_party/eigen/scripts/buildtests.in.

Changes to 3rd_party/eigen/scripts/check.in.

Changes to 3rd_party/eigen/scripts/eigen_gen_docs.

Changes to 3rd_party/eigen/test/CMakeLists.txt.

Changes to 3rd_party/eigen/test/adjoint.cpp.

Changes to 3rd_party/eigen/test/array.cpp.

Changes to 3rd_party/eigen/test/array_for_matrix.cpp.

Added 3rd_party/eigen/test/array_of_string.cpp.

Changes to 3rd_party/eigen/test/array_replicate.cpp.

Changes to 3rd_party/eigen/test/array_reverse.cpp.

Changes to 3rd_party/eigen/test/bandmatrix.cpp.

Changes to 3rd_party/eigen/test/basicstuff.cpp.

Added 3rd_party/eigen/test/bdcsvd.cpp.

Changes to 3rd_party/eigen/test/bicgstab.cpp.

Changes to 3rd_party/eigen/test/block.cpp.

Added 3rd_party/eigen/test/boostmultiprec.cpp.

Added 3rd_party/eigen/test/bug1213.cpp.

Added 3rd_party/eigen/test/bug1213.h.

Added 3rd_party/eigen/test/bug1213_main.cpp.

Changes to 3rd_party/eigen/test/cholesky.cpp.

Changes to 3rd_party/eigen/test/cholmod_support.cpp.

Changes to 3rd_party/eigen/test/commainitializer.cpp.

Changes to 3rd_party/eigen/test/conjugate_gradient.cpp.

Added 3rd_party/eigen/test/constructor.cpp.

Added 3rd_party/eigen/test/ctorleak.cpp.

Added 3rd_party/eigen/test/cuda_basic.cu.

Added 3rd_party/eigen/test/cuda_common.h.

Deleted 3rd_party/eigen/test/cwiseop.cpp.

Added 3rd_party/eigen/test/dense_storage.cpp.

Changes to 3rd_party/eigen/test/diagonal.cpp.

Changes to 3rd_party/eigen/test/diagonalmatrices.cpp.

Changes to 3rd_party/eigen/test/dynalloc.cpp.

Deleted 3rd_party/eigen/test/eigen2/CMakeLists.txt.

Deleted 3rd_party/eigen/test/eigen2/eigen2_adjoint.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_alignedbox.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_array.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_basicstuff.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_bug_132.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_cholesky.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_commainitializer.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_cwiseop.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_determinant.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_dynalloc.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_eigensolver.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_first_aligned.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_geometry.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_geometry_with_eigen2_prefix.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_hyperplane.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_inverse.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_linearstructure.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_lu.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_map.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_meta.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_miscmatrices.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_mixingtypes.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_newstdvector.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_nomalloc.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_packetmath.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_parametrizedline.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_prec_inverse_4x4.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_product_large.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_product_small.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_qr.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_qtvector.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_regression.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_sizeof.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_smallvectors.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_sparse_basic.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_sparse_product.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_sparse_solvers.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_sparse_vector.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_stdvector.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_submatrices.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_sum.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_svd.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_swap.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_triangular.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_unalignedassert.cpp.

Deleted 3rd_party/eigen/test/eigen2/eigen2_visitor.cpp.

Deleted 3rd_party/eigen/test/eigen2/gsl_helper.h.

Deleted 3rd_party/eigen/test/eigen2/main.h.

Deleted 3rd_party/eigen/test/eigen2/product.h.

Deleted 3rd_party/eigen/test/eigen2/runtest.sh.

Deleted 3rd_party/eigen/test/eigen2/sparse.h.

Deleted 3rd_party/eigen/test/eigen2/testsuite.cmake.

Changes to 3rd_party/eigen/test/eigen2support.cpp.

Changes to 3rd_party/eigen/test/eigensolver_complex.cpp.

Changes to 3rd_party/eigen/test/eigensolver_generalized_real.cpp.

Changes to 3rd_party/eigen/test/eigensolver_generic.cpp.

Changes to 3rd_party/eigen/test/eigensolver_selfadjoint.cpp.

Added 3rd_party/eigen/test/evaluator_common.h.

Added 3rd_party/eigen/test/evaluators.cpp.

Added 3rd_party/eigen/test/fastmath.cpp.

Changes to 3rd_party/eigen/test/first_aligned.cpp.

Changes to 3rd_party/eigen/test/geo_alignedbox.cpp.

Changes to 3rd_party/eigen/test/geo_eulerangles.cpp.

Changes to 3rd_party/eigen/test/geo_homogeneous.cpp.

Changes to 3rd_party/eigen/test/geo_hyperplane.cpp.

Changes to 3rd_party/eigen/test/geo_orthomethods.cpp.

Changes to 3rd_party/eigen/test/geo_parametrizedline.cpp.

