--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/flankBed/flankBed.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,163 @@
+/*****************************************************************************
+  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);
+    }   
+}
+
+