--- a/BEDTools-Version-2.14.3/src/windowBed/windowBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,253 +0,0 @@
-/*****************************************************************************
-  windowBed.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 "windowBed.h"
-
-
-/*
-    Constructor
-*/
-BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
-                     bool anyHit, bool noHit, bool writeCount, bool strandWindows,
-                     bool matchOnSameStrand, bool matchOnDiffStrand, bool bamInput, bool bamOutput, bool isUncompressedBam) {
-
-    _bedAFile      = bedAFile;
-    _bedBFile      = bedBFile;
-
-    _leftSlop      = leftSlop;
-    _rightSlop     = rightSlop;
-
-    _anyHit              = anyHit;
-    _noHit               = noHit;
-    _writeCount          = writeCount;
-    _strandWindows       = strandWindows;
-    _matchOnSameStrand   = matchOnSameStrand;
-    _matchOnDiffStrand   = matchOnDiffStrand;
-    _bamInput            = bamInput;
-    _bamOutput           = bamOutput;
-    _isUncompressedBam   = isUncompressedBam;
-
-    _bedA          = new BedFile(bedAFile);
-    _bedB          = new BedFile(bedBFile);
-
-    if (_bamInput == false)
-        WindowIntersectBed();
-    else
-        WindowIntersectBam(_bedAFile);
-}
-
-
-
-/*
-    Destructor
-*/
-BedWindow::~BedWindow(void) {
-}
-
-
-
-void BedWindow::FindWindowOverlaps(const BED &a, vector<BED> &hits) {
-
-    /*
-        Adjust the start and end of a based on the requested window
-    */
-
-    // update the current feature's start and end
-    // according to the slop requested (slop = 0 by default)
-    CHRPOS aFudgeStart = 0;
-    CHRPOS aFudgeEnd;
-    AddWindow(a, aFudgeStart, aFudgeEnd);
-
-    /*
-        Now report the hits (if any) based on the window around a.
-    */
-    // get the hits in B for the A feature
-    _bedB->FindOverlapsPerBin(a.chrom, aFudgeStart, aFudgeEnd, a.strand, hits, _matchOnSameStrand, _matchOnDiffStrand);
-
-    int numOverlaps = 0;
-
-    // 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) {
-
-        int s = max(aFudgeStart, h->start);
-        int e = min(aFudgeEnd, h->end);
-        int overlapBases = (e - s);             // the number of overlapping bases b/w a and b
-        int aLength = (a.end - a.start);        // the length of a in b.p.
-
-        if (s < e) {
-            // is there enough overlap (default ~ 1bp)
-            if ( ((float) overlapBases / (float) aLength) > 0 ) {
-                numOverlaps++;
-                if (_anyHit == false && _noHit == false && _writeCount == false) {
-                    _bedA->reportBedTab(a);
-                    _bedB->reportBedNewLine(*h);
-                }
-            }
-        }
-    }
-    if (_anyHit == true && (numOverlaps >= 1)) {
-        _bedA->reportBedNewLine(a); }
-    else if (_writeCount == true) {
-        _bedA->reportBedTab(a); printf("\t%d\n", numOverlaps);
-    }
-    else if (_noHit == true && (numOverlaps == 0)) {
-        _bedA->reportBedNewLine(a);
-    }
-}
-
-
-bool BedWindow::FindOneOrMoreWindowOverlaps(const BED &a) {
-
-    // update the current feature's start and end
-    // according to the slop requested (slop = 0 by default)
-    CHRPOS aFudgeStart = 0;
-    CHRPOS aFudgeEnd;
-    AddWindow(a, aFudgeStart, aFudgeEnd);
-
-    bool overlapsFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _matchOnSameStrand, _matchOnDiffStrand);
-    return overlapsFound;
-}
-
-
-void BedWindow::WindowIntersectBed() {
-
-    // load the "B" bed file into a map so
-    // that we can easily compare "A" to it for overlaps
-    _bedB->loadBedFileIntoMap();
-
-    BED a, nullBed;
-    int lineNum = 0;                    // current input line number
-    BedLineStatus bedStatus;