Changes to 3rd_party/eigen/test/geo_quaternion.cpp.

Changes to 3rd_party/eigen/test/geo_transformations.cpp.

Added 3rd_party/eigen/test/half_float.cpp.

Added 3rd_party/eigen/test/incomplete_cholesky.cpp.

Added 3rd_party/eigen/test/inplace_decomposition.cpp.

Changes to 3rd_party/eigen/test/integer_types.cpp.

Changes to 3rd_party/eigen/test/inverse.cpp.

Added 3rd_party/eigen/test/is_same_dense.cpp.

Changes to 3rd_party/eigen/test/jacobisvd.cpp.

Changes to 3rd_party/eigen/test/linearstructure.cpp.

Added 3rd_party/eigen/test/lscg.cpp.

Changes to 3rd_party/eigen/test/lu.cpp.

Changes to 3rd_party/eigen/test/main.h.

Changes to 3rd_party/eigen/test/mapped_matrix.cpp.

Changes to 3rd_party/eigen/test/mapstaticmethods.cpp.

Changes to 3rd_party/eigen/test/mapstride.cpp.

Changes to 3rd_party/eigen/test/meta.cpp.

Changes to 3rd_party/eigen/test/metis_support.cpp.

Changes to 3rd_party/eigen/test/mixingtypes.cpp.

Added 3rd_party/eigen/test/mpl2only.cpp.

Changes to 3rd_party/eigen/test/nesting_ops.cpp.

Changes to 3rd_party/eigen/test/nomalloc.cpp.

Changes to 3rd_party/eigen/test/nullary.cpp.

Added 3rd_party/eigen/test/numext.cpp.

Changes to 3rd_party/eigen/test/packetmath.cpp.

Changes to 3rd_party/eigen/test/pastix_support.cpp.

Changes to 3rd_party/eigen/test/permutationmatrices.cpp.

Changes to 3rd_party/eigen/test/prec_inverse_4x4.cpp.

Changes to 3rd_party/eigen/test/product.h.

Changes to 3rd_party/eigen/test/product_extra.cpp.

Changes to 3rd_party/eigen/test/product_large.cpp.

Changes to 3rd_party/eigen/test/product_mmtr.cpp.

Changes to 3rd_party/eigen/test/product_notemporary.cpp.

Changes to 3rd_party/eigen/test/product_selfadjoint.cpp.

Changes to 3rd_party/eigen/test/product_small.cpp.

Changes to 3rd_party/eigen/test/product_symm.cpp.

Changes to 3rd_party/eigen/test/product_syrk.cpp.

Changes to 3rd_party/eigen/test/product_trmm.cpp.

Changes to 3rd_party/eigen/test/product_trmv.cpp.

Changes to 3rd_party/eigen/test/product_trsolve.cpp.

Changes to 3rd_party/eigen/test/qr.cpp.

Changes to 3rd_party/eigen/test/qr_colpivoting.cpp.

Changes to 3rd_party/eigen/test/qr_fullpivoting.cpp.

Added 3rd_party/eigen/test/rand.cpp.

Changes to 3rd_party/eigen/test/real_qz.cpp.

Changes to 3rd_party/eigen/test/redux.cpp.

Changes to 3rd_party/eigen/test/ref.cpp.

Deleted 3rd_party/eigen/test/runtest.sh.

Added 3rd_party/eigen/test/rvalue_types.cpp.

Changes to 3rd_party/eigen/test/schur_complex.cpp.

Changes to 3rd_party/eigen/test/schur_real.cpp.

Changes to 3rd_party/eigen/test/selfadjoint.cpp.

Changes to 3rd_party/eigen/test/simplicial_cholesky.cpp.

Changes to 3rd_party/eigen/test/sizeof.cpp.

Changes to 3rd_party/eigen/test/sizeoverflow.cpp.

Changes to 3rd_party/eigen/test/sparse.h.

Changes to 3rd_party/eigen/test/sparse_basic.cpp.

Added 3rd_party/eigen/test/sparse_block.cpp.

Changes to 3rd_party/eigen/test/sparse_permutations.cpp.

Changes to 3rd_party/eigen/test/sparse_product.cpp.

Added 3rd_party/eigen/test/sparse_ref.cpp.

Changes to 3rd_party/eigen/test/sparse_solver.h.

Changes to 3rd_party/eigen/test/sparse_vector.cpp.

Changes to 3rd_party/eigen/test/sparselu.cpp.

Changes to 3rd_party/eigen/test/sparseqr.cpp.

Changes to 3rd_party/eigen/test/spqr_support.cpp.

Changes to 3rd_party/eigen/test/stable_norm.cpp.

Added 3rd_party/eigen/test/stddeque_overload.cpp.

Added 3rd_party/eigen/test/stdlist_overload.cpp.

Changes to 3rd_party/eigen/test/stdvector.cpp.

Changes to 3rd_party/eigen/test/stdvector_overload.cpp.

