--- a/BEDTools-Version-2.14.3/src/linksBed/linksMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-/*****************************************************************************
-  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);
-}