cmake_minimum_required(VERSION 3.0.0)

# project name and it is C++ only
project(scATACseq CXX)


# libraries
## boost library
# set(BOOST_INCLUDEDIR "/usr/local/include/boost/")
# set(BOOST_LIBRARYDIR "/usr/local/lib/boost")
set( BOOST_ROOT "" CACHE PATH "Boost library path" )
set(Boost_NO_SYSTEM_PATHS on CACHE BOOL "Do not search system for Boost")
set(BOOST_INCLUDEDIR "/local/groux/scATAC-seq/lib/boost/include/")
set(BOOST_LIBRARYDIR "/local/groux/scATAC-seq/lib/")
find_package(Boost 1.70 COMPONENTS program_options REQUIRED)

## UnitTest++ library
## TODO write a FindUnitTest++.cmake file to use find_package()
# find_library(UNITTEST_LIB
#              NAMES "UnitTest++"
#              PATHS "/usr/local/lib/UnitTest++")
# find_path(UNITTEST_INCLUDE
#           NAMES "UnitTest++.h"
#           PATHS "/usr/local/include/UnitTest++/")
find_library(UNITTEST_LIB
             NAMES "UnitTest++"
             PATHS "/local/groux/scATAC-seq/lib/UnitTest++/lib")
find_path(UNITTEST_INCLUDE
          NAMES "UnitTest++.h"
          PATHS "/local/groux/scATAC-seq/lib/UnitTest++/include")
include_directories(${UNITTEST_INCLUDE})
# link_directories(${UNITTEST_LIB})

## zlib (for seqan Bam I/O)
find_package(ZLIB REQUIRED)

## SeqAn
find_package (SeqAn REQUIRED)

## threads
find_package(Threads REQUIRED)

add_subdirectory(src)