Changes to 3rd_party/eigen/test/superlu_support.cpp.

Added 3rd_party/eigen/test/svd_common.h.

Added 3rd_party/eigen/test/svd_fill.h.

Changes to 3rd_party/eigen/test/swap.cpp.

Deleted 3rd_party/eigen/test/testsuite.cmake.

Changes to 3rd_party/eigen/test/triangular.cpp.

Changes to 3rd_party/eigen/test/umfpack_support.cpp.

Changes to 3rd_party/eigen/test/unalignedassert.cpp.

Changes to 3rd_party/eigen/test/unalignedcount.cpp.

Changes to 3rd_party/eigen/test/upperbidiagonalization.cpp.

Changes to 3rd_party/eigen/test/vectorization_logic.cpp.

Changes to 3rd_party/eigen/test/vectorwiseop.cpp.

Changes to 3rd_party/eigen/test/visitor.cpp.

Changes to 3rd_party/eigen/test/zerosized.cpp.

Changes to 3rd_party/eigen/unsupported/Eigen/AdolcForward.

Changes to 3rd_party/eigen/unsupported/Eigen/AlignedVector3.

Changes to 3rd_party/eigen/unsupported/Eigen/CMakeLists.txt.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/CMakeLists.txt.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/Tensor.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/TensorSymmetry.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/ThreadPool.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/README.md.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h.

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Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h.

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Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h.

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Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h.

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Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclConvertToDeviceExpression.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExprConstructor.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractAccessor.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclExtractFunctors.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclLeafCount.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclPlaceHolderExpr.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclRun.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorSyclTuple.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/SimpleThreadPool.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/util/EmulateCXX11Meta.h.

Added 3rd_party/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h.

Added 3rd_party/eigen/unsupported/Eigen/EulerAngles.

Changes to 3rd_party/eigen/unsupported/Eigen/IterativeSolvers.

Changes to 3rd_party/eigen/unsupported/Eigen/KroneckerProduct.

Changes to 3rd_party/eigen/unsupported/Eigen/MPRealSupport.

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Changes to 3rd_party/eigen/unsupported/Eigen/SparseExtra.

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Deleted 3rd_party/eigen/unsupported/Eigen/src/SVD/CMakeLists.txt.

Deleted 3rd_party/eigen/unsupported/Eigen/src/SVD/JacobiSVD.h.

Deleted 3rd_party/eigen/unsupported/Eigen/src/SVD/SVDBase.h.

Deleted 3rd_party/eigen/unsupported/Eigen/src/SVD/TODOBdcsvd.txt.

Deleted 3rd_party/eigen/unsupported/Eigen/src/SVD/doneInBDCSVD.txt.

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Added 3rd_party/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h.

Deleted 3rd_party/eigen/unsupported/Eigen/src/SparseExtra/CMakeLists.txt.

Changes to 3rd_party/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h.

Changes to 3rd_party/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h.

Changes to 3rd_party/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h.

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Added 3rd_party/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h.

Added 3rd_party/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h.

Added 3rd_party/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h.

Added 3rd_party/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h.

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Added 3rd_party/eigen/unsupported/test/cxx11_eventcount.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_non_blocking_thread_pool.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_runqueue.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_argmax_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_assign.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_broadcast_sycl.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_broadcasting.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_cast_float16_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_casts.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_chipping.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_comparisons.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_complex_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_complex_cwise_ops_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_concatenation.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_const.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_contract_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_contraction.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_convolution.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_custom_index.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_custom_op.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_device.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_device_sycl.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_dimension.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_empty.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_expr.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_fft.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_fixed_size.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_forced_eval.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_forced_eval_sycl.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_ifft.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_image_patch.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_index_list.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_inflation.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_mixed_indices.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_of_const_values.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_of_float16_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_of_strings.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_random_cuda.cu.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_reduction_sycl.cpp.

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Added 3rd_party/eigen/unsupported/test/cxx11_tensor_scan_cuda.cu.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_shuffling.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_simple.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_striding.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_sugar.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_sycl.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_symmetry.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_thread_pool.cpp.

Added 3rd_party/eigen/unsupported/test/cxx11_tensor_uint128.cpp.

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Deleted 3rd_party/eigen/unsupported/test/jacobisvd.cpp.

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Added 3rd_party/eigen/wscript.

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Added 3rd_party/zlib/win32/zlib1.rc.

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Changes to appcontext/include/appcontext/ApplicationContext.hpp.

Changes to appcontext/include/appcontext/OptionDefinition.hpp.

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Changes to appcontext/src/ApplicationContext.cpp.

Changes to appcontext/src/OptionDefinition.cpp.

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Changes to appcontext/wscript.

Added apps/bingwa.cpp.

Deleted apps/binit.cpp.

Deleted apps/checkvcf.cpp.

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Added apps/hptest.cpp.

