--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/overlap/overlap.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,202 @@
+/*****************************************************************************
+  overlap.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 <vector>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+#include "version.h"
+#include "lineFileUtilities.h"
+#include "bedFile.h"
+using namespace std;
+
+
+// define our program name
+#define PROGRAM_NAME "overlap"
+
+// 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);
+void DetermineInput(string &inFile, short &s1Col, short &e1Col, short &s2Col, short &e2Col);
+void ComputeOverlaps(istream &input, short &s1Col, short &e1Col, short &s2Col, short &e2Col);
+
+int main(int argc, char* argv[]) {
+
+    // input files
+    string inFile = "stdin";
+    string columns;
+
+    // our configuration variables
+    bool showHelp = false;
+    bool haveInFile  = true;
+    bool haveColumns = false;
+
+
+    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) {
+                inFile     = argv[i + 1];
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-cols", 5, parameterLength)) {
+            haveColumns = true;
+            columns     = argv[i + 1];
+            i++;
+        }
+        else {
+            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+            showHelp = true;
+        }
+    }
+
+    // make sure we have an input files
+    if (!haveInFile ) {
+        cerr << endl << "*****" << endl << "*****ERROR: Need -i file. " << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (!showHelp) {
+
+        // Split the column string sent by the user into discrete column numbers
+        // A comma separated string is expected.
+        vector<string> posColumns;
+        Tokenize(columns, posColumns, ",");
+
+        if (posColumns.size() != 4) {
+            cerr << endl << "*****" << endl << "*****ERROR: Please specify 4, comma-separated position columns. " << endl << "*****" << endl;
+            ShowHelp();
+        }
+        else {
+            short s1, e1, s2, e2;
+            s1 = atoi(posColumns[0].c_str());
+            e1 = atoi(posColumns[1].c_str());
+            s2 = atoi(posColumns[2].c_str());
+            e2 = atoi(posColumns[3].c_str());
+
+            DetermineInput(inFile, s1, e1, s2, e2);
+        }
+    }
+    else {
+        ShowHelp();
+    }
+}
+
+void ShowHelp(void) {
+
+    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+
+    cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+    cerr << "Summary: Computes the amount of overlap (positive values)" << endl;
+    cerr << "\t or distance (negative values) between genome features" << endl;
+    cerr << "\t and reports the result at the end of the same line." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <input> -cols s1,e1,s2,e2 " << endl << endl;
+
+    cerr << "Options: " << endl;
+    cerr << "\t-i\t"        << "Input file. Use \"stdin\" for pipes." << endl << endl;
+
+    cerr << "\t-cols\t"     << "Specify the columns (1-based) for the starts and ends of the" << endl;
+    cerr                    << "\t\tfeatures for which you'd like to compute the overlap/distance." << endl;
+    cerr                    << "\t\tThe columns must be listed in the following order: " << endl << endl;
+    cerr                    << "\t\tstart1,end1,start2,end2" << endl << endl;
+
+    cerr << "Example: " << endl;
+    cerr << "\t$ windowBed -a A.bed -b B.bed -w 10" << endl;
+    cerr << "\tchr1 10  20  A   chr1    15  25  B" << endl;
+    cerr << "\tchr1 10  20  C   chr1    25  35  D" << endl << endl;
+    cerr << "\t$ windowBed -a A.bed -b B.bed -w 10 | overlap -i stdin -cols 2,3,6,7" << endl;
+    cerr << "\tchr1 10  20  A   chr1    15  25  B   5" << endl;
+    cerr << "\tchr1 10  20  C   chr1    25  35  D   -5" << endl;
+
+    // end the program here
+    exit(1);
+
+}
+
+
+void DetermineInput(string &inFile, short &s1Col, short &e1Col, short &s2Col, short &e2Col) {
+
+
+    if (inFile != "stdin") {   // process a file
+
+        ifstream in(inFile.c_str(), ios::in);
+        if ( !in ) {
+            cerr << "Error: The requested input file (" << inFile << ") could not be opened. Exiting!" << endl;
+            exit (1);
+        }
+        ComputeOverlaps(in, s1Col, e1Col, s2Col, e2Col);
+    }
+    else ComputeOverlaps(cin, s1Col, e1Col, s2Col, e2Col);
+}
+
+
+void ComputeOverlaps(istream &input, short &s1Col, short &e1Col, short &s2Col, short &e2Col) {
+
+    int lineNum = 0;
+    string inLine;
+    vector<string> inFields;
+
+    int overlap;
+
+    char *s1End, *e1End, *s2End, *e2End;
+    long s1, e1, s2, e2;
+
+    while (getline(input, inLine)) {
+        lineNum++;
+        Tokenize(inLine, inFields);
+
+        if (inFields.size() > 1) {
+
+            // test if columns  2 and 3 are integers.  If so, assume BED.
+            s1 = strtol(inFields[s1Col-1].c_str(), &s1End, 10);
+            e1 = strtol(inFields[e1Col-1].c_str(), &e1End, 10);
+            s2 = strtol(inFields[s2Col-1].c_str(), &s2End, 10);
+            e2 = strtol(inFields[e2Col-1].c_str(), &e2End, 10);
+
+            // strtol will set pointers to the start of the string if non-integral, base 10
+            // if they all check out, we have valid numeric columns.  Otherwise, complain.
+            if (s1End != inFields[s1Col-1].c_str() &&
+                e1End != inFields[e1Col-1].c_str() &&
+                s2End != inFields[s2Col-1].c_str() &&
+                e2End != inFields[e2Col-1].c_str()) {
+
+                overlap = overlaps(s1, e1, s2, e2);
+                printf("%s\t%d\n", inLine.c_str(), overlap);
+            }
+            else {
+                cerr << "One of your columns appears to be non-numeric at line " << lineNum << ". Exiting..." << endl << endl;
+                exit(1);
+            }
+        }
+        inFields.clear();
+    }
+}