--- a/BEDTools-Version-2.14.3/src/multiBamCov/multiBamCov.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-/*****************************************************************************
-  multiBamCov.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 "multiBamCov.h"
-#include "api/BamMultiReader.h"
-
-
-/*
-    Constructor
-*/
-MultiCovBam::MultiCovBam(const vector<string> &bam_files, const string bed_file, 
-                         int minQual, bool properOnly,
-                         bool keepDuplicates, bool keepFailedQC)
-:
-_bam_files(bam_files),
-_bed_file(bed_file),
-_minQual(minQual),
-_properOnly(properOnly),
-_keepDuplicates(keepDuplicates),
-_keepFailedQC(keepFailedQC)
-{
-	_bed = new BedFile(_bed_file);
-    LoadBamFileMap();
-}
-
-
-/*
-    Destructor
-*/
-MultiCovBam::~MultiCovBam(void) 
-{}
-
-
-
-void MultiCovBam::CollectCoverage()
-{
-    BamMultiReader reader;
-    
-    if ( !reader.Open(_bam_files) )
-    {
-        cerr << "Could not open input BAM files." << endl;
-        exit(1);
-    }
-    else
-    {
-        // attempt to find index files
-        reader.LocateIndexes();
-
-        // if index data available for all BAM files, we can use SetRegion
-        if ( reader.HasIndexes() ) {
-            BED bed, nullBed;
-            int lineNum = 0;
-            BedLineStatus bedStatus;
-
-            _bed->Open();
-            // loop through each BED entry, jump to it, 
-            // and collect coverage from each BAM
-            while ((bedStatus = _bed->GetNextBed(bed, lineNum)) != BED_INVALID)
-            {
-                if (bedStatus == BED_VALID)
-                {
-                    // initialize counts for each file to 0
-                    vector<int> counts(_bam_files.size(), 0);
-                    // get the BAM refId for this chrom.
-                    int refId = reader.GetReferenceID(bed.chrom);
-                    // set up a BamRegion to which to attempt to jump
-                    BamRegion region(refId, (int)bed.start, refId, (int)bed.end);
-                    
-                    // everything checks out, just iterate through specified region, counting alignments
-                    if ( (refId != -1) && (reader.SetRegion(region)) ) {
-                        BamAlignment al;
-                        while ( reader.GetNextAlignment(al) )
-                        {
-                            bool duplicate = al.IsDuplicate();
-                            bool failedQC  = al.IsFailedQC();
-                            if (_keepDuplicates) duplicate = false;
-                            if (_keepFailedQC)    failedQC = false;
-                            // map qual must exceed minimum
-                            if ((al.MapQuality >= _minQual) && (!duplicate) && (!failedQC)) {
-                                // ignore if not properly paired and we actually care.
-                                if (_properOnly && !al.IsProperPair())
-                                    continue;
-
-                                // lookup the offset of the file name and tabulate 
-                                //coverage for the appropriate file
-                                counts[bamFileMap[al.Filename]]++;
-                            }
-                        }
-                    }
-                    // report the cov at this interval for each file and reset
-                    _bed->reportBedTab(bed);
-                    ReportCounts(counts);
-                    bed = nullBed;
-                }
-            }
-            _bed->Close();
-        }
-        else {
-            cerr << "Could not find indexes." << endl;
-            reader.Close();
-            exit(1);
-        }
-    }
-}
-
-
-void MultiCovBam::LoadBamFileMap(void) 
-{
-    for (size_t i = 0; i < _bam_files.size(); ++i)
-    {
-        bamFileMap[_bam_files[i]] = i;
-    }
-}
-
-void MultiCovBam::ReportCounts(const vector<int> &counts) 
-{
-    for (size_t i = 0; i < counts.size(); ++i)
-    {
-        if (i < counts.size() - 1)
-            cout << counts[i] << "\t";
-        else
-            cout << counts[i];
-    }
-    cout << endl;
-}