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Deleted apps/inflation.cpp.

Changes to apps/inthinnerator.cpp.

Added apps/ldbird.cpp.

Added apps/multifinemap.cpp.

Deleted apps/overrep.cpp.

Changes to apps/qctool.cpp.

Changes to apps/selfmap.cpp.

Added apps/wscript.

Added bingwa/include/bingwa/BingwaComputation.hpp.

Added bingwa/include/bingwa/EffectParameterNamePack.hpp.

Added bingwa/include/bingwa/FlatFileFrequentistGenomeWideAssociationResults.hpp.

Added bingwa/include/bingwa/FrequentistGenomeWideAssociationResults.hpp.

Added bingwa/include/bingwa/MMMResults.hpp.

Added bingwa/include/bingwa/ModelAveragingBayesFactorAnalysis.hpp.

Added bingwa/include/bingwa/MultivariateFixedEffectMetaAnalysis.hpp.

Added bingwa/include/bingwa/PerCohortBayesFactor.hpp.

Added bingwa/include/bingwa/PerCohortCountsReporter.hpp.

Added bingwa/include/bingwa/PerCohortValueReporter.hpp.

Added bingwa/include/bingwa/SNPTESTResults.hpp.

Added bingwa/include/bingwa/impl/impl.hpp.

Added bingwa/include/bingwa/special_values.hpp.

Added bingwa/src/EffectParameterNamePack.cpp.

Added bingwa/src/FlatFileFrequentistGenomeWideAssociationResults.cpp.

Added bingwa/src/MMMResults.cpp.

Added bingwa/src/ModelAveragingBayesFactorAnalysis.cpp.

Added bingwa/src/MultivariateFixedEffectMetaAnalysis.cpp.

Added bingwa/src/PerCohortBayesFactor.cpp.

Added bingwa/src/PerCohortCountsReporter.cpp.

Added bingwa/src/PerCohortValueReporter.cpp.

Added bingwa/src/SNPTESTResults.cpp.

Added bingwa/src/impl/impl.cpp.

Added bingwa/wscript.

Deleted bitbucket-pipelines.yml.

Deleted components/AssociationTestComponent/wscript.

Changes to components/HaplotypeFrequencyComponent/include/components/HaplotypeFrequencyComponent/FlatTableDBOutputter.hpp.

Changes to components/HaplotypeFrequencyComponent/include/components/HaplotypeFrequencyComponent/HaplotypeFrequencyComponent.hpp.

Changes to components/HaplotypeFrequencyComponent/src/FlatTableDBOutputter.cpp.

Changes to components/HaplotypeFrequencyComponent/src/HaplotypeFrequencyComponent.cpp.

Changes to components/HaplotypeFrequencyComponent/wscript.

Deleted components/Illumina/include/components/Illumina/include/IlluminaManifest.hpp.

Deleted components/Illumina/wscript.

Changes to components/RelatednessComponent/include/components/RelatednessComponent/KinshipCoefficientComputer.hpp.

Changes to components/RelatednessComponent/src/KinshipCoefficientComputer.cpp.

Changes to components/RelatednessComponent/src/RelatednessComponent.cpp.

Changes to components/RelatednessComponent/wscript.

Changes to components/SNPOutputComponent/include/components/SNPOutputComponent/SQLiteGenotypesSNPDataSink.hpp.

Changes to components/SNPOutputComponent/include/components/SNPOutputComponent/SQLiteHaplotypesSNPDataSink.hpp.

Changes to components/SNPOutputComponent/src/SQLiteGenotypesSNPDataSink.cpp.

Changes to components/SNPOutputComponent/src/SQLiteHaplotypesSNPDataSink.cpp.

Changes to components/SNPOutputComponent/wscript.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/AssociationTest.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/Bed3Annotation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/Bed4Annotation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/CallComparerComponent.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/ClusterFitComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/CrossDataSetConcordanceComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/CrossDataSetHaplotypeComparisonComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/DifferentialMissingnessComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/FileOutputter.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/GeneticMapAnnotation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/GenomeSequence.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/HWEComputation.hpp.

Added components/SNPSummaryComponent/include/components/SNPSummaryComponent/InfoComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/IntensitySummaryComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/SNPSummaryComponent.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/SNPSummaryComputation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/SNPSummaryComputationManager.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/SequenceAnnotation.hpp.

Changes to components/SNPSummaryComponent/include/components/SNPSummaryComponent/StratifyingSNPSummaryComputation.hpp.

Changes to components/SNPSummaryComponent/src/Bed3Annotation.cpp.

Changes to components/SNPSummaryComponent/src/Bed4Annotation.cpp.

Changes to components/SNPSummaryComponent/src/CallComparerComponent.cpp.

Changes to components/SNPSummaryComponent/src/ClusterFitComputation.cpp.

