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set(htslib_PREFIX ${CMAKE_BINARY_DIR}/contrib/htslib-prefix)
set(htslib_INSTALL ${CMAKE_BINARY_DIR}/contrib/htslib-install)
if (CMAKE_GENERATOR STREQUAL "Unix Makefiles")
# when using the makefile generator, use the special variable $(MAKE) to invoke make
# this enables the jobserver to work correctly
set(MAKE_COMMAND "$(MAKE)")
else()
# invoke make explicitly
# in this case, we assume the parent build system is running in parallel already so no -j flag is added
find_program(MAKE_COMMAND NAMES make gmake)
endif()
include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
set(HTSLIB_ZLIB_INC)
set(HTSLIB_ZLIB_LIB)
if ((NOT ZLIB_FOUND))
if(NOT EXISTS "${zlib_INSTALL}")
include(${CMAKE_SOURCE_DIR}/cmake/zlib.cmake)
endif()
message(STATUS "Using local build of zlib at ${zlib_INSTALL} with htslib")
set(HTSLIB_ZLIB_INC "CPPFLAGS=-I${zlib_INSTALL}/include")
set(HTSLIB_ZLIB_LIB "LDFLAGS=-L${zlib_INSTALL}/lib/")
endif()
ExternalProject_Add(htslib
PREFIX ${htslib_PREFIX}
GIT_REPOSITORY "https://github.com/samtools/htslib.git"
GIT_TAG "1.20"
UPDATE_COMMAND ""
BUILD_IN_SOURCE 1
#CONFIGURE_COMMAND "${CMAKE_CURRENT_SOURCE_DIR}/contrib/htslib-prefix/src/htslib/configure"
#CONFIGURE_COMMAND "autoheader"
#CONFIGURE_COMMAND "autoconf"
CONFIGURE_COMMAND autoheader && autoconf && autoreconf --install && ./configure --disable-bz2 --disable-lzma --disable-libcurl --without-libdeflate ${HTSLIB_ZLIB_INC} ${HTSLIB_ZLIB_LIB}
BUILD_COMMAND ${MAKE_COMMAND} lib-static
INSTALL_COMMAND ${MAKE_COMMAND} install prefix=${htslib_INSTALL}
LOG_DOWNLOAD 1
)
if (NOT ZLIB_FOUND)
message(STATUS "Adding zlib built via external project as dependency for htslib")
add_dependencies(htslib zlib)
endif()
include_directories(${htslib_INSTALL}/include)
set(HTSlib_LIBRARIES ${htslib_INSTALL}/lib/libhts.a)
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