--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/utils/bedFilePE/bedFilePE.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,93 @@
+#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 */