--- a/BEDTools-Version-2.14.3/src/pairToPair/pairToPairMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,188 +0,0 @@
-/*****************************************************************************
-  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);
-}