--- a/BEDTools-Version-2.14.3/src/pairToBed/pairToBed.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,161 +0,0 @@
-/*****************************************************************************
-  pairToBed.h
-
-  (c) 2009 - Aaron Quinlan
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#ifndef INTERSECTBED_H
-#define INTERSECTBED_H
-
-#include "api/BamReader.h"
-#include "api/BamWriter.h"
-#include "api/BamAux.h"
-using namespace BamTools;
-
-#include "bedFile.h"
-#include "bedFilePE.h"
-#include <vector>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-
-
-
-/**************************************************
-Helper function protoypes
-**************************************************/
-void IsCorrectMappingForBEDPE (const BamAlignment &bam, const RefVector &refs, BEDPE &a);
-
-
-
-//************************************************
-// Class methods and elements
-//************************************************
-class BedIntersectPE {
-
-public:
-
-    // constructor
-    BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction,
-        string searchType, bool sameStrand, bool diffStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance);
-    // destructor
-    ~BedIntersectPE(void);
-
-    void FindOverlaps(const BEDPE &, vector<BED> &hits1, vector<BED> &hits2, const string &type);
-
-    bool FindOneOrMoreOverlaps(const BEDPE &, const string &type);
-
-    void FindSpanningOverlaps(const BEDPE &a, vector<BED> &hits, const string &type);
-    bool FindOneOrMoreSpanningOverlaps(const BEDPE &a, const string &type);
-
-    void IntersectBedPE();
-    void IntersectBamPE(string bamFile);
-
-    void DetermineBedPEInput();
-
-private:
-
-    string _bedAFilePE;
-    string _bedBFile;
-    float _overlapFraction;
-    string _searchType;
-    bool _sameStrand;
-    bool _diffStrand;
-    bool _useEditDistance;
-    bool _bamInput;
-    bool _bamOutput;
-    bool  _isUncompressedBam;
-
-    // instance of a paired-end bed file class.
-    BedFilePE *_bedA;
-
-    // instance of a bed file class.
-    BedFile *_bedB;
-
-    inline
-    void ConvertBamToBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVector &refs, BEDPE &a) {
-
-        // initialize BEDPE variables
-        a.start1 = a.start2 = a.end1 = a.end2 = -1;
-        a.chrom1 = a.chrom2 = ".";
-        a.strand1 = a.strand2 = '.';
-        uint32_t editDistance1, editDistance2;
-        editDistance1 = editDistance2 = 0;
-
-        // take the qname from end 1.
-        a.name = bam1.Name;
-
-        // end 1
-        if (bam1.IsMapped()) {
-            a.chrom1  = refs.at(bam1.RefID).RefName;
-            a.start1  = bam1.Position;
-            a.end1    = bam1.GetEndPosition(false, false);
-            a.strand1 = "+";
-            if (bam1.IsReverseStrand()) a.strand1 = "-";
-
-            // extract the edit distance from the NM tag
-            // if possible. otherwise, complain.
-            if (_useEditDistance == true) {
-                if (bam1.GetTag("NM", editDistance1) == false) {
-                    cerr << "The edit distance tag (NM) was not found in the BAM file.  Please disable -ed.  Exiting\n";
-                    exit(1);
-                }
-            }
-        }
-
-        // end 2
-        if (bam2.IsMapped()) {
-            a.chrom2  = refs.at(bam2.RefID).RefName;
-            a.start2  = bam2.Position;
-            a.end2    = bam2.GetEndPosition(false, false);
-            a.strand2 = "+";
-            if (bam2.IsReverseStrand()) a.strand2 = "-";
-
-            // extract the edit distance from the NM tag
-            // if possible. otherwise, complain.
-            if (_useEditDistance == true) {
-                if (bam2.GetTag("NM", editDistance2) == false) {
-                    cerr << "The edit distance tag (NM) was not found in the BAM file.  Please disable -ed.  Exiting\n";
-                    exit(1);
-                }
-            }
-        }
-
-        // swap the ends if necessary
-        if ( a.chrom1 > a.chrom2 || ((a.chrom1 == a.chrom2) && (a.start1 > a.start2)) ) {
-            swap(a.chrom1, a.chrom2);
-            swap(a.start1, a.start2);
-            swap(a.end1, a.end2);
-            swap(a.strand1, a.strand2);
-        }
-
-        // compute the minimum mapping quality b/w the two ends of the pair.
-        a.score = "0";
-        if (_useEditDistance == false) {
-            if (bam1.IsMapped() == true && bam2.IsMapped() == true)
-                a.score = ToString(min(bam1.MapQuality, bam2.MapQuality));
-        }
-        // BEDPE using edit distance
-        else {
-            if (bam1.IsMapped() == true && bam2.IsMapped() == true)
-                a.score = ToString((int) (editDistance1 + editDistance2));
-            else if (bam1.IsMapped() == true)
-                a.score = ToString((int) editDistance1);
-            else if (bam2.IsMapped() == true)
-                a.score = ToString((int) editDistance2);
-        }
-    };
-
-    inline
-    void ProcessBamBlock (const BamAlignment &bam1, const BamAlignment &bam2,
-                                          const RefVector &refs,
-                                          BamWriter &writer);
-};
-
-#endif /* PEINTERSECTBED_H */