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Merged
jermp merged 1 commit into from
Sep 3, 2026
Merged

Update CMake for easier inclusion #94

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2 changes: 1 addition & 1 deletion .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ jobs:
sudo apt-get install --assume-yes --no-install-recommends clang-${{ matrix.compiler.version }}
echo "CC=/usr/bin/clang-${{ matrix.compiler.version }}" >> $GITHUB_ENV
echo "CXX=/usr/bin/clang++-${{ matrix.compiler.version }}" >> $GITHUB_ENV
- uses: actions/checkout@v4
- uses: actions/checkout@v6
with:
submodules: recursive
- name: Build
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6 changes: 3 additions & 3 deletions .github/workflows/codeql.yml
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Expand Up @@ -23,11 +23,11 @@ jobs:

steps:
- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v6

# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
uses: github/codeql-action/init@v4
with:
languages: ${{ matrix.language }}

Expand All @@ -48,6 +48,6 @@ jobs:

# Perform Analysis
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v3
uses: github/codeql-action/analyze@v4
with:
category: "/language:${{matrix.language}}"
177 changes: 80 additions & 97 deletions CMakeLists.txt
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Expand Up @@ -2,124 +2,107 @@ cmake_minimum_required(VERSION 3.5...4.0)
project(SSHASH)

set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
if (NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release")
set(CMAKE_BUILD_TYPE "Release")
endif ()

set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})

# Options
option(SSHASH_BUILD_EXECUTABLES "Build sshash executables" ON)
option(SSHASH_USE_ARCH_NATIVE "Build with -march=native" OFF)
option(SSHASH_USE_MAX_KMER_LENGTH_63 "Use max kmer length 63" OFF)
option(SSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING "Use traditional nucleotide encoding" OFF)
option(SSHASH_USE_SANITIZERS "Build with sanitizers" OFF)

if (UNIX AND (CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64"))
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mbmi2 -mavx2")
if (SSHASH_USE_ARCH_NATIVE AND NOT CMAKE_CROSSCOMPILING)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
endif()
endif()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mbmi2 -mavx2")
if (SSHASH_USE_ARCH_NATIVE AND NOT CMAKE_CROSSCOMPILING)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
endif ()
endif ()

if (SSHASH_USE_MAX_KMER_LENGTH_63)
MESSAGE(STATUS "SSHash uses a maximum kmer length of 63")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSSHASH_USE_MAX_KMER_LENGTH_63")
else()
MESSAGE(STATUS "SSHash uses a maximum kmer length of 31")
endif()
message(STATUS "SSHash uses a maximum kmer length of 63")
add_compile_definitions(SSHASH_USE_MAX_KMER_LENGTH_63)
else ()
message(STATUS "SSHash uses a maximum kmer length of 31")
endif ()

if (SSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING)
MESSAGE(STATUS "SSHash maps {'A','a'}->0, {'C','c'}->1, {'G','g'}->2, and {'T','t'}->3")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING")
else()
MESSAGE(STATUS "SSHash maps {'A','a'}->0, {'C','c'}->1, {'T','t'}->2, and {'G','g'}->3")
endif()
message(STATUS "SSHash maps {'A','a'}->0, {'C','c'}->1, {'G','g'}->2, and {'T','t'}->3")
add_compile_definitions(SSHASH_USE_TRADITIONAL_NUCLEOTIDE_ENCODING)
else ()
message(STATUS "SSHash maps {'A','a'}->0, {'C','c'}->1, {'T','t'}->2, and {'G','g'}->3")
endif ()

if (UNIX)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -ggdb -Wall -Wextra -Werror -Wno-missing-braces -Wno-unknown-attributes -Wno-unused-function -pthread")

