--- a/BEDTools-Version-2.14.3/src/slopBed/slopBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-/*****************************************************************************
-  slopBed.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 "slopBed.h"
-
-
-BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) {
-
-    _bedFile     = bedFile;
-    _genomeFile  = genomeFile;
-    _forceStrand = forceStrand;
-    _leftSlop    = leftSlop;
-    _rightSlop   = rightSlop;
-    _fractional  = fractional; 
-
-    _bed    = new BedFile(bedFile);
-    _genome = new GenomeFile(genomeFile);
-
-    // get going, slop it up.
-    SlopBed();
-}
-
-
-BedSlop::~BedSlop(void) {
-
-}
-
-
-void BedSlop::SlopBed() {
-
-    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) {
-            if (_fractional == false) {
-                AddSlop(bedEntry, (int) _leftSlop, (int) _rightSlop);
-            }
-            else {
-                int leftSlop  = (int) (_leftSlop  * bedEntry.size());
-                int rightSlop = (int) (_rightSlop * bedEntry.size());
-                AddSlop(bedEntry, leftSlop, rightSlop);
-            }
-            _bed->reportBedNewLine(bedEntry);
-            bedEntry = nullBed;
-        }
-        bedStatus = _bed->GetNextBed(bedEntry, lineNum);
-    }
-    _bed->Close();
-}
-
-
-void BedSlop::AddSlop(BED &bed, int leftSlop, int rightSlop) {
-
-    // special handling if the BED entry is on the negative
-    // strand and the user cares about strandedness.
-    CHRPOS chromSize = _genome->getChromSize(bed.chrom);
-
-    if ( (_forceStrand) && (bed.strand == "-") ) {
-        // inspect the start
-        if ( (static_cast<int>(bed.start) - rightSlop) > 0 ) bed.start -= rightSlop;
-        else bed.start = 0;
-
-        // inspect the start
-        if ( (static_cast<int>(bed.end) + leftSlop) <= static_cast<int>(chromSize)) bed.end += leftSlop;
-        else bed.end = chromSize;
-    }
-    else {
-        // inspect the start
-        if ( (static_cast<int>(bed.start) - leftSlop) > 0) bed.start -= leftSlop;
-        else bed.start = 0;
-
-        // inspect the end
-        if ( (static_cast<int>(bed.end) + rightSlop) <= static_cast<int>(chromSize)) bed.end += rightSlop;
-        else bed.end = chromSize;
-    }
-}
-
-