Docopt (#58)

* switching docopt.cpp to upstream version 0.6.2
 - contains Boost fix for borken C++11 std::regex on GCC 4.8.x

* success exit code for `--help`

.gitmodules

@@ -5,3 +5,6 @@
 	path = external/googletest
 	url = https://github.com/google/googletest.git
 	branch = master
+[submodule "external/docopt.cpp"]
+	path = external/docopt.cpp
+	url = https://github.com/docopt/docopt.cpp.git

CMakeLists.txt

@@ -38,5 +38,6 @@ include(hc-compilerflags)
 include(hc-dependencies)
 
 add_subdirectory(${HC_EXTERNALDIR}/BamTools external/bamtools)
+add_subdirectory(${HC_EXTERNALDIR}/docopt.cpp external/docopt.cpp)
 add_subdirectory(src)
 add_subdirectory(test)

src/CMakeLists.txt

@@ -27,21 +27,29 @@ target_include_directories(hc PUBLIC
 	${HC_SRCDIR}
 	${Boost_INCLUDE_DIR}
 	${HC_EXTERNALDIR}/BamTools/src
+	${HC_EXTERNALDIR}/docopt.cpp
+	${PROJECT_BINARY_DIR}
 )
 target_link_libraries(hc
 	${Boost_LIBRARIES}
 )
 if (HC_STATIC)
-	target_link_libraries(hc BamTools-static)
+	target_link_libraries(hc BamTools-static docopt_s)
 else()
-	target_link_libraries(hc BamTools)
+	target_link_libraries(hc BamTools docopt_s)
 endif()
 
 set_target_properties(hc PROPERTIES COMPILE_FLAGS ${HC_COMPILE_FLAGS})
 if (HC_LINK_FLAGS)
 	set_target_properties(hc PROPERTIES LINK_FLAGS ${HC_LINK_FLAGS})
 endif()
 
+# Version
+configure_file (
+	"${HC_SRCDIR}/version.h.in"
+	"${PROJECT_BINARY_DIR}/version.h"
+)
+
 # Haploclique executable
 add_executable (haploclique	haploclique.cpp)
 set_target_properties(haploclique PROPERTIES COMPILE_FLAGS ${HC_COMPILE_FLAGS})
@@ -55,4 +63,4 @@ set_target_properties(haploclique PROPERTIES
 
 target_link_libraries(haploclique hc)
 
-install(TARGETS haploclique RUNTIME DESTINATION bin)
+install(TARGETS haploclique RUNTIME DESTINATION bin)