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Add MONI v0.1.0
1 parent b314e83 commit eb2f285

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‎.gitignore‎

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*.exe
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*.out
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*.app
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# Folders
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build/*
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debug/*
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data/*
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!data/yeast.fasta

‎CMakeLists.txt‎

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CMAKE_MINIMUM_REQUIRED(VERSION 3.15)
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set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules")
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# Set a default build type if none was specified
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# ------------------------------------------------------------------------------
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if(NOT CMAKE_BUILD_TYPE)
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message(STATUS "Setting build type to 'Release' as none was specified.")
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set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
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endif()
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# About this project
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# ------------------------------------------------------------------------------
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project(moni)
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SET(VERSION_MAJOR "0")
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SET(VERSION_MINOR "1")
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SET(VERSION_PATCH "0")
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SET(VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
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# Set environment
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# ------------------------------------------------------------------------------
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set(CMAKE_INSTALL_PREFIX ${CMAKE_BINARY_DIR}/install)
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find_package(Git)
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if(GIT_FOUND)
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message("git found: ${GIT_EXECUTABLE}")
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else()
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message(WARNING "git not found. Cloning of submodules will not work.")
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endif()
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# Configure thirdparty
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# ------------------------------------------------------------------------------
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set(CMAKE_INSTALL_INCLUDEDIR "include") # This is an hack because include(GUIInstallDirs) doesn't work
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add_subdirectory(thirdparty)
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# Configure the compiler with the appropriate flags
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# ------------------------------------------------------------------------------
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if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang" OR "${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang")
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# using Clang
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include(ConfigureCompilerClang)
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elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
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# using GCC
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include(ConfigureCompilerGcc)
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else ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
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message(FATAL_ERROR "Only the compiler gcc and clang are supported")
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endif()
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add_subdirectory(src)
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add_subdirectory(utils)
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configure_file(${PROJECT_SOURCE_DIR}/pipeline/moni ${PROJECT_BINARY_DIR}/moni)

