move to submodule deps

Author: ekg

.gitmodules

@@ -0,0 +1,21 @@
+[submodule "deps/BBHash"]
+	path = deps/BBHash
+	url = https://github.com/vgteam/BBHash.git
+[submodule "deps/sdsl-lite"]
+	path = deps/sdsl-lite
+	url = https://github.com/simongog/sdsl-lite.git
+[submodule "deps/libhandlegraph"]
+	path = deps/libhandlegraph
+	url = https://github.com/vgteam/libhandlegraph.git
+[submodule "deps/mmmultimap"]
+	path = deps/mmmultimap
+	url = https://github.com/ekg/mmmultimap.git
+[submodule "deps/ips4o"]
+	path = deps/ips4o
+	url = https://github.com/SaschaWitt/ips4o.git
+[submodule "deps/args"]
+	path = deps/args
+	url = https://github.com/Taywee/args.git
+[submodule "deps/gfakluge"]
+	path = deps/gfakluge
+	url = https://github.com/vgteam/gfakluge.git

CMakeLists.txt

@@ -69,21 +69,16 @@ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
 
 # libhandlegraph (full build using its cmake config)
 ExternalProject_Add(handlegraph
-  GIT_REPOSITORY "https://github.com/vgteam/libhandlegraph.git"
-  GIT_TAG "7b788bfaea21d976e372b130a2353deff99757f1"
-  CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR}
-  #BUILD_COMMAND ""
-  UPDATE_COMMAND ""
-  INSTALL_COMMAND "")
+  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/libhandlegraph"
+  CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>")
 ExternalProject_Get_property(handlegraph INSTALL_DIR)
-set(handlegraph_INCLUDE "${INSTALL_DIR}/src/handlegraph/src/include")
-set(handlegraph_LIB "${INSTALL_DIR}/src/handlegraph-build")
+set(handlegraph_INCLUDE "${INSTALL_DIR}/include")
+set(handlegraph_LIB "${INSTALL_DIR}/lib")
 
 # sdsl-lite (full build using its cmake config)
 ExternalProject_Add(sdsl-lite
-  GIT_REPOSITORY "https://github.com/simongog/sdsl-lite.git"
-  GIT_TAG "ddb0fbbc33bb183baa616f17eb48e261ac2a3672"
-  CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} # TODO ADD static build flag
+  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite"
+  CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>"
   UPDATE_COMMAND ""
   INSTALL_COMMAND "")
 ExternalProject_Get_property(sdsl-lite INSTALL_DIR)
@@ -94,46 +89,43 @@ set(sdsl-lite-divsufsort_LIB "${INSTALL_DIR}/src/sdsl-lite-build/external/libdiv
 
 # mmmultimap (memory mapped multimap)
 ExternalProject_Add(mmmultimap
-  GIT_REPOSITORY "https://github.com/ekg/mmmultimap.git"
-  GIT_TAG "38d5d70f4f9e10aae4548b022c2a7d55024c5e99"
+  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/mmmultimap"
   BUILD_COMMAND ""
   UPDATE_COMMAND ""
   INSTALL_COMMAND "")
 ExternalProject_Get_property(mmmultimap SOURCE_DIR)
 set(mmmultimap_INCLUDE "${SOURCE_DIR}/src")
 
+# In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
+ExternalProject_Add(ips4o
+  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/ips4o"
+  INSTALL_COMMAND ""
+  BUILD_COMMAND ""
+  CONFIGURE_COMMAND "")
+ExternalProject_Get_property(ips4o SOURCE_DIR)
+set(ips4o_INCLUDE "${SOURCE_DIR}")
+
 # taywee's C++ args library, header only
 ExternalProject_Add(tayweeargs
-  GIT_REPOSITORY "https://github.com/Taywee/args.git"
-  GIT_TAG "3de44ec671db452cc0c4ef86399b108939768abb"
+  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/args"
   UPDATE_COMMAND ""
   INSTALL_COMMAND "")
 ExternalProject_Get_property(tayweeargs SOURCE_DIR)
 set(tayweeargs_INCLUDE "${SOURCE_DIR}")
 
-# gfakluge (header only)
+# gfakluge (now header only)
 ExternalProject_Add(gfakluge
-  GIT_REPOSITORY "https://github.com/vgteam/gfakluge.git"
-  GIT_TAG "3b9faa69fc27f34b9f65d78dd66bc4c97f11014b"
-  BUILD_IN_SOURCE TRUE
-  CMAKE_ARGS -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} # TODO ADD static build flag
+  SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/gfakluge"
+  CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>"
   UPDATE_COMMAND ""
   INSTALL_COMMAND ""
   BUILD_COMMAND ""
   CONFIGURE_COMMAND "")
+ExternalProject_Get_property(gfakluge SOURCE_DIR)
+set(gfakluge_INCLUDE "${SOURCE_DIR}/src")
+set(gfakluge_tinyFA_INCLUDE "${SOURCE_DIR}/src/tinyFA")
 ExternalProject_Get_property(gfakluge INSTALL_DIR)
-set(gfakluge_INCLUDE "${INSTALL_DIR}/src/gfakluge/src")
-set(gfakluge_tinyFA_INCLUDE "${INSTALL_DIR}/src/gfakluge/src/tinyFA")
-
-# In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
-ExternalProject_Add(ips4o
-  GIT_REPOSITORY "https://github.com/vgteam/ips4o.git"
-  GIT_TAG "22069381cc1bf2df07ee1ff47f6b6073fcfb4508"
-  INSTALL_COMMAND ""
-  BUILD_COMMAND ""
-  CONFIGURE_COMMAND "")
-ExternalProject_Get_property(ips4o SOURCE_DIR)
-set(ips4o_INCLUDE "${SOURCE_DIR}")
+set(gfakluge_LIB "${INSTALL_DIR}/src/gfakluge")
 
 #set(CMAKE_BUILD_TYPE Release)
 

deps/BBHash

@@ -55,8 +55,12 @@ XG::~XG(void) {
         paths.pop_back();
     }
 }
+
+uint32_t XG::get_magic_number(void) const {
+    return 4143290017ul;
+}
 
-void XG::deserialize(std::istream& in) {
+void XG::deserialize_members(std::istream& in) {
     // simple alias to match an external interface
     load(in);
 }
@@ -518,7 +522,7 @@ handle_t XGPath::external_handle(const handle_t& handle) const {
     return as_handle(as_integer(handle)+as_integer(min_handle));
 }
 
-void XG::serialize(ostream& out) const {
+void XG::serialize_members(ostream& out) const {
     serialize_and_measure(out);
 }