Merge pull request #429 from pgangwar-ucsd/ripples-server-tbb-update

Ripples server integration with namespace changes

Author: yatisht

CMakeLists.txt

@@ -22,9 +22,9 @@ if ("${VERSION_PATCH}" MATCHES "[0-9]+")
 endif()
 message(STATUS "${usher_VERSION}")
 
-if(NOT APPLE)
-  add_link_options("-Wl,--undefined-version")
-endif()
+#if(NOT APPLE)
+#  add_link_options("-Wl,--undefined-version")
+#endif()
 
 include(FetchContent)
 set(TBB_VERSION "v2022.2.0")
@@ -43,7 +43,8 @@ configure_file(src/version.hpp.in version.hpp)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -pipe -g -ggdb3 -Wno-unused-function  -Wno-deprecated-declarations") 
 #-DDEBUG_PARSIMONY_SCORE_CHANGE_CORRECT -fsanitize=address -DCHECK_PAR_MAIN  -DEASY_DEBUG -DSTOP_ON_ERROR  -DDETAILED_MERGER_CHECK -O0
-set(CMAKE_CXX_FLAGS_DEBUG "  -fno-eliminate-unused-debug-symbols -O0")
+set(CMAKE_CXX_FLAGS_DEBUG " -fsanitize=address -fno-eliminate-unused-debug-symbols -O0")
+#set(CMAKE_CXX_FLAGS_DEBUG "  -fno-eliminate-unused-debug-symbols -O0")
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-DNDEBUG -O3")
 set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG -O3 ")
 set(CMAKE_INCLUDE_CURRENT_DIR ON)
@@ -77,9 +78,12 @@ AUX_SOURCE_DIRECTORY(src/matOptimize/apply_move patch_tree)
 AUX_SOURCE_DIRECTORY(src/check_samples_place check_samples_place) 
 file(GLOB MATUTIL_SRCS "src/matUtils/*.cpp" "src/matUtils/*.hpp")
 file(GLOB RIPPLES_SRCS "src/ripples/*.cpp" "src/ripples/*.hpp")
+file(GLOB RIPPLES_SERVER_SRCS "src/ripples/server/*.cpp" "src/ripples/server/*.hpp")
 file(GLOB USHER_SAMPLED_SRCS "src/usher-sampled/static_tree_mapper/*" "src/usher-sampled/*.cpp" "src/usher-sampled/*.hpp")
 file(GLOB RIPPLES_FAST_SRCS "src/ripples/ripples_fast/*.cpp" "src/ripples/ripples_fast/*.hpp")
 file(GLOB RIPPLES_UTILS_SRCS "src/ripples/util/*.cpp" "src/ripples/util/*.hpp")
+file(GLOB RIPPLES_COPY_UTIL_SRCS "src/ripples/util/copy/*.cpp" "src/ripples/util/copy/*.hpp")
+file(GLOB RIPPLES_FILTRATION_SRCS "src/ripples/post_filtration/*.cpp" "src/ripples/post_filtration/*.hpp")
 
 set_source_files_properties(src/mutation_annotated_tree.cpp PROPERTIES COMPILE_FLAGS -O3)
 set_source_files_properties(src/usher-sampled/wait_debug.cpp PROPERTIES COMPILE_FLAGS -O0)
@@ -108,13 +112,15 @@ if(DEFINED Protobuf_PATH)
             src/usher_mapper.cpp
             ${RIPPLES_SRCS}
         )
+
         if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
             add_executable(ripples-fast
                 src/mutation_annotated_tree.cpp
                 src/usher_mapper.cpp
                 ${RIPPLES_FAST_SRCS}
             )
         endif()
+
         add_executable(usher-sampled
             ${USHER_SAMPLED_SRCS}
             src/matOptimize/main_helper.cpp
@@ -226,6 +232,7 @@ if(DEFINED Protobuf_PATH)
                 TARGET ripples-fast 
                 PROTOS parsimony.proto)
         endif()
+
         protobuf_generate(
             LANGUAGE cpp
             TARGET compareVCF 
@@ -321,6 +328,7 @@ if(DEFINED Protobuf_PATH)
             ${TAXO_HDRS}
         )
 
