Remove odgi

Author: adamnovak

CMakeLists.txt

@@ -272,8 +272,6 @@ add_library(bdsg_objs OBJECT
   ${bdsg_DIR}/src/hash_graph.cpp
   ${bdsg_DIR}/src/is_single_stranded.cpp
   ${bdsg_DIR}/src/mapped_structs.cpp
-  ${bdsg_DIR}/src/node.cpp
-  ${bdsg_DIR}/src/odgi.cpp
   ${bdsg_DIR}/src/packed_graph.cpp
   ${bdsg_DIR}/src/packed_path_position_overlay.cpp
   ${bdsg_DIR}/src/packed_reference_path_overlay.cpp

Makefile

@@ -15,8 +15,6 @@ OBJS = $(OBJ_DIR)/eades_algorithm.o
 OBJS += $(OBJ_DIR)/hash_graph.o 
 OBJS += $(OBJ_DIR)/is_single_stranded.o 
 OBJS += $(OBJ_DIR)/mapped_structs.o 
-OBJS += $(OBJ_DIR)/node.o 
-OBJS += $(OBJ_DIR)/odgi.o 
 OBJS += $(OBJ_DIR)/packed_graph.o 
 OBJS += $(OBJ_DIR)/path_position_overlays.o 
 OBJS += $(OBJ_DIR)/packed_path_position_overlay.o

README.md

@@ -6,12 +6,13 @@ Optimized **b**i**d**irected **s**equence **g**raph implementations for graph ge
 
 ## About
 
-The main purpose of `libbdsg` is to provide high performance implementations of sequence graphs for graph-based pangenomics applications. The repository contains three graph implementations with different performance tradeoffs:
+The main purpose of `libbdsg` is to provide high performance implementations of sequence graphs for graph-based pangenomics applications. The repository contains two graph implementations with different performance tradeoffs:
 
 - HashGraph: prioritizes speed
-- ODGI: balances speed and low memory usage
 - PackedGraph: prioritizes low memory usage
 
+Previously, a third implementation, ODGI, was provided, but that implementation is now part of its own [odgi project](https://github.com/pangenome/odgi#odgi).
+
 All of these graph objects implement a common interface defined by [`libhandlegraph`](https://github.com/vgteam/libhandlegraph), so they can be used interchangeably and swapped easily.
 
 Additionally, `libbdsg` provides a few "overlays", which are applied to the graph implementations in order to expand their functionality. The expanded functionality is also described generically using `libhandlegraph` interfaces.

bdsg/cmake_bindings/bdsg.cpp

@@ -26,10 +26,9 @@ void bind_bdsg_internal_is_single_stranded(std::function< pybind11::module &(std
 void bind_bdsg_internal_eades_algorithm(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_snarl_decomposition(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_std_bdsg_internal_binder_hook_bind(std::function< pybind11::module &(std::string const &namespace_) > &M);
-void bind_bdsg_odgi(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_handlegraph_path_position_handle_graph(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_packed_path_position_overlay(std::function< pybind11::module &(std::string const &namespace_) > &M);
-void bind_bdsg_overlays_packed_subgraph_overlay(std::function< pybind11::module &(std::string const &namespace_) > &M);
+void bind_bdsg_overlays_packed_path_position_overlay_1(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_path_position_overlays(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_path_subgraph_overlay(std::function< pybind11::module &(std::string const &namespace_) > &M);
 void bind_bdsg_overlays_vectorizable_overlays(std::function< pybind11::module &(std::string const &namespace_) > &M);
@@ -80,10 +79,9 @@ PYBIND11_MODULE(bdsg, root_module) {
 	bind_bdsg_internal_eades_algorithm(M);
 	bind_handlegraph_snarl_decomposition(M);
 	bind_std_bdsg_internal_binder_hook_bind(M);
-	bind_bdsg_odgi(M);
 	bind_handlegraph_path_position_handle_graph(M);
 	bind_bdsg_overlays_packed_path_position_overlay(M);
-	bind_bdsg_overlays_packed_subgraph_overlay(M);
+	bind_bdsg_overlays_packed_path_position_overlay_1(M);
 	bind_bdsg_overlays_path_position_overlays(M);
 	bind_bdsg_overlays_path_subgraph_overlay(M);
 	bind_bdsg_overlays_vectorizable_overlays(M);

