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#===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# External
if( NOT WIN32)
add_compile_definitions( __mod__="tools/bam-loader" )
include_directories( /usr/include/ncbi-vdb/interfaces/ext/ ) # zlib.h
include_directories(./)
set( SRC
bam-loader
bam
sam
alignment-writer
reference-writer
sequence-writer
loader-imp
mem-bank
low-match-count
)
set_source_files_properties(bam-loader.c PROPERTIES LANGUAGE CXX )
set_source_files_properties(loader-imp.c PROPERTIES LANGUAGE CXX )
GenerateExecutableWithDefs( bam-load "${SRC}" "" "${CMAKE_SOURCE_DIR}/libs/inc" "loader;${COMMON_LINK_LIBRARIES};${COMMON_LIBS_WRITE}" )
target_compile_features(bam-load PRIVATE cxx_std_17)
if (COMPILER_OPTION_SSE42_SUPPORTED)
target_compile_options( bam-load PRIVATE -msse4.2 -DBMSSE42OPT)
endif()
target_include_directories( bam-load PRIVATE ${CMAKE_SOURCE_DIR}/libs/inc)
target_link_libraries( bam-load loader ${COMMON_LINK_LIBRARIES} ${COMMON_LIBS_WRITE} -lz )
MakeLinksExe( bam-load false )
# Internal
GenerateExecutableWithDefs( samview "bam;sam;samview" "" "" "${COMMON_LINK_LIBRARIES};${COMMON_LIBS_READ};-lz" )
MakeLinksExe( samview false )
endif()
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