--- a/BEDTools-Version-2.14.3/src/fjoin/fjoin.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,350 +0,0 @@
-/*****************************************************************************
-  intersectBed.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 "fjoin.h"
-#include <queue>
-#include <set>
-
-bool leftOf(const BED &a, const BED &b);
-
-
-bool BedIntersect::processHits(BED &a, vector<BED> &hits) {
-    // how many overlaps are there b/w the bed and the set of hits?
-    int s, e, overlapBases;
-    int  numOverlaps = 0;
-    bool hitsFound   = false;
-    int aLength      = (a.end - a.start);   // the length of a in b.p.
-
-    // loop through the hits and report those that meet the user's criteria
-    vector<BED>::const_iterator h       = hits.begin();
-    vector<BED>::const_iterator hitsEnd = hits.end();
-    for (; h != hitsEnd; ++h) {
-        s            = max(a.start, h->start);
-        e            = min(a.end, h->end);
-        overlapBases = (e - s);             // the number of overlapping bases b/w a and b
-
-        // is there enough overlap relative to the user's request? (default ~ 1bp)
-        if ( ( (float) overlapBases / (float) aLength ) >= _overlapFraction ) {
-            // Report the hit if the user doesn't care about reciprocal overlap between A and B.
-            if (_reciprocal == false) {
-                hitsFound = true;
-                numOverlaps++;
-                if (_printable == true)
-                    ReportOverlapDetail(overlapBases, a, *h, s, e);
-            }
-            // we require there to be sufficient __reciprocal__ overlap
-            else {
-                int bLength    = (h->end - h->start);
-                float bOverlap = ( (float) overlapBases / (float) bLength );
-                if (bOverlap >= _overlapFraction) {
-                    hitsFound = true;
-                    numOverlaps++;
-                    if (_printable == true)
-                        ReportOverlapDetail(overlapBases, a, *h, s, e);
-                }
-            }
-        }
-    }
-    // report the summary of the overlaps if requested.
-    ReportOverlapSummary(a, numOverlaps);
-    // were hits found for this BED feature?
-    return hitsFound;
-}
-
-/*
-    Constructor
-*/
-BedIntersect::BedIntersect(string bedAFile, string bedBFile, bool anyHit,
-                           bool writeA, bool writeB, bool writeOverlap, bool writeAllOverlap,
-                           float overlapFraction, bool noHit, bool writeCount, bool forceStrand,
-                           bool reciprocal, bool obeySplits, bool bamInput, bool bamOutput) {
-
-    _bedAFile            = bedAFile;
-    _bedBFile            = bedBFile;
-    _anyHit              = anyHit;
-    _noHit               = noHit;
-    _writeA              = writeA;
-    _writeB              = writeB;
-    _writeOverlap        = writeOverlap;
-    _writeAllOverlap     = writeAllOverlap;
-    _writeCount          = writeCount;
-    _overlapFraction     = overlapFraction;
-    _forceStrand         = forceStrand;
-    _reciprocal          = reciprocal;
-    _obeySplits          = obeySplits;
-    _bamInput            = bamInput;
-    _bamOutput           = bamOutput;
-
-    if (_anyHit || _noHit || _writeCount)
-        _printable = false;
-    else
-        _printable = true;
-
-    // create new BED file objects for A and B
-    _bedA = new BedFile(bedAFile);
-    _bedB = new BedFile(bedBFile);
-
-    IntersectBed();
-}
-
-
-/*
-    Destructor
-*/
-BedIntersect::~BedIntersect(void) {
-}
-
-
-bool leftOf(const BED &a, const BED &b) {
-    return (a.end <= b.start);
-}
-
-
-void BedIntersect::ReportOverlapDetail(const int &overlapBases, const BED &a, const BED &b,
-                                       const CHRPOS &s, const CHRPOS &e) {
-    // default. simple intersection only
-    if (_writeA == false && _writeB == false && _writeOverlap == false) {
-        _bedA->reportBedRangeNewLine(a,s,e);
-    }
-    //  -wa -wbwrite the original A and B
-    else if (_writeA == true && _writeB == true) {
-        _bedA->reportBedTab(a);
-        _bedB->reportBedNewLine(b);
-    }
-    // -wa write just the original A
-    else if (_writeA == true) {
-        _bedA->reportBedNewLine(a);
-    }
-    // -wb write the intersected portion of A and the original B
-    else if (_writeB == true) {
-        _bedA->reportBedRangeTab(a,s,e);
-        _bedB->reportBedNewLine(b);
-    }
-    // -wo write the original A and B plus the no. of overlapping bases.
