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DEVELOP.md
README.md
pyproject.toml
setup.py
tox.ini
docs/.gitignore
docs/source/conf.py
docs/source/index.md
docs/source/python.md
docs/source/_static/switcher.json
docs/source/_templates/autosummary/class.rst
docs/source/api/fragments.rst
docs/source/api/matrix.rst
docs/source/notebooks/.gitignore
docs/source/notebooks/fragment_basics.md
docs/source/notebooks/matrix_basics.md
scripts/build_docs.sh
scripts/clean_all.sh
scripts/install_ccache_linux.sh
scripts/install_deps.py
scripts/install_eigen.sh
scripts/install_hdf5.sh
scripts/install_highway.sh
scripts/run_tests.sh
src/bindings.cpp
src/fragments.cpp
src/fragments.hpp
src/matrix.cpp
src/matrix.hpp
src/py_interrupts.hpp
src/bpcells/__init__.py
src/bpcells/version.py
src/bpcells-cpp/arrayIO/array_interfaces.cpp
src/bpcells-cpp/arrayIO/array_interfaces.h
src/bpcells-cpp/arrayIO/binaryfile.cpp
src/bpcells-cpp/arrayIO/binaryfile.h
src/bpcells-cpp/arrayIO/bp128.cpp
src/bpcells-cpp/arrayIO/bp128.h
src/bpcells-cpp/arrayIO/design_doc.md
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src/bpcells-cpp/factorization/GLMFactorization.cpp
src/bpcells-cpp/factorization/GLMFactorization.h
src/bpcells-cpp/fragmentIterators/BedFragments.cpp
src/bpcells-cpp/fragmentIterators/BedFragments.h
src/bpcells-cpp/fragmentIterators/CellSelect.cpp
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src/bpcells-cpp/fragmentIterators/ChrSelect.cpp
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src/bpcells-cpp/fragmentUtils/FootprintMatrix.cpp
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src/bpcells-cpp/matrixIterators/MatrixMarketImport.cpp
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src/bpcells-cpp/matrixIterators/MatrixMultiply.h
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src/bpcells-cpp/matrixIterators/RenameDims.h
src/bpcells-cpp/matrixIterators/SVD.cpp
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src/bpcells-cpp/matrixIterators/StoredMatrixTransposeWriter.h
src/bpcells-cpp/matrixIterators/StoredMatrixWriter.h
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src/bpcells-cpp/matrixUtils/Quantile.cpp
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src/bpcells-cpp/simd/bp128/d1z_maxbits.cpp
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src/bpcells-cpp/simd/bp128/diff_maxbits.cpp
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src/bpcells-cpp/simd/bp128/diff_unpack.cpp
src/bpcells-cpp/simd/bp128/for_maxbits.cpp
src/bpcells-cpp/simd/bp128/for_pack.cpp
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src/vendor/Spectra/AUTHORS.md
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src/vendor/Spectra/MatOp/internal/SymGEigsShiftInvertOp.h
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src/vendor/Spectra/Util/GEigsMode.h
src/vendor/Spectra/Util/SelectionRule.h
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src/vendor/Spectra/Util/Version.h
src/vendor/Spectra/contrib/LOBPCGSolver.h
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src/vendor/dary_heap/LICENSE
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