--- a/BEDTools-Version-2.14.3/src/pairToPair/pairToPair.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,216 +0,0 @@
-/*****************************************************************************
-  pairToPair.cpp
-
-  (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.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "pairToPair.h"
-
-
-/*
-    Constructor
-*/
-PairToPair::PairToPair(string &bedAFilePE, string &bedBFilePE, float &overlapFraction,
-                           string searchType, bool ignoreStrand, bool reqDiffNames, int slop, bool strandedSlop) {
-
-    _bedAFilePE      = bedAFilePE;
-    _bedBFilePE      = bedBFilePE;
-    _overlapFraction = overlapFraction;
-    _searchType      = searchType;
-    _ignoreStrand    = ignoreStrand;
-    _reqDiffNames    = reqDiffNames;
-    _slop            = slop;
-    _strandedSlop    = strandedSlop;
-
-    _bedA = new BedFilePE(bedAFilePE);
-    _bedB = new BedFilePE(bedBFilePE);
-
-    IntersectPairs();
-}
-
-
-/*
-    Destructor
-*/
-PairToPair::~PairToPair(void) {
-}
-
-
-
-void PairToPair::IntersectPairs() {
-
-    // load the "B" bed file into a map so
-    // that we can easily compare "A" to it for overlaps
-    _bedB->loadBedPEFileIntoMap();
-
-    int lineNum = 0;
-    BedLineStatus bedStatus;
-    BEDPE a, nullBedPE;
-
-    _bedA->Open();
-    while ((bedStatus = _bedA->GetNextBedPE(a, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            // identify overlaps b/w the pairs
-            FindOverlaps(a);
-            a = nullBedPE;
-        }
-    }
-    _bedA->Close();
-}
-// END IntersectPE
-
-
-
-void PairToPair::FindOverlaps(const BEDPE &a) {
-    //
-    vector<MATE> hitsA1B1, hitsA1B2, hitsA2B1, hitsA2B2;
-
-    // add the appropriate slop to the starts and ends
-    int start1 = a.start1;
-    int end1   = a.end1;
-    int start2 = a.start2;
-    int end2   = a.end2;
-
-    if (_strandedSlop == true) {
-        if (a.strand1 == "+")
-            end1   += _slop;
-        else
-            start1 -= _slop;
-        if (a.strand2 == "+")
-            end2   += _slop;
-        else
-            start2 -= _slop;
-    }
-    else {
-        (start1 - _slop) >= 0 ? start1 -= _slop : start1 = 0;
-        (start2 - _slop) >= 0 ? start2 -= _slop : start2 = 0;
-        end1   += _slop;
-        end2   += _slop;
-    }
-
-    // Find the _potential_ hits between each end of A and B
-    _bedB->FindOverlapsPerBin(1, a.chrom1, start1, end1, a.name, a.strand1, hitsA1B1, _overlapFraction, !(_ignoreStrand), _reqDiffNames);   // hits b/w A1 & B1
-    _bedB->FindOverlapsPerBin(1, a.chrom2, start2, end2, a.name, a.strand2, hitsA2B1, _overlapFraction, !(_ignoreStrand), _reqDiffNames);   // hits b/w A2 & B1
-    _bedB->FindOverlapsPerBin(2, a.chrom1, start1, end1, a.name, a.strand1, hitsA1B2, _overlapFraction, !(_ignoreStrand), _reqDiffNames);   // hits b/w A1 & B2
-    _bedB->FindOverlapsPerBin(2, a.chrom2, start2, end2, a.name, a.strand2, hitsA2B2, _overlapFraction, !(_ignoreStrand), _reqDiffNames);   // hits b/w A2 & B2
-
-    unsigned int matchCount1 = (hitsA1B1.size() + hitsA2B2.size());
-    unsigned int matchCount2 = (hitsA2B1.size() + hitsA1B2.size());
-
-    
-    // report the fact that no hits were found iff _searchType is neither.
