################################################################################
##
## Copyright (c) 2007-2009 Illumina, Inc.
##
## This software is covered by the "Illumina Genome Analyzer Software
## License Agreement" and the "Illumina Source Code License Agreement",
## and certain third party copyright/licenses, and any user of this
## source file is bound by the terms therein (see accompanying files
## Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
## Illumina_Source_Code_License_Agreement.pdf and third party
## copyright/license notices).
##
## This file is part of the Consensus Assessment of Sequence And VAriation 
## (CASAVA) software package.
##
## file configure
##
## Configuration file for the c++/libexec subdirectory
##
## author Roman Petrovski
##
################################################################################

include(${CASAVA_CXX_EXECUTABLE_CMAKE})

set(BLT_SOURCES "blt.cpp" "starling.cpp")
foreach(BLT_SOURCE ${BLT_SOURCES})
    get_filename_component(BLT_PROGRAM ${BLT_SOURCE} NAME_WE)
    add_executable(${BLT_PROGRAM} ${BLT_SOURCE})
    target_link_libraries (${BLT_PROGRAM} casava_${BLT_PROGRAM} casava_blt_common casava_blt_util casava_common
                           ${Boost_LIBRARIES} ${SAMTOOLS_DIR}/libbam.a ${CASAVA_ADDITIONAL_LIB})
    install(TARGETS ${BLT_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})
endforeach(BLT_SOURCE)

set(SAMMD_SOURCES "samMD.cpp" "samMD2Export.cpp")

foreach(SAMMD_SOURCE ${SAMMD_SOURCES})
    get_filename_component(SAMMD_PROGRAM ${SAMMD_SOURCE} NAME_WE)
    add_executable(${SAMMD_PROGRAM} ${SAMMD_SOURCE})
    target_link_libraries (${SAMMD_PROGRAM} ${CASAVA_AVAILABLE_LIBRARIES} ${Boost_LIBRARIES} ${CASAVA_ADDITIONAL_LIB})
    install(TARGETS ${SAMMD_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})
endforeach(SAMMD_SOURCE)

set(KAGU_SOURCES "kagu.cpp")
foreach(KAGU_SOURCE ${KAGU_SOURCES})
    get_filename_component(KAGU_PROGRAM ${KAGU_SOURCE} NAME_WE)
    add_executable(${KAGU_PROGRAM} ${KAGU_SOURCE})
    target_link_libraries(${KAGU_PROGRAM} ${CASAVA_AVAILABLE_LIBRARIES} ${Boost_LIBRARIES} ${CASAVA_ADDITIONAL_LIB})
    install(TARGETS ${KAGU_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})
endforeach(KAGU_SOURCE)

set(SIMPLE_SOURCES "countFastaBases.cpp")

foreach(CASAVA_SOURCE ${SIMPLE_SOURCES})
    get_filename_component(CASAVA_PROGRAM ${CASAVA_SOURCE} NAME_WE)
    add_executable(${CASAVA_PROGRAM} ${CASAVA_SOURCE})
    target_link_libraries (${CASAVA_PROGRAM} ${Boost_LIBRARIES} ${CASAVA_ADDITIONAL_LIB})
    install(TARGETS ${CASAVA_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})
endforeach(CASAVA_SOURCE)

set(GSIDX_SOURCE "makeGStudioBAMIndex.cpp")
get_filename_component(GSIDX_PROGRAM ${GSIDX_SOURCE} NAME_WE)
include_directories(${SAMTOOLS_DIR} ${ILMNSAMTOOLS_DIR})
add_executable(${GSIDX_PROGRAM} ${GSIDX_SOURCE})
target_link_libraries(${GSIDX_PROGRAM} casava_blt_util ${Boost_LIBRARIES} ${SAMTOOLS_DIR}/libbam.a ${CASAVA_ADDITIONAL_LIB})
add_dependencies(${GSIDX_PROGRAM} CASAVA_SAMTOOLS)
add_dependencies(${GSIDX_PROGRAM} CASAVA_ILMNSAMTOOLS)
install(TARGETS ${GSIDX_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})

set(CX_SOURCE "compressXPair.cpp")
get_filename_component(CX_PROGRAM ${CX_SOURCE} NAME_WE)
add_executable(${CX_PROGRAM} ${CX_SOURCE})
target_link_libraries (${CX_PROGRAM} casava_blt_util 
                       ${Boost_LIBRARIES} ${CASAVA_ADDITIONAL_LIB})
install(TARGETS ${CX_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})

set(CX_SOURCE "sortedToBam.cpp")
get_filename_component(CX_PROGRAM ${CX_SOURCE} NAME_WE)
add_executable(${CX_PROGRAM} ${CX_SOURCE})
target_link_libraries (${CX_PROGRAM} casava_starling casava_blt_util casava_common
                       ${Boost_LIBRARIES} ${SAMTOOLS_DIR}/libbam.a ${CASAVA_ADDITIONAL_LIB})
install(TARGETS ${CX_PROGRAM} RUNTIME DESTINATION ${CASAVA_LIBEXECDIR})