Changes to components/SNPSummaryComponent/src/CrossDataSetConcordanceComputation.cpp.

Changes to components/SNPSummaryComponent/src/CrossDataSetHaplotypeComparisonComputation.cpp.

Changes to components/SNPSummaryComponent/src/DifferentialMissingnessComputation.cpp.

Changes to components/SNPSummaryComponent/src/GeneticMapAnnotation.cpp.

Changes to components/SNPSummaryComponent/src/GenomeSequence.cpp.

Changes to components/SNPSummaryComponent/src/GenotypeFrequencyTestCallComparer.cpp.

Changes to components/SNPSummaryComponent/src/HWEComputation.cpp.

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Changes to components/SNPSummaryComponent/src/IntensitySummaryComputation.cpp.

Changes to components/SNPSummaryComponent/src/PairwiseCallComparerManager.cpp.

Changes to components/SNPSummaryComponent/src/SNPSummaryComponent.cpp.

Changes to components/SNPSummaryComponent/src/SNPSummaryComputation.cpp.

Changes to components/SNPSummaryComponent/src/SNPSummaryComputationManager.cpp.

Changes to components/SNPSummaryComponent/src/SequenceAnnotation.cpp.

Changes to components/SNPSummaryComponent/src/StratifyingSNPSummaryComputation.cpp.

Changes to components/SNPSummaryComponent/wscript.

Changes to components/SampleSummaryComponent/include/components/SampleSummaryComponent/FlatTableDBOutputter.hpp.

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Changes to components/SampleSummaryComponent/wscript.

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Deleted db/include/db/Connection.hpp.

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Deleted db/include/db/MySQLConnection.hpp.

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Deleted db/include/db/SQLite3Connection.hpp.

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Deleted db/include/db/SQLite3Statement.hpp.

Deleted db/include/db/Transaction.hpp.

Deleted db/include/db/fill_SQL.hpp.

Deleted db/include/db/get_unique_id.hpp.

Deleted db/include/db/load_key_value_pairs.hpp.

Deleted db/src/Connection.cpp.

Deleted db/src/Error.cpp.

Deleted db/src/MySQLConnection.cpp.

Deleted db/src/SQLStatement.cpp.

Deleted db/src/SQLite3Connection.cpp.

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Deleted db/src/get_unique_id.cpp.

Deleted db/test/test_case.hpp.

Deleted db/test/test_fill_SQL.cpp.

Deleted db/test/test_get_unique_id.cpp.

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Added doc/html/qctool/content/documentation/examples/intensities.content.html.

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Changes to doc/html/qctool/documentation/examples/combining.html.

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Changes to doc/html/qctool/documentation/examples/computing_pcs.html.

Changes to doc/html/qctool/documentation/examples/converting.html.

Changes to doc/html/qctool/documentation/examples/converting_genotypes.html.

Changes to doc/html/qctool/documentation/examples/filtering_samples.html.

Changes to doc/html/qctool/documentation/examples/filtering_variants.html.

Changes to doc/html/qctool/documentation/examples/inferring_ploidy.html.

Changes to doc/html/qctool/documentation/examples/intensities.html.

Changes to doc/html/qctool/documentation/examples/merging.html.

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Changes to doc/html/qctool/documentation/examples/sorting.html.

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Changes to doc/html/qctool/documentation/genotype_file_formats.html.

Changes to doc/html/qctool/documentation/sample_file_formats.html.

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Changes to fputils/wscript.

Changes to genfile/include/genfile/BGenFileSNPDataSource.hpp.

Changes to genfile/include/genfile/BedFileSNPDataSource.hpp.

Added genfile/include/genfile/CartesianProductVisitor.hpp.

Changes to genfile/include/genfile/CategoricalCrossCohortCovariateValueMapping.hpp.

Changes to genfile/include/genfile/CountingCohortIndividualSource.hpp.

Changes to genfile/include/genfile/CrossCohortCovariateValueMapping.hpp.

Changes to genfile/include/genfile/DosageFileSNPDataSource.hpp.

Added genfile/include/genfile/GPThresholdingGTSetter.hpp.

Changes to genfile/include/genfile/GenFileSNPDataSource.hpp.

Changes to genfile/include/genfile/HLAIMPAsBiallelicVariantDataSource.hpp.

Changes to genfile/include/genfile/HapmapHaplotypesSNPDataSource.hpp.

Changes to genfile/include/genfile/ImputeHapProbsSNPDataSource.hpp.

Changes to genfile/include/genfile/ImputeHaplotypesSNPDataSource.hpp.

Added genfile/include/genfile/ListSNPDataSink.hpp.

Changes to genfile/include/genfile/LongFormatSNPDataSource.hpp.

Changes to genfile/include/genfile/MergingSNPDataSource.hpp.

Added genfile/include/genfile/MultiSourceVisitor.hpp.

Changes to genfile/include/genfile/PloidyConvertingSNPDataSource.hpp.