bdsg/cmake_bindings/bdsg.sources

@@ -17,10 +17,9 @@ bdsg/internal/is_single_stranded.cpp
 bdsg/internal/eades_algorithm.cpp
 handlegraph/snarl_decomposition.cpp
 std/bdsg/internal/binder_hook_bind.cpp
-bdsg/odgi.cpp
 handlegraph/path_position_handle_graph.cpp
 bdsg/overlays/packed_path_position_overlay.cpp
-bdsg/overlays/packed_subgraph_overlay.cpp
+bdsg/overlays/packed_path_position_overlay_1.cpp
 bdsg/overlays/path_position_overlays.cpp
 bdsg/overlays/path_subgraph_overlay.cpp
 bdsg/overlays/vectorizable_overlays.cpp

bdsg/cmake_bindings/bdsg/odgi.cpp

@@ -425,6 +425,32 @@ struct PyCallBack_bdsg_PackedPositionOverlay : public bdsg::PackedPositionOverla
 		}
 		return PackedPositionOverlay::get_path_handle_of_step(a0);
 	}
+	bool for_each_path_handle_impl(const class std::function<bool (const struct handlegraph::path_handle_t &)> & a0) const override { 
+		pybind11::gil_scoped_acquire gil;
+		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "for_each_path_handle_impl");
+		if (overload) {
+			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0);
+			if (pybind11::detail::cast_is_temporary_value_reference<bool>::value) {
+				static pybind11::detail::overload_caster_t<bool> caster;
+				return pybind11::detail::cast_ref<bool>(std::move(o), caster);
+			}
+			else return pybind11::detail::cast_safe<bool>(std::move(o));
+		}
+		return PackedPositionOverlay::for_each_path_handle_impl(a0);
+	}
+	bool for_each_step_on_handle_impl(const struct handlegraph::handle_t & a0, const class std::function<bool (const struct handlegraph::step_handle_t &)> & a1) const override { 
+		pybind11::gil_scoped_acquire gil;
+		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "for_each_step_on_handle_impl");
+		if (overload) {
+			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0, a1);
+			if (pybind11::detail::cast_is_temporary_value_reference<bool>::value) {
+				static pybind11::detail::overload_caster_t<bool> caster;
+				return pybind11::detail::cast_ref<bool>(std::move(o), caster);
+			}
+			else return pybind11::detail::cast_safe<bool>(std::move(o));
+		}
+		return PackedPositionOverlay::for_each_step_on_handle_impl(a0, a1);
+	}
 	unsigned long get_path_length(const struct handlegraph::path_handle_t & a0) const override { 
 		pybind11::gil_scoped_acquire gil;
 		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "get_path_length");
@@ -477,48 +503,35 @@ struct PyCallBack_bdsg_PackedPositionOverlay : public bdsg::PackedPositionOverla
 		}
 		return PackedPositionOverlay::get_underlying_handle(a0);
 	}
-	bool for_each_step_position_on_handle(const struct handlegraph::handle_t & a0, const class std::function<bool (const struct handlegraph::step_handle_t &, const bool &, const unsigned long &)> & a1) const override { 
+	unsigned long scan_path(const struct handlegraph::path_handle_t & a0, void *& a1) override { 
 		pybind11::gil_scoped_acquire gil;
-		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "for_each_step_position_on_handle");
+		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "scan_path");
 		if (overload) {
 			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0, a1);
-			if (pybind11::detail::cast_is_temporary_value_reference<bool>::value) {
-				static pybind11::detail::overload_caster_t<bool> caster;
-				return pybind11::detail::cast_ref<bool>(std::move(o), caster);
-			}
-			else return pybind11::detail::cast_safe<bool>(std::move(o));
-		}
-		return PathPositionHandleGraph::for_each_step_position_on_handle(a0, a1);
-	}
-	unsigned long get_step_count(const struct handlegraph::handle_t & a0) const override { 
-		pybind11::gil_scoped_acquire gil;
-		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "get_step_count");
-		if (overload) {
-			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0);
 			if (pybind11::detail::cast_is_temporary_value_reference<unsigned long>::value) {
 				static pybind11::detail::overload_caster_t<unsigned long> caster;
