add -m option to merge intervals

src/fisher/fisherMain.cpp

@@ -34,7 +34,7 @@ void fisher_help(void) {
     cerr << "Summary: Calculate Fisher statistic b/w two feature files."
          << endl << endl;
 
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf> -c <possible counts>" << endl << endl;
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf> -g <genome file>" << endl << endl;
 
     cerr << "Options: " << endl;
 
@@ -43,6 +43,9 @@ void fisher_help(void) {
     cerr                        << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
     cerr                        << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
 
+    cerr << "\t-m\t"            << "Merge overlapping intervals before" << endl;
+    cerr                        << "\t\t- looking at overlap." << endl << endl;
+
     cerr << "\t-r\t"            << "Require that the fraction overlap be reciprocal for A and B." << endl;
     cerr                        << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
     cerr                        << "\t\t  that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;

src/utils/Contexts/ContextFisher.cpp

@@ -43,6 +43,10 @@ bool ContextFisher::parseCmdArgs(int argc, char **argv, int skipFirstArgs)
         if (strcmp(_argv[_i], "-g") == 0) {
               if (!handle_g()) return false;
         }
+        if(strcmp(_argv[_i], "-m") == 0) {
+            markUsed(_i - _skipFirstArgs);
+	        setUseMergedIntervals(true);
+        }
 	}
 	return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs);
 }