--- a/BEDTools-Version-2.14.3/src/closestBed/closestMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
-/*****************************************************************************
-  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);
-}