 				return pybind11::detail::cast_ref<unsigned long>(std::move(o), caster);
 			}
 			else return pybind11::detail::cast_safe<unsigned long>(std::move(o));
 		}
-		return PathHandleGraph::get_step_count(a0);
+		return PackedPositionOverlay::scan_path(a0, a1);
 	}
-	bool for_each_path_handle_impl(const class std::function<bool (const struct handlegraph::path_handle_t &)> & a0) const override { 
+	void set_index_count(unsigned long a0) override { 
 		pybind11::gil_scoped_acquire gil;
-		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "for_each_path_handle_impl");
+		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "set_index_count");
 		if (overload) {
 			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0);
-			if (pybind11::detail::cast_is_temporary_value_reference<bool>::value) {
-				static pybind11::detail::overload_caster_t<bool> caster;
-				return pybind11::detail::cast_ref<bool>(std::move(o), caster);
+			if (pybind11::detail::cast_is_temporary_value_reference<void>::value) {
+				static pybind11::detail::overload_caster_t<void> caster;
+				return pybind11::detail::cast_ref<void>(std::move(o), caster);
 			}
-			else return pybind11::detail::cast_safe<bool>(std::move(o));
+			else return pybind11::detail::cast_safe<void>(std::move(o));
 		}
-		pybind11::pybind11_fail("Tried to call pure virtual function \"PathHandleGraph::for_each_path_handle_impl\"");
+		return PackedPositionOverlay::set_index_count(a0);
 	}
-	bool for_each_step_on_handle_impl(const struct handlegraph::handle_t & a0, const class std::function<bool (const struct handlegraph::step_handle_t &)> & a1) const override { 
+	bool for_each_step_position_on_handle(const struct handlegraph::handle_t & a0, const class std::function<bool (const struct handlegraph::step_handle_t &, const bool &, const unsigned long &)> & a1) const override { 
 		pybind11::gil_scoped_acquire gil;
-		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "for_each_step_on_handle_impl");
+		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "for_each_step_position_on_handle");
 		if (overload) {
 			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0, a1);
 			if (pybind11::detail::cast_is_temporary_value_reference<bool>::value) {
@@ -527,7 +540,20 @@ struct PyCallBack_bdsg_PackedPositionOverlay : public bdsg::PackedPositionOverla
 			}
 			else return pybind11::detail::cast_safe<bool>(std::move(o));
 		}
-		pybind11::pybind11_fail("Tried to call pure virtual function \"PathHandleGraph::for_each_step_on_handle_impl\"");
+		return PathPositionHandleGraph::for_each_step_position_on_handle(a0, a1);
+	}
+	unsigned long get_step_count(const struct handlegraph::handle_t & a0) const override { 
+		pybind11::gil_scoped_acquire gil;
+		pybind11::function overload = pybind11::get_overload(static_cast<const bdsg::PackedPositionOverlay *>(this), "get_step_count");
+		if (overload) {
+			auto o = overload.operator()<pybind11::return_value_policy::reference>(a0);
+			if (pybind11::detail::cast_is_temporary_value_reference<unsigned long>::value) {
+				static pybind11::detail::overload_caster_t<unsigned long> caster;
+				return pybind11::detail::cast_ref<unsigned long>(std::move(o), caster);
+			}
+			else return pybind11::detail::cast_safe<unsigned long>(std::move(o));
+		}
+		return PathHandleGraph::get_step_count(a0);
 	}
 	class std::vector<handlegraph::step_handle_t> steps_of_handle(const struct handlegraph::handle_t & a0, bool a1) const override { 
 		pybind11::gil_scoped_acquire gil;
@@ -721,8 +747,10 @@ void bind_bdsg_overlays_packed_path_position_overlay(std::function< pybind11::mo
 		cl.def( pybind11::init( [](const class handlegraph::PathHandleGraph * a0){ return new bdsg::PackedPositionOverlay(a0); }, [](const class handlegraph::PathHandleGraph * a0){ return new PyCallBack_bdsg_PackedPositionOverlay(a0); } ), "doc");
 		cl.def( pybind11::init<const class handlegraph::PathHandleGraph *, unsigned long>(), pybind11::arg("graph"), pybind11::arg("steps_per_index") );
 
