diff --git a/src/multiBamCov/multiBamCov.cpp b/src/multiBamCov/multiBamCov.cpp
index 920cbf96..1ec88e9e 100644
--- a/src/multiBamCov/multiBamCov.cpp
+++ b/src/multiBamCov/multiBamCov.cpp
@@ -22,7 +22,7 @@ MultiCovBam::MultiCovBam(const vector<string> &bam_files, const string bed_file,
                          bool keepDuplicates, bool keepFailedQC,
                          bool obeySplits, bool sameStrand, 
                          bool diffStrand, float overlapFraction,
-                         bool reciprocal)
+                         bool reciprocal, bool extendOneRead)
 :
 _bam_files(bam_files),
 _bed_file(bed_file),
@@ -34,7 +34,8 @@ _obeySplits(obeySplits),
 _sameStrand(sameStrand),
 _diffStrand(diffStrand),
 _overlapFraction(overlapFraction),
-_reciprocal(reciprocal)
+_reciprocal(reciprocal),
+_extendOneRead(extendOneRead)
 {
 	_bed = new BedFile(_bed_file);
     LoadBamFileMap();
@@ -157,6 +158,8 @@ void MultiCovBam::CollectCoverage()
                                 (_diffStrand && strands_are_same)   || 
                                 (al.MapQuality < _minQual)          ||
                                 (duplicate)                         ||
+                                (_extendOneRead && al.IsSecondMate()) ||
+                                (_extendOneRead && !al.IsProperPair()) ||
                                 (failedQC)
                             )
                             {
@@ -185,6 +188,32 @@ void MultiCovBam::CollectCoverage()
                                         counts[bamFileMap[al.Filename]]++;
                                 }
                             }
+                            else if (_extendOneRead) {
+                            	int al_start = al.Position;
+                            	if (al.IsReverseStrand()) 
+                            		al_start = al.MatePosition;
+								
+								int al_end = al.InsertSize + al_start;
+                            	                            		
+                                CHRPOS s = max(al.Position, (int) bed.start);
+                                CHRPOS e = min(al_end, (int) bed.end);
+                                CHRPOS aLength = (bed.end - bed.start);
+                                CHRPOS bLength = (al_end - al.Position);
+                                int overlapBases = (e - s);
+                                float aOverlap = 
+                                    ( (float) overlapBases / (float) aLength );
+                                float bOverlap = 
+                                    ( (float) overlapBases / (float) bLength );
+                                
+                                if ( aOverlap >= _overlapFraction) 
+                                {
+                                    if (!_reciprocal)
+                                        counts[bamFileMap[al.Filename]]++;
+                                    else if (bOverlap >= _overlapFraction)
+                                        counts[bamFileMap[al.Filename]]++;
+                                }
+                            	
+                            }
                             else {
                                 // break alignment into discrete blocks,
                                 bedVector bed_blocks, hits;
diff --git a/src/multiBamCov/multiBamCov.h b/src/multiBamCov/multiBamCov.h
index d0f96d80..87b66021 100644
--- a/src/multiBamCov/multiBamCov.h
+++ b/src/multiBamCov/multiBamCov.h
@@ -36,7 +36,7 @@ class MultiCovBam {
                 bool keepDuplicates, bool keepFailedQC,
                 bool obeySplits, bool sameStrand,
                 bool diffStrand, float overlapFraction,
-                bool reciprocal);
+                bool reciprocal, bool extendOneRead);
 
     // destructor
     ~MultiCovBam(void);
@@ -62,6 +62,7 @@ class MultiCovBam {
     bool _diffStrand;
     float _overlapFraction;
     bool _reciprocal;
+    bool _extendOneRead;
 
 
     map<string, int> bamFileMap;
diff --git a/src/multiBamCov/multiBamCovMain.cpp b/src/multiBamCov/multiBamCovMain.cpp
index 798a5a0c..5e806e75 100644
--- a/src/multiBamCov/multiBamCovMain.cpp
+++ b/src/multiBamCov/multiBamCovMain.cpp
@@ -46,6 +46,7 @@ int multibamcov_main(int argc, char* argv[]) {
     float overlapFraction = 1E-9;
     bool haveFraction       = false;
     bool reciprocalFraction = false;
+    bool extendOneRead		= false;
      
     // check to see if we should print out some help
     if(argc <= 1) showHelp = true;
@@ -121,11 +122,21 @@ int multibamcov_main(int argc, char* argv[]) {
         else if (PARAMETER_CHECK("-S", 2, parameterLength)) {
             diffStrand = true;
         }
+        else if (PARAMETER_CHECK("-E", 2, parameterLength)) {
+            extendOneRead = true;
+        }
         else {
             cerr << endl << "*****ERROR: Unrecognized parameter: " << 
                 argv[i] << " *****" << endl << endl;
             showHelp = true;
         }
+        
+        if (extendOneRead && (sameStrand || diffStrand)) 
+           cerr << endl << "*****ERROR: read extension cannot be used with strand constrains" << endl;
+        if (extendOneRead && obeySplits) 
+           cerr << endl << "*****ERROR: read extension cannot be used with split option" << endl;
+    	
+
     }
 
     if (!showHelp) {
@@ -134,7 +145,7 @@ int multibamcov_main(int argc, char* argv[]) {
                                           keepDuplicates, keepFailedQC,
                                           obeySplits, sameStrand,
                                           diffStrand, overlapFraction,
-                                          reciprocalFraction);
+                                          reciprocalFraction, extendOneRead);
         mc->CollectCoverage();
         delete mc;
     }
@@ -185,6 +196,8 @@ void multibamcov_help(void) {
     cerr << "\t-p\t"           << "Only count proper pairs.  Default counts all alignments with" << endl;
     cerr << "\t\t"             << "MAPQ > -q argument, regardless of the BAM FLAG field." << endl << endl;
 
+    cerr << "\t-E\t"           << "Extend one read (R1) to the extent of insert size" << endl << endl;
+
     // end the program here
     exit(1);