--- a/BEDTools-Version-2.14.3/src/utils/BamTools-Ancillary/BamAncillary.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,73 +0,0 @@
-/*****************************************************************************
-  bamAncillary.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 "BamAncillary.h"
-using namespace std;
-
-// 10   15   20      25    30               4000
-// acccctttggacct---ataggga.................aaaa
-// acccc---ggaccttttataggga.................aaaa
-// 5M   3D 6M    2I 7M      20N             4M
-
-namespace BamTools {
-    void getBamBlocks(const BamAlignment &bam, const RefVector &refs,
-                      vector<BED> &blocks, bool breakOnDeletionOps) {
-
-        CHRPOS currPosition = bam.Position;
-        CHRPOS blockStart   = bam.Position;
-        string chrom        = refs.at(bam.RefID).RefName;
-        string name         = bam.Name;
-        string strand       = "+";
-        string score        = ToString(bam.MapQuality);
-        char  prevOp        = '\0';
-        if (bam.IsReverseStrand()) strand = "-";
-        bool blocksFound = false;
-
-        vector<CigarOp>::const_iterator cigItr = bam.CigarData.begin();
-        vector<CigarOp>::const_iterator cigEnd = bam.CigarData.end();
-        for ( ; cigItr != cigEnd; ++cigItr ) {
-            if (cigItr->Type == 'M') {
-                currPosition += cigItr->Length;
-                // we only want to create a new block if the current M op
-                // was preceded by an N op or a D op (and we are breaking on D ops)
-                if ((prevOp == 'D' && breakOnDeletionOps == true) || (prevOp == 'N')) {
-                    blocks.push_back( BED(chrom, blockStart, currPosition, name, score, strand) );
-                    blockStart = currPosition;
-                }
-            }
-            else if (cigItr->Type == 'D') {
-                if (breakOnDeletionOps == false)
-                    currPosition += cigItr->Length;
-                else {
-                    currPosition += cigItr->Length;
-                    blockStart    = currPosition;
-                }
-            }
-            else if (cigItr->Type == 'N') {
-                currPosition += cigItr->Length;
-                blockStart    = currPosition;
-            }
-            else if (cigItr->Type == 'S' || cigItr->Type == 'H' || cigItr->Type == 'P' || cigItr->Type == 'I') {
-                // do nothing
-            }
-            else {
-                cerr << "Input error: invalid CIGAR type (" << cigItr->Type
-                    << ") for: " << bam.Name << endl;
-                exit(1);
-            }
-            prevOp = cigItr->Type;
-        }
-        // if there were no splits, we just create a block representing the contiguous alignment.
-        if (blocksFound == false) {
-            blocks.push_back( BED(chrom, bam.Position, currPosition, name, score, strand) );
-        }
-    }
-}