Changes to genfile/include/genfile/ReorderingSNPDataSource.hpp.

Changes to genfile/include/genfile/SNPDataSource.hpp.

Changes to genfile/include/genfile/SNPDataSourceChain.hpp.

Changes to genfile/include/genfile/SNPDataSourceRack.hpp.

Changes to genfile/include/genfile/SNPFilteringSNPDataSource.hpp.

Deleted genfile/include/genfile/SNPIdentifyingDataFilteringSNPDataSource.hpp.

Changes to genfile/include/genfile/SNPTranslatingSNPDataSource.hpp.

Changes to genfile/include/genfile/SampleFilteringSNPDataSource.hpp.

Changes to genfile/include/genfile/SampleMappingSNPDataSource.hpp.

Changes to genfile/include/genfile/SampleRange.hpp.

Changes to genfile/include/genfile/ShapeITHaplotypesSNPDataSource.hpp.

Changes to genfile/include/genfile/StrandAligningSNPDataSource.hpp.

Changes to genfile/include/genfile/ThreshholdingSNPDataSource.hpp.

Changes to genfile/include/genfile/ToGP.hpp.

Changes to genfile/include/genfile/VCFFormatSNPDataSource.hpp.

Changes to genfile/include/genfile/VariantEntry.hpp.

Added genfile/include/genfile/VariantIdentifyingDataFilteringSNPDataSource.hpp.

Added genfile/include/genfile/bgen/IndexQuery.hpp.

Added genfile/include/genfile/bgen/Query.hpp.

Added genfile/include/genfile/bgen/View.hpp.

Added genfile/include/genfile/db/Connection.hpp.

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Added genfile/include/genfile/db/get_unique_id.hpp.

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Changes to genfile/include/genfile/vcf/Types.hpp.

Changes to genfile/src/BGenFileSNPDataSource.cpp.

Changes to genfile/src/BedFileSNPDataSink.cpp.

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Changes to genfile/src/CategoricalCrossCohortCovariateValueMapping.cpp.

Changes to genfile/src/Chromosome.cpp.

Changes to genfile/src/CohortIndividualSource.cpp.

Changes to genfile/src/CountingCohortIndividualSource.cpp.

Changes to genfile/src/CrossCohortBaselineRemapping.cpp.

Changes to genfile/src/CrossCohortCovariateValueMapping.cpp.

Changes to genfile/src/FromFileCohortIndividualSource.cpp.

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Changes to genfile/src/GenFileSNPDataSource.cpp.

Changes to genfile/src/GenLikeSNPDataSink.cpp.

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Changes to genfile/src/LongFormatSNPDataSource.cpp.

Changes to genfile/src/MergingSNPDataSource.cpp.

Changes to genfile/src/ReorderingSNPDataSource.cpp.

Changes to genfile/src/SNPDataSink.cpp.

Changes to genfile/src/SNPDataSource.cpp.

Changes to genfile/src/SNPDataSourceChain.cpp.

Changes to genfile/src/SNPDataSourceRack.cpp.

Changes to genfile/src/SNPFilteringSNPDataSource.cpp.

Changes to genfile/src/SNPIdentifyingDataFilteringSNPDataSource.cpp.

Changes to genfile/src/SampleFilteringSNPDataSource.cpp.

Changes to genfile/src/SampleMappingSNPDataSource.cpp.

Changes to genfile/src/SampleRange.cpp.

Changes to genfile/src/SampleStratification.cpp.

Changes to genfile/src/SortingBGenFileSNPDataSink.cpp.

Changes to genfile/src/StrandAligningSNPDataSource.cpp.

Changes to genfile/src/ThreshholdingSNPDataSource.cpp.

Changes to genfile/src/VCFFormatSNPDataSink.cpp.

Changes to genfile/src/VCFFormatSNPDataSource.cpp.

Changes to genfile/src/VariableInSetSampleFilter.cpp.

Changes to genfile/src/VariantEntry.cpp.

Changes to genfile/src/VariantIdentifyingData.cpp.

Added genfile/src/bgen/IndexQuery.cpp.

Added genfile/src/bgen/View.cpp.

Added genfile/src/db/Connection.cpp.

Added genfile/src/db/Error.cpp.

Added genfile/src/db/SQLStatement.cpp.

Added genfile/src/db/SQLite3Connection.cpp.

Added genfile/src/db/SQLite3Statement.cpp.

Added genfile/src/db/fill_SQL.cpp.

Added genfile/src/db/get_unique_id.cpp.

Changes to genfile/src/vcf/CallReader.cpp.

Added genfile/test/catch.hpp.

Added genfile/test/db/test_fill_SQL.cpp.

Added genfile/test/db/test_get_unique_id.cpp.

Added genfile/test/db/test_load_key_value_pairs.cpp.

Changes to genfile/test/test_case.cpp.

