no major update, troubleshooting variants errors

andersen-lab · Dec 7, 2023 · 839b0dd · 839b0dd
1 parent 184627e
commit 839b0dd
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Showing 3 changed files with 26 additions and 10 deletions.
diff --git a/src/allele_functions.h b/src/allele_functions.h
@@ -26,7 +26,7 @@ struct allele {
 class position {
   public:
     uint32_t pos;
-    uint32_t depth;
+    uint32_t depth=0;
     std::vector<allele> alleles;
     void update_alleles(std::string nt, uint32_t count);
     bool flux;

diff --git a/src/interval_tree.cpp b/src/interval_tree.cpp
@@ -13,7 +13,8 @@ void add_allele_vectors(std::vector<allele> new_alleles, std::vector<allele> ret
     for(uint32_t j=0; j < return_alleles.size(); j++){
       if (return_alleles[j].nuc == new_alleles[i].nuc){
         if(use){
-          std::cerr << return_alleles[j].depth << " " << return_alleles[j].nuc << std::endl;
+          std::cerr<<"";
+        //  std::cerr << "\nin found " << return_alleles[j].depth << " " << return_alleles[j].nuc << std::endl;
         }
         return_alleles[j].depth += new_alleles[i].depth;
         found = true;
@@ -55,27 +56,34 @@ void IntervalTree::set_haplotypes(ITNode *root, primer prim){
     // we found the matching amplion, now we add this cigarotype to the amplicon     
     std::vector<position> tmp_pos = prim.get_positions();
     for (uint32_t i=0; i < tmp_pos.size(); i++){
+      if(tmp_pos[i].pos == 350){
+        std::cerr << "posssssss" << std::endl;
+      }
       position add_pos = tmp_pos[i];
       bool found = false;
       // check if we already have a pos for this pos
       for(uint32_t j=0; j < root->amp_positions.size(); j++){
         position here_pos = root->amp_positions[j];
         bool use = false;
         if(add_pos.pos == 350 && here_pos.pos == add_pos.pos){
-          std::cerr << " " << std::endl;
+          /*
+          std::cerr << "\nthe original thing" << std::endl;
           print_allele_depths(root->amp_positions[j].alleles);
           std::cerr << root->data->low << " " << root->data->high << std::endl;
-          std::cerr << "amp " << here_pos.depth << " prim "<< add_pos.depth << std::endl;
+          std::cerr << "position depth " << root->amp_positions[j].depth << " prim depth "<< tmp_pos[i].depth << std::endl;
+          std::cerr << "thing being added" << std::endl;
           print_allele_depths(add_pos.alleles);
+          */
           use = true;
         }
         if(here_pos.pos == add_pos.pos){
           found = true;
           root->amp_positions[j].depth += add_pos.depth;
           add_allele_vectors(add_pos.alleles, root->amp_positions[j].alleles, use);
-          if(add_pos.pos == 350){
-            print_allele_depths(root->amp_positions[j].alleles);
-          }
+          //if(add_pos.pos == 350){
+          //  std::cerr << "after being added " << std::endl;
+          //  print_allele_depths(root->amp_positions[j].alleles);
+          //}
           break;
         }
       }
@@ -85,6 +93,11 @@ void IntervalTree::set_haplotypes(ITNode *root, primer prim){
         tmp.depth = add_pos.depth;
         tmp.alleles = add_pos.alleles;
         tmp.pos = add_pos.pos;
+        if(add_pos.pos == 350){
+          std::cerr << "initiate " << tmp.depth << " " << add_pos.depth << std::endl;
+          std::cerr << root->data->low << " " << root->data->high << std::endl;
+          print_allele_depths(tmp.alleles);
+        }
         root->amp_positions.push_back(tmp);
       }
     }

diff --git a/src/primer_bed.cpp b/src/primer_bed.cpp
@@ -460,14 +460,14 @@ void primer::transform_mutations() {
       std::ostringstream convert;
       convert << sequence[j];
       std::string nuc = convert.str(); 
-      if (current_pos == 350 && nuc != "C"){
-        std::cerr << current_pos << " " << nuc << "  " << ccount << std::endl;
-      }
       if (exists) {
         if (qname == test){
           //std::cerr << qname << " " << nuc << std::endl;
           std::cerr << current_pos  << " j " << j << " nuc " << nuc << " del pos " << deletion_positions.size() << " insert pos " << ignore_sequence.size() << std::endl;
         }
+        if(current_pos ==350){
+          std::cerr << "primer " << ccount << " " << nuc << std::endl;
+        }
         positions[exists].update_alleles(nuc, ccount);  
       } else {
         //add position to vector
@@ -476,6 +476,9 @@ void primer::transform_mutations() {
         add_pos.pos = current_pos; //don't add a position
         add_pos.update_alleles(nuc, ccount);            
         positions.push_back(add_pos);
+        if(current_pos ==350){
+          std::cerr << "primer " << ccount << " " << nuc << std::endl;
+        }
       }         
     }
   }