Merge branch 'master' into 'master'

Make thresholds command line options instead of hard coded

Also:
- Fix a crash when -i option is missing
- Add Makefile dependency

See merge request !4

src/snpCaller/Makefile

@@ -13,8 +13,8 @@ all: snpCall
 snpCall: snpCall.o
 	$(CC) snpCall.o -o snpCall
 
-snpCall.o:
-	$(CC) -I$(BOOST) -I$(INCLUDE) $(CFLAGS) call_vC.cpp -o snpCall.o
+snpCall.o: call_vC.cpp
+	$(CC) -I$(BOOST) -I$(INCLUDE) $(CFLAGS) $< -o $@
 
 clean:
 	rm -rf *o snpCall

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;
@@ -638,13 +656,28 @@ std::map<std::string, char> CodonMap(codons, codons + sizeof codons / sizeof cod
       s.erase(0,1);//There's an extra comma here
 
     //We now have information about all of the snp's. If multiple, sperate them by ,
-    fprintf(stdout,"%s\t%s\t%ld\t%c\t%s\t%s\n",name.c_str(),geneName.c_str(),lP+1,//again, this one gets converted to 1 based representation                                                  
-	    base,getCoverageString(map,nrSamples,"actgACTG,.").c_str(),s.c_str());
-    } 
+    fprintf(stdout,"%s\t%s\t%ld\t%c\t%s\t%s\n",
+                name.c_str(),
+                geneName.c_str(),
+                long(lP+1),//again, this one gets converted to 1 based representation
+	            base,
+                getCoverageString(map,nrSamples,"actgACTG,.").c_str(),
+                s.c_str());
+    }
     if (indiv.length() != 0) {
       indiv.erase(0,1);
-      fprintf(individualFile,"%s\t%s\t%ld\t%c\t%s\t%s\n",name.c_str(),geneName.c_str(),lP+1,//again, this one gets converted to 1 based representation
-	      base,getCoverageString(map,nrSamples,"actgACTG,.").c_str(),indiv.c_str());
+      if (individualFile == NULL) {
+          fprintf(stderr, "Individual SNPs detected, but no individual output file specified (-i option).\n");
+          individualFile = fopen("/dev/null", "w"); // This way, in the next iteration, warning above will not be printed
+      } else {
+          fprintf(individualFile,"%s\t%s\t%ld\t%c\t%s\t%s\n",
+            name.c_str(),
+            geneName.c_str(),
+            long(lP+1),//again, this one gets converted to 1 based representation
+	        base,
+            getCoverageString(map,nrSamples,"actgACTG,.").c_str(),
+            indiv.c_str());
+      }
     }
   }