diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..1875aef
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,3 @@
+bin/
+!bin/config/
+DirCMake/
diff --git a/src/ProcessPairs.cpp b/src/ProcessPairs.cpp
index a320563..8e4962b 100644
--- a/src/ProcessPairs.cpp
+++ b/src/ProcessPairs.cpp
@@ -48,7 +48,6 @@ void ProcessBAM::Initialize(std::string bamfilename, int nOfExp, int padd, int r
     bLog << bamfilename << "  opened" << std::endl;
     
     // retrieve 'metadata' from BAM files, these are required by BamWriter
-    const SamHeader header = reader.GetHeader();
     const RefVector references = reader.GetReferenceData();
     
     // Make a map of chr names to RefIDs
@@ -113,9 +112,13 @@ void ProcessBAM::ProcessSortedBamFile_NegCtrls(ProbeSet& ProbeClass, RESitesClas
 			probeRegion.RightPosition =  Design_NegCtrl[DesignName].Probes[i].end + padding;
 		}
 		else if(Design_NegCtrl[DesignName].Probes[i].side=="R"){
-			probeRegion.LeftPosition =  Design_NegCtrl[DesignName].Probes[i].start- padding;;
+			probeRegion.LeftPosition =  Design_NegCtrl[DesignName].Probes[i].start - padding;
 			probeRegion.RightPosition =  Design_NegCtrl[DesignName].Probes[i].end;
 		}
+		else if(Design_NegCtrl[DesignName].Probes[i].side=="M"){
+			probeRegion.LeftPosition =  Design_NegCtrl[DesignName].Probes[i].start - padding;
+			probeRegion.RightPosition =  Design_NegCtrl[DesignName].Probes[i].end  + padding;
+		}
 		
 		reader.SetRegion(probeRegion);
 
@@ -237,9 +240,13 @@ void ProcessBAM::ProcessSortedBAMFile(ProbeSet& ProbeClass, RESitesClass& dpnII,
 			probeRegion.RightPosition =  Design[DesignName].Probes[i].end + padding;
 		}
 		else if(Design[DesignName].Probes[i].side=="R"){
-			probeRegion.LeftPosition =  Design[DesignName].Probes[i].start- padding;;
+			probeRegion.LeftPosition =  Design[DesignName].Probes[i].start - padding;
 			probeRegion.RightPosition =  Design[DesignName].Probes[i].end;
 		}
+		else if(Design[DesignName].Probes[i].side=="M"){
+			probeRegion.LeftPosition =  Design[DesignName].Probes[i].start - padding;
+			probeRegion.RightPosition =  Design[DesignName].Probes[i].end + padding;
+		}
 		
 		reader.SetRegion(probeRegion);
 		while(reader.GetNextAlignmentCore(al)){
@@ -368,9 +375,13 @@ void ProcessBAM::ProcessSortedBAMFile(ProbeSet& ProbeClass, RESitesClass& dpnII,
 			probeRegion.RightPosition =  Design_NegCtrl[DesignName].Probes[i].end + padding;
 		}
 		else if(Design_NegCtrl[DesignName].Probes[i].side=="R"){
-			probeRegion.LeftPosition =  Design_NegCtrl[DesignName].Probes[i].start- padding;;
+			probeRegion.LeftPosition =  Design_NegCtrl[DesignName].Probes[i].start - padding;
 			probeRegion.RightPosition =  Design_NegCtrl[DesignName].Probes[i].end;
 		}
+		else if(Design_NegCtrl[DesignName].Probes[i].side=="M"){
+			probeRegion.LeftPosition =  Design_NegCtrl[DesignName].Probes[i].start - padding;
+			probeRegion.RightPosition =  Design_NegCtrl[DesignName].Probes[i].end + padding;
+		}
 		
 		reader.SetRegion(probeRegion);