--- a/BEDTools-Version-2.14.3/src/overlap/overlap.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,202 +0,0 @@
-/*****************************************************************************
-  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();
-    }
-}