+        
         add_executable(ripples
             src/mutation_annotated_tree.cpp
             src/usher_mapper.cpp
@@ -497,6 +505,19 @@ if(DEFINED Protobuf_PATH)
                 src/matOptimize/main_load_tree.cpp
                 src/matOptimize/priority_conflict_resolver.cpp
                 src/usher-sampled/driver/socket.cpp
+                src/mutation_annotated_tree.cpp
+                src/usher_mapper.cpp
+                src/usher_common.cpp
+                # ripples server
+                src/ripples/ripples_fast/ripples_util.cpp
+                src/ripples/ripples_fast/ripples.cpp
+                src/ripples/ripples_fast/ripple_aux.cpp
+                src/ripples/ripples_fast/ripples_mapper.cpp
+                src/ripples/ripples_fast/ripple_merger.cpp
+                src/ripples/util/text_parser.cpp
+                ${RIPPLES_SERVER_SRCS}
+                ${RIPPLES_COPY_UTIL_SRCS}
+                ${RIPPLES_FILTRATION_SRCS}
                 ${patch_tree}
                 ${New_Profitable_Moves_Enumerators}
             )
@@ -566,6 +587,7 @@ TARGET_LINK_LIBRARIES(ripplesInit PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${
 
 TARGET_COMPILE_OPTIONS(ripples PRIVATE)
 TARGET_LINK_LIBRARIES(ripples PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
+
 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
     TARGET_LINK_LIBRARIES(ripples-fast PRIVATE stdc++  ${Boost_LIBRARIES} TBB::tbb ${Protobuf_LIBRARIES}) # OpenMP::OpenMP_CXX)
 endif()

src/check_samples_place/check_samples.cpp

@@ -10,7 +10,8 @@
 #include <unordered_set>
 #include <utility>
 #include <vector>
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT =  MatOptimize::Mutation_Annotated_Tree;
+using namespace MatOptimize;
 //add mutation m to parent_mutations, which represent the mutation of a node relative to root,
 //or update major allele if already present
 void ins_mut(Mutation_Set &parent_mutations,const Mutation_Annotated_Tree::Mutation &m,bool is_leaf) {

src/check_samples_place/import_vcf.cpp

@@ -31,7 +31,7 @@
 #include <unordered_set>
 #include <utility>
 #include <vector>
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT = MatOptimize::Mutation_Annotated_Tree;
 #define ZLIB_BUFSIZ 0x10000
 size_t read_size;
 size_t alloc_size;

src/check_samples_place/main.cpp

@@ -2,7 +2,7 @@
 #include <cstdio>
 #include <unordered_set>
 #include <string>
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT = MatOptimize::Mutation_Annotated_Tree;
 #include "src/matOptimize/check_samples.hpp"
 void Sample_Input(const char *name, Original_State_t& ori_state,
                   MAT::Tree &tree);

src/matOptimize/Fitch_Sankoff.cpp

@@ -15,7 +15,7 @@
 #include <emmintrin.h>
 #include <smmintrin.h>
 #endif
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT = MatOptimize::Mutation_Annotated_Tree;
 //get state of ancestor at position
 nuc_one_hot get_this_state(MAT::Node* ancestor,int position) {
     auto iter = ancestor->mutations.find(position);
@@ -311,6 +311,8 @@ int FS_forward_assign_states_only(const std::vector<MAT::Node*>& bfs_ordered_nod
     return mutation_count;
 }
 #endif
+
+using namespace MatOptimize;
 void Fitch_Sankoff_Whole_Tree(const std::vector<backward_pass_range>& child_idx_range,const std::vector<forward_pass_range>& parent_idx,const MAT::Mutation & base,const mutated_t& mutated,Fitch_Sankoff_Out_Container& output,MAT::Tree* try_similar) {
 
