--- a/BEDTools-Version-2.14.3/src/coverageBed/coverageMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,182 +0,0 @@
-/*****************************************************************************
-  coverageMain.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 "coverageBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define the version
-#define PROGRAM_NAME "coverageBed"
-
-// 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;
-
-    // parm flags
-    bool sameStrand    = false;
-    bool diffStrand    = false;
-    bool writeHistogram = false;
-    bool eachBase       = false;
-    bool obeySplits     = false;
-    bool bamInput       = false;
-    bool haveBedA       = false;
-    bool haveBedB       = false;
-    bool countsOnly     = 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("-abam", 5, parameterLength)) {
-            if ((i+1) < argc) {
-                haveBedA = true;
-                bamInput = 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("-hist", 5, parameterLength)) {
-            writeHistogram = true;
-        }
-        else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
-            eachBase = true;
-        }
-        else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
-            obeySplits = true;
-        }
-        else if (PARAMETER_CHECK("-counts", 7, parameterLength)) {
-            countsOnly = true;
-        }
-        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 (sameStrand && diffStrand) {
-        cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-        BedCoverage *bg = new BedCoverage(bedAFile, bedBFile, sameStrand, diffStrand,
-                                          writeHistogram, bamInput, obeySplits, eachBase, countsOnly);
-        delete bg;
-        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: Returns the depth and breadth of coverage of features from A" << endl;
-    cerr << "\t on the intervals in B." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -b <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options: " << endl;
-
-    cerr << "\t-abam\t"         << "The A input file is in BAM format." << endl << endl;
-
-    cerr << "\t-s\t"            << "Require same strandedness.  That is, only counts hits in A that" << endl;
-    cerr                        << "\t\toverlap B on 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 report hits in A that" << endl;
-    cerr                        << "\t\toverlap B on the _opposite_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are counted without respect to strand." << endl << endl;
-
-    cerr << "\t-hist\t"         << "Report a histogram of coverage for each feature in B" << endl;
-    cerr                        << "\t\tas well as a summary histogram for _all_ features in B." << endl << endl;
-    cerr                        << "\t\tOutput (tab delimited) after each feature in B:" << endl;
-    cerr                        << "\t\t  1) depth\n\t\t  2) # bases at depth\n\t\t  3) size of B\n\t\t  4) % of B at depth" << endl << endl;
-
-    cerr << "\t-d\t"            << "Report the depth at each position in each B feature." << endl;
-    cerr                        << "\t\tPositions reported are one based.  Each position" << endl;
-    cerr                        << "\t\tand depth follow the complete B feature." << endl << endl;
-    
-    cerr << "\t-counts\t"       << "Only report the count of overlaps, don't compute fraction, etc." << endl << endl;
-
-    cerr << "\t-split\t"        << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl;
-    cerr                        << "\t\twhen computing coverage." << endl;
-    cerr                        << "\t\tFor BAM files, this uses the CIGAR \"N\" and \"D\" operations " << endl;
-    cerr                        << "\t\tto infer the blocks for computing coverage." << endl;
-    cerr                        << "\t\tFor BED12 files, this uses the BlockCount, BlockStarts," << endl;
-    cerr                        << "\t\tand BlockEnds fields (i.e., columns 10,11,12)." << endl << endl;
-
-    cerr << "Default Output:  " << endl;
-    cerr << "\t" << " After each entry in B, reports: " << endl;
-    cerr << "\t   1) The number of features in A that overlapped the B interval." << endl;
-    cerr << "\t   2) The number of bases in B that had non-zero coverage." << endl;
-    cerr << "\t   3) The length of the entry in B." << endl;
-    cerr << "\t   4) The fraction of bases in B that had non-zero coverage." << endl << endl;
-
-    exit(1);
-}