--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/closestBed/closestMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,202 @@
+/*****************************************************************************
+  closestMain.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 "closestBed.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "closestBed"
+
+// 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 bedAFile;
+    string bedBFile;
+    string tieMode = "all";
+    string strandedDistMode = "";
+
+    bool haveBedA       = false;
+    bool haveBedB       = false;
+    bool haveTieMode    = false;
+    bool sameStrand     = false;
+    bool diffStrand     = false;
+    bool ignoreOverlaps = false;
+    bool reportDistance = false;
+    bool signDistance   = false;
+    bool haveStrandedDistMode = false;
+
+
+    // check to see if we should print out some help
+    if(argc <= 1) showHelp = 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("-a", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveBedA = true;
+                bedAFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveBedB = true;
+                bedBFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
+            sameStrand = true;
+        }
+        else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
+            diffStrand = true;
+        }
+        else if (PARAMETER_CHECK("-d", 2, parameterLength)) {
+            reportDistance = true;
+        }
+        else if (PARAMETER_CHECK("-D", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                reportDistance = true;
+                signDistance = true;
+                haveStrandedDistMode = true;
+                strandedDistMode = argv[i + 1];
+                i++;
+            }
+        }
+        else if (PARAMETER_CHECK("-io", 3, parameterLength)) {
+            ignoreOverlaps = true;
+        }
+        else if (PARAMETER_CHECK("-t", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveTieMode = true;
+                tieMode = argv[i + 1];
+                i++;
+            }
+        }
+        else {
+            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    // make sure we have both input files
+    if (!haveBedA || !haveBedB) {
+        cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (haveTieMode && (tieMode != "all") && (tieMode != "first")
+                    && (tieMode != "last")) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request \"all\" or \"first\" or \"last\" for Tie Mode (-t)" << endl << "*****" << endl;
+        showHelp = true;
+    }
+    
+    if (haveStrandedDistMode && (strandedDistMode != "a") && (strandedDistMode != "b")
+                             && (strandedDistMode != "ref")) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request \"a\" or \"b\" or \"ref\" for Stranded Distance Mode (-D)" << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (sameStrand && diffStrand) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+    
+    if (!showHelp) {
+        BedClosest *bc = new BedClosest(bedAFile, bedBFile, sameStrand, diffStrand, tieMode, reportDistance, signDistance, strandedDistMode, ignoreOverlaps);
+        delete bc;
+        return 0;
+    }
+    else {
+        ShowHelp();
+    }
+}
+
+void ShowHelp(void) {
+
+    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+    cerr << "Authors: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+    cerr       << "\t Erik Arner, Riken" << endl << endl;
+
+    cerr << "Summary: For each feature in A, finds the closest " << endl;
+    cerr << "\t feature (upstream or downstream) in B." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-s\t"            << "Require same strandedness.  That is, find the closest feature in B" << endl;
+    cerr                        << "\t\tthat overlaps A on the _same_ strand." << endl;
+    cerr                        << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+    cerr << "\t-S\t"            << "Require opposite strandedness.  That is, find the closest feature in B" << endl;
+    cerr                        << "\t\tthat overlaps A on the _opposite_ strand." << endl;
+    cerr                        << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+    cerr << "\t-d\t"            << "In addition to the closest feature in B, " << endl;
+    cerr                        << "\t\treport its distance to A as an extra column." << endl;
+    cerr                        << "\t\t- The reported distance for overlapping features will be 0." << endl << endl;
+    
+    cerr << "\t-D\t"            << "Like -d, report the closest feature in B, and its distance to A" << endl;
+    cerr                        << "\t\tas an extra column. Unlike -d, use negative distances to report" << endl;
+    cerr                        << "\t\tupstream features. You must specify which orientation defines \"upstream\"." << endl;
+    cerr                        << "\t\tThe options are:" << endl;
+    cerr                        << "\t\t- \"ref\"   Report distance with respect to the reference genome. " << endl;
+    cerr                        << "\t\t            B features with a lower (start, stop) are upstream" << endl;
+    cerr                        << "\t\t- \"a\"     Report distance with respect to A." << endl;
+    cerr                        << "\t\t            When A is on the - strand, \"upstream\" means B has a higher (start,stop)." << endl;
+    cerr                        << "\t\t- \"b\"     Report distance with respect to B." << endl;
+    cerr                        << "\t\t            When B is on the - strand, \"upstream\" means A has a higher (start,stop)." << endl << endl;
+
+    cerr << "\t-io\t"           << "Ignore features in B that overlap A.  That is, we want close, but " << endl;
+    cerr                        << "\t\tnot touching features only." << endl << endl;
+
+    cerr << "\t-t\t"            << "How ties for closest feature are handled.  This occurs when two" << endl;
+    cerr                        << "\t\tfeatures in B have exactly the same \"closeness\" with A." << endl;
+    cerr                        << "\t\tBy default, all such features in B are reported." << endl;
+    cerr                        << "\t\tHere are all the options:" << endl;
+    cerr                        << "\t\t- \"all\"    Report all ties (default)." << endl;
+    cerr                        << "\t\t- \"first\"  Report the first tie that occurred in the B file." << endl;
+    cerr                        << "\t\t- \"last\"   Report the last tie that occurred in the B file." << endl << endl;
+
+    cerr << "Notes: " << endl;
+    cerr << "\tReports \"none\" for chrom and \"-1\" for all other fields when a feature" << endl;
+    cerr << "\tis not found in B on the same chromosome as the feature in A." << endl;
+    cerr << "\tE.g. none\t-1\t-1" << endl << endl;
+
+    // end the program here
+    exit(1);
+}