--- a/BEDTools-Version-2.14.3/src/nucBed/nucBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,147 +0,0 @@
-/*****************************************************************************
-  nucBedMain.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 "nucBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "nucBed"
-
-
-// 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 fastaDbFile;
-    string bedFile;
-    string pattern;
-
-    // checks for existence of parameters
-    bool haveFastaDb = false;
-    bool haveBed     = false;
-    bool printSeq    = false;
-    bool hasPattern  = false;
-    bool forceStrand = 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("-fi", 3, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFastaDb = true;
-                fastaDbFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBed = true;
-                bedFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-seq", 4, parameterLength)) {
-            printSeq = true;
-        }
-        else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
-            forceStrand = true;
-        }
-        else if(PARAMETER_CHECK("-pattern", 8, parameterLength)) {
-            if ((i+1) < argc) {
-                hasPattern = true;
-                pattern = argv[i + 1];
-                i++;
-            }
-        }
-        else {
-            cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    if (!haveFastaDb || !haveBed) {
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-
-        NucBed *nuc = new NucBed(fastaDbFile, bedFile, printSeq, hasPattern, pattern, forceStrand);
-        delete nuc;
-
-        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: Profiles the nucleotide content of intervals in a fasta file." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -bed <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options: " << endl;
-    cerr << "\t-fi\tInput FASTA file" << endl << endl;
-    cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl << endl;
-    cerr << "\t-s\tProfile the sequence according to strand." << endl << endl;
-    cerr << "\t-seq\tPrint the extracted sequence" << endl << endl;
-    cerr << "\t-pattern\tReport the number of times a user-defined sequence is observed (case-insensitive)." << endl << endl;
-    
-    
-    cerr << "Output format: " << endl;
-    cerr << "\tThe following information will be reported after each original BED entry:" << endl;
-    cerr << "\t    1) %AT content" << endl;
-    cerr << "\t    2) %GC content" << endl;
-    cerr << "\t    3) Number of As observed" << endl;
-    cerr << "\t    4) Number of Cs observed" << endl;
-    cerr << "\t    5) Number of Gs observed" << endl;
-    cerr << "\t    6) Number of Ts observed" << endl;
-    cerr << "\t    7) Number of Ns observed" << endl;
-    cerr << "\t    8) Number of other bases observed" << endl;
-    cerr << "\t    9) The length of the explored sequence/interval." << endl;
-    cerr << "\t    10) The sequence extracted from the FASTA file. (optional, if -seq is used)" << endl;
-    cerr << "\t    11) The number of times a user defined pattern was observed. (optional, if -pattern is used.)" << endl;
-
-    // end the program here
-    exit(1);
-
-}