--- a/BEDTools-Version-2.14.3/src/flankBed/flankBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,163 +0,0 @@
-/*****************************************************************************
-  flankBed.cpp
-
-  (c) 2009 - Aaron Quinlan
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licensed under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include "lineFileUtilities.h"
-#include "flankBed.h"
-
-
-BedFlank::BedFlank(string &bedFile, string &genomeFile, bool forceStrand, float leftFlank, float rightFlank, bool fractional) {
-
-    _bedFile      = bedFile;
-    _genomeFile   = genomeFile;
-    _forceStrand  = forceStrand;
-    _leftFlank    = leftFlank;
-    _rightFlank   = rightFlank;
-    _fractional   = fractional; 
-
-    _bed    = new BedFile(bedFile);
-    _genome = new GenomeFile(genomeFile);
-
-    // get going, slop it up.
-    FlankBed();
-}
-
-
-BedFlank::~BedFlank(void) {
-
-}
-
-
-void BedFlank::FlankBed() {
-
-    int lineNum = 0;
-    BED bedEntry, nullBed;     // used to store the current BED line from the BED file.
-    BedLineStatus bedStatus;
-
-    _bed->Open();
-    bedStatus = _bed->GetNextBed(bedEntry, lineNum);
-    while (bedStatus != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-
-            int leftFlank  = _leftFlank;
-            int rightFlank = _rightFlank;            
-            if (_fractional == true) {
-                leftFlank  = (int) (_leftFlank  * bedEntry.size());
-                rightFlank = (int) (_rightFlank * bedEntry.size());
-            }
-            
-            if ((_forceStrand == false) || (bedEntry.strand == "+"))
-            {
-                AddFlank(bedEntry,  leftFlank, rightFlank);
-            }
-            else if ((_forceStrand == true) && (bedEntry.strand == "-" ))
-            {
-                AddStrandedFlank(bedEntry,  leftFlank, rightFlank);                    
-            }
-            bedEntry = nullBed;
-        }
-        bedStatus = _bed->GetNextBed(bedEntry, lineNum);
-    }
-    _bed->Close();
-}
-
-
-void BedFlank::AddFlank(BED &bed, int leftFlank, int rightFlank) {
-
-    int chromSize = _genome->getChromSize(bed.chrom);
-    if (chromSize == -1) {
-        cerr << "ERROR: chrom \"" << bed.chrom << "\" not found in genome file. Exiting." << endl;
-        exit(1);
-    }
-
-    // init. our left and right flanks to the original BED entry.
-    // we'll create the flanks from these coordinates.
-    BED left  = bed;
-    BED right = bed;
-    
-    // make the left flank (if necessary)
-    if (leftFlank > 0) {
-        if ( (static_cast<int>(left.start) - leftFlank) > 0) 
-        {
-            left.end    = left.start;
-            left.start -= leftFlank;
-        }
-        else 
-        {
-            left.end    = left.start;
-            left.start  = 0;
-        }
-        // report the left flank
-        _bed->reportBedNewLine(left);
-    }
-    
-    // make the left flank (if necessary)
-    if (rightFlank > 0) {
-        if ( (static_cast<int>(right.end) + (rightFlank+1)) <= static_cast<int>(chromSize)) 
-        {
-            right.start    = right.end;
-            right.end     += (rightFlank);
-        }
-        else {
-            right.start    = right.end;
-            right.end     += chromSize;
-        }
-        // report the right flank
-        _bed->reportBedNewLine(right);
-    }    
-}
-
-
-void BedFlank::AddStrandedFlank(BED &bed, int leftFlank, int rightFlank) {
-
-    int chromSize = _genome->getChromSize(bed.chrom);
-    if (chromSize == -1) {
-        cerr << "ERROR: chrom \"" << bed.chrom << "\" not found in genome file. Exiting." << endl;
-        exit(1);
-    }
-
-    // init. our left and right flanks to the original BED entry.
-    // we'll create the flanks from these coordinates.
-    BED left  = bed;
-    BED right = bed;
-    
-    // make the left flank (if necessary)
-    if (rightFlank > 0) {
-        if ( (static_cast<int>(left.start) - rightFlank) > 0) 
-        {
-            left.end    = left.start;
-            left.start -= rightFlank;
-        }
-        else 
-        {
-            left.end    = left.start;
-            left.start  = 0;
-        }
-        // report the left flank
-        _bed->reportBedNewLine(left);
-    }
-    
-    // make the left flank (if necessary)
-    if (leftFlank > 0) {
-        if ( (static_cast<int>(right.end) + leftFlank) <= static_cast<int>(chromSize)) 
-        {
-            right.start    = right.end;
-            right.end     += leftFlank;
-        }
-        else {
-            right.start    = right.end;
-            right.end      = chromSize;
-        }
-        // report the right flank
-        _bed->reportBedNewLine(right);
-    }   
-}
-
-