overload populate_from_file()

src/get_masked_amplicons.cpp

@@ -1,8 +1,7 @@
 #include "get_masked_amplicons.h"
 
 int get_primers_with_mismatches(std::string bed, std::string vpath, std::string out, std::string primer_pair_file){
-  int32_t primer_offset = 0;
-  std::vector<primer> primers = populate_from_file(bed, primer_offset);
+  std::vector<primer> primers = populate_from_file(bed);
   std::vector<primer> mismatches_primers;
   std::vector<primer> tmp;
   if(primers.size() == 0){

src/primer_bed.cpp

@@ -154,6 +154,75 @@ std::vector<primer> populate_from_file(std::string path, int32_t offset = 0){
   return primers;
 }
 
+std::vector<primer> populate_from_file(std::string path){
+  std::ifstream  data(path.c_str());
+  std::string line;
+  std::vector<primer> primers;
+  int16_t indice = 0;
+  while(std::getline(data,line)){ // Remove extra lineStream
+    std::stringstream lineStream(line);
+    std::string cell;
+    int ctr = 0;
+    primer p;
+    p.set_strand(0);		// Set strand to NULL
+    while(std::getline(lineStream,cell,'\t')){
+      switch(ctr){
+      case 0:
+	p.set_region(cell);
+	break;
+      case 1:
+	if(std::all_of(cell.begin(), cell.end(), ::isdigit)) {
+	  p.set_start(std::stoul(cell));
+	} else {
+	  print_bed_format();
+	  primers.clear();
+	  return primers;
+	}
+	break;
+      case 2:
+	if(std::all_of(cell.begin(), cell.end(), ::isdigit)) {
+	  p.set_end(std::stoul(cell) - 1); // Bed format - End is not 0 based
+	} else {
+	  print_bed_format();
+	  primers.clear();
+	  return primers;
+	}
+	break;
+      case 3:
+	p.set_name(cell);
+	break;
+      case 4:
+	if(std::all_of(cell.begin(), cell.end(), ::isdigit)) {
+	  p.set_score(stoi(cell));
+	} else {
+	  print_bed_format();  // score is missing, send warning but continue populating
+    std::cout << "\nWARNING: The BED file provided did not have the expected score column, but iVar will continue trimming\n" << std::endl;
+    p.set_score(-1);
+	}
+	break;
+      case 5:
+	if(cell[0] == '+' || cell[0] == '-')
+	  p.set_strand(cell[0]);
+	else {
+	  print_bed_format();
+	  primers.clear();
+	  return primers;
+	}
+      }
+      ctr++;
+    }
+    if(indice == 0 && ctr < 6)
+      std::cout << "Strand not found in primer BED file so strand will not be considered for trimming" << std::endl;
+    p.set_indice(indice);
+    p.set_pair_indice(-1);
+    p.set_read_count(0);
+    primers.push_back(p);
+    indice++;
+  }
+  std::cout << "Found " << primers.size() << " primers in BED file" << std::endl;
+  return primers;
+}
+
 std::vector<primer> get_primers(std::vector<primer> p, unsigned int pos){
   std::vector<primer> primers_with_mismatches;
   for(std::vector<primer>::iterator it = p.begin(); it != p.end(); ++it) {

src/primer_bed.h

@@ -47,6 +47,7 @@ class primer {
 };
 
 std::vector<primer> populate_from_file(std::string path, int32_t offset);
+std::vector<primer> populate_from_file(std::string path);
 std::vector<primer> get_primers(std::vector<primer> p, unsigned int pos);
 int get_primer_indice(std::vector<primer> p, std::string name);
 int populate_pair_indices(std::vector<primer> &primers, std::string path);

src/remove_reads_from_amplicon.cpp

@@ -1,8 +1,7 @@
 #include "remove_reads_from_amplicon.h"
 
 int rmv_reads_from_amplicon(std::string bam, std::string region_, std::string bam_out, std::vector<std::string> amp, std::string bed, std::string cmd){
-  int32_t primer_offset = 0;
-  std::vector<primer> primers = populate_from_file(bed, primer_offset);
+  std::vector<primer> primers = populate_from_file(bed);
   if(primers.size() == 0){
     return 0;
   }

tests/test_primer_bed.cpp

@@ -7,8 +7,7 @@ int main(){
   int num_tests = 2;
   int success = 0;
   std::vector<primer>::iterator it;
-  int32_t primer_offset = 0;
-  std::vector<primer> primers = populate_from_file("../data/test.bed", primer_offset);
+  std::vector<primer> primers = populate_from_file("../data/test.bed");
   std::string primer_names[] = {"WNV_400_1_LEFT", "WNV_400_1_LEFT_alt", "WNV_400_2_LEFT", "WNV_400_1_RIGHT", "WNV_400_2_RIGHT", "WNV_400_3_LEFT", "WNV_400_2_LEFT_alt", "WNV_400_2_RIGHT_alt"};
   int primer_indices[] = {0,1,2,3,4,5,6,7,8};
   unsigned int primer_start[] = {8,7, 230, 359,658,569,251,352};

tests/test_primer_trim.cpp

@@ -7,8 +7,7 @@
 int main(){
   int success = 0;
   std::string bam = "../data/test.unmapped.sorted.bam";
-  int32_t primer_offset = 0;
-  std::vector<primer> primers = populate_from_file("../data/test.bed", primer_offset);
+  std::vector<primer> primers = populate_from_file("../data/test.bed");
   int max_primer_len = 0;
   max_primer_len = get_bigger_primer(primers);
   std::string region_;

tests/test_unpaired_trim.cpp

@@ -7,8 +7,7 @@
 int main(){
   int success = 0;
   std::string bam = "../data/test.sim.merged.sorted.bam";
-  int32_t primer_offset = 0;
-  std::vector<primer> primers = populate_from_file("../data/test_merged.bed", primer_offset);
+  std::vector<primer> primers = populate_from_file("../data/test_merged.bed");
   int max_primer_len = 0;
   max_primer_len = get_bigger_primer(primers);
   std::string region_;