--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/slopBed/slopBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,190 @@
+/*****************************************************************************
+  slopBedMain.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 "slopBed.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "slopBed"
+
+
+// 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 genomeFile;
+
+    bool haveBed    = true;
+    bool haveGenome = false;
+    bool haveLeft   = false;
+    bool haveRight  = false;
+    bool haveBoth   = false;
+
+    bool forceStrand = false;
+    float leftSlop   = 0.0;
+    float rightSlop  = 0.0;
+    bool  fractional = 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("-l", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveLeft = true;
+                leftSlop = atof(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveRight = true;
+                rightSlop = atof(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveBoth = true;
+                leftSlop = atof(argv[i + 1]);
+                rightSlop = atof(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-s", 2, parameterLength)) {
+            forceStrand = true;
+        }
+        else if(PARAMETER_CHECK("-pct", 4, parameterLength)) {
+            fractional = true;
+        }
+        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 (!haveLeft && !haveRight && !haveBoth) {
+      cerr << endl << "*****" << endl << "*****ERROR: Need -l and -r together or -b alone. " << endl << "*****" << endl;
+      showHelp = true;
+    }
+    if ((!haveLeft && haveRight) || (haveLeft && !haveRight)) {
+      cerr << endl << "*****" << endl << "*****ERROR: Need both -l and -r. " << endl << "*****" << endl;
+      showHelp = true;
+    }
+    if (forceStrand && (!(haveLeft) || !(haveRight))) {
+      cerr << endl << "*****" << endl << "*****ERROR: Must supply -l and -r with -s. " << endl << "*****" << endl;
+      showHelp = true;
+    }
+
+    if (!showHelp) {
+        BedSlop *bc = new BedSlop(bedFile, genomeFile, forceStrand, leftSlop, rightSlop, fractional);
+        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: Add requested base pairs of \"slop\" to each feature." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome> [-b <int> or (-l and -r)]" << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-b\t"                << "Increase the BED/GFF/VCF entry by -b base pairs in each direction." << endl;
+    cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+
+    cerr << "\t-l\t"                << "The number of base pairs to subtract from the start coordinate." << endl;
+    cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+        
+    cerr << "\t-r\t"                << "The number of base pairs to add to the end coordinate." << endl;
+    cerr                            << "\t\t- (Integer) or (Float, e.g. 0.1) if used with -pct." << endl << endl;
+        
+    cerr << "\t-s\t"                << "Define -l and -r based on strand." << endl;
+    cerr                            << "\t\tE.g. if used, -l 500 for a negative-stranded feature, " << endl;
+    cerr                            << "\t\tit will add 500 bp downstream.  Default = false." << endl << endl;
+
+    cerr << "\t-pct\t"              << "Define -l and -r as a fraction of the feature's length." << endl;
+    cerr                            << "\t\tE.g. if used on a 1000bp feature, -l 0.50, " << endl;
+    cerr                            << "\t\twill add 500 bp \"upstream\".  Default = false." << endl << endl;
+
+    cerr << "Notes: " << endl;
+    cerr << "\t(1)  Starts will be set to 0 if options would force it below 0." << endl;
+    cerr << "\t(2)  Ends will be set to the chromosome length if  requested slop would" << endl;
+    cerr <<        "\tforce it above the max chrom length." << endl;
+
+    cerr << "\t(3)  The genome file should tab delimited and structured as follows:" << endl;
+    cerr << "\n\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);
+}