+		cl.def( pybind11::init( [](){ return new bdsg::PackedPositionOverlay(); }, [](){ return new PyCallBack_bdsg_PackedPositionOverlay(); } ) );
 		cl.def( pybind11::init( [](PyCallBack_bdsg_PackedPositionOverlay const &o){ return new PyCallBack_bdsg_PackedPositionOverlay(o); } ) );
 		cl.def( pybind11::init( [](bdsg::PackedPositionOverlay const &o){ return new bdsg::PackedPositionOverlay(o); } ) );
+		cl.def("assign", (class bdsg::PackedPositionOverlay & (bdsg::PackedPositionOverlay::*)(const class bdsg::PackedPositionOverlay &)) &bdsg::PackedPositionOverlay::operator=, "C++: bdsg::PackedPositionOverlay::operator=(const class bdsg::PackedPositionOverlay &) --> class bdsg::PackedPositionOverlay &", pybind11::return_value_policy::automatic, pybind11::arg("other"));
 		cl.def("has_node", (bool (bdsg::PackedPositionOverlay::*)(long long) const) &bdsg::PackedPositionOverlay::has_node, "Method to check if a node exists by ID\n\nC++: bdsg::PackedPositionOverlay::has_node(long long) const --> bool", pybind11::arg("node_id"));
 		cl.def("get_handle", [](bdsg::PackedPositionOverlay const &o, const long long & a0) -> handlegraph::handle_t { return o.get_handle(a0); }, "", pybind11::arg("node_id"));
 		cl.def("get_handle", (struct handlegraph::handle_t (bdsg::PackedPositionOverlay::*)(const long long &, bool) const) &bdsg::PackedPositionOverlay::get_handle, "Look up the handle for the node with the given ID in the given orientation\n\nC++: bdsg::PackedPositionOverlay::get_handle(const long long &, bool) const --> struct handlegraph::handle_t", pybind11::arg("node_id"), pybind11::arg("is_reverse"));
@@ -759,23 +787,4 @@ void bind_bdsg_overlays_packed_path_position_overlay(std::function< pybind11::mo
 		cl.def("get_step_at_position", (struct handlegraph::step_handle_t (bdsg::PackedPositionOverlay::*)(const struct handlegraph::path_handle_t &, const unsigned long &) const) &bdsg::PackedPositionOverlay::get_step_at_position, "Returns the step at this position, measured in bases of sequence starting at\n the step returned by path_begin(). If the position is past the end of the\n path, returns path_end().\n\nC++: bdsg::PackedPositionOverlay::get_step_at_position(const struct handlegraph::path_handle_t &, const unsigned long &) const --> struct handlegraph::step_handle_t", pybind11::arg("path"), pybind11::arg("position"));
 		cl.def("get_underlying_handle", (struct handlegraph::handle_t (bdsg::PackedPositionOverlay::*)(const struct handlegraph::handle_t &) const) &bdsg::PackedPositionOverlay::get_underlying_handle, "Returns the handle in the underlying graph that corresponds to a handle in the\n overlay\n\nC++: bdsg::PackedPositionOverlay::get_underlying_handle(const struct handlegraph::handle_t &) const --> struct handlegraph::handle_t", pybind11::arg("handle"));
