--- a/BEDTools-Version-2.14.3/src/complementBed/complementBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-/*****************************************************************************
-  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++;
-        }
-    }
-}
-