--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/complementBed/complementBed.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,83 @@
+/*****************************************************************************
+  complementBed.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 "complementBed.h"
+
+BedComplement::BedComplement(string &bedFile, string &genomeFile) {
+
+    _bedFile = bedFile;
+    _genomeFile = genomeFile;
+
+    _bed    = new BedFile(bedFile);
+    _genome = new GenomeFile(genomeFile);
+
+}
+
+
+BedComplement::~BedComplement(void) {
+}
+
+
+//
+// Merge overlapping BED entries into a single entry
+//
+void BedComplement::ComplementBed() {
+
+    // load the "B" bed file into a map so
+    // that we can easily compare "A" to it for overlaps
+    _bed->loadBedFileIntoMapNoBin();
+
+    // get a list of the chroms in the user's genome
+    vector<string> chromList =  _genome->getChromList();
+
+    // process each chrom in the genome
+    for (size_t c = 0; c < chromList.size(); ++c) {
+        string currChrom = chromList[c];
+
+        // create a "bit vector" for the chrom
+        CHRPOS currChromSize = _genome->getChromSize(currChrom);
+        vector<bool> chromMasks(currChromSize, 0);
+
+        // mask the chrom for every feature in the BED file
+        bedVector::const_iterator bItr = _bed->bedMapNoBin[currChrom].begin();
+        bedVector::const_iterator bEnd = _bed->bedMapNoBin[currChrom].end();
+        for (; bItr != bEnd; ++bItr) {
+            if (bItr->end > currChromSize) {
+                cout << "Warninge: end of BED entry exceeds chromosome length. Please correct." << endl;
+                _bed->reportBedNewLine(*bItr);
+                exit(1);
+            }
+
+            // mask all of the positions spanned by this BED entry.
+            for (CHRPOS b = bItr->start; b < bItr->end; b++)
+                chromMasks[b] = 1;
+        }
+
+        // report the unmasked, that is, complemented parts of the chrom
+        CHRPOS i = 0;
+        CHRPOS start;
+        while (i < chromMasks.size()) {
+            if (chromMasks[i] == 0) {
+                start = i;
+                while ((chromMasks[i] == 0) && (i < chromMasks.size()))
+                    i++;
+
+                if (start > 0)
+                    cout << currChrom << "\t" << start << "\t" << i << endl;
+                else
+                    cout << currChrom << "\t" << 0 << "\t" << i << endl;
+            }
+            i++;
+        }
+    }
+}
+