--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/bed12ToBed6/bed12ToBed6.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,168 @@
+/*****************************************************************************
+  bed12ToBed6.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 "lineFileUtilities.h"
+#include "bedFile.h"
+#include "version.h"
+
+#include <vector>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+
+// define our program name
+#define PROGRAM_NAME "bed12ToBed6"
+
+// 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);
+void DetermineBedInput(BedFile *bed);
+void ProcessBed(istream &bedInput, BedFile *bed);
+
+
+bool addBlockNums = false;
+
+int main(int argc, char* argv[]) {
+
+    // our configuration variables
+    bool showHelp = false;
+
+    // input files
+    string bedFile       = "stdin";
+    bool haveBed         = 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("-i", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                bedFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-n", 2, parameterLength)) {
+            addBlockNums = true;
+            i++;
+        }
+        else {
+            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    // make sure we have an input files
+    if (!haveBed ) {
+        cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (!showHelp) {
+        BedFile *bed       = new BedFile(bedFile);
+        DetermineBedInput(bed);
+    }
+    else {
+        ShowHelp();
+    }
+}
+
+
+void ShowHelp(void) {
+
+    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+    cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+    cerr << "Summary: Splits BED12 features into discrete BED6 features." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed12>" << endl << endl;
+
+    cerr << "Options: " << endl;
+
+    cerr << "\t-n\t"        << "Force the score to be the (1-based) block number from the BED12." << endl << endl;
+
+
+    // end the program here
+    exit(1);
+}
+
+
+void DetermineBedInput(BedFile *bed) {
+
+    // dealing with a proper file
+    if (bed->bedFile != "stdin") {
+
+        ifstream bedStream(bed->bedFile.c_str(), ios::in);
+        if ( !bedStream ) {
+            cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl;
+            exit (1);
+        }
+        ProcessBed(bedStream, bed);
+    }
+    // reading from stdin
+    else {
+        ProcessBed(cin, bed);
+    }
+}
+
+
+void ProcessBed(istream &bedInput, BedFile *bed) {
+
+    // process each BED entry and convert to BAM
+    BED bedEntry, nullBed;
+    int lineNum = 0;
+    BedLineStatus bedStatus;
+    // open the BED file for reading.
+    bed->Open();
+    while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
+        if (bedStatus == BED_VALID) {
+
+            bedVector bedBlocks;  // vec to store the discrete BED "blocks" from a
+            splitBedIntoBlocks(bedEntry, lineNum, bedBlocks);
+
+            for (int i = 0; i < (int) bedBlocks.size(); ++i) {
+                if (addBlockNums == false) {
+                    printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(),
+                                                        bedBlocks[i].score.c_str(), bedBlocks[i].strand.c_str());
+                }
+                else {
+                    if (bedBlocks[i].strand == "+")
+                        printf ("%s\t%d\t%d\t%s\t%d\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(),
+                                                        i+1, bedBlocks[i].strand.c_str());
+                    else 
+                        printf ("%s\t%d\t%d\t%s\t%d\t%s\n", bedBlocks[i].chrom.c_str(), bedBlocks[i].start, bedBlocks[i].end, bedBlocks[i].name.c_str(),
+                                                        (int) ((bedBlocks.size()+1)-i), bedBlocks[i].strand.c_str());
+                }
+            }
+            bedEntry = nullBed;
+        }
+    }
+    // close up
+    bed->Close();
+}