--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/pairToPair/pairToPairMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,188 @@
+/*****************************************************************************
+  pairToPairMain.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 "pairToPair.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "pairToPair"
+
+// 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;
+    int slop = 0;
+    string searchType = "both";
+
+    // flags to track parameters
+    bool haveBedA = false;
+    bool haveBedB = false;
+    bool haveSearchType = false;
+    bool haveFraction = false;
+    bool ignoreStrand = false;
+    bool requireDifferentNames = false;
+    bool haveSlop = false;
+    bool strandedSlop = 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("-type", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                haveSearchType = true;
+                searchType = 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("-slop", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                haveSlop = true;
+                slop = atoi(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-ss", 3, parameterLength)) {
+            strandedSlop = true;
+        }
+        else if(PARAMETER_CHECK("-rdn", 4, parameterLength)) {
+            requireDifferentNames = true;
+        }
+        else if(PARAMETER_CHECK("-is", 3, parameterLength)) {
+            ignoreStrand = 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 (haveSearchType && (searchType != "neither") && (searchType != "both") && (searchType != "either") && (searchType != "notboth")) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request \"both\",\"neither\",\"either\",or \"notboth\"" << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (strandedSlop == true && haveSlop == false) {
+        cerr << endl << "*****" << endl << "*****ERROR: Need a -slop value if requesting -ss." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (!showHelp) {
+
+        PairToPair *bi = new PairToPair(bedAFile, bedBFile, overlapFraction, searchType,
+                                        ignoreStrand, requireDifferentNames, slop, strandedSlop);
+        delete bi;
+        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: Report overlaps between two paired-end BED files (BEDPE)." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <BEDPE> -b <BEDPE>" << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-f\t"                    << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl;
+    cerr                                << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
+
+    cerr << "\t-type \t"                << "Approach to reporting overlaps between A and B." << endl << endl;
+    cerr                                << "\t\tneither\tReport overlaps if neither end of A overlaps B." << endl;
+    cerr                                << "\t\teither\tReport overlaps if either ends of A overlap B." << endl;
+    cerr                                << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl;
+    cerr                                << "\t\tnotboth\tReport overlaps if one or neither of ends of A overlap B." << endl;
+    
+    cerr                                << "\t\t- Default = both." << endl << endl;
+
+    cerr << "\t-slop \t"                << "The amount of slop (in b.p.). to be added to each footprint." << endl;
+    cerr                                << "\t\t*Note*: Slop is subtracted from start1 and start2 and added to end1 and end2." << endl << endl;
+
+    cerr << "\t-ss\t"                   << "Add slop based to each BEDPE footprint based on strand." << endl;
+    cerr                                << "\t\t- If strand is \"+\", slop is only added to the end coordinates." << endl;
+    cerr                                << "\t\t- If strand is \"-\", slop is only added to the start coordinates." << endl;
+    cerr                                << "\t\t- By default, slop is added in both directions." << endl << endl;
+
+    cerr << "\t-is\t"                   << "Ignore strands when searching for overlaps." << endl;
+    cerr                                << "\t\t- By default, strands are enforced." << endl << endl;
+
+    cerr << "\t-rdn\t"                  << "Require the hits to have different names (i.e. avoid self-hits)." << endl;
+    cerr                                << "\t\t- By default, same names are allowed." << endl << endl;
+
+
+    cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl;
+
+    // end the program here
+    exit(1);
+}