From b8d6ab38c57e02d0047e10aed93d66f63e47de3a Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Fri, 3 Sep 2021 09:53:13 -0400
Subject: [PATCH] fix up build script with hacky hack

---
 build-tools/CMakeLists.txt | 78 ++++++++++++++++++++++++++++++++++++++
 build-tools/makeBinRelease |  5 ++-
 2 files changed, 82 insertions(+), 1 deletion(-)
 create mode 100644 build-tools/CMakeLists.txt

diff --git a/build-tools/CMakeLists.txt b/build-tools/CMakeLists.txt
new file mode 100644
index 0000000..87ee3d2
--- /dev/null
+++ b/build-tools/CMakeLists.txt
@@ -0,0 +1,78 @@
+# Specify the minimum version for CMake
+cmake_minimum_required(VERSION 3.10)
+
+# This defines default install directories like "lib"
+include(GNUInstallDirs)
+
+# Project's name
+project(libhandlegraph)
+# We build using c++14
+set(CMAKE_CXX_STANDARD 14)
+
+# Use all standard-compliant optimizations
+set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -g")
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -g")
+
+# Let cmake decide where to put the output files, allowing for out-of-tree builds.
+
+if(CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_SOURCE_DIR)
+    # We are probably an external project. Don't use @rpath in Mac builds'
+    # install_name fields (AKA LC_ID_DYLIB in otool -l output). Populate with
+    # an absolute path instead. This will let us actually find the library when
+    # we use it as a CMake external project and don't fully install it to any
+    # normal lib directory.
+    message("libhandlegraph is root project or external_project")
+    set (CMAKE_MACOSX_RPATH OFF)
+else()
+    # We are probably an add_subdirectory. We will expect to be in the root
+    # project's lib directory, so we do want to have our non-installed
+    # install_name use @rpath.
+    message("libhandlegraph is add_subdirectory project")
+    set (CMAKE_MACOSX_RPATH ON)
+endif()
+
+# The install_name gets modified on installation to be this.
+set (CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
+
+add_library(handlegraph_objs OBJECT
+  src/handle.cpp
+  src/include/handlegraph/handle_graph.hpp
+  src/include/handlegraph/mutable_handle_graph.hpp
+  src/include/handlegraph/deletable_handle_graph.hpp
+  src/include/handlegraph/path_handle_graph.hpp
+  src/include/handlegraph/path_position_handle_graph.hpp
+  src/include/handlegraph/mutable_path_handle_graph.hpp
+  src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
+  src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
+  src/include/handlegraph/expanding_overlay_graph.hpp
+  src/include/handlegraph/util.hpp
+  src/include/handlegraph/types.hpp
+  src/include/handlegraph/iteratee.hpp
+  )
+
+# Use the include directory when building the objects.
+# It can't be picked up via dependency by the other libraries even if it's public.
+target_include_directories(handlegraph_objs PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/src/include")
+
+# Build objects position-independent to allow a shared library
+set_target_properties(handlegraph_objs PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
+
+# Make static and shared versions with the same base name.
+# Make sure to give them interface include directories that depending targets can use.
+#add_library(handlegraph_shared SHARED $<TARGET_OBJECTS:handlegraph_objs>)
+#set_target_properties(handlegraph_shared PROPERTIES OUTPUT_NAME handlegraph)
+#target_include_directories(handlegraph_shared INTERFACE "${CMAKE_CURRENT_SOURCE_DIR}/src/include")
+add_library(handlegraph_static STATIC $<TARGET_OBJECTS:handlegraph_objs>)
+set_target_properties(handlegraph_static PROPERTIES OUTPUT_NAME handlegraph)
+target_include_directories(handlegraph_static INTERFACE "${CMAKE_CURRENT_SOURCE_DIR}/src/include")
+
+# Set up for installability
+#install(TARGETS handlegraph_shared handlegraph_static
+install(TARGETS handlegraph_static 
+  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install(DIRECTORY src/include/handlegraph
+  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+  FILES_MATCHING PATTERN "*.hpp"
+  )
diff --git a/build-tools/makeBinRelease b/build-tools/makeBinRelease
index fb2729a..c7d5356 100755
--- a/build-tools/makeBinRelease
+++ b/build-tools/makeBinRelease
@@ -28,6 +28,9 @@ REL_TAG=$(getLatestReleaseTag)
 git checkout "${REL_TAG}"
 git submodule update --init --recursive
 
+# todo: update / figure out / remove hack:
+cp ./build-tools/CMakeLists.txt ./deps/libbdsg-easy/deps/libhandlegraph/CMakeLists.txt
+
 if [ $(man gcc | grep nehalem | wc -l) -ge 1 ]
 then
 	 # attempt to increase portability by using older architecture
@@ -36,5 +39,5 @@ else
 	 make check-static
 fi
 
-cp hal2vg clip-vg halRemoveDupes halMergeChroms ${buildDir}/
+cp hal2vg clip-vg halRemoveDupes halMergeChroms halUnclip ${buildDir}/