--- a/BEDTools-Version-2.14.3/src/complementBed/complementMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,116 +0,0 @@
-/*****************************************************************************
-  complementBedMain.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 "complementBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "complementBed"
-
-
-// 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";
-    string genomeFile;
-
-    bool haveBed = true;
-    bool haveGenome = 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("-g", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveGenome = true;
-                genomeFile = 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 || !haveGenome) {
-      cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file and -g Genome file. " << endl << "*****" << endl;
-      showHelp = true;
-    }
-    if (!showHelp) {
-        BedComplement *bc = new BedComplement(bedFile, genomeFile);
-        bc->ComplementBed();
-        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: Returns the base pair complement of a feature file." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
-
-    cerr << "Notes: " << endl;
-    cerr << "\t(1)  The genome file should tab delimited and structured as follows:" << endl;
-    cerr << "\t     <chromName><TAB><chromSize>" << endl << endl;
-    cerr << "\tFor example, Human (hg19):" << endl;
-    cerr << "\tchr1\t249250621" << endl;
-    cerr << "\tchr2\t243199373" << endl;
-    cerr << "\t..." << endl;
-    cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
-
-    cerr << "Tips: " << endl;
-    cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
-    cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
-    cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
-    cerr << "\t\"select chrom, size from hg19.chromInfo\"  > hg19.genome" << endl << endl;
-
-    exit(1);
-
-}