restylized.

src/matOptimize/main.cpp

@@ -313,8 +313,8 @@ int main(int argc, char **argv) {
             }
             if (allow_drift) {
                 nodes_to_search=bfs_ordered_nodes;
-            }else {
-                find_nodes_to_move(bfs_ordered_nodes, nodes_to_search,isfirst,radius,t);                
+            } else {
+                find_nodes_to_move(bfs_ordered_nodes, nodes_to_search,isfirst,radius,t);
             }
             if (search_proportion<1) {
                 std::vector<MAT::Node *> nodes_to_search_temp;

src/matOptimize/optimize_tree.cpp

@@ -267,9 +267,9 @@ void optimize_tree_main_thread(std::vector<size_t> &nodes_to_search,
     tbb::flow::graph g;
     std::vector<std::string> defered_node_identifier;
     resolver_node_t resover_node(g, 1,
-                                          Conflict_Resolver(potential_crosses,
-                                                  deferred_moves,
-                                                  &defered_node_identifier));
+                                 Conflict_Resolver(potential_crosses,
+                                         deferred_moves,
+                                         &defered_node_identifier));
     std::thread move_reciever(MPI_recieve_move,std::ref(dfs_ordered_nodes),std::ref(resover_node));
     //progress bar
     searcher_node_t searcher(g,num_threads+1,move_searcher{dfs_ordered_nodes,radius,allow_drift});

src/matUtils/annotate.cpp

@@ -205,8 +205,7 @@ void assignLineages (MAT::Tree& T, const std::string& clade_to_nid_filename, boo
     fprintf(stderr, "Completed in %ld msec \n\n", timer.Stop());
 }
 
-MAT::Mutation* mutation_from_string(const std::string& mut_string)
-{
+MAT::Mutation* mutation_from_string(const std::string& mut_string) {
     // Parse string like /[A-Z][0-9]+[A-Z]/ e.g. A23403G; create & return (pointer to) MAT::Mutation
     // with par_nuc set to ref_nuc (same as VCF parsing code in usher.cpp).
     // If mut_string is not in expected format, print error message and return NULL.
@@ -231,8 +230,7 @@ MAT::Mutation* mutation_from_string(const std::string& mut_string)
 }
 
 void parse_clade_mutations(const std::string& clade_mutations_filename,
-                           std::map<std::string, std::vector<MAT::Mutation>>& clade_mutations)
-{
+                           std::map<std::string, std::vector<MAT::Mutation>>& clade_mutations) {
     std::ifstream infile(clade_mutations_filename);
     if (!infile) {
         fprintf(stderr, "ERROR: Could not open the clade mutations file: %s!\n", clade_mutations_filename.c_str());
@@ -296,16 +294,15 @@ void parse_clade_mutations(const std::string& clade_mutations_filename,
 void parse_clade_names(const std::string& clade_filename,
                        std::map<std::string, std::vector<MAT::Mutation>>& clade_mutations,
                        std::map<std::string, std::vector<MAT::Node*>>& clade_map,
-                       MAT::Tree& uncondensed_T, float min_freq, float mask_freq)
-{
+                       MAT::Tree& uncondensed_T, float min_freq, float mask_freq) {
     std::ifstream infile(clade_filename);
     if (!infile) {
         fprintf(stderr, "ERROR: Could not open the clade assignment file: %s!\n", clade_filename.c_str());
         exit(1);
     }
     std::string line;
 
-     //Read the clade assignment file line by line and fill up map values
+    //Read the clade assignment file line by line and fill up map values
     fprintf(stderr, "Reading clade assignment file %s.\n", clade_filename.c_str());
     timer.Start();
     while (std::getline(infile, line)) {
@@ -514,7 +511,7 @@ void assignLineages (MAT::Tree& T, const std::string& clade_filename,
     if (clade_filename != "") {
         parse_clade_names(clade_filename, clade_mutations_map, clade_map, uncondensed_T,
                           min_freq, mask_freq);
-                        
+
     }
 
     struct Node_freq {
@@ -552,8 +549,7 @@ void assignLineages (MAT::Tree& T, const std::string& clade_filename,
                 return true;
             } else if (this->clade_size > 0 && c.clade_size == 0) {
                 return false;
-            }
-            else {
+            } else {
                 return ((this->best_node_frequencies.size() < c.best_node_frequencies.size()) ||
                         ((this->best_node_frequencies.size() == c.best_node_frequencies.size()) && (this->clade_size > c.clade_size)));
             }

src/matUtils/convert.cpp

@@ -769,7 +769,7 @@ std::unordered_map<std::string, std::vector<std::string>> read_metafiles_tax(std
                     exit(1);
                 }
                 continue;
-            }            
+            }
             std::string key = words[strain_column];
             if ( seen_in_this_file.find(key) != seen_in_this_file.end() ) {
                 continue; // ignore duplicates in each metadata file
@@ -779,13 +779,13 @@ std::unordered_map<std::string, std::vector<std::string>> read_metafiles_tax(std
                 // if we haven't seen this sample yet
                 metadata[key] = std::vector<std::string>();
             }
-            for (auto word : words){
+            for (auto word : words) {
                 metadata[key].push_back(word);
             }
             if (metadata[key].size() == header.size() - 1) {
                 metadata[key].push_back(""); // the case where the last column is empty
             }
-        }   
+        }
         infile.close();
     }
     // Then use map to make taxodium encodings and check for defined/generic fields
@@ -849,7 +849,7 @@ std::unordered_map<std::string, std::vector<std::string>> read_metafiles_tax(std
             fprintf(stderr, "-- %s\n", name.c_str());
         }
     }
-    
+
 
     for (auto &v : metadata) { // for each metadata value
         // Build mappings for generic metadata types
@@ -864,7 +864,7 @@ std::unordered_map<std::string, std::vector<std::string>> read_metafiles_tax(std
 
     }
 
-    
+
 
     fprintf(stderr, "\nPerforming conversion.\n");
 

src/matUtils/extract.cpp

@@ -393,7 +393,7 @@ usher_single_subtree_size == 0 && usher_minimum_subtrees_size == 0) {
             tv = add_random + samples.size();
         }
         samples = fill_random_samples(&T, samples, tv, limit_lca);
-    } 
+    }
     //the final step of selection is to invert the set if prune is set
     //this is done by getting all sample names which are not in the samples vector.
     if (prune_samples) {