--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/coverageBed/coverageMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,182 @@
+/*****************************************************************************
+  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);
+}