‎CMakeModules/ConfigureCompilerClang.cmake‎

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# ##############################################################################
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# Compiler configuration
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# @author Massimiliano Rossi
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# ##############################################################################
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# Add the basic compiler options
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add_compile_options("-std=c++11")
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# add_compile_options("-Werror")
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add_compile_options("-Wall")
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add_compile_options("-Wextra")
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add_compile_options("-Wcomment")
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add_compile_options("-Wformat=2")
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add_compile_options("-Wnonnull")
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add_compile_options("-Winit-self")
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add_compile_options("-Wmain")
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add_compile_options("-Wmissing-braces")
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add_compile_options("-Wmissing-include-dirs")
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add_compile_options("-Wparentheses")
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add_compile_options("-Wsequence-point")
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add_compile_options("-Wreturn-type")
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add_compile_options("-Wdate-time")
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add_compile_options("-Wswitch")
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add_compile_options("-Wswitch-default")
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add_compile_options("-Wswitch-enum")
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add_compile_options("-Wunused-function")
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add_compile_options("-Wunused-label")
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add_compile_options("-Wunused-local-typedefs")
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add_compile_options("-Wunused-parameter")
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add_compile_options("-Wunused-variable")
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add_compile_options("-Wunused-value")
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add_compile_options("-Wunused")
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add_compile_options("-Wuninitialized")
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add_compile_options("-Wunknown-pragmas")
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add_compile_options("-Wstrict-aliasing")
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add_compile_options("-Wstrict-overflow=5")
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add_compile_options("-Warray-bounds")
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add_compile_options("-Wundef")
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add_compile_options("-Wendif-labels")
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add_compile_options("-Wshadow")
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add_compile_options("-Wpointer-arith")
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add_compile_options("-Wtype-limits")
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add_compile_options("-Wcast-qual")
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add_compile_options("-Wwrite-strings")
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add_compile_options("-Wconversion")
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add_compile_options("-Wenum-compare")
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add_compile_options("-Wsign-compare")
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add_compile_options("-Waddress")
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add_compile_options("-Wattributes")
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add_compile_options("-Wbuiltin-macro-redefined")
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add_compile_options("-Wmissing-declarations")
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add_compile_options("-Wmissing-field-initializers")
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add_compile_options("-Wdeprecated")
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add_compile_options("-Wdeprecated-declarations")
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add_compile_options("-Woverflow")
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add_compile_options("-Wpacked")
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add_compile_options("-Winline")
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add_compile_options("-Wint-to-pointer-cast")
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add_compile_options("-Winvalid-pch")
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add_compile_options("-Wno-long-long")
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add_compile_options("-Wno-variadic-macros")
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add_compile_options("-Wvarargs")
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add_compile_options("-Wvla")
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add_compile_options("-Wvolatile-register-var")
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add_compile_options("-Wdisabled-optimization")
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add_compile_options("-Wstack-protector")
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add_compile_options("-Woverlength-strings")
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add_compile_options("-fvisibility=hidden")
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add_compile_options("-Wc++11-compat")
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add_compile_options("-Wconversion-null")
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add_compile_options("-Winherited-variadic-ctor")
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add_compile_options("-Winvalid-offsetof")
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add_compile_options("-pedantic")
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add_compile_options("-fno-gnu-keywords")
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add_compile_options("-Wctor-dtor-privacy")
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add_compile_options("-Wdelete-non-virtual-dtor")
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add_compile_options("-Wnarrowing")
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add_compile_options("-Wnon-virtual-dtor")
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add_compile_options("-Wreorder")
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add_compile_options("-Weffc++")
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add_compile_options("-Wold-style-cast")
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add_compile_options("-Wsign-promo")
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add_compile_options("-Wchar-subscripts")
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add_compile_options("-Wno-ignored-qualifiers")
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add_compile_options("-Wuninitialized")
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add_compile_options("-Wdiv-by-zero")
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add_compile_options("-Wfloat-equal")
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add_compile_options("-Wcast-align")
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add_compile_options("-Wempty-body")
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add_compile_options("-Wsizeof-pointer-memaccess")
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add_compile_options("-Wmultichar")
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add_compile_options("-fPIC")
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# Add the basic compiler options for debug version
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb3")
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# Add the basic compiler options for release version
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -ansi -march=native -funroll-loops -O3 -DNDEBUG")

