subtractMain.cpp

/*****************************************************************************
  subtractMain.cpp

  (c) 2009 - Aaron Quinlan
  Hall Laboratory
  Department of Biochemistry and Molecular Genetics
  University of Virginia
  aaronquinlan@gmail.com

  Licenced under the GNU General Public License 2.0+ license.
******************************************************************************/
#include "subtractBed.h"
#include "version.h"

using namespace std;

// define our program name
#define PROGRAM_NAME "subtractBed"


// define our parameter checking macro
#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)

// function declarations
void ShowHelp(void);

int main(int argc, char* argv[]) {

	// our configuration variables
	bool showHelp = false;

	// input files
	string bedAFile;
	string bedBFile;

	// input arguments
	float overlapFraction = 1E-9;

	bool haveBedA = false;
	bool haveBedB = false;
	bool haveFraction = false;
	bool forceStrand = false;

	// check to see if we should print out some help
	if(argc <= 1) showHelp = true;

	for(int i = 1; i < argc; i++) {
		int parameterLength = (int)strlen(argv[i]);

		if((PARAMETER_CHECK("-h", 2, parameterLength)) || 
		(PARAMETER_CHECK("--help", 5, parameterLength))) {
			showHelp = true;
		}
	}

	if(showHelp) ShowHelp();

	// do some parsing (all of these parameters require 2 strings)
	for(int i = 1; i < argc; i++) {

		int parameterLength = (int)strlen(argv[i]);

		if(PARAMETER_CHECK("-a", 2, parameterLength)) {
			if ((i+1) < argc) {
				haveBedA = true;
				bedAFile = argv[i + 1];
			}
			i++;
		}
		else if(PARAMETER_CHECK("-b", 2, parameterLength)) {