### add -m option to merge intervals

parent 3594e98a
 ... @@ -34,7 +34,7 @@ void fisher_help(void) { ... @@ -34,7 +34,7 @@ void fisher_help(void) { cerr << "Summary: Calculate Fisher statistic b/w two feature files." cerr << "Summary: Calculate Fisher statistic b/w two feature files." << endl << endl; << endl << endl; cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a -b -c " << endl << endl; cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a -b -g " << endl << endl; cerr << "Options: " << endl; cerr << "Options: " << endl; ... @@ -43,6 +43,9 @@ void fisher_help(void) { ... @@ -43,6 +43,9 @@ void fisher_help(void) { cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; cerr << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl; cerr << "\t\t- FLOAT (e.g. 0.50)" << endl << 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-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- 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; cerr << "\t\t that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl; ... ...
 ... @@ -43,6 +43,10 @@ bool ContextFisher::parseCmdArgs(int argc, char **argv, int skipFirstArgs) ... @@ -43,6 +43,10 @@ bool ContextFisher::parseCmdArgs(int argc, char **argv, int skipFirstArgs) if (strcmp(_argv[_i], "-g") == 0) { if (strcmp(_argv[_i], "-g") == 0) { if (!handle_g()) return false; if (!handle_g()) return false; } } if(strcmp(_argv[_i], "-m") == 0) { markUsed(_i - _skipFirstArgs); setUseMergedIntervals(true); } } } return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs); return ContextIntersect::parseCmdArgs(argc, argv, _skipFirstArgs); } } ... ...
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