‎CMakeModules/ConfigureCompilerGcc.cmake‎

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# ##############################################################################
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# Compiler configuration
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# @author Massimiliano Rossi
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# ##############################################################################
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# Add the basic compiler options
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add_compile_options("-std=c++11")
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# add_compile_options("-Werror")
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add_compile_options("-Wall")
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add_compile_options("-Wextra")
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add_compile_options("-Wcomment")
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add_compile_options("-Wdouble-promotion")
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add_compile_options("-Wformat=2")
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add_compile_options("-Wnonnull")
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add_compile_options("-Winit-self")
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add_compile_options("-Wmain")
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add_compile_options("-Wmissing-braces")
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add_compile_options("-Wmissing-include-dirs")
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add_compile_options("-Wparentheses")
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add_compile_options("-Wsequence-point")
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add_compile_options("-Wreturn-local-addr")
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add_compile_options("-Wreturn-type")
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add_compile_options("-Wswitch")
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add_compile_options("-Wswitch-default")
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add_compile_options("-Wswitch-enum")
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add_compile_options("-Wunused-but-set-parameter")
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add_compile_options("-Wunused-but-set-variable")
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add_compile_options("-Wunused-function")
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add_compile_options("-Wunused-label")
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add_compile_options("-Wunused-local-typedefs")
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add_compile_options("-Wunused-parameter")
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add_compile_options("-Wunused-variable")
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add_compile_options("-Wunused-value")
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add_compile_options("-Wunused")
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add_compile_options("-Wuninitialized")
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add_compile_options("-Wunknown-pragmas")
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add_compile_options("-Wstrict-aliasing")
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add_compile_options("-Wstrict-overflow=5")
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add_compile_options("-Warray-bounds")
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add_compile_options("-Wundef")
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add_compile_options("-Wendif-labels")
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add_compile_options("-Wshadow")
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add_compile_options("-Wfree-nonheap-object")
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add_compile_options("-Wunsafe-loop-optimizations")
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add_compile_options("-Wpointer-arith")
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add_compile_options("-Wtype-limits")
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add_compile_options("-Wcast-qual")
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add_compile_options("-Wwrite-strings")
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add_compile_options("-Wclobbered")
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add_compile_options("-Wconversion")
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add_compile_options("-Wenum-compare")
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add_compile_options("-Wsign-compare")
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add_compile_options("-Wsign-conversion")
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add_compile_options("-Waddress")
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add_compile_options("-Wlogical-op")
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add_compile_options("-Wno-aggressive-loop-optimizations")
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add_compile_options("-Wattributes")
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add_compile_options("-Wbuiltin-macro-redefined")
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add_compile_options("-Wmissing-declarations")
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add_compile_options("-Wmissing-field-initializers")
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add_compile_options("-Wdeprecated")
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add_compile_options("-Wdeprecated-declarations")
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add_compile_options("-Woverflow")
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add_compile_options("-Wpacked")
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add_compile_options("-Wno-packed-bitfield-compat")
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add_compile_options("-Winline")
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add_compile_options("-Wint-to-pointer-cast")
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add_compile_options("-Winvalid-pch")
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add_compile_options("-Wno-long-long")
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add_compile_options("-Wno-variadic-macros")
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add_compile_options("-Wvarargs")
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add_compile_options("-Wvector-operation-performance")
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add_compile_options("-Wvla")
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add_compile_options("-Wvolatile-register-var")
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add_compile_options("-Wdisabled-optimization")
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add_compile_options("-Wstack-protector")
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add_compile_options("-Woverlength-strings")
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add_compile_options("-fvisibility=hidden")
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add_compile_options("-Wc++11-compat")
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add_compile_options("-Wconversion-null")
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add_compile_options("-Wuseless-cast")
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add_compile_options("-Winherited-variadic-ctor")
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add_compile_options("-Winvalid-offsetof")
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add_compile_options("-Wvirtual-move-assign")
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add_compile_options("-pedantic")
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add_compile_options("-fno-gnu-keywords")
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add_compile_options("-foptional-diags")
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add_compile_options("-Wctor-dtor-privacy")
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add_compile_options("-Wdelete-non-virtual-dtor")
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add_compile_options("-Wliteral-suffix")
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add_compile_options("-Wnarrowing")
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add_compile_options("-Wnon-virtual-dtor")
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add_compile_options("-Wreorder")
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add_compile_options("-Weffc++")
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add_compile_options("-fno-ext-numeric-literals")
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add_compile_options("-Wnon-template-friend")
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add_compile_options("-Wold-style-cast")
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add_compile_options("-Wpmf-conversions")
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add_compile_options("-Wsign-promo")
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add_compile_options("-Wchar-subscripts")
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add_compile_options("-Wno-ignored-qualifiers")
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add_compile_options("-Wmaybe-uninitialized")
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add_compile_options("-Wdiv-by-zero")
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add_compile_options("-Wtrampolines")
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add_compile_options("-Wfloat-equal")
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add_compile_options("-Wcast-align")
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add_compile_options("-Wempty-body")
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add_compile_options("-Wsizeof-pointer-memaccess")
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add_compile_options("-Wmultichar")
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add_compile_options("-Wnormalized=nfc")
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add_compile_options("-Wnoexcept")
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add_compile_options("-Wstrict-null-sentinel")
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# Add the basic compiler options for debug version
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -ggdb3")
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# Add the basic compiler options for release version
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -ansi -march=native -funroll-loops -O3 -DNDEBUG")

‎LICENSE‎

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MIT License
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3-
Copyright (c) 2021 Massimiliano Rossi
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Copyright (c) 2020 Massimiliano Rossi
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

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