--- a/BEDTools-Version-2.14.3/src/annotateBed/annotateMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,170 +0,0 @@
-/*****************************************************************************
-  annotateMain.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 "annotateBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define the version
-#define PROGRAM_NAME "annotateBed"
-
-// 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 file
-    string mainFile;
-
-    // parm flags
-    bool sameStrand     = false;
-    bool diffStrand     = false;
-    bool haveBed        = false;
-    bool haveFiles      = false;
-    bool haveTitles     = false;
-    bool reportCounts   = false;
-    bool reportBoth     = false;
-
-    // list of annotation files / names
-    vector<string> inputFiles;
-    vector<string> inputTitles;
-
-    // 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("-i", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBed  = true;
-                mainFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-files", 6, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFiles = true;
-                i = i+1;
-                string file = argv[i];
-                while (file[0] != '-' && i < argc) {
-                    inputFiles.push_back(file);
-                    i++;
-                    if (i < argc)
-                        file = argv[i];
-                }
-                i--;
-            }
-        }
-        else if(PARAMETER_CHECK("-names", 6, parameterLength)) {
-            if ((i+1) < argc) {
-                haveTitles = true;
-                i = i+1;
-                string title = argv[i];
-                while (title[0] != '-' && i < argc) {
-                    inputTitles.push_back(title);
-                    i++;
-                    if (i < argc)
-                        title = argv[i];
-                }
-                i--;
-            }
-        }
-        else if(PARAMETER_CHECK("-counts", 7, parameterLength)) {
-            reportCounts = true;
-        }
-        else if(PARAMETER_CHECK("-both", 5, parameterLength)) {
-            reportBoth = true;
-        }
-        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
-            sameStrand = true;
-        }
-        else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
-            diffStrand = true;
-        }
-        else {
-            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    // make sure we have both input files
-    if (!haveBed || !haveFiles) {
-        cerr << endl << "*****" << endl << "*****ERROR: Need -i and -files files. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-    if (sameStrand && diffStrand) {
-        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-        BedAnnotate *ba = new BedAnnotate(mainFile, inputFiles, inputTitles, sameStrand, diffStrand, reportCounts, reportBoth);
-        ba->AnnotateBed();
-        delete ba;
-        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: Annotates the depth & breadth of coverage of features from multiple files" << endl;
-    cerr << "\t on the intervals in -i." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -files FILE1 FILE2 .. FILEn" << endl << endl;
-
-    cerr << "Options: " << endl;
-
-    cerr << "\t-names\t"        << "A list of names (one / file) to describe each file in -i." << endl;
-    cerr                        << "\t\tThese names will be printed as a header line." << endl << endl;
-
-    cerr << "\t-counts\t"       << "Report the count of features in each file that overlap -i." << endl;
-    cerr                        << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
-
-    cerr << "\t-both\t"         << "Report the counts followed by the % coverage." << endl;
-    cerr                        << "\t\t- Default is to report the fraction of -i covered by each file." << endl << endl;
-
-    cerr << "\t-s\t"            << "Require same strandedness.  That is, only counts overlaps" << endl;
-    cerr                        << "\t\ton the _same_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
-
-    cerr << "\t-S\t"            << "Require different strandedness.  That is, only count overlaps" << endl;
-    cerr                        << "\t\ton the _opposite_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
-    exit(1);
-}