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cmake/FindHTSLIB.cmake: adding
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‎cmake/FindHTSLIB.cmake‎

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# SPDX-License-Identifier: GPL-3.0-or-later; (c) 2025 Andrew D Smith (author)
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#[=======================================================================[.rst:
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FindHTSLIB
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--------
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Find the native HTSLib includes and library. Based on the ZLIB module.
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#]=======================================================================]
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cmake_policy(PUSH)
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cmake_policy(SET CMP0159 NEW) # file(STRINGS) with REGEX updates CMAKE_MATCH_<n>
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if(HTSLIB_FIND_COMPONENTS AND NOT HTSLIB_FIND_QUIETLY)
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message(AUTHOR_WARNING
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"HTSLib does not provide any COMPONENTS. Calling\n"
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" find_package(HTSLIB COMPONENTS ...)\n"
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"will always fail."
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)
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endif()
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set(_HTSLIB_SEARCHES)
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# Search HTSLIB_ROOT first if it is set.
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if(HTSLIB_ROOT)
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set(_HTSLIB_SEARCH_ROOT PATHS ${HTSLIB_ROOT} NO_DEFAULT_PATH)
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list(APPEND _HTSLIB_SEARCHES _HTSLIB_SEARCH_ROOT)
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endif()
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# Normal search.
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# Windows stuff
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set(_HTSLIB_x86 "(x86)")
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set(_HTSLIB_SEARCH_NORMAL
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PATHS "$ENV{ProgramFiles}/htslib"
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"$ENV{ProgramFiles${_HTSLIB_x86}}/htslib")
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unset(_HTSLIB_x86)
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list(APPEND _HTSLIB_SEARCHES _HTSLIB_SEARCH_NORMAL)
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if(HTSLIB_USE_STATIC_LIBS)
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set(HTSLIB_NAMES hts)
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set(HTSLIB_NAMES_DEBUG hts)
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else()
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set(HTSLIB_NAMES hts)
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set(HTSLIB_NAMES_DEBUG hts)
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endif()
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# Try each search configuration.
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foreach(search ${_HTSLIB_SEARCHES})
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find_path(HTSLIB_INCLUDE_DIR NAMES htslib ${${search}} PATH_SUFFIXES include)
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endforeach()
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# Allow HTSLIB_LIBRARY to be set manually, as the location of the htslib library
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if(NOT HTSLIB_LIBRARY)
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if(DEFINED CMAKE_FIND_LIBRARY_PREFIXES)
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set(_htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES "${CMAKE_FIND_LIBRARY_PREFIXES}")
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else()
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set(_htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES)
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endif()
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if(DEFINED CMAKE_FIND_LIBRARY_SUFFIXES)
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set(_htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES "${CMAKE_FIND_LIBRARY_SUFFIXES}")
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else()
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set(_htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES)
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endif()
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# Prefix/suffix of the win32/Makefile.gcc build
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if(WIN32)
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list(APPEND CMAKE_FIND_LIBRARY_PREFIXES "" "lib")
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list(APPEND CMAKE_FIND_LIBRARY_SUFFIXES ".dll.a")
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endif()
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# Support preference of static libs by adjusting CMAKE_FIND_LIBRARY_SUFFIXES
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if(HTSLIB_USE_STATIC_LIBS)
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if(WIN32)
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set(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
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else()
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set(CMAKE_FIND_LIBRARY_SUFFIXES .a)
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endif()
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endif()
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foreach(search ${_HTSLIB_SEARCHES})
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find_library(HTSLIB_LIBRARY_RELEASE NAMES ${HTSLIB_NAMES} NAMES_PER_DIR ${${search}} PATH_SUFFIXES lib)
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find_library(HTSLIB_LIBRARY_DEBUG NAMES ${HTSLIB_NAMES_DEBUG} NAMES_PER_DIR ${${search}} PATH_SUFFIXES lib)
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endforeach()
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# Restore the original find library ordering
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if(DEFINED _htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES)
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set(CMAKE_FIND_LIBRARY_SUFFIXES "${_htslib_ORIG_CMAKE_FIND_LIBRARY_SUFFIXES}")
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else()
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set(CMAKE_FIND_LIBRARY_SUFFIXES)
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endif()
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if(DEFINED _htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES)
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set(CMAKE_FIND_LIBRARY_PREFIXES "${_htslib_ORIG_CMAKE_FIND_LIBRARY_PREFIXES}")
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else()
