--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/annotateBed/annotateMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,170 @@
+/*****************************************************************************
+  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);
+}