--- a/BEDTools-Version-2.14.3/src/utils/bedFilePE/bedFilePE.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,93 +0,0 @@
-#ifndef BEDFILEPE_H
-#define BEDFILEPE_H
-
-#include <vector>
-#include <map>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <cstring>
-#include <algorithm>
-#include "bedFile.h"
-#include "lineFileUtilities.h"
-
-using namespace std;
-
-
-/*
-    Structure for paired-end records
-*/
-struct BEDPE {
-
-    // UCSC BED fields
-    string chrom1;
-    CHRPOS start1;
-    CHRPOS end1;
-
-    string chrom2;
-    CHRPOS start2;
-    CHRPOS end2;
-
-    string name;
-    string score;
-
-    string strand1;
-    string strand2;
-
-    vector<string> otherFields;
-};
-
-
-
-
-//************************************************
-// BedFile Class methods and elements
-//************************************************
-class BedFilePE {
-
-public:
-
-    // Constructor
-    BedFilePE(string &);
-
-    // Destructor
-    ~BedFilePE(void);
-
-    // Open a BEDPE file for reading (creates an istream pointer)
-    void Open(void);
-
-    // Close an opened BEDPE file.
-    void Close(void);
-
-    // Get the next BED entry in an opened BED file.
-    BedLineStatus GetNextBedPE (BEDPE &bedpe, int &lineNum);
-
-
-    // Methods
-
-    void reportBedPETab(const BEDPE &a);
-    void reportBedPENewLine(const BEDPE &a);
-    void loadBedPEFileIntoMap();
-    void splitBedPEIntoBeds(const BEDPE &a, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2);
-
-
-    void FindOverlapsPerBin(int bEnd, string chrom, CHRPOS start, CHRPOS end, string name, string strand,
-        vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames);
-
-
-    string bedFile;
-    unsigned int bedType;
-
-    masterMateMap bedMapEnd1;
-    masterMateMap bedMapEnd2;
-
-private:
-    istream *_bedStream;
-
-    // methods
-    BedLineStatus parseLine (BEDPE &bedpe, const vector<string> &lineVector, int &lineNum);
-    bool parseBedPELine (BEDPE &bed, const vector<string> &lineVector, const int &lineNum);
-};
-
-#endif /* BEDFILEPE_H */