removing more floats and excess code

Author: cmaceves

src/gmm.cpp

@@ -813,7 +813,7 @@ std::vector<uint32_t> find_deletion_positions(std::string filename, uint32_t dep
   return(deletion_positions);
 }
 
-void parse_internal_variants(std::string filename, std::vector<variant> &variants, uint32_t depth_cutoff, float lower_bound, float upper_bound, std::vector<uint32_t> deletion_positions, uint32_t round_val, double quality_threshold){
+void parse_internal_variants(std::string filename, std::vector<variant> &variants, uint32_t depth_cutoff, double lower_bound, double upper_bound, std::vector<uint32_t> deletion_positions, uint32_t round_val, double quality_threshold){
   /*
    * Parses the variants file produced internally by reading bam file line-by-line.
    */
@@ -829,7 +829,7 @@ void parse_internal_variants(std::string filename, std::vector<variant> &variant
      std::vector<std::string> row_values;
     //split the line by delimiter
     uint32_t pos = 0, depth = 0;
-    float freq = 0, gapped_freq=0, qual=0, std_dev=0;
+    double freq = 0, gapped_freq=0, qual=0, std_dev=0;
     bool version_1_var = false;
     std::string flag = "";
     std::string amp_flag = "";
@@ -840,7 +840,7 @@ void parse_internal_variants(std::string filename, std::vector<variant> &variant
     depth = std::stoi(row_values[7]);
     freq = std::stof(row_values[10]);
 
-    float multiplier = pow(10, round_val);
+    double multiplier = pow(10, round_val);
     freq = round(freq * multiplier) / multiplier;
     qual = std::stof(row_values[9]);
 
@@ -898,7 +898,7 @@ void parse_internal_variants(std::string filename, std::vector<variant> &variant
     } else {
       tmp.outside_freq_range = false;
     }
-    if((double)qual < quality_threshold){
+    if(qual < quality_threshold){
       tmp.qual_flag = true;
     } else {
       tmp.qual_flag = false;

src/gmm.h

@@ -26,12 +26,12 @@ struct variant {
   uint32_t position;
   std::string nuc;
   uint32_t depth;
-  float qual;
-  float freq;
-  float gapped_freq = 0;
+  double qual;
+  double freq;
+  double gapped_freq = 0;
   int cluster_assigned = -1;
   bool version_1_var=false;  
-  float std_dev;
+  double std_dev;
 
   //for these true means flagged as problematic
   bool vague_assignment=false; //cannot be distinguished between two groups
@@ -51,16 +51,16 @@ struct variant {
 };
 void split(const std::string &s, char delim, std::vector<std::string> &elems);
 std::vector<variant> gmm_model(std::string prefix, std::string output_prefix);
-void parse_internal_variants(std::string filename, std::vector<variant> &base_variants, uint32_t depth_cutoff, float lower_bound, float upper_bound, std::vector<uint32_t> deletion_positions, uint32_t round_val, double quality_threshold);
-std::vector<uint32_t> find_deletion_positions(std::string filename, uint32_t depth_cutoff, float lower_bound, float upper_bound, uint32_t round_val);
-std::vector<uint32_t> find_low_quality_positions(std::string filename, uint32_t depth_cutoff, float lower_bound, float upper_bound, float quality_threshold, uint32_t round_val);
+void parse_internal_variants(std::string filename, std::vector<variant> &base_variants, uint32_t depth_cutoff, double lower_bound, double upper_bound, std::vector<uint32_t> deletion_positions, uint32_t round_val, double quality_threshold);
+std::vector<uint32_t> find_deletion_positions(std::string filename, uint32_t depth_cutoff, double lower_bound, double upper_bound, uint32_t round_val);
+std::vector<uint32_t> find_low_quality_positions(std::string filename, uint32_t depth_cutoff, double lower_bound, double upper_bound, double quality_threshold, uint32_t round_val);
 std::vector<std::vector<double>> solve_possible_solutions(std::vector<float> tmp_means, double error);
 uint32_t smallest_value_index(std::vector<double> values);
 std::vector<std::vector<double>> transpose_vector(const std::vector<std::vector<double>>& input_vector);
 void assign_variants_simple(std::vector<variant> &variants, std::vector<std::vector<double>> prob_matrix, uint32_t index, std::vector<double> means, uint32_t lower_n);
 gaussian_mixture_model retrain_model(uint32_t n, arma::mat data, std::vector<variant> variants, uint32_t lower_n, double var_floor);
 void assign_clusters(std::vector<variant> &variants, gaussian_mixture_model gmodel, uint32_t lower_n);
 double calculate_mean(const std::vector<double>& data);
-void calculate_reference_frequency(std::vector<variant> &variants, std::string filename, uint32_t depth_cutoff, float lower_bound, float upper_bound, std::vector<uint32_t> deletion_positions);
+void calculate_reference_frequency(std::vector<variant> &variants, std::string filename, uint32_t depth_cutoff, double lower_bound, double upper_bound, std::vector<uint32_t> deletion_positions);
 kmeans_model train_model(uint32_t n, arma::mat data);
 #endif

src/interval_tree.h

@@ -1,5 +1,4 @@
 #include <iostream>
-
 #include "primer_bed.h"
 using namespace std;
 

src/primer_bed.h

@@ -23,7 +23,6 @@ class primer {
   std::vector<position> positions; //allele counts for this primer
 
  public:
-  uint32_t hardcoded_length=300; //CHANGE
   std::string get_name();
   std::string get_region();
   std::vector<position> get_positions();
@@ -64,7 +63,6 @@ primer get_max_end(std::vector<primer> primers);
 std::vector<uint32_t> get_nlengths();
 std::vector<uint32_t> get_start_positions();
 std::vector<bool> get_direction();
-std::vector<std::vector<std::string>> get_qnames();
 void set_positions(position pos);
 std::vector<position> get_positions();
 void populate_positions();

src/saga.cpp

@@ -631,9 +631,9 @@ int preprocess_reads(std::string bam, std::string bed, std::string bam_out, std:
       }
     }
     for(uint32_t j=0; j < variants[i].alleles.size(); j++){
-      float freq = (float)variants[i].alleles[j].depth / ((float)variants[i].depth-del_depth);
-      float gapped_freq = (float)variants[i].alleles[j].depth / (float)variants[i].depth;
-      if((float)variants[i].alleles[j].depth == 0){
+      double freq = (double)variants[i].alleles[j].depth / ((double)variants[i].depth-del_depth);
+      double gapped_freq = (double)variants[i].alleles[j].depth / (double)variants[i].depth;
+      if((double)variants[i].alleles[j].depth == 0){
         continue;
       }
       file << "NA\t"; //region