--- a/BEDTools-Version-2.14.3/src/sortBed/sortMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,157 +0,0 @@
-/*****************************************************************************
-  sortBedMain.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 "sortBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "sortBed"
-
-
-// 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 bedFile  = "stdin";
-    bool haveBed    = true;
-    int sortChoices = 0;
-
-    bool sortBySizeAsc            = false;
-    bool sortBySizeDesc           = false;
-    bool sortByChromThenSizeAsc   = false;
-    bool sortByChromThenSizeDesc  = false;
-    bool sortByChromThenScoreAsc  = false;
-    bool sortByChromThenScoreDesc = false;
-
-
-    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("-sizeA", 6, parameterLength)) {
-            sortBySizeAsc = true;
-            sortChoices++;
-        }
-        else if(PARAMETER_CHECK("-sizeD", 6, parameterLength)) {
-            sortBySizeDesc = true;
-            sortChoices++;
-        }
-        else if(PARAMETER_CHECK("-chrThenSizeA", 13, parameterLength)) {
-            sortByChromThenSizeAsc = true;
-            sortChoices++;
-        }
-        else if(PARAMETER_CHECK("-chrThenSizeD", 13, parameterLength)) {
-            sortByChromThenSizeDesc = true;
-            sortChoices++;
-        }
-        else if(PARAMETER_CHECK("-chrThenScoreA", 14, parameterLength)) {
-            sortByChromThenScoreAsc = true;
-            sortChoices++;
-        }
-        else if(PARAMETER_CHECK("-chrThenScoreD", 14, parameterLength)) {
-            sortByChromThenScoreDesc = true;
-            sortChoices++;
-        }
-        else {
-            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    // make sure we have both input files
-    if (!haveBed) {
-        cerr << endl << "*****" << endl << "*****ERROR: Need -i BED file. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-    if (sortChoices > 1) {
-        cerr << endl << "*****" << endl << "*****ERROR: Sorting options are mutually exclusive.  Please choose just one. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-
-    if (!showHelp) {
-        BedSort *bm = new BedSort(bedFile);
-
-        if (sortBySizeAsc) {
-            bm->SortBedBySizeAsc();
-        }
-        else if (sortBySizeDesc) {
-            bm->SortBedBySizeDesc();
-        }
-        else if (sortByChromThenSizeAsc) {
-            bm->SortBedByChromThenSizeAsc();
-        }
-        else if (sortByChromThenSizeDesc) {
-            bm->SortBedByChromThenSizeDesc();
-        }
-        else if (sortByChromThenScoreAsc) {
-            bm->SortBedByChromThenScoreAsc();
-        }
-        else if (sortByChromThenScoreDesc) {
-            bm->SortBedByChromThenScoreDesc();
-        }
-        else {
-            bm->SortBed();
-        }
-        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: Sorts a feature file in various and useful ways." << endl << endl;
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options: " << endl;
-    cerr << "\t" << "-sizeA\t\t"    << "Sort by feature size in ascending order." << endl;
-    cerr << "\t" << "-sizeD\t\t"    << "Sort by feature size in descending order." << endl;
-    cerr << "\t" << "-chrThenSizeA\t"   << "Sort by chrom (asc), then feature size (asc)." << endl;
-    cerr << "\t" << "-chrThenSizeD\t"   << "Sort by chrom (asc), then feature size (desc)." << endl;
-    cerr << "\t" << "-chrThenScoreA\t"  << "Sort by chrom (asc), then score (asc)." << endl;
-    cerr << "\t" << "-chrThenScoreD\t"  << "Sort by chrom (asc), then score (desc)." << endl << endl;
-
-    exit(1);
-
-}