--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/slopBed/slopBed.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,91 @@
+/*****************************************************************************
+  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;
+    }
+}
+
+