Refactored SNP calling/determination code for clarity.

src/snpCaller/call_vC.cpp

@@ -587,26 +587,31 @@ std::map<std::string, char> CodonMap(codons, codons + sizeof codons / sizeof cod
     std::string oldCodon = "";
     bool write = false;
     for (int i=0; i<snps.length(); ++i) {
-      //Skip same base
-      if (snps[i] == base) continue;
-      std::ostringstream internal;
-      char check[3];
-      sprintf(check,"%c%c",snps[i],toupper(snps[i]));
-      snpCount = getSum(map,check);
-      bool writeThis = false;
-      std::string* sToWrite = NULL;
-
-      if (snpCount >= 2*CALLING_THRESHOLD) {//Could be that this is a sample specific SNP.
-	if (isPersonalSNP(map,nrSamples,check)) {
-	  writeThis = true;
-	  sToWrite = &indiv;
-	}
-      }
-      if ((snpCount >= CALLING_THRESHOLD) && (snpCount >= cov*CALLING_MIN_FRACTION)) {
-	write = true;
-	writeThis = true;
-	sToWrite = &s;
-      }
+        
+        //Skip same base
+        if (snps[i] == base) continue;
+        std::ostringstream internal;
+        char check[3];
+        sprintf(check,"%c%c",snps[i],toupper(snps[i]));
+        snpCount = getSum(map,check);//How many times do we see this position as a variant in the entire population?
+        bool writeThis = false;
+        std::string* sToWrite = NULL;
+        
+        if ((snpCount >= CALLING_THRESHOLD) && (snpCount >= cov*CALLING_MIN_FRACTION)) { // This is a "common" variant
+            write = true;
+            writeThis = true;
+            sToWrite = &s;
+        } else { //May be a individual variant
+            for (int i=1; i<=nrSamples; ++i) {
+                int s = getSum(map,snp,i);
+                if (s >= CALLING_THRESHOLD) {//We observe the variant "CALLING_THRESHOLD" times in one sample.
+                    writeThis = true;
+    	            sToWrite = &indiv;
+    	            break;
+                }
+            }
+        }
+      
       if (writeThis) {
 	if ((hasGenes) && (isInGene)) {
 	  //TODO: consider multiple genes!