--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/linksBed/linksMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,129 @@
+/*****************************************************************************
+  linksBedMain.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 "linksBed.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "linksBed"
+
+
+// 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";
+    bool haveBed   = true;
+
+    /* Defaults for everyone else */
+    string org = "human";
+    string db = "hg18";
+    string base = "http://genome.ucsc.edu";
+
+    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("-base", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                base = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-org", 4, parameterLength)) {
+            if ((i+1) < argc) {
+                org = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-db", 3, parameterLength)) {
+            if ((i+1) < argc) {
+                db = 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 (!showHelp) {
+        BedLinks *bl = new BedLinks(bedFile, base, org, db);
+        delete bl;
+        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: Creates HTML links to an UCSC Genome Browser from a feature file." << endl << endl;
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> > out.html" << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-base\t" << "The browser basename.  Default: http://genome.ucsc.edu " << endl;
+    cerr << "\t-org\t"  << "The organism. Default: human" << endl;
+    cerr << "\t-db\t"   << "The build.  Default: hg18" << endl << endl;
+
+    cerr << "Example: " << endl;
+    cerr << "\t" << "By default, the links created will point to human (hg18) UCSC browser." << endl;
+    cerr <<         "\tIf you have a local mirror, you can override this behavior by supplying" << endl;
+    cerr <<         "\tthe -base, -org, and -db options."  << endl << endl;
+    cerr << "\t" << "For example, if the URL of your local mirror for mouse MM9 is called: " << endl;
+    cerr <<         "\thttp://mymirror.myuniversity.edu, then you would use the following:" << endl;
+    cerr <<         "\t" << "-base http://mymirror.myuniversity.edu" << endl;
+    cerr <<         "\t" << "-org mouse" << endl;
+    cerr <<         "\t" << "-db mm9" << endl;
+
+
+    exit(1);
+}