--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCovMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,145 @@
+/*****************************************************************************
+  multiBamCovMain.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 "multiBamCov.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "multiBamCov"
+
+
+// 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;
+    vector<string> bamFiles;
+    int minQual = 0;
+
+    // input arguments
+    bool haveBed           = false;
+    bool haveBams          = false;
+    bool properOnly        = false;
+    bool keepDuplicates    = false;
+    bool keepFailedQC      = 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("-bed", 4, parameterLength)) {
+            if ((i+1) < argc) {
+                haveBed = true;
+                bedFile = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-bams", 5, parameterLength)) {
+            if ((i+1) < argc) {
+                haveBams = true;
+                i = i+1;
+                string file = argv[i];
+                while (file[0] != '-' && i < argc) {
+                    bamFiles.push_back(file);
+                    i++;
+                    if (i < argc)
+                        file = argv[i];
+                }
+                i--;
+            }
+        }
+        else if(PARAMETER_CHECK("-q", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                minQual = atoi(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-p", 2, parameterLength)) {
+            properOnly = true;
+        }
+        else if(PARAMETER_CHECK("-D", 2, parameterLength)) {
+            keepDuplicates = true;
+        }
+        
+        else if(PARAMETER_CHECK("-F", 2, parameterLength)) {
+            keepFailedQC = true;
+        }
+        else {
+            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    if (!showHelp) {
+        MultiCovBam *mc = new MultiCovBam(bamFiles, bedFile, minQual, properOnly, keepDuplicates, keepFailedQC);
+        mc->CollectCoverage();
+        delete mc;
+        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: Counts sequence coverage for multiple bams at specific loci." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>" << endl << endl;
+
+    cerr << "Options: " << endl;
+
+    cerr << "\t-bams\t"        << "The bam files." << endl << endl;
+
+    cerr << "\t-bed\t"         << "The bed file." << endl << endl;
+
+    cerr << "\t-q\t"           << "Minimum mapping quality allowed. Default is 0." << endl << endl;
+
+    cerr << "\t-D\t"           << "Include duplicate-marked reads.  Default is to count non-duplicates only" << endl << endl;
+
+    cerr << "\t-F\t"           << "Include failed-QC reads.  Default is to count pass-QC reads only" << endl << endl;
+
+    cerr << "\t-p\t"           << "Only count proper pairs.  Default is to count all alignments with MAPQ" << endl;
+    cerr << "\t\t"             << "greater than the -q argument, regardless of the BAM FLAG field." << endl << endl;
+
+    // end the program here
+    exit(1);
+
+}