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Refactor FileStream and HiCFileWriter to be more robust against data races #275

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wants to merge 33 commits into from
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Refactor FileStream and HiCFileWriter to be more robust against data races #275

wants to merge 33 commits into from

Commits on Oct 2, 2024

  1. Add thread-safe API to FileStream

    @robomics
    robomics committed Oct 2, 2024
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  2. Update and add new tests

    @robomics
    robomics committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Merge branch 'fix/convert-tmpdir' into fix/data-race

    @robomics
    robomics committed Oct 3, 2024
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  2. Bugfix

    @robomics
    robomics committed Oct 3, 2024
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  3. Fix deadlock

    @robomics
    robomics committed Oct 3, 2024
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  4. Bugfix

    @robomics
    robomics committed Oct 3, 2024
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  5. Bugfix

    @robomics
    robomics committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. Rework code related to .hic parallel serialization

    @robomics
    robomics committed Oct 4, 2024
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  2. Add more tests

    @robomics
    robomics committed Oct 4, 2024
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  3. Bugfix

    @robomics
    robomics committed Oct 4, 2024
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  4. wip

    @robomics
    robomics committed Oct 4, 2024
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Commits on Oct 6, 2024

  1. Implement FileStream::resize()

    @robomics
    robomics committed Oct 6, 2024
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  2. Minor optimization to MatrixInteractionBlock<N>::compress()

    @robomics
    robomics committed Oct 6, 2024
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  3. Bugfix. .hic file creation now appears to be working as expected

    @robomics
    robomics committed Oct 6, 2024
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  4. Remove debug code

    @robomics
    robomics committed Oct 6, 2024
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  5. Forgot that Catch2 assertions are not thread-safe...

    @robomics
    robomics committed Oct 6, 2024
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  6. Remove debug code

    @robomics
    robomics committed Oct 6, 2024
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  7. Reduce peak memory usage of SerializedBlockPQueue

    @robomics
    robomics committed Oct 6, 2024
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  8. Address static-analysis warnings

    @robomics
    robomics committed Oct 6, 2024
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Commits on Oct 7, 2024

  1. Add tests covering overwritig of weights in .hic files

    @robomics
    robomics committed Oct 7, 2024
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  2. Address clang-tidy warnings

    @robomics
    robomics committed Oct 7, 2024
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  3. Fix builds on old compilers

    @robomics
    robomics committed Oct 7, 2024
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  4. Fix windows builds

    @robomics
    robomics committed Oct 7, 2024
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  5. Fix GCC8 builds

    @robomics
    robomics committed Oct 7, 2024
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  6. Fix clang8 builds

    @robomics
    robomics committed Oct 7, 2024
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  7. Fix macOS builds

    @robomics
    robomics committed Oct 7, 2024
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  8. Fix tests

    @robomics
    robomics committed Oct 7, 2024
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  9. Fix clang8 builds

    @robomics
    robomics committed Oct 7, 2024
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  10. Fix windows builds

    @robomics
    robomics committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. Bugfix

    @robomics
    robomics committed Oct 8, 2024
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  2. Merge branch 'main' into fix/data-race

    @robomics
    robomics committed Oct 8, 2024
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  3. Fix mysterious compilation error on Windows 

    I have no clue why this code stopped compiling all of a sudden.
    @robomics
    robomics committed Oct 8, 2024
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  4. Fix tests on Windows

    @robomics
    robomics committed Oct 8, 2024
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