faster Ripples

.devcontainer/Dockerfile

@@ -0,0 +1,22 @@
+FROM ubuntu:20.04
+ENV APT_KEY_DONT_WARN_ON_DANGEROUS_USAGE=DontWarn
+ENV DEBIAN_FRONTEND=noninteractive
+USER root
+RUN apt-get update && apt-get install -yq --no-install-recommends \
+    git wget \
+    ca-certificates \
+wget cmake  libboost-filesystem-dev libboost-program-options-dev libboost-iostreams-dev libboost-date-time-dev \
+ libprotoc-dev libprotoc-dev protobuf-compiler openssl openssh-client vim \
+ mafft rsync libtbb-dev mpich libmpich-dev automake libtool autoconf make nasm gdb && apt clean
+
+RUN mkdir ISAL&& \
+    cd ISAL&& \
+    wget https://github.com/intel/isa-l/archive/refs/tags/v2.30.0.tar.gz && \
+    tar -xvf v2.30.0.tar.gz && \
+    cd isa-l-2.30.0 && \
+    ./autogen.sh && \
+    ./configure && \
+    make -j$(nproc) && \
+    make install && \
+    cd .. && rm -rf ISAL
+LABEL Name=usher-dev

.devcontainer/devcontainer.json

@@ -0,0 +1,32 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
+// https://github.com/microsoft/vscode-dev-containers/tree/v0.209.6/containers/docker-existing-dockerfile
+{
+	"name": "Existing Dockerfile",
+
+	// Sets the run context to one level up instead of the .devcontainer folder.
+	"context": ".",
+
+	// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
+	"dockerFile": "./Dockerfile",
+
+	// Set *default* container specific settings.json values on container create.
+	"settings": {},
+
+	// Add the IDs of extensions you want installed when the container is created.
+	"extensions": [],
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Uncomment the next line to run commands after the container is created - for example installing curl.
+	// "postCreateCommand": "apt-get update && apt-get install -y curl",
+
+	// Uncomment when using a ptrace-based debugger like C++, Go, and Rust
+	 "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ]
+
+	// Uncomment to use the Docker CLI from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker.
+	// "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ],
+
+	// Uncomment to connect as a non-root user if you've added one. See https://aka.ms/vscode-remote/containers/non-root.
+	// "remoteUser": "vscode"
+}

CMakeLists.txt

@@ -20,7 +20,7 @@ configure_file(src/version.hpp.in version.hpp)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -std=c++17 -Wall -g -Wno-unused-function  -Wno-deprecated-declarations") 
 #-DDEBUG_PARSIMONY_SCORE_CHANGE_CORRECT  -DCHECK_PAR_MAIN  -DEASY_DEBUG -DSTOP_ON_ERROR    -fsanitize=address
-set(CMAKE_CXX_FLAGS_DEBUG "-fsanitize=address")
+set(CMAKE_CXX_FLAGS_DEBUG "-fsanitize=address -O0 -ggdb3 -fno-eliminate-unused-debug-symbols")
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-DNDEBUG -O3")
 set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3")
 set(CMAKE_INCLUDE_CURRENT_DIR ON) 
@@ -52,9 +52,10 @@ AUX_SOURCE_DIRECTORY(src/matOptimize/Profitable_Moves_Enumerators New_Profitable
 AUX_SOURCE_DIRECTORY(src/matOptimize/apply_move patch_tree) 
 file(GLOB MATUTIL_SRCS "src/matUtils/*.cpp" "src/matUtils/*.hpp")
 file(GLOB RIPPLES_SRCS "src/ripples/*.cpp" "src/ripples/*.hpp")
+file(GLOB RIPPLES_FAST_SRCS "src/ripples/ripples_fast/*.cpp" "src/ripples/ripples_fast/*.hpp")
 
-#set_source_files_properties(src/matOptimize/Profitable_Moves_Enumerators/upward_integrated.cpp PROPERTIES COMPILE_FLAGS -O0)
-#set_source_files_properties(src/matOptimize/Profitable_Moves_Enumerators/downward_integrated.cpp PROPERTIES COMPILE_FLAGS -O0)
+set_source_files_properties(src/mutation_annotated_tree.cpp PROPERTIES COMPILE_FLAGS -O3)
+#set_source_files_properties(src/usher_mapper.cpp PROPERTIES COMPILE_FLAGS -O3)
 #set_source_files_properties(src/matOptimize/Profitable_Moves_Enumerators/range_tree.cpp PROPERTIES COMPILE_FLAGS -O0)
 
 #set_source_files_properties(src/matOptimize/detailed_mutations_store.cpp PROPERTIES COMPILE_FLAGS -O0)
@@ -214,6 +215,13 @@ else()
         ${PROTO_HDRS}
         )
 
+    add_executable(ripples-fast
+        src/mutation_annotated_tree.cpp
+        src/usher_mapper.cpp
+        ${RIPPLES_FAST_SRCS}
+        ${PROTO_SRCS}
+        ${PROTO_HDRS}
+        )
 
     add_executable(compareVCF
         src/mutation_annotated_tree.cpp
@@ -347,6 +355,7 @@ TARGET_LINK_LIBRARIES(matUtils PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED
 
 TARGET_COMPILE_OPTIONS(ripples PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)
 TARGET_LINK_LIBRARIES(ripples PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+TARGET_LINK_LIBRARIES(ripples-fast PRIVATE stdc++  ${Boost_LIBRARIES} ${TBB_IMPORTED_TARGETS} ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
 
 if(USHER_SERVER)
     TARGET_COMPILE_OPTIONS(usher_server PRIVATE -DTBB_SUPPRESS_DEPRECATED_MESSAGES)

src/mutation_annotated_tree.cpp

@@ -13,7 +13,7 @@
 #include <google/protobuf/io/coded_stream.h>
 #include <google/protobuf/io/zero_copy_stream_impl.h>
 #include "usher_graph.hpp"
-
+#include <signal.h>
 // Uses one-hot encoding if base is unambiguous
 // A:1,C:2,G:4,T:8
 int8_t Mutation_Annotated_Tree::get_nuc_id (char nuc) {
@@ -1141,10 +1141,12 @@ std::vector<Mutation_Annotated_Tree::Node*> Mutation_Annotated_Tree::Tree::bread
 }
 
 void Mutation_Annotated_Tree::Tree::depth_first_expansion_helper(Mutation_Annotated_Tree::Node* node, std::vector<Mutation_Annotated_Tree::Node*>& vec) const {
+    node->dfs_idx=vec.size();
     vec.push_back(node);
     for (auto c: node->children) {
         depth_first_expansion_helper(c, vec);
     }
+    node->dfs_end_idx=vec.size();
 }
 
 std::vector<Mutation_Annotated_Tree::Node*> Mutation_Annotated_Tree::Tree::depth_first_expansion(Mutation_Annotated_Tree::Node* node) const {

src/mutation_annotated_tree.hpp

@@ -86,6 +86,8 @@ class Node {
     Node* parent;
     std::vector<Node*> children;
     std::vector<Mutation> mutations;
+    size_t dfs_idx;
+    size_t dfs_end_idx;
 
     bool is_leaf();
     bool is_root();