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set(CMAKE_FIND_LIBRARY_PREFIXES)
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endif()
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include(SelectLibraryConfigurations)
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select_library_configurations(HTSLIB)
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endif()
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unset(HTSLIB_NAMES)
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unset(HTSLIB_NAMES_DEBUG)
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mark_as_advanced(HTSLIB_INCLUDE_DIR)
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if(HTSLIB_INCLUDE_DIR AND EXISTS "${HTSLIB_INCLUDE_DIR}/htslib/hts.h")
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# Example: #define HTS_VERSION 101300
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file(STRINGS "${HTSLIB_INCLUDE_DIR}/htslib/hts.h" HTSLIB_H_LIST REGEX "^#define HTS_VERSION")
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list(GET HTSLIB_H_LIST 0 HTSLIB_H) # Take the first matching line
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if (HTSLIB_H MATCHES "#define[ \t]+HTS_VERSION[ \t]+\([0-9]+\)")
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set(NUMERIC_VERSION "${CMAKE_MATCH_1}")
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# Extract digits by position in string
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# XYYYZZ => X = major, YYY = minor, ZZ = patch
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string(SUBSTRING "${NUMERIC_VERSION}" 0 1 HTSLIB_VERSION_MAJOR)
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string(SUBSTRING "${NUMERIC_VERSION}" 1 3 HTSLIB_VERSION_MINOR)
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string(SUBSTRING "${NUMERIC_VERSION}" 4 2 HTSLIB_VERSION_PATCH)
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else()
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set(HTSLIB_VERSION_STRING "")
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set(HTSLIB_VERSION_MAJOR "")
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set(HTSLIB_VERSION_MINOR "")
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set(HTSLIB_VERSION_PATCH "")
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endif()
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# Make sure the version numbers don't have leading zeros
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# The minor version is encoded in such a way that it often will
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foreach(part HTSLIB_VERSION_MAJOR HTSLIB_VERSION_MINOR HTSLIB_VERSION_PATCH)
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if(${${part}} MATCHES "^[0]+$")
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set(${part} "0")
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else()
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string(REGEX REPLACE "^0+" "" ${part} "${${part}}")
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endif()
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endforeach()
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# Set canonical variables
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set(HTSLIB_MAJOR_VERSION "${HTSLIB_VERSION_MAJOR}")
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set(HTSLIB_MINOR_VERSION "${HTSLIB_VERSION_MINOR}")
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set(HTSLIB_PATCH_VERSION "${HTSLIB_VERSION_PATCH}")
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# Build the standard version string
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set(HTSLIB_VERSION "${HTSLIB_VERSION_MAJOR}.${HTSLIB_VERSION_MINOR}")
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# Only append patch if it's not "00"
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if(NOT HTSLIB_VERSION_PATCH STREQUAL "00")
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set(HTSLIB_VERSION "${HTSLIB_VERSION}.${HTSLIB_VERSION_PATCH}")
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endif()
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endif()
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include(FindPackageHandleStandardArgs)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(
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HTSLIB
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REQUIRED_VARS
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HTSLIB_LIBRARY
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HTSLIB_INCLUDE_DIR
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VERSION_VAR
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HTSLIB_VERSION
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HANDLE_COMPONENTS
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)
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if(HTSLIB_FOUND)
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set(HTSLIB_INCLUDE_DIRS ${HTSLIB_INCLUDE_DIR})
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if(NOT HTSLIB_LIBRARIES)
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set(HTSLIB_LIBRARIES ${HTSLIB_LIBRARY})
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endif()
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if(NOT TARGET HTSLIB::HTSLIB)
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add_library(HTSLIB::HTSLIB UNKNOWN IMPORTED)
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set_target_properties(HTSLIB::HTSLIB PROPERTIES
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INTERFACE_INCLUDE_DIRECTORIES "${HTSLIB_INCLUDE_DIRS}")
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if(HTSLIB_LIBRARY_RELEASE)
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set_property(TARGET HTSLIB::HTSLIB APPEND PROPERTY
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IMPORTED_CONFIGURATIONS RELEASE)
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set_target_properties(HTSLIB::HTSLIB PROPERTIES
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IMPORTED_LOCATION_RELEASE "${HTSLIB_LIBRARY_RELEASE}")
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endif()
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if(HTSLIB_LIBRARY_DEBUG)
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set_property(TARGET HTSLIB::HTSLIB APPEND PROPERTY
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IMPORTED_CONFIGURATIONS DEBUG)
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set_target_properties(HTSLIB::HTSLIB PROPERTIES
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IMPORTED_LOCATION_DEBUG "${HTSLIB_LIBRARY_DEBUG}")
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endif()
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if(NOT HTSLIB_LIBRARY_RELEASE AND NOT HTSLIB_LIBRARY_DEBUG)
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set_property(TARGET HTSLIB::HTSLIB APPEND PROPERTY
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IMPORTED_LOCATION "${HTSLIB_LIBRARY}")
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endif()
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endif()
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endif()
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cmake_policy(POP)

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