--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/nucBed/nucBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,147 @@
+/*****************************************************************************
+  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);
+
+}