--- a/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCovMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-/*****************************************************************************
-  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);
-
-}