ENH Make thresholds command line options

src/snpCaller/call_vC.cpp

@@ -20,9 +20,17 @@
 #include <boost/lexical_cast.hpp>
 using namespace boost::icl;
 
-#define MIN_COVERAGE_FOR_CALLING 4
-#define CALLING_THRESHOLD 4
-#define CALLING_MIN_FRACTION 0.01
+struct SNPCallOptions {
+    SNPCallOptions()
+        :min_coverage(4)
+        ,calling_threshold(4)
+        ,calling_min_fraction(0.01)
+    { }
+
+    int min_coverage;
+    int calling_threshold;
+    double calling_min_fraction;
+};
 
 #define READ_BUFFER_SIZE 10000000
 
@@ -342,8 +350,9 @@ int main(int argc, char** argv) {
 
   //Define the char map!
   std::map<char,long*> map;
+  SNPCallOptions options;
 
-  while ((c = getopt (argc, argv, "hdab:f:g:i:")) != -1)
+  while ((c = getopt (argc, argv, "hdab:f:g:i:c:p:t:")) != -1)
     switch (c)
       {
       case 'h':		// help message
@@ -380,7 +389,16 @@ int main(int argc, char** argv) {
           return -1;
 	}
 //        printf("Writing individual SNPs to %s \n", optarg);
-        break; 
+        break;
+      case 'c':
+        options.min_coverage = atol(optarg);
+        break;
+      case 'p':
+        options.calling_min_fraction = atof(optarg);
+        break;
+      case 't':
+        options.calling_threshold = atol(optarg);
+        break;
       case '?':
         if (( optopt == 'f') || ( optopt == 'g') || ( optopt == 'i') ){
 	  if ( optopt == 'f'){
@@ -540,10 +558,10 @@ std::map<std::string, char> CodonMap(codons, codons + sizeof codons / sizeof cod
 
     cov = getSum(map,"actgACTG,.");
 
-    if (cov < MIN_COVERAGE_FOR_CALLING) {//We don't have enough coverage
+    if (cov < options.min_coverage) {//We don't have enough coverage
       continue;
     }
-    if (getSum(map,"actgACTG") < CALLING_THRESHOLD) {//We don't have enough SNP calls
+    if (getSum(map,"actgACTG") < options.calling_threshold) {//We don't have enough SNP calls
       continue;
     }
 
@@ -581,14 +599,14 @@ std::map<std::string, char> CodonMap(codons, codons + sizeof codons / sizeof cod
         bool writeThis = false;
         std::string* sToWrite = NULL;
         
-        if ((snpCount >= CALLING_THRESHOLD) && (snpCount >= cov*CALLING_MIN_FRACTION)) { // This is a "common" variant
+        if ((snpCount >= options.calling_threshold) && (snpCount >= cov*options.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,check,i);
-                if (s >= CALLING_THRESHOLD) {//We observe the variant "CALLING_THRESHOLD" times in one sample.
+                if (s >= options.calling_threshold) {//We observe the variant "options.calling_threshold" times in one sample.
                     writeThis = true;
     	            sToWrite = &indiv;
     	            break;