--- a/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,294 +0,0 @@
-/*****************************************************************************
-  unionBedGraphsMain.cpp
-
-  (c) 2010 - Assaf Gordon, CSHL
-           - Aaron Quinlan, UVA
-  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 <climits>
-#include <cstring>
-#include <cstdlib>
-#include <vector>
-#include <string>
-#include <iostream>
-#include <getopt.h>
-#include <libgen.h> //for basename()
-#include "version.h"
-
-#include "genomeFile.h"
-#include "multiIntersectBed.h"
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "multiIntersectBed"
-
-// define our parameter checking macro
-#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
-
-//STLized version of basename()
-// (because POSIX basename() modifies the input string pointer)
-// Additionally: removes any extension the basename might have.
-std::string stl_basename(const std::string& path);
-
-// function declarations
-void ShowHelp(void);
-void ShowExamples(void);
-
-
-int main(int argc, char* argv[])
-{
-    bool haveFiles         = false;
-    bool haveTitles        = false;
-    bool haveGenome        = false;
-    bool haveFiller        = true;
-    bool printHeader       = false;
-    bool printEmptyRegions = false;
-    bool showHelp          = false;
-    string genomeFile;
-    string basePath;
-    string noCoverageValue = "0";
-    vector<string> inputFiles;
-    vector<string> inputTitles;
-
-    //Parse command line options
-    if(argc <= 1)
-        ShowHelp();
-
-    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 == true) {
-        ShowHelp();
-        exit(1);
-    }
-
-    // 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) {
-                haveFiles = true;
-                i = i+1;
-                string file = argv[i];
-                while (file[0] != '-' && i < argc) {
-                    inputFiles.push_back(file);
-                    i++;
-                    if (i < argc)
-                        file = argv[i];
-                }
-                i--;
-            }
-        }
-        else if(PARAMETER_CHECK("-names", 6, parameterLength)) {
-            if ((i+1) < argc) {
-                haveTitles = true;
-                i = i+1;
-                string title = argv[i];
-                while (title[0] != '-' && i < argc) {
-                    inputTitles.push_back(title);
-                    i++;
-                    if (i < argc)
-                        title = argv[i];
-                }
-                i--;
-            }
-        }
-        else if(PARAMETER_CHECK("-g", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveGenome = true;
-                genomeFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-filler", 7, parameterLength)) {
-            if ((i+1) < argc) {
-                haveFiller      = true;
-                noCoverageValue = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-header", 7, parameterLength)) {
-            printHeader = true;
-        }
-        else if(PARAMETER_CHECK("-empty", 6, parameterLength)) {
-            printEmptyRegions = true;
-        }
-        else if(PARAMETER_CHECK("-examples", 9, parameterLength)) {
-            ShowHelp();
-            ShowExamples();
-            exit(1);
-        }
-    }
-
-    //Sanity checks
-    if (inputFiles.empty() == true) {
-        cerr << "Error: missing BedGraph file names (-i) to combine." << endl;
-        exit(1);
-    }
-    if (inputFiles.size() == 1) {
-        cerr << "Error: Only a single BedGraph file was specified. Nothing to combine, exiting." << endl;
-        exit(1);
-    }
-    if (printEmptyRegions && (genomeFile.empty() == true)) {
-        cerr << "Error: when using -empty, the genome sizes file (-g) must be specified using '-g FILE'." << endl;
-        exit(1);
-    }
-    if ((haveTitles == true) && (inputFiles.size() != inputTitles.size())) {
-        cerr << "Error: The number of file titles (-names) does not match the number of files (-i)." << endl;
-        exit(1);
-    }
-
-    MultiIntersectBed mbi(cout, inputFiles, inputTitles, printEmptyRegions, genomeFile, noCoverageValue);
-    if (printHeader)
-        mbi.PrintHeader();
-    mbi.MultiIntersect();
-}
-
-void ShowHelp(void) {
-
-    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
-
-    cerr << "Authors: Assaf Gordon, CSHL" << endl;
-    cerr << "         Aaron Quinlan (aaronquinlan@gmail.com)" << endl << endl;
-
-    cerr << "Summary: Combines multiple BedGraph files into a single file," << endl;
