--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/shuffleBed/shuffleBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,188 @@
+/*****************************************************************************
+  shuffleBedMain.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 "shuffleBed.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "shuffleBed"
+
+
+// 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";
+    string excludeFile;
+    string includeFile;
+    string genomeFile;
+
+    bool haveBed          = true;
+    bool haveGenome       = false;
+    bool haveExclude      = false;
+    bool haveInclude      = false;
+    bool haveSeed         = false;
+    float overlapFraction = 0.0;
+    int seed              = -1;
+    bool sameChrom        = 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("-g", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveGenome = true;
+                genomeFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-excl", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                haveExclude = true;
+                excludeFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-incl", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                haveInclude = true;
+                includeFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-seed", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                haveSeed = true;
+                seed = atoi(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-chrom", 6, parameterLength)) {
+            sameChrom = true;
+        }
+        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                overlapFraction = atof(argv[i + 1]);
+                i++;
+            }
+        }
+        else {
+          cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    // make sure we have both input files
+    if (!haveBed || !haveGenome) {
+      cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
+      showHelp = true;
+    }
+    
+    if (haveInclude && haveExclude) {
+      cerr << endl << "*****" << endl << "*****ERROR: Cannot use -incl and -excl together." << endl << "*****" << endl;
+      showHelp = true;
+    }
+
+    if (!showHelp) {
+        BedShuffle *bc = new BedShuffle(bedFile, genomeFile, excludeFile, includeFile, 
+                                        haveSeed, haveExclude, haveInclude, sameChrom, 
+                                        overlapFraction, seed);
+        delete bc;
+        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: Randomly permute the locations of a feature file among a genome." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-excl\t"             << "A BED/GFF/VCF file of coordinates in which features in -i" << endl;
+    cerr                            << "\t\tshould not be placed (e.g. gaps.bed)." << endl << endl;
+
+    cerr << "\t-incl\t"             << "Instead of randomly placing features in a genome, the -incl" << endl;
+    cerr                            << "\t\toptions defines a BED/GFF/VCF file of coordinates in which " << endl;
+    cerr                            << "\t\tfeatures in -i should be randomly placed (e.g. genes.bed). " << endl << endl;
+
+    cerr << "\t-chrom\t"            << "Keep features in -i on the same chromosome."<< endl;
+    cerr                            << "\t\t- By default, the chrom and position are randomly chosen." << endl << endl;
+
+    cerr << "\t-seed\t"             << "Supply an integer seed for the shuffling." << endl;
+    cerr                            << "\t\t- By default, the seed is chosen automatically." << endl;
+    cerr                            << "\t\t- (INTEGER)" << endl << endl;
+
+    cerr << "\t-f\t"                << "Maximum overlap (as a fraction of the -i feature) with an -excl" << endl;
+    cerr                            << "\t\tfeature that is tolerated before searching for a new, " << endl;
+    cerr                            << "\t\trandomized locus. For example, -f 0.10 allows up to 10%" << endl;
+    cerr                            << "\t\tof a randomized feature to overlap with a given feature" << endl;
+    cerr                            << "\t\tin the -excl file. **Cannot be used with -incl file.**" << endl;
+    cerr                            << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
+    cerr                            << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
+
+    cerr << "Notes: " << endl;
+    cerr << "\t(1)  The genome file should tab delimited and structured as follows:" << endl;
+    cerr << "\t     <chromName><TAB><chromSize>" << endl << endl;
+    cerr << "\tFor example, Human (hg19):" << endl;
+    cerr << "\tchr1\t249250621" << endl;
+    cerr << "\tchr2\t243199373" << endl;
+    cerr << "\t..." << endl;
+    cerr << "\tchr18_gl000207_random\t4262" << endl << endl;
+
+
+    cerr << "Tips: " << endl;
+    cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
+    cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
+    cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\" << endl;
+    cerr << "\t\"select chrom, size from hg19.chromInfo\"  > hg19.genome" << endl << endl;
+
+
+    // end the program here
+    exit(1);
+}