--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/maskFastaFromBed/maskFastaFromBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,146 @@
+/*****************************************************************************
+  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);
+
+}