Changes to genfile/test/test_case.hpp.

Changes to genfile/test/test_cohort_individual_source.cpp.

Changes to genfile/test/test_endianness_utils.cpp.

Changes to genfile/test/test_filter_grammar.cpp.

Changes to genfile/test/test_genfile_io.cpp.

Changes to genfile/test/test_sample_filtering_snp_data_source.cpp.

Changes to genfile/test/test_slice.cpp.

Changes to genfile/test/test_snp_data_source_chain.cpp.

Changes to genfile/test/test_snp_data_source_rack.cpp.

Changes to genfile/test/test_snp_identifying_data.cpp.

Changes to genfile/test/test_strand_aligning_snp_data_source.cpp.

Changes to genfile/test/test_string_utils.cpp.

Changes to genfile/test/test_strtod.cpp.

Changes to genfile/test/test_variant_identifying_data.cpp.

Changes to genfile/test/test_vcf_call_reader.cpp.

Changes to genfile/test/test_vcf_format_source.cpp.

Changes to genfile/test/test_vcf_metadata.cpp.

Changes to genfile/test/test_vcf_types.cpp.

Changes to genfile/wscript.

Deleted include/compute_maximum_likelihood_allele_frequency.hpp.

Deleted include/gamma.hpp.

Deleted integration/include/integration/ModifiedCholesky.hpp.

Deleted integration/include/integration/ModifiedNewtonRaphson.hpp.

Deleted integration/test/test_modified_cholesky.cpp.

Changes to integration/wscript.

Added metro/include/metro/CholeskyStepper.hpp.

Added metro/include/metro/Error.hpp.

Added metro/include/metro/IndependentParameterDistribution.hpp.

Changes to metro/include/metro/LogLikelihood.hpp.

Added metro/include/metro/ModifiedCholesky.hpp.

Added metro/include/metro/ModifiedNewtonRaphson.hpp.

Added metro/include/metro/NewtonRaphson.hpp.

Added metro/include/metro/SampleRange.hpp.

Added metro/include/metro/SampleStratification.hpp.

Added metro/include/metro/ShotgunStochasticSearch.hpp.

Added metro/include/metro/SmoothFunction.hpp.

Added metro/include/metro/Snptest25StoppingCondition.hpp.

Added metro/include/metro/UnivariateLogDensity.hpp.

Added metro/include/metro/concurrency/threadpool.hpp.

Added metro/include/metro/constants.hpp.

Added metro/include/metro/count_range.hpp.

Added metro/include/metro/distributions/Flat.hpp.

Added metro/include/metro/distributions/LogF.hpp.

Added metro/include/metro/fit_model.hpp.

Added metro/include/metro/intersect_ranges.hpp.

Changes to metro/include/metro/likelihood/Mixture.hpp.

Changes to metro/include/metro/likelihood/Multinomial.hpp.

Changes to metro/include/metro/likelihood/MultivariateT.hpp.

Changes to metro/include/metro/likelihood/ProductOfMultinomials.hpp.

Changes to metro/include/metro/log_sum_exp.hpp.

Added metro/include/metro/maximisation.hpp.

Added metro/include/metro/regression/BinomialLogistic.hpp.

Added metro/include/metro/regression/Design.hpp.

Added metro/include/metro/regression/IndependentLogFWeightedLogLikelihood.hpp.

Added metro/include/metro/regression/IndependentNormalWeightedLogLikelihood.hpp.

Added metro/include/metro/regression/LogLikelihood.hpp.

Added metro/include/metro/regression/LogPosteriorDensity.hpp.

Added metro/include/metro/regression/LogUnnormalisedPosterior.hpp.

Added metro/include/metro/regression/Logistic.hpp.

Added metro/include/metro/regression/MultinomialRegressionLogLikelihood.hpp.

Added metro/include/metro/regression/NormalWeightedLogLikelihood.hpp.

Added metro/include/metro/regression/ThreadedLogLikelihood.hpp.

Added metro/include/metro/summation.hpp.

Added metro/include/metro/union_ranges.hpp.

Added metro/src/CholeskyStepper.cpp.

Changes to metro/src/DataSubset.cpp.

Added metro/src/Error.cpp.

Added metro/src/IndependentParameterDistribution.cpp.

Added metro/src/SampleRange.cpp.

Added metro/src/SampleStratification.cpp.

Added metro/src/ShotgunStochasticSearch.cpp.

Added metro/src/UnivariateLogDensity.cpp.

Added metro/src/concurrency/threadpool.cpp.

Added metro/src/count_range.cpp.

Added metro/src/distributions/Flat.cpp.

Added metro/src/distributions/LogF.cpp.

Added metro/src/fit_model.cpp.

Added metro/src/intersect_ranges.cpp.

Changes to metro/src/log_sum_exp.cpp.

Added metro/src/regression/BinomialLogistic.cpp.

