--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/subtractBed/subtractMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,145 @@
+/*****************************************************************************
+  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);
+}