--- a/BEDTools-Version-2.14.3/src/subtractBed/subtractMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-/*****************************************************************************
-  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 sameStrand = false;
-    bool diffStrand = 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)) {
-            if ((i+1) < argc) {
-                haveBedB = true;
-                bedBFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFraction = true;
-                overlapFraction = atof(argv[i + 1]);
-                i++;
-            }
-        }
-        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
-            sameStrand = true;
-        }
-        else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
-            diffStrand = true;
-        }
-        else {
-            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    // make sure we have both input files
-    if (!haveBedA || !haveBedB) {
-        cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-    
-    if (sameStrand && diffStrand) {
-        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-
-        BedSubtract *bs = new BedSubtract(bedAFile, bedBFile, overlapFraction, sameStrand, diffStrand);
-        delete bs;
-        return 0;
-    }
-    else {
-        ShowHelp();
-    }
-}
-
-void ShowHelp(void) {
-
-    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
-
-    cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
-
-    cerr << "Summary: Removes the portion(s) of an interval that is overlapped" << endl;
-    cerr << "\t by another feature(s)." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options: " << endl;
-    cerr << "\t-f\t"            << "Minimum overlap required as a fraction of A." << endl;
-    cerr                        << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
-    cerr                        << "\t\t- (FLOAT) (e.g. 0.50)" << endl << endl;
-
-    cerr << "\t-s\t"            << "Require same strandedness.  That is, only subtract hits in B that" << endl;
-    cerr                        << "\t\toverlap A on the _same_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are subtracted without respect to strand." << endl << endl;
-
-    cerr << "\t-S\t"            << "Force strandedness.  That is, only subtract hits in B that" << endl;
-    cerr                        << "\t\toverlap A on the _opposite_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are subtracted without respect to strand." << endl << endl;
-
-    // end the program here
-    exit(1);
-}