-    else if (_writeOverlap == true) {
-        _bedA->reportBedTab(a);
-        _bedB->reportBedTab(b);
-        printf("%d\n", overlapBases);
-    }
-}
-
-
-void BedIntersect::ReportOverlapSummary(const BED &a, const int &numOverlapsFound) {
-    // -u  just report the fact that there was >= 1 overlaps
-    if (_anyHit && (numOverlapsFound >= 1)) {
-        _bedA->reportBedNewLine(a);
-    }
-    // -c  report the total number of features overlapped in B
-    else if (_writeCount) {
-        _bedA->reportBedTab(a);
-        printf("%d\n", numOverlapsFound);
-    }
-    // -v  report iff there were no overlaps
-    else if (_noHit && (numOverlapsFound == 0)) {
-        _bedA->reportBedNewLine(a);
-    }
-    // -wao the user wants to force the reporting of 0 overlap
-    else if (_writeAllOverlap && (numOverlapsFound == 0)) {
-        _bedA->reportBedTab(a);
-        _bedB->reportNullBedTab();
-        printf("0\n");
-    }
-}
-
-
-
-void BedIntersect::Scan(BED *x, vector<BED *> *windowX, BedLineStatus xStatus,
-                  const BED &y, vector<BED *> *windowY, BedLineStatus yStatus) {
-
-    if (xStatus != BED_VALID) {
-        return;
-    }
-
-    std::vector<BED *>::iterator wYIter = windowY->begin();
-    while (wYIter != windowY->end()) {
-        if (leftOf(*(*wYIter), *x) == true) {
-            (*wYIter)->finished = true;
-            wYIter = windowY->erase(wYIter);  // erase auto-increments to the next position
-        }
-        else if (overlaps((*wYIter)->start, (*wYIter)->end, x->start, x->end) > 0) {
-            if (_lastPick == 0) {
-                AddHits(x, *(*wYIter));
-            }
-            else {
-                AddHits(*wYIter, *x);
-            }
-            ++wYIter;  // force incrementing
-        }
-    }
-    if (leftOf(*x,y) == false)
-        windowX->push_back(x);
-    else {
-        x->finished = true;
-    }
-    // dump the buffered results (if any)
-    FlushOutputBuffer();
-}
-
-
-void BedIntersect::AddHits(BED *x, const BED &y) {
-    if (x->overlaps.empty() == true)
-        _outputBuffer.push(x);
-    x->overlaps.push_back(y);
-}
-
-
-void BedIntersect::FlushOutputBuffer(bool final) {
-    while (_outputBuffer.empty() == false)
-    {
-        if (final == false && _outputBuffer.front()->finished == false)
-            break;
-
-        processHits(*_outputBuffer.front(), _outputBuffer.front()->overlaps);
-        // remove the finished BED entry from the heap
-        delete _outputBuffer.front();
-        _outputBuffer.pop();
-    }
-}
-
-
-vector<BED*>* BedIntersect::GetWindow(const string &chrom, bool isA) {
-
-    // iterator to test if a window for a given chrom exists.
-    map<string, vector<BED*> >::iterator it;
-
-    // grab the current window for A or B, depending on
-    // the request.  if a window hasn't yet been created
-    // for the requested chrom, create one.
