Merge pull request #59 from ComparativeGenomicsToolkit/path-sense

Update libhandle graph

build-tools/CMakeLists.txt

@@ -35,7 +35,38 @@ endif()
 set (CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}")
 
 add_library(handlegraph_objs OBJECT
-  src/handle.cpp
+  src/deletable_handle_graph.cpp
+  src/handle_graph.cpp
+  src/mutable_handle_graph.cpp
+  src/path_metadata.cpp
+  src/mutable_path_metadata.cpp 
+  src/path_handle_graph.cpp 
+  src/path_position_handle_graph.cpp
+  src/mutable_path_handle_graph.cpp
+  src/ranked_handle_graph.cpp
+  src/serializable.cpp
+  src/snarl_decomposition.cpp
+  src/trivially_serializable.cpp
+  src/types.cpp
+  src/copy_graph.cpp
+  src/append_graph.cpp
+  src/are_equivalent.cpp
+  src/find_tips.cpp
+  src/topological_sort.cpp
+  src/apply_orientations.cpp
+  src/is_single_stranded.cpp
+  src/count_walks.cpp
+  src/eades_algorithm.cpp
+  src/dagify.cpp
+  src/strongly_connected_components.cpp
+  src/find_shortest_paths.cpp
+  src/dijkstra.cpp
+  src/is_acyclic.cpp
+  src/reverse_complement.cpp
+  src/split_strands.cpp
+  src/chop.cpp
+  src/weakly_connected_components.cpp
+  src/extend.cpp
   src/include/handlegraph/handle_graph.hpp
   src/include/handlegraph/mutable_handle_graph.hpp
   src/include/handlegraph/deletable_handle_graph.hpp
@@ -48,6 +79,25 @@ add_library(handlegraph_objs OBJECT
   src/include/handlegraph/util.hpp
   src/include/handlegraph/types.hpp
   src/include/handlegraph/iteratee.hpp
+  src/include/handlegraph/algorithms/copy_graph.hpp
+  src/include/handlegraph/algorithms/append_graph.hpp
+  src/include/handlegraph/algorithms/are_equivalent.hpp
+  src/include/handlegraph/algorithms/find_tips.hpp
+  src/include/handlegraph/algorithms/topological_sort.hpp
+  src/include/handlegraph/algorithms/apply_orientations.hpp
+  src/include/handlegraph/algorithms/is_single_stranded.hpp
+  src/include/handlegraph/algorithms/count_walks.hpp
+  src/include/handlegraph/algorithms/eades_algorithm.hpp
+  src/include/handlegraph/algorithms/dagify.hpp
+  src/include/handlegraph/algorithms/strongly_connected_components.hpp
+  src/include/handlegraph/algorithms/find_shortest_paths.hpp
+  src/include/handlegraph/algorithms/dijkstra.hpp
+  src/include/handlegraph/algorithms/reverse_complement.hpp
+  src/include/handlegraph/algorithms/is_acyclic.hpp
+  src/include/handlegraph/algorithms/split_strands.hpp
+  src/include/handlegraph/algorithms/chop.hpp
+  src/include/handlegraph/algorithms/weakly_connected_components.hpp
+  src/include/handlegraph/algorithms/extend.hpp
   )
 
 # Use the include directory when building the objects.

build-tools/makeBinRelease

@@ -20,7 +20,7 @@ set -x
 rm -rf ${binBuildDir}
 mkdir -p ${binBuildDir}
 cd ${binBuildDir}
-git clone --recursive https://github.com/ComparativeGenomicsToolkit/hal2vg.git
+git clone https://github.com/ComparativeGenomicsToolkit/hal2vg.git
 cd hal2vg
 git fetch --tags origin
 
@@ -34,8 +34,13 @@ cp ./build-tools/CMakeLists.txt ./deps/libbdsg-easy/deps/libhandlegraph/CMakeLis
 if [ $(man gcc | grep nehalem | wc -l) -ge 1 ]
 then
 	 # attempt to increase portability by using older architecture
+	 # this make/sed/make thing is a hack to get around a linking error that just cropped up
+	 CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make static || true
+	 sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g"	 
 	 CFLAGS="-march=nehalem" CXXFLAGS="-march=nehalem" make check-static
 else
+	 make static || true
+	 sed -i deps/libbdsg-easy/deps/libbdsg/Makefile -e "s/-lomp//g"
 	 make check-static
 fi