-    vector<BED> hits;                   // vector of potential hits
-    hits.reserve(100);
-
-    _bedA->Open();
-    while ((bedStatus = _bedA->GetNextBed(a, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            FindWindowOverlaps(a, hits);
-            hits.clear();
-            a = nullBed;
-        }
-    }
-    _bedA->Close();
-}
-
-
-void BedWindow::WindowIntersectBam(string bamFile) {
-
-    // load the "B" bed file into a map so
-    // that we can easily compare "A" to it for overlaps
-    _bedB->loadBedFileIntoMap();
-
-    // open the BAM file
-    BamReader reader;
-    BamWriter writer;
-    reader.Open(bamFile);
-
-    // get header & reference information
-    string bamHeader  = reader.GetHeaderText();
-    RefVector refs    = reader.GetReferenceData();
-
-    // open a BAM output to stdout if we are writing BAM
-    if (_bamOutput == true) {
-        // set compression mode
-        BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
-        if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
-        writer.SetCompressionMode(compressionMode);
-        // open our BAM writer
-        writer.Open("stdout", bamHeader, refs);
-    }
-
-    vector<BED> hits;                   // vector of potential hits
-    // reserve some space
-    hits.reserve(100);
-
-    _bedA->bedType = 6;
-    BamAlignment bam;
-    bool overlapsFound;
-    // get each set of alignments for each pair.
-    while (reader.GetNextAlignment(bam)) {
-
-        if (bam.IsMapped()) {
-            BED a;
-            a.chrom = refs.at(bam.RefID).RefName;
-            a.start = bam.Position;
-            a.end   = bam.GetEndPosition(false, false);
-
-            // build the name field from the BAM alignment.
-            a.name = bam.Name;
-            if (bam.IsFirstMate()) a.name += "/1";
-            if (bam.IsSecondMate()) a.name += "/2";
-
-            a.score  = ToString(bam.MapQuality);
-            a.strand = "+"; if (bam.IsReverseStrand()) a.strand = "-";
-
-            if (_bamOutput == true) {
-                overlapsFound = FindOneOrMoreWindowOverlaps(a);
-                if (overlapsFound == true) {
-                    if (_noHit == false)
-                        writer.SaveAlignment(bam);
-                }
-                else {
-                    if (_noHit == true)
-                        writer.SaveAlignment(bam);
-                }
-            }
-            else {
-                FindWindowOverlaps(a, hits);
-                hits.clear();
-            }
-        }
-        // BAM IsMapped() is false
-        else if (_noHit == true) {
-            writer.SaveAlignment(bam);
-        }
-    }
-
-    // close the relevant BAM files.
-    reader.Close();
-    if (_bamOutput == true) {
-        writer.Close();
-    }
-}
-
-
-void BedWindow::AddWindow(const BED &a, CHRPOS &fudgeStart, CHRPOS &fudgeEnd) {
-    // Does the user want to treat the windows based on strand?
-    // If so,
-    // if "+", then left is left and right is right
-    // if "-", the left is right and right is left.
-    if (_strandWindows) {
-        if (a.strand == "+") {
-            if ((int) (a.start - _leftSlop) > 0) 
-                fudgeStart = a.start - _leftSlop;
-            else fudgeStart = 0;
-            fudgeEnd = a.end + _rightSlop;
-        }
-        else {
-            if ((int) (a.start - _rightSlop) > 0) 
-                fudgeStart = a.start - _rightSlop;
-            else fudgeStart = 0;
-            fudgeEnd = a.end + _leftSlop;
-        }
-    }
-    // If not, add the windows irrespective of strand
-    else {
-        if ((int) (a.start - _leftSlop) > 0) 
-            fudgeStart = a.start - _leftSlop;
-        else fudgeStart = 0;
-        fudgeEnd = a.end + _rightSlop;
-    }
-}
-