cmake_minimum_required(VERSION 2.6)
project (TransBorrow_graph)

set(CMAKE_CXX_COMPILER "g++")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")

#Warning: The followings need your settings...(we have shown some examples below them.)
set(BOOST_LIB_DIR <Path_To_BOOST_LIB_DIR>)
#set(BOOST_LIB_DIR /storage/juntaosdu/razor-home/juntaosdu/local/boost/lib)
set(BOOST_INCLUDE_DIR <Path_To_BOOST_INCLUDE_DIR>)
#set(BOOST_INCLUDE_DIR /storage/juntaosdu/razor-home/juntaosdu/local/boost/include)
set(BAMTOOLS_LIB_DIR <Path_To_BAMTOOLS_LIB_DIR>)
#set(BAMTOOLS_LIB_DIR /storage/juntaosdu/yuting/bamtools/lib)
set(BAMTOOLS_INCLUDE_DIR <Path_To_BAMTOOLS_INCLUDE_DIR>
#set(BAMTOOLS_INCLUDE_DIR /storage/juntaosdu/yuting/bamtools/include)

include_directories(. ${BOOST_INCLUDE_DIR} ${BAMTOOLS_INCLUDE_DIR})
link_directories(${BOOST_LIB_DIR} ${BAMTOOLS_LIB_DIR})

#add_executable(Assemble Graph_NH_old_combine_filter.cc expression_level.h
#Find_junc_last_map.h Insert.h Sort.h edge_node_pair.h False_junc.h sep_gene.h
#Trim.h Function.h get_junction_graph.h junction_paths_new.h recover_paths.h
#PairPacker.h)
#add_executable(Assemble Graph_strand.cc process.h graph_division.h)
add_executable(TransBorrow_build SCTie_build.cc SCTie_build.h get_plus_minus_from_gtf.h sort_gtf.h get_bound.h)
add_executable(TransBorrow_single get_single.cc)
add_executable(TransBorrow_revise revise_gtf.cc)
add_executable(TransBorrow SCTie.cc SCTie.h gtf2fa.h abundance.h get_info_gene.h get_info_gene_single.h get_junction_graph.h junction_paths.h recover_paths.h PairPacker.h extract_UnmapRead.h combine_gtf.h)
add_executable(${PROJECT_NAME} Pre_Alignment.cc assembler.cpp simplify_graph.cc junction_graph.cc QuadProg++.cc)

target_link_libraries(${PROJECT_NAME} boost_math_c99 bamtools boost_program_options boost_regex boost_graph boost_thread boost_system boost_filesystem)