     FS_backward_pass(child_idx_range,output.minor_major_allele,mutated,base.get_ref_one_hot());

src/matOptimize/Fitch_Sankoff.hpp

@@ -4,7 +4,6 @@
 #include <tbb/concurrent_vector.h>
 #include <tbb/enumerable_thread_specific.h>
 #include <vector>
-namespace MAT=Mutation_Annotated_Tree;
 struct backward_pass_range {
     size_t first_child_bfs_idx;
     size_t child_size;
@@ -28,7 +27,7 @@ struct mutated_t_comparator {
         return lhs.first>rhs.first;
     }
 };
-typedef std::vector<MAT::Mutation> mut_vect_t;
+typedef std::vector<MatOptimize::MAT::Mutation> mut_vect_t;
 struct Fitch_Sankoff_Out_Container {
     std::vector<mut_vect_t> output;
     std::vector<uint8_t> minor_major_allele;
@@ -39,13 +38,13 @@ struct Fitch_Sankoff_Out_Container {
         }
     }
 };
-void Fitch_Sankoff_prep(const std::vector<Mutation_Annotated_Tree::Node*>& bfs_ordered_nodes, std::vector<backward_pass_range>& child_idx_range,std::vector<forward_pass_range>& parent_idx);
-void Fitch_Sankoff_Whole_Tree(const std::vector<backward_pass_range>& child_idx_range,const std::vector<forward_pass_range>& parent_idx,const Mutation_Annotated_Tree::Mutation & base,const mutated_t& mutated,Fitch_Sankoff_Out_Container& output,Mutation_Annotated_Tree::Tree* try_similar=nullptr);
+void Fitch_Sankoff_prep(const std::vector<MatOptimize::MAT::Node*>& bfs_ordered_nodes, std::vector<backward_pass_range>& child_idx_range,std::vector<forward_pass_range>& parent_idx);
+void Fitch_Sankoff_Whole_Tree(const std::vector<backward_pass_range>& child_idx_range,const std::vector<forward_pass_range>& parent_idx,const MatOptimize::Mutation_Annotated_Tree::Mutation & base,const mutated_t& mutated,Fitch_Sankoff_Out_Container& output,MatOptimize::Mutation_Annotated_Tree::Tree* try_similar=nullptr);
 #if defined CHECK_STATE_REASSIGN||defined DEBUG_PARSIMONY_SCORE_CHANGE_CORRECT
-void FS_backward_pass(const std::vector<Mutation_Annotated_Tree::Node*> bfs_ordered_nodes, std::vector<uint8_t>& boundary1_major_allele,const std::unordered_map<std::string, nuc_one_hot>& mutated,nuc_one_hot ref_nuc);
-int FS_forward_assign_states_only(const std::vector<Mutation_Annotated_Tree::Node*>& bfs_ordered_nodes,const std::vector<uint8_t>& boundary1_major_allele,const nuc_one_hot parent_state,std::vector<uint8_t>& states_out,std::vector<std::vector<Mutation_Annotated_Tree::Node*>>& children_mutation_count);
+void FS_backward_pass(const std::vector<MatOptimize::MAT::Node*> bfs_ordered_nodes, std::vector<uint8_t>& boundary1_major_allele,const std::unordered_map<std::string, nuc_one_hot>& mutated,nuc_one_hot ref_nuc);
+int FS_forward_assign_states_only(const std::vector<MatOptimize::MAT::Node*>& bfs_ordered_nodes,const std::vector<uint8_t>& boundary1_major_allele,const nuc_one_hot parent_state,std::vector<uint8_t>& states_out,std::vector<std::vector<MatOptimize::Mutation_Annotated_Tree::Node*>>& children_mutation_count);
 #endif
 void set_state_from_cnt(const std::array<int,4>& data, uint8_t& boundary1_major_allele_out);
 typedef tbb::enumerable_thread_specific<Fitch_Sankoff_Out_Container> FS_result_per_thread_t;
 void deallocate_FS_cache(FS_result_per_thread_t& in);
-void fill_muts(FS_result_per_thread_t& in, std::vector<MAT::Node*>& bfs_ordered_nodes);
+void fill_muts(FS_result_per_thread_t& in, std::vector<MatOptimize::MAT::Node*>& bfs_ordered_nodes);

