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Modernize cpp #91

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@pb-dseifert pb-dseifert commented Nov 2, 2024

  • Makefile should adhere to common Linux packaging conventions
  • State dependency on C++11 explicitly
  • Allow using all APIs without calling strlen() internally
  • Modernize to C++ code:
    • Avoid manual memory management with new/delete and use RAII types instead
    • Avoid passing pointers when references suffice
    • Avoid references for input values
    • Reduce code duplication in the Align() function

@pb-dseifert pb-dseifert force-pushed the modernize-cpp branch 2 times, most recently from 07c4158 to a9623e3 Compare November 2, 2024 19:44
// A C G
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
// T
4, 4, 4, 4, 3, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
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@mengyao I assume the 0 after the t/Ts are a typo?

@pb-dseifert pb-dseifert force-pushed the modernize-cpp branch 2 times, most recently from c8626a3 to 5b4fcb6 Compare November 8, 2024 13:00
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