--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/sortBed/sortMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,157 @@
+/*****************************************************************************
+  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);
+
+}