-    if ((matchCount1 == 0) && (matchCount2 == 0) && (_searchType == "neither")) {
-        _bedA->reportBedPENewLine(a);
-    }
-    else if (_searchType == "both")  {
-        bool found1 = false;
-        bool found2 = false;
-        if ((hitsA1B1.size() > 0) || (hitsA2B2.size() > 0))
-            found1 = FindHitsOnBothEnds(a, hitsA1B1, hitsA2B2);
-        if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0))
-            found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2);
-    }
-    else if (_searchType == "notboth")  {
-        bool found1 = false;
-        bool found2 = false;
-        if ((hitsA1B1.size() > 0) || (hitsA2B2.size() > 0))
-            found1 = FindHitsOnBothEnds(a, hitsA1B1, hitsA2B2);
-        if ((hitsA2B1.size() > 0) || (hitsA1B2.size() > 0))
-            found2 = FindHitsOnBothEnds(a, hitsA2B1, hitsA1B2);
-        if (found1 == false && found2 == false)
-            _bedA->reportBedPENewLine(a);
-    }
-    else if (_searchType == "either") {
-        FindHitsOnEitherEnd(a, hitsA1B1, hitsA2B2);
-        FindHitsOnEitherEnd(a, hitsA2B1, hitsA1B2);
-    }
-}
-
-
-bool PairToPair::FindHitsOnBothEnds(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
-                                    const vector<MATE> &qualityHitsEnd2) {
-
-    map<unsigned int, vector<MATE>, less<int> > hitsMap;
-
-    for (vector<MATE>::const_iterator h = qualityHitsEnd1.begin(); h != qualityHitsEnd1.end(); ++h) {
-        hitsMap[h->lineNum].push_back(*h);
-    }
-    for (vector<MATE>::const_iterator h = qualityHitsEnd2.begin(); h != qualityHitsEnd2.end(); ++h) {
-        hitsMap[h->lineNum].push_back(*h);
-    }
-
-
-    bool bothFound = false;
-    for (map<unsigned int, vector<MATE>, less<unsigned int> >::iterator m = hitsMap.begin(); m != hitsMap.end(); ++m) {
-        
-        // hits on both sides
-        if (m->second.size() >= 2) {
-            bothFound = true;
-            MATE b1 = m->second[0];
-            MATE b2 = m->second[1];
-
-            if (_searchType == "both") {
-                _bedA->reportBedPETab(a);
-                printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", b1.bed.chrom.c_str(), b1.bed.start, b1.bed.end,
-                                                                   b2.bed.chrom.c_str(), b2.bed.start, b2.bed.end,
-                                                                   b1.bed.name.c_str(), b1.bed.score.c_str(),
-                                                                   b1.bed.strand.c_str(), b2.bed.strand.c_str());
-                for (size_t i = 0; i < b1.bed.otherFields.size(); ++i)
-                    printf("\t%s", b1.bed.otherFields[i].c_str());
-                printf("\n");
-            }
-        }
-    }
-    return bothFound;
-}
-
-
-void PairToPair::FindHitsOnEitherEnd(const BEDPE &a, const vector<MATE> &qualityHitsEnd1,
-                                    const vector<MATE> &qualityHitsEnd2) {
-
-    map<unsigned int, vector<MATE>, less<int> > hitsMap;
-
-    for (vector<MATE>::const_iterator h = qualityHitsEnd1.begin(); h != qualityHitsEnd1.end(); ++h) {
-        hitsMap[h->lineNum].push_back(*h);
-    }
-    for (vector<MATE>::const_iterator h = qualityHitsEnd2.begin(); h != qualityHitsEnd2.end(); ++h) {
-        hitsMap[h->lineNum].push_back(*h);
-    }
-
-    for (map<unsigned int, vector<MATE>, less<unsigned int> >::iterator m = hitsMap.begin(); m != hitsMap.end(); ++m) {
-        if (m->second.size() >= 1) {
-
-            if ((m->second.size()) == 2) {
-                MATE b1 = m->second[0];
-                MATE b2 = m->second[1];
-
-                _bedA->reportBedPETab(a);
-                printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", b1.bed.chrom.c_str(), b1.bed.start, b1.bed.end,
-                                                                   b2.bed.chrom.c_str(), b2.bed.start, b2.bed.end,
-                                                                   b1.bed.name.c_str(), b1.bed.score.c_str(),
-                                                                   b1.bed.strand.c_str(), b2.bed.strand.c_str());
-                for (size_t i = 0; i < b1.bed.otherFields.size(); ++i)
-                    printf("\t%s", b1.bed.otherFields[i].c_str());
-                printf("\n");
-            }
-            else {
-                MATE b1 = m->second[0];
-
-                _bedA->reportBedPETab(a);
-                printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", b1.bed.chrom.c_str(), b1.bed.start, b1.bed.end,
-                                                                   b1.mate->bed.chrom.c_str(), b1.mate->bed.start, b1.mate->bed.end,
-                                                                   b1.bed.name.c_str(), b1.bed.score.c_str(),
-                                                                   b1.bed.strand.c_str(), b1.mate->bed.strand.c_str());
-                for (size_t i = 0; i < b1.bed.otherFields.size(); ++i)
-                    printf("\t%s", b1.bed.otherFields[i].c_str());
-                printf("\n");
-            }
-        }
-    }
-}