--- a/BEDTools-Version-2.14.3/src/bed12ToBed6/bed12ToBed6.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +0,0 @@
-/*****************************************************************************
-  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();
-}