src/matOptimize/Mutation_Collection.cpp

@@ -5,7 +5,7 @@
 #include <tbb/blocked_range.h>
 #include <tbb/parallel_for.h>
 #include <vector>
-using namespace Mutation_Annotated_Tree;
+using namespace MatOptimize::Mutation_Annotated_Tree;
 void Mutations_Collection::merge_out(const Mutations_Collection &other,
                                      Mutations_Collection &out,
                                      char keep_self) const {
@@ -165,7 +165,7 @@ Mutations_Collection::iterator Mutations_Collection::find_next(int pos) {
 }
 
 
-int Mutation_Annotated_Tree::Mutations_Collection::count_valid_mutations() const {
+int MatOptimize::Mutation_Annotated_Tree::Mutations_Collection::count_valid_mutations() const {
     int count=0;
     for(const auto & mut:mutations) {
         if (mut.is_valid()) {
@@ -174,8 +174,8 @@ int Mutation_Annotated_Tree::Mutations_Collection::count_valid_mutations() const
     }
     return count;
 }
-void Mutation_Annotated_Tree::Mutations_Collection::remove_invalid() {
-    std::vector<Mutation_Annotated_Tree::Mutation> out;
+void MatOptimize::Mutation_Annotated_Tree::Mutations_Collection::remove_invalid() {
+    std::vector<MatOptimize::Mutation_Annotated_Tree::Mutation> out;
     out.reserve(mutations.size());
     for (const auto& mut : mutations) {
         if (mut.is_valid()) {
@@ -185,11 +185,11 @@ void Mutation_Annotated_Tree::Mutations_Collection::remove_invalid() {
     mutations.swap(out);
 }
 
-bool Mutation_Annotated_Tree::Mutations_Collection::no_valid_mutation()const {
+bool MatOptimize::Mutation_Annotated_Tree::Mutations_Collection::no_valid_mutation()const {
     for(auto& mut:mutations) {
         if (mut.is_valid()) {
             return false;
         }
     }
     return true;
-}
+}

src/matOptimize/Profitable_Moves_Enumerators/Profitable_Moves_Enumerators-debug.cpp

@@ -3,7 +3,7 @@
 #include <string>
 #ifndef NDEBUG
 #include "../mutation_annotated_tree.hpp"
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT = MatOptimize::Mutation_Annotated_Tree;
 #include "../Fitch_Sankoff.hpp"
 #include "../check_samples.hpp"
 #include <unordered_set>
@@ -173,4 +173,4 @@ int get_parsimmony_score_only(MAT::Node *src, MAT::Node *dst, MAT::Node *LCA,con
     return parsimony_score_change;
 }
 #endif
-#endif
+#endif

src/matOptimize/Profitable_Moves_Enumerators/Profitable_Moves_Enumerators.hpp

@@ -10,7 +10,7 @@
 #include "../stack_allocator.hpp"
 typedef std::vector<std::array<std::vector<unsigned int>, 4>> mutated_node_dfs_idx_t;
 extern mutated_node_dfs_idx_t mutated_node_dfs_idx;
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT = MatOptimize::Mutation_Annotated_Tree;
 //Class for recording change in major allele set
 class Mutation_Count_Change {
     int position;

src/matOptimize/Profitable_Moves_Enumerators/possible_change.cpp

@@ -20,7 +20,7 @@
 void make_range_tree(const std::vector<MAT::Node *> &dfs_ordered_nodes,
                      tbb::concurrent_vector<node_info> &in, range_tree &out,
                      size_t idx);
-namespace MAT = Mutation_Annotated_Tree;
+namespace MAT = MatOptimize::Mutation_Annotated_Tree;
 short default_decrement_effect[4];
 short default_increment_effect[4];
 struct initer {