Added metro/src/regression/Design.cpp.

Added metro/src/regression/IndependentLogFWeightedLogLikelihood.cpp.

Added metro/src/regression/IndependentNormalWeightedLogLikelihood.cpp.

Added metro/src/regression/LogLikelihood.cpp.

Added metro/src/regression/LogUnnormalisedPosterior.cpp.

Added metro/src/regression/Logistic.cpp.

Added metro/src/regression/MultinomialRegressionLogLikelihood.cpp.

Added metro/src/regression/NormalWeightedLogLikelihood.cpp.

Added metro/src/regression/ThreadedLogLikelihood.cpp.

Added metro/src/union_ranges.cpp.

Added metro/test/test_binomial_logistic_regression.cpp.

Changes to metro/test/test_case.cpp.

Added metro/test/test_log_sum_exp.cpp.

Added metro/test/test_logistic_regression.cpp.

Changes to metro/test/test_mixture.cpp.

Added metro/test/test_modified_cholesky.cpp.

Added metro/test/test_modified_newton_raphson.cpp.

Added metro/test/test_multinomial_regression.cpp.

Added metro/test/test_regression_design.cpp.

Changes to metro/wscript.

Changes to qcdb/include/qcdb/DBOutputter.hpp.

Added qcdb/include/qcdb/FlatFileMultiVariantOutputter.hpp.

Changes to qcdb/include/qcdb/FlatTableDBOutputter.hpp.

Added qcdb/include/qcdb/FlatTableMultiVariantDBOutputter.hpp.

Added qcdb/include/qcdb/MultiFileOutputter.hpp.

Added qcdb/include/qcdb/MultiTableDBOutputter.hpp.

Added qcdb/include/qcdb/MultiTableStorage.hpp.

Added qcdb/include/qcdb/MultiVariantStorage.hpp.

Changes to qcdb/include/qcdb/Storage.hpp.

Changes to qcdb/include/qcdb/StorageOptions.hpp.

Changes to qcdb/src/DBOutputter.cpp.

Added qcdb/src/FlatFileMultiVariantOutputter.cpp.

Changes to qcdb/src/FlatTableDBOutputter.cpp.

Added qcdb/src/FlatTableMultiVariantDBOutputter.cpp.

Added qcdb/src/MultiFileOutputter.cpp.

Added qcdb/src/MultiTableDBOutputter.cpp.

Added qcdb/src/MultiVariantStorage.cpp.

Added qcdb/src/Storage.cpp.

Changes to qcdb/src/store_samples_in_db.cpp.

Changes to qcdb/wscript.

Changes to release/Release/ReleaseBuilder.py.

Changes to release/Release/SingleTest.py.

Changes to release/Release/TestHarness.py.

Changes to release/test/QctoolRunner.py.

Changes to release/test/data/complex.backward.vcf.

Changes to release/test/data/complex.reordered.vcf.

Changes to release/test/data/complex.vcf.

Added release/test/data/correlation.sample.

Added release/test/data/correlation.vcf.

Changes to release/test/data/diploid.converted.vcf.

Changes to release/test/data/diploid.vcf.

Deleted release/test/data/excluded_samples.txt.

Added release/test/data/finemap.bgen.

Added release/test/data/finemap.sample.

Added release/test/data/host-parasite/host.large.vcf.

Added release/test/data/host-parasite/host.vcf.

Added release/test/data/host-parasite/host_spec.txt.

Added release/test/data/host-parasite/parasite.large.vcf.

Added release/test/data/host-parasite/parasite.vcf.

Added release/test/data/host-parasite/samples.large.sample.

Added release/test/data/host-parasite/samples.sample.

Added release/test/data/imputed.bgen.bgi.

Added release/test/data/imputed.vcf.

Added release/test/data/merge1_merged_merge2.gen.

Added release/test/data/test.bgen.bgi.

Changes to release/test/data/test.sample-filtered.vcf.

Changes to release/test/data/test.twice.vcf.

Changes to release/test/data/test.v4.1.vcf.

Changes to release/test/data/test.v4.1.vcf.gz.

Changes to release/test/data/test.v4.2.vcf.

Changes to release/test/data/test.vcf.

Added release/test/data/test.wrongids.sample.

Changes to release/test/info_test.R.

Changes to release/test/run_tests.sh.

Changes to release/test/stats_test.R.

Changes to release/test/tests.txt.

Changes to src/FileBackupCreator.cpp.

Changes to statfile/include/statfile/DelimitedStatSource.hpp.

Changes to statfile/include/statfile/SNPDataSourceAdapter.hpp.

Changes to statfile/wscript.

Changes to string_utils/wscript.

Added waf.

Deleted waf-1.5.18.

Changes to worker/test/test_case.hpp.

Changes to worker/test/test_workers.cpp.

Changes to worker/test/wscript.

Changes to worker/wscript.

Changes to wscript.