 	}
-	{ // bdsg::BBHashHelper file:bdsg/overlays/packed_path_position_overlay.hpp line:288
-		pybind11::class_<bdsg::BBHashHelper, std::shared_ptr<bdsg::BBHashHelper>> cl(M("bdsg"), "BBHashHelper", "");
-		{ // bdsg::BBHashHelper::iterator file:bdsg/overlays/packed_path_position_overlay.hpp line:298
-			auto & enclosing_class = cl;
-			pybind11::class_<bdsg::BBHashHelper::iterator, std::shared_ptr<bdsg::BBHashHelper::iterator>> cl(enclosing_class, "iterator", "");
-			cl.def( pybind11::init( [](bdsg::BBHashHelper::iterator const &o){ return new bdsg::BBHashHelper::iterator(o); } ) );
-			cl.def("assign", (struct bdsg::BBHashHelper::iterator & (bdsg::BBHashHelper::iterator::*)(const struct bdsg::BBHashHelper::iterator &)) &bdsg::BBHashHelper::iterator::operator=, "C++: bdsg::BBHashHelper::iterator::operator=(const struct bdsg::BBHashHelper::iterator &) --> struct bdsg::BBHashHelper::iterator &", pybind11::return_value_policy::automatic, pybind11::arg("other"));
-			cl.def("plus_plus", (struct bdsg::BBHashHelper::iterator & (bdsg::BBHashHelper::iterator::*)()) &bdsg::BBHashHelper::iterator::operator++, "C++: bdsg::BBHashHelper::iterator::operator++() --> struct bdsg::BBHashHelper::iterator &", pybind11::return_value_policy::automatic);
-			cl.def("__mul__", (struct handlegraph::step_handle_t (bdsg::BBHashHelper::iterator::*)() const) &bdsg::BBHashHelper::iterator::operator*, "C++: bdsg::BBHashHelper::iterator::operator*() const --> struct handlegraph::step_handle_t");
-			cl.def("__eq__", (bool (bdsg::BBHashHelper::iterator::*)(const struct bdsg::BBHashHelper::iterator &) const) &bdsg::BBHashHelper::iterator::operator==, "C++: bdsg::BBHashHelper::iterator::operator==(const struct bdsg::BBHashHelper::iterator &) const --> bool", pybind11::arg("other"));
-			cl.def("__ne__", (bool (bdsg::BBHashHelper::iterator::*)(const struct bdsg::BBHashHelper::iterator &) const) &bdsg::BBHashHelper::iterator::operator!=, "C++: bdsg::BBHashHelper::iterator::operator!=(const struct bdsg::BBHashHelper::iterator &) const --> bool", pybind11::arg("other"));
-		}
-
-		cl.def( pybind11::init<const class handlegraph::PathHandleGraph *>(), pybind11::arg("graph") );
-
-		cl.def( pybind11::init( [](bdsg::BBHashHelper const &o){ return new bdsg::BBHashHelper(o); } ) );
-		cl.def("begin", (struct bdsg::BBHashHelper::iterator (bdsg::BBHashHelper::*)() const) &bdsg::BBHashHelper::begin, "C++ style range begin over steps\n\nC++: bdsg::BBHashHelper::begin() const --> struct bdsg::BBHashHelper::iterator");
-		cl.def("end", (struct bdsg::BBHashHelper::iterator (bdsg::BBHashHelper::*)() const) &bdsg::BBHashHelper::end, "C++ style range end over steps\n\nC++: bdsg::BBHashHelper::end() const --> struct bdsg::BBHashHelper::iterator");
-	}
 }