-
-    if (isA) {
-        it = _windowA.find(chrom);
-        if (it != _windowA.end()) {
-            return & _windowA[chrom];
-        }
-        else {
-            _windowA.insert(pair<string, vector<BED *> >(chrom, vector<BED *>()));
-            return & _windowA[chrom];
-        }
-    }
-    else {
-        it = _windowB.find(chrom);
-        if (it != _windowB.end()) {
-            return & _windowB[chrom];
-        }
-        else {
-            _windowB.insert(pair<string, vector<BED *> >(chrom, vector<BED *>()));
-            return & _windowB[chrom];
-        }
-    }
-}
-
-
-void BedIntersect::ChromSwitch(const string &chrom) {
-
-    vector<BED*>::iterator windowAIter = _windowA[chrom].begin();
-    vector<BED*>::iterator windowAEnd  = _windowA[chrom].end();
-    for (; windowAIter != windowAEnd; ++windowAIter)
-        (*windowAIter)->finished = true;
-
-    vector<BED*>::iterator windowBIter = _windowB[chrom].begin();
-    vector<BED*>::iterator windowBEnd  = _windowB[chrom].end();
-    for (; windowBIter != windowBEnd; ++windowBIter)
-        (*windowBIter)->finished = true;
-
-    FlushOutputBuffer();
-}
-
-
-void BedIntersect::IntersectBed() {
-
-    int aLineNum = 0;
-    int bLineNum = 0;
-
-    // current feature from each file
-    BED *a, *b, *prevA, *prevB;
-
-    // status of the current lines
-    BedLineStatus aStatus, bStatus;
-
-    // open the files; get the first line from each
-    _bedA->Open();
-    _bedB->Open();
-
-    prevA = NULL;
-    prevB = NULL;
-    a = new BED();
-    b = new BED();
-    aStatus = _bedA->GetNextBed(*a, aLineNum);
-    bStatus = _bedB->GetNextBed(*b, bLineNum);
-
-    cout << a->chrom << " " << a->start << " " << a->chrom << " " << b->start << endl;
-    while (aStatus != BED_INVALID || bStatus != BED_INVALID) {
-        
-        if ((a->start <= b->start) && (a->chrom == b->chrom)) {
-            prevA = a;
-            _lastPick = 0;
-            Scan(a, GetWindow(a->chrom, true),  aStatus,
-                *b, GetWindow(a->chrom, false), bStatus);
-
-            a = new BED();
-            aStatus = _bedA->GetNextBed(*a, aLineNum);
-        }
-        else if ((a->start > b->start) && (a->chrom == b->chrom)) {
-            prevB = b;
-            _lastPick = 1;
-            Scan(b, GetWindow(b->chrom, false), bStatus,
-                *a, GetWindow(b->chrom, true),  aStatus);
-
-            b = new BED();
-            bStatus = _bedB->GetNextBed(*b, bLineNum);
-        }
-        else if (a->chrom != b->chrom) {
-            // A was most recently read
-            if (_lastPick == 0) {
-                prevB = b;
-                while (b->chrom == prevA->chrom){
-                    _windowB[prevA->chrom].push_back(b);
-                    b = new BED();
-                    bStatus = _bedB->GetNextBed(*b, bLineNum);
-                }
-                Scan(prevA, GetWindow(prevA->chrom, true),  aStatus,
-                    *prevB, GetWindow(prevA->chrom, false),  bStatus);
-            }
-            // B was most recently read
-            else {
-                prevA = a;
-                while (a->chrom == prevB->chrom) {
-                    _windowA[prevB->chrom].push_back(a);
-                    a = new BED();
-                    aStatus = _bedA->GetNextBed(*a, aLineNum);
-                }
-                Scan(prevB, GetWindow(prevB->chrom, false), bStatus,
-                    *prevA, GetWindow(prevB->chrom, true),  aStatus);
-            }
-            FlushOutputBuffer(true);
-        }
-        if (prevA!=NULL&&prevB!=NULL)
-            //cout << prevA->chrom << " " << a->chrom << " " << a->start << " "
-            //     << prevB->chrom << " " << b->chrom << " " << b->start << "\n";
-        if (aStatus == BED_INVALID) a->start = INT_MAX;
-        if (bStatus == BED_INVALID) b->start = INT_MAX;
-    }
-
-    // clear out the final bit of staged output
-    FlushOutputBuffer(true);
-
-    // close the files
-    _bedA->Close();
-    _bedB->Close();
-}
-
-