--- a/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,146 +0,0 @@
-/*****************************************************************************
-  maskFastaFromBedMain.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 "maskFastaFromBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "maskFastaFromBed"
-
-
-// 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 fastaInFile;
-    string bedFile;
-
-    // output files
-    string fastaOutFile;
-
-    // defaults for parameters
-    bool haveFastaIn  = false;
-    bool haveBed      = false;
-    bool haveFastaOut = false;
-    bool softMask     = false;
-    char maskChar     = 'N';
-
-    // 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) {
-                haveFastaIn = true;
-                fastaInFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-fo", 3, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFastaOut = true;
-                fastaOutFile = 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("-soft", 5, parameterLength)) {
-            softMask = true;
-        }
-        else if(PARAMETER_CHECK("-mc", 3, parameterLength)) {
-            if ((i+1) < argc) {
-                string mask = argv[i + 1];
-                if (mask.size() > 1) {
-                    cerr << "*****ERROR: The mask character (-mc) should be a single character.*****" << endl << endl;
-                    showHelp = true;
-                }
-                else {
-                    maskChar = mask[0];
-                }
-                i++;
-            }
-        }
-        else {
-            cerr << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    if (!haveFastaIn || !haveFastaOut || !haveBed) {
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-
-        MaskFastaFromBed *maskFasta = new MaskFastaFromBed(fastaInFile, bedFile, fastaOutFile, softMask, maskChar);
-        delete maskFasta;
-        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: Mask a fasta file based on feature coordinates." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -fi <fasta> -out <fasta> -bed <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options:" << endl;
-    cerr << "\t-fi\tInput FASTA file" << endl;
-    cerr << "\t-bed\tBED/GFF/VCF file of ranges to mask in -fi" << endl;
-    cerr << "\t-fo\tOutput FASTA file" << endl;
-    cerr << "\t-soft\tEnforce \"soft\" masking.  That is, instead of masking with Ns," << endl;
-    cerr << "\t\tmask with lower-case bases." << endl;
-    cerr << "\t-mc\tReplace masking character.  That is, instead of masking with Ns, use another character." << endl;
-
-    // end the program here
-    exit(1);
-
-}