--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,294 @@
+/*****************************************************************************
+  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;
+}
+