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ggdb")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Werror -Wno-missing-braces -Wno-unknown-attributes -Wno-unused-function")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
if (SSHASH_USE_SANITIZERS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fno-omit-frame-pointer")
endif ()
endif ()

if (SSHASH_USE_SANITIZERS)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fno-omit-frame-pointer")
endif()
if (CONDA_BUILD)
set(CONDA_BUILD TRUE)
else ()
set(CONDA_BUILD FALSE)
endif ()

endif()
message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
message(STATUS "Conda build: ${CONDA_BUILD}")
message(STATUS "Installation prefix: ${CMAKE_INSTALL_PREFIX}")
message(STATUS "Compiling for processor: ${CMAKE_SYSTEM_PROCESSOR}")
message(STATUS "Compiling with flags:${CMAKE_CXX_FLAGS}")
message(STATUS "Build executables: ${SSHASH_BUILD_EXECUTABLES}")

if (CONDA_BUILD)
set(CONDA_BUILD TRUE)
else()
set(CONDA_BUILD FALSE)
endif()
# Find dependencies
find_package(ZLIB REQUIRED)

option(SSHASH_BUILD_EXECUTABLES "Build sshash executables" ON)
MESSAGE(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
MESSAGE(STATUS "Conda build: ${CONDA_BUILD}")
MESSAGE(STATUS "Installation prefix: ${CMAKE_INSTALL_PREFIX}")
MESSAGE(STATUS "Compiling for processor: ${CMAKE_SYSTEM_PROCESSOR}")
MESSAGE(STATUS "Compiling with flags:${CMAKE_CXX_FLAGS}")
MESSAGE(STATUS "Build executables: ${SSHASH_BUILD_EXECUTABLES}")

set(Z_LIB_SOURCES
external/gz/zip_stream.cpp
# SSHash static library target
add_library(sshash_static STATIC
external/gz/zip_stream.cpp
external/cityhash/cityhash.cpp
src/builder/build.cpp
src/dictionary.cpp
src/query.cpp
src/info.cpp
)

set(CITYHASH_SOURCES
external/cityhash/cityhash.cpp
# PUBLIC: Only expose SSHash's own API headers to consuming projects
target_include_directories(sshash_static PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/external/pthash/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/external/pthash/external/bits/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/external/pthash/external/fastmod>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/external/pthash/external/bits/external/essentials/include>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/external/pthash/external/xxHash>
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/external/pthash/external/mm_file/include>
)

set(SSHASH_SOURCES
src/builder/build.cpp
src/dictionary.cpp
src/query.cpp
src/info.cpp
)
# Link dependencies
target_link_libraries(sshash_static PUBLIC ZLIB::ZLIB)

set(SSHASH_INCLUDE_DIRS
external/pthash/include
external/pthash/external/bits/include
external/pthash/external/fastmod
external/pthash/external/bits/external/essentials/include
external/pthash/external/xxHash
external/pthash/external/mm_file/include
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_SOURCE_DIR}/include
)
# Create standard target alias
add_library(sshash::sshash ALIAS sshash_static)

# Create a static lib
add_library(sshash_static STATIC
${Z_LIB_SOURCES}
${CITYHASH_SOURCES}
${SSHASH_SOURCES}
)
if (SSHASH_BUILD_EXECUTABLES)
add_executable(sshash tools/sshash.cpp)
target_link_libraries(sshash PRIVATE sshash_static)

target_include_directories(sshash_static PUBLIC ${SSHASH_INCLUDE_DIRS})

if(SSHASH_BUILD_EXECUTABLES)
add_executable(sshash tools/sshash.cpp)
target_include_directories(sshash PUBLIC ${SSHASH_INCLUDE_DIRS})
target_link_libraries(sshash
sshash_static
z
)

# tests:

add_executable(test_alphabet test/test_alphabet.cpp)
target_link_libraries(test_alphabet
sshash_static
)

add_executable(test_minimizer test/test_minimizer.cpp)
target_link_libraries(test_minimizer
sshash_static
)

add_executable(check test/check.cpp)
target_link_libraries(check
sshash_static
z
)

if (CONDA_BUILD)
install(TARGETS sshash
RUNTIME DESTINATION bin
)
endif()
endif()
add_executable(test_alphabet test/test_alphabet.cpp)
target_link_libraries(test_alphabet PRIVATE sshash_static)

add_executable(test_minimizer test/test_minimizer.cpp)
target_link_libraries(test_minimizer PRIVATE sshash_static)

add_executable(check test/check.cpp)
target_link_libraries(check PRIVATE sshash_static)

if (CONDA_BUILD)
install(TARGETS sshash RUNTIME DESTINATION bin)
endif ()
endif ()
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