--- a/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,125 +0,0 @@
-/*****************************************************************************
-  multiIntersectBed.h
-
-  (c) 2010 - Aaron Quinlan, UVA
-           - Assaf Gordon, CSHL
-  Quinlan Laboratory
-  Department of Public Health Sciences
-  Center for Public Health Genomics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef MULTIINTERSECTBED_H
-#define MULTIINTERSECTBED_H
-
-#include <vector>
-#include <string>
-#include "bedFile.h"
-#include "genomeFile.h"
-#include "intervalItem.h"
-
-class MultiIntersectBed
-{
-private:
-
-    vector<string>  filenames;
-    vector<string>  titles;
-
-    vector<BedFile*>   input_files;
-    vector<int>        current_depth;
-    vector<BED>        current_item;
-
-    std::ostream    &output;
-
-    INTERVALS_PRIORITY_QUEUE queue;
-    std::string              current_chrom;
-    map<int, bool>           files_with_coverage;
-    int                      current_non_zero_inputs;
-    bool                     print_empty_regions;
-    bool                     haveTitles;
-    
-    GenomeFile* genome_sizes;
-
-    std::string no_coverage_value;
-
-public:
-    MultiIntersectBed(std::ostream& _output,
-            const vector<string>& _filenames,
-            const vector<string>& _titles,
-            bool _print_empty_regions,
-            const std::string& _genomeFileName,
-            const std::string& _no_coverage_value);
-
-    virtual ~MultiIntersectBed();
-
-    // Combines all interval files
-    void MultiIntersect();
-
-    // Print the header line: chrom/start/end + name of each bedgraph file.
-    void PrintHeader();
-
-
-private:
-
-    // Open all input files, initialize "current_XXX" vectors
-    void OpenFiles();
-
-    // Close the input files.
-    void CloseFiles();
-
-    /*
-       Add an interval from BedGraph file 'index' into the queue.
-       will only be added if it belongs to the current chromosome.
-
-       If the interval was added (=consumed), the next interval will be read from the file
-       using 'LoadNextItem'
-     */
-    void AddInterval(int index);
-
-    /*
-       Loads the next interval from Bed file 'index'.
-       Stores it in 'current_bed_item' vector.
-     */
-    void LoadNextItem(int index);
-
-    /*
-       Scans the 'current_bedgraph_item' vector,
-       find the 'first' chromosome to use (different BedGraph files can start with different chromosomes).
-     */
-    std::string DetermineNextChrom();
-
-    /*
-       Returns 'true' if ALL intervals from ALL BedGraph files were used
-    */
-    bool        AllFilesDone();
-
-    /*
-       Extract the next coordinate from the queue, and updates the current coverage information.
-       If multiple interval share the same coordinate values, all of them are handled.
-       If an END coordinate is consumed, the next interval (from the corresponding file) is read.
-     */
-    CHRPOS ConsumeNextCoordinate();
-
-    /*
-       Updates the coverage information based on the given item.
-       Item can be a START coordinate or an END coordiante.
-     */
-    void UpdateInformation(const IntervalItem &item);
-
-    /*
-       prints chrom/start/end and the current depth coverage values of all the files.
-     */
-    void PrintCoverage(CHRPOS start, CHRPOS end);
-
-    /*
-       prints chrom/start/end and the ZERO depth coverage values of all the files.
-     */
-    void PrintEmptyCoverage(CHRPOS start, CHRPOS end);
-
-    void DebugPrintQueue();
-};
-
-
-#endif