--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/mergeBed/mergeMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,163 @@
+/*****************************************************************************
+  mergeMain.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 "mergeBed.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "mergeBed"
+
+
+// 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 bedFile  = "stdin";
+    int maxDistance = 0;
+    string scoreOp  = "";
+
+    // input arguments
+    bool haveBed         = true;
+    bool numEntries      = false;
+    bool haveMaxDistance = false;
+    bool forceStrand     = false;
+    bool reportNames     = false;
+    bool reportScores    = false;
+
+    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("-i", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                bedFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-n", 2, parameterLength)) {
+            numEntries = true;
+        }
+        else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveMaxDistance = true;
+                maxDistance = atoi(argv[i + 1]);
+                i++;
+            }
+        }
+        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
+            forceStrand = true;
+        }
+        else if (PARAMETER_CHECK("-nms", 4, parameterLength)) {
+            reportNames = true;
+        }
+        else if (PARAMETER_CHECK("-scores", 7, parameterLength)) {
+            reportScores = true;
+            if ((i+1) < argc) {
+                scoreOp      = argv[i + 1];
+                i++;
+            }
+        }
+        else {
+            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    // make sure we have both input files
+    if (!haveBed) {
+        cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
+        showHelp = true;
+    }
+    if (reportNames && numEntries) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -n OR -nms, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+    if ((reportScores == true) && (scoreOp != "sum")  && (scoreOp != "max")    && (scoreOp != "min") && (scoreOp != "mean") &&
+        (scoreOp != "mode") && (scoreOp != "median") && (scoreOp != "antimode") && (scoreOp != "collapse")) 
+    {
+        cerr << endl << "*****" << endl << "*****ERROR: Invalid scoreOp selection \"" << scoreOp << endl << "\"  *****" << endl;
+        showHelp = true;
+    }
+
+    if (!showHelp) {
+        BedMerge *bm = new BedMerge(bedFile, numEntries, maxDistance, forceStrand, reportNames, reportScores, scoreOp);
+        delete bm;
+        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: Merges overlapping BED/GFF/VCF entries into a single interval." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-s\t"                     << "Force strandedness.  That is, only merge features" << endl;
+    cerr                                 << "\t\tthat are the same strand." << endl;
+    cerr                                 << "\t\t- By default, merging is done without respect to strand." << endl << endl;
+
+    cerr << "\t-n\t"                     << "Report the number of BED entries that were merged." << endl;
+    cerr                                 << "\t\t- Note: \"1\" is reported if no merging occurred." << endl << endl;
+
+
+    cerr << "\t-d\t"                     << "Maximum distance between features allowed for features" << endl;
+    cerr                                 << "\t\tto be merged." << endl;
+    cerr                                 << "\t\t- Def. 0. That is, overlapping & book-ended features are merged." << endl;
+    cerr                                 << "\t\t- (INTEGER)" << endl << endl;
+
+    cerr << "\t-nms\t"                   << "Report the names of the merged features separated by semicolons." << endl << endl;
+    
+    cerr << "\t-scores\t"                << "Report the scores of the merged features. Specify one of " << endl;
+    cerr                                 << "\t\tthe following options for reporting scores:" << endl;
+    cerr                                 << "\t\t  sum, min, max," << endl;
+    cerr                                 << "\t\t  mean, median, mode, antimode," << endl;
+    cerr                                 << "\t\t  collapse (i.e., print a semicolon-separated list)," << endl;
+    cerr                                 << "\t\t- (INTEGER)" << endl << endl;
+    
+    cerr << "Notes: " << endl;
+    cerr << "\t(1) All output, regardless of input type (e.g., GFF or VCF)" << endl;
+    cerr << "\t    will in BED format with zero-based starts" << endl << endl;
+
+
+    // end the program here
+    exit(1);
+
+}