-    cerr << "\t allowing coverage comparisons between them." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i FILE1 FILE2 .. FILEn" << endl;
-    cerr << "\t Assumes that each BedGraph file is sorted by chrom/start " << endl;
-    cerr << "\t and that the intervals in each are non-overlapping." << endl << endl;
-
-    cerr << "Options: " << endl;
-
-    cerr << "\t-header\t\t"     << "Print a header line." << endl;
-    cerr                        << "\t\t\t(chrom/start/end + names of each file)." << endl << endl;
-
-    cerr << "\t-names\t\t"      << "A list of names (one / file) to describe each file in -i." << endl;
-    cerr                        << "\t\t\tThese names will be printed in the header line." << endl << endl;
-
-    cerr << "\t-g\t\t"          << "Use genome file to calculate empty regions." << endl;
-    cerr                        << "\t\t\t- STRING." << endl << endl;
-
-    cerr << "\t-empty\t\t"      << "Report empty regions (i.e., start/end intervals w/o" << endl;
-    cerr                        << "\t\t\tvalues in all files)." << endl;
-    cerr                        << "\t\t\t- Requires the '-g FILE' parameter.\n" << endl;
-
-    cerr << "\t-filler TEXT\t"  << "Use TEXT when representing intervals having no value." << endl;
-    cerr                        << "\t\t\t- Default is '0', but you can use 'N/A' or any other text." << endl << endl;
-
-    cerr << "\t-examples\t"     << "Show detailed usage examples." << endl << endl;
-}
-
-
-
-void ShowExamples()
-{
-    cerr << "Example usage:\n\n"  \
-"== Input files: ==\n" \
-"\n" \
-" $ cat 1.bg\n" \
-" chr1  1000    1500    10\n" \
-" chr1  2000    2100    20\n" \
-"\n" \
-" $ cat 2.bg\n" \
-" chr1  900 1600    60\n" \
-" chr1  1700    2050    50\n" \
-"\n" \
-" $ cat 3.bg\n" \
-" chr1  1980    2070    80\n" \
-" chr1  2090    2100    20\n" \
-"\n" \
-" $ cat sizes.txt\n" \
-" chr1  5000\n" \
-"\n" \
-"== Union/combine the files: ==\n" \
-"\n" \
-" $ unionBedGraphs -i 1.bg 2.bg 3.bg\n" \
-" chr1  900 1000    0   60  0\n" \
-" chr1  1000    1500    10  60  0\n" \
-" chr1  1500    1600    0   60  0\n" \
-" chr1  1700    1980    0   50  0\n" \
-" chr1  1980    2000    0   50  80\n" \
-" chr1  2000    2050    20  50  80\n" \
-" chr1  2050    2070    20  0   80\n" \
-" chr1  2070    2090    20  0   0\n" \
-" chr1  2090    2100    20  0   20\n" \
-"\n" \
-"== Union/combine the files, with a header line (titles are the file names): ==\n" \
-"\n" \
-" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg\n" \
-" chrom start   end 1   2   3\n" \
-" chr1  900 1000    0   60  0\n" \
-" chr1  1000    1500    10  60  0\n" \
-" chr1  1500    1600    0   60  0\n" \
-" chr1  1700    1980    0   50  0\n" \
-" chr1  1980    2000    0   50  80\n" \
-" chr1  2000    2050    20  50  80\n" \
-" chr1  2050    2070    20  0   80\n" \
-" chr1  2070    2090    20  0   0\n" \
-" chr1  2090    2100    20  0   20\n" \
-"\n" \
-"== Union/combine the files, with a header line and custom names: ==\n" \
-"\n" \
-" $ unionBedGraphs -header -i 1.bg 2.bg 3.bg -names WT-1 WT-2 KO-1\n" \
-" chrom start   end WT-1    WT-2    KO-1\n" \
-" chr1  900 1000    0   60  0\n" \
-" chr1  1000    1500    10  60  0\n" \
-" chr1  1500    1600    0   60  0\n" \
-" chr1  1700    1980    0   50  0\n" \
-" chr1  1980    2000    0   50  80\n" \
-" chr1  2000    2050    20  50  80\n" \
-" chr1  2050    2070    20  0   80\n" \
-" chr1  2070    2090    20  0   0\n" \
-" chr1  2090    2100    20  0   20\n" \
-"\n" \
-"== Union/combine, showing empty regions (note, requires -g): ==\n" \
-"\n" \
-" $ unionBedGraphs -header -empty -g sizes.TXT -i 1.bg 2.bg 3.bg\n" \
-" chrom start   end 1   2   3\n" \
-" chr1  0   900 0   0   0\n" \
-" chr1  900 1000    0   60  0\n" \
-" chr1  1000    1500    10  60  0\n" \
-" chr1  1500    1600    0   60  0\n" \
-" chr1  1600    1700    0   0   0\n" \
-" chr1  1700    1980    0   50  0\n" \
-" chr1  1980    2000    0   50  80\n" \
-" chr1  2000    2050    20  50  80\n" \
-" chr1  2050    2070    20  0   80\n" \
-" chr1  2070    2090    20  0   0\n" \
-" chr1  2090    2100    20  0   20\n" \
-" chr1  2100    5000    0   0   0\n" \
-"\n" \
-;
-}
-
-std::string stl_basename(const std::string& path)
-{
-    string result;
-
-    char* path_dup = strdup(path.c_str());
-    char* basename_part = basename(path_dup);
-    result = basename_part;
-    free(path_dup);
-
-    size_t pos = result.find_last_of('.');
-    if (pos != string::npos )
-        result = result.substr(0,pos);
-
-    return result;
-}
-