added option to display time for each step

amkram · Dec 17, 2024 · 05daa8b · 05daa8b
1 parent b53876a
commit 05daa8b
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Showing 4 changed files with 24 additions and 5 deletions.
diff --git a/src/main.cpp b/src/main.cpp
@@ -96,6 +96,7 @@ Other options:
                                  [default: ]
   -Q <seed>                 Integer seed for random number generation. [default: 42]
   -V --version              Show version.
+  --time                    Show time taken at each step
   -h --help                 Show this screen.
   -D --dump                 Dump all seeds to file.
   -X --dump-real            Dump true seeds to file.
@@ -293,6 +294,8 @@ int main(int argc, const char** argv) {
     bool placement_per_read = args["--place-per-read"] && args["--place-per-read"].isBool() ? args["--place-per-read"].asBool() : false;
     bool genotype_from_sam = args["--genotype-from-sam"] && args["--genotype-from-sam"].isBool() ? args["--genotype-from-sam"].asBool() : false;
     bool save_jaccard = args["--save-jaccard"] && args["--save-jaccard"].isBool() ? args["--save-jaccard"].asBool() : false;
+    bool show_time = args["--time"] && args["--time"].isBool() ? args["--time"].asBool() : false;
+
 
     int k = std::stoi(args["-k"].asString());
     int s = std::stoi(args["-s"].asString());
@@ -454,7 +457,7 @@ int main(int argc, const char** argv) {
         std::cerr << "Reference node (" << refNode << ") specified but not found in the pangenome." << std::endl;
         return 1;
       }
-      pmi::place(T, index_input, reads1, reads2, mutMat, prefix, refFileName, samFileName, bamFileName, mpileupFileName, vcfFileName, aligner, refNode, save_jaccard);
+      pmi::place(T, index_input, reads1, reads2, mutMat, prefix, refFileName, samFileName, bamFileName, mpileupFileName, vcfFileName, aligner, refNode, save_jaccard, show_time);
     }
 
     auto end = std::chrono::high_resolution_clock::now();

diff --git a/src/pmi.cpp b/src/pmi.cpp
@@ -2363,8 +2363,9 @@ void pmi::place(
   Tree *T, Index::Reader &index, const std::string &reads1Path, const std::string &reads2Path,
   seed_annotated_tree::mutationMatrices &mutMat, std::string prefix,std::string refFileName,
   std::string samFileName, std::string bamFileName, std::string mpileupFileName, std::string vcfFileName,
-  std::string aligner, const std::string& refNode, const bool& save_jaccard)
+  std::string aligner, const std::string& refNode, const bool& save_jaccard, bool show_time)
 {
+    time_stamp();
     // Setup for seed indexing
     seed_annotated_tree::mutableTreeData data;
 
@@ -2564,6 +2565,10 @@ void pmi::place(
     }
 
     if (aligner == "minimap2") {
+      double time = time_stamp();
+      if(show_time){
+        std::cerr << "Placement time: " << time << "\n";
+      }
       //Create SAM
       std::vector<char *> samAlignments;
       std::string samHeader;
@@ -2582,6 +2587,12 @@ void pmi::place(
           samAlignments,             
           samHeader                  
       );
+
+      time = time_stamp();
+      if(show_time){
+        std::cerr << "Alignment time: " << time << "\n";
+      }
+
       //Convert to BAM
       sam_hdr_t *header;
       bam1_t **bamRecords;
@@ -2611,6 +2622,11 @@ void pmi::place(
         0.0011
       );
 
+      time = time_stamp();
+      if(show_time){
+        std::cerr << "Genotyping time: " << time << "\n";
+      }
+
       // //std::string mpileupFileName = "MPILEUP";
       // //Convert to Mplp
       // char *mplpString;

diff --git a/src/seed_annotated_tree.cpp b/src/seed_annotated_tree.cpp
@@ -15,12 +15,12 @@ std::chrono::time_point<std::chrono::high_resolution_clock> global_timer =
     std::chrono::high_resolution_clock::now();
 
 
-void time_stamp() {
+double time_stamp() {
   std::chrono::time_point<std::chrono::high_resolution_clock> newtime =
       std::chrono::high_resolution_clock::now();
   std::chrono::duration<float> duration = newtime - global_timer;
-  std::cerr << "timing " << duration.count() << "\n\n";
   global_timer = newtime;
+  return duration.count();
 }
 
 

diff --git a/src/seed_annotated_tree.hpp b/src/seed_annotated_tree.hpp
@@ -8,7 +8,7 @@
 #include <unordered_map>
 #include <vector>
 
-void time_stamp();
+double time_stamp();
 
 using namespace seeding;