Adding full cs sequence capabilities

cpp/Vihgo.cpp

@@ -1740,44 +1740,20 @@ void Vihgo::writeFullConsensus() {
   cerr << "Writing full consensus sequence ... " << endl;
   ofstream csStream;
   csStream.open((this->getConsensusFile()).c_str(), ios::out);
+  csStream << ">" << "full_cs_sequence" << endl;
 
-  map<string, map<int, map<string, int>>>::iterator myIterA;
-  map<int, map<string, int>>::iterator myIterB;
-  map<string, int>::iterator myIterC;
-
-  map<string, map<int, string>>::iterator myIterE;
-  map<int, string>::iterator myIterF;
-
-  for (myIterE = this->protCodon.begin(); myIterE != this->protCodon.end();
-       myIterE++) {
-    string prot = myIterE->first;
-    string chrom = getChrFromProt(prot);
-
-    if (!(this->sampleData.count(chrom) > 0)) {
-      continue;
-    }
-    csStream << ">" << prot << endl;
-
-    for (myIterF = (myIterE->second).begin();
-         myIterF != (myIterE->second).end(); myIterF++) {
-      int aaPosition = myIterF->first;
-      int gPosition;
-      map<int, int> tmpMap = this->refProtCorresp[prot];
-      map<int, int>::iterator myIterG;
-      for (myIterG = tmpMap.begin(); myIterG != tmpMap.end(); myIterG++) {
-        if (myIterG->second == aaPosition) {
-          gPosition = myIterG->first;
-          break;
-        }
-      }
-
-      // cerr << "ppos : " << aaPosition << " ; genomic position is : " <<
-      // gPosition << endl;
+  map<string, map<int, string>>::iterator myIterA;
+  map<int, string>::iterator myIterB;
 
-      // determine most frequent codon
+  for (myIterA = this->referenceCodon.begin(); myIterA != this->referenceCodon.end();
+       myIterA++) {
+    string chrom = myIterA->first;
+    for (myIterB = (myIterA->second).begin();
+         myIterB != (myIterA->second).end(); myIterB++) {
+      int gPosition = myIterB->first;
+      // determine most frequent codon at this position
       string codon = "NNN";
       int count = 0;
-
       if (this->sampleData[chrom].count(gPosition) > 0) {
         map<string, int> tmpMapCodon;
         tmpMapCodon = this->sampleData[chrom][gPosition];
@@ -1790,6 +1766,7 @@ void Vihgo::writeFullConsensus() {
           }
         }
       }
+      // write codon : if found will be a true codon, other wise will be a NNN
       csStream << codon;
     }
     csStream << endl;