diff --git a/Code_v1.5.1/python.calculateReadsDepthOfAmp.py b/Code_v1.5.1/python.calculateReadsDepthOfAmp.py
index 88656b5..9a49859 100644
--- a/Code_v1.5.1/python.calculateReadsDepthOfAmp.py
+++ b/Code_v1.5.1/python.calculateReadsDepthOfAmp.py
@@ -177,7 +177,7 @@ def MapReadinBamPCR(inBamFile, ampliconDic, ampTree, dedupOp, MQList):
             if(read.is_duplicate):
                 if(dedupOp=="true"):
                     continue
-            overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].search(read.pos+1, read.pos+read.alen+1) ## [start, end)
+            overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].overlap(read.pos+1, read.pos+read.alen+1) ## [start, end)
             if(len(overlapAmpTreeList)==0):
                 pass
             else:
@@ -242,7 +242,7 @@ def MapReadinBamHYB(inBamFile, ampliconDic, ampTree, dedupOp, MQList):
             if(read.is_duplicate):
                 if(dedupOp=="true"):
                     continue
-            overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].search(read.pos+1, read.pos+read.alen+1) ## [start, end)
+            overlapAmpTreeList=ampTree[inBam.getrname(read.rname).replace("chr","")].overlap(read.pos+1, read.pos+read.alen+1) ## [start, end)
             if(len(overlapAmpTreeList)==0):
                 pass
             else:          
diff --git a/Code_v1.5.1/python.getCNVPerSample.py b/Code_v1.5.1/python.getCNVPerSample.py
index c9dffad..a27df84 100644
--- a/Code_v1.5.1/python.getCNVPerSample.py
+++ b/Code_v1.5.1/python.getCNVPerSample.py
@@ -137,20 +137,20 @@ def getCandidateRegion(self, qType, CBSTree):
         #### UnifiedRegions ##############################
         UnifiedRegion={}
         ID=1
-        segmentList=CBSTree[self.chrom].search(self.start, self.end+1) 
+        segmentList=CBSTree[self.chrom].overlap(self.start, self.end+1) 
         segmentList=sorted(segmentList,key=itemgetter(1))
         for segment in segmentList:
           [segChr, segStart, segEnd, segNo, segMean]=segment[-1]
           if(self.qType=="dup"):
             dupList=[]
-            for overlapAmps in list(self.dupTree[segChr].search(segStart, segEnd)):
+            for overlapAmps in list(self.dupTree[segChr].overlap(segStart, segEnd)):
               dupList.append(overlapAmps[-1])
             if(dupList!=[] and len(dupList)>=minAmpCntInRegion):
               dupList=sorted(dupList,key=attrgetter('inS'))
               UnifiedRegion[self.sample+"_"+self.gene+"_"+"dup"+":"+str(ID)]=dupList  
           if(self.qType=="del"):
             delList=[]
-            for overlapAmps in list(self.delTree[segChr].search(segStart, segEnd)):
+            for overlapAmps in list(self.delTree[segChr].overlap(segStart, segEnd)):
               delList.append(overlapAmps[-1])
             if(delList!=[] and len(delList)>=minAmpCntInRegion):
               delList=sorted(delList,key=attrgetter('inS'))
@@ -519,4 +519,4 @@ def readCBSFile(inFileName, dupTh, delTh):
       getRegionCandidate(genePerSampleDic, outFileName, pTh, CBSTree,minAmpCntInRegion, dupTh, delTh, MQ)
       #except:
       #    print("Unexpected error:", sys.exc_info()[0])
-      #    print("Maybe all values are nan for "+inSample)
\ No newline at end of file
+      #    print("Maybe all values are nan for "+inSample)
diff --git a/Code_v1.5.1/python.scoreCNV.py b/Code_v1.5.1/python.scoreCNV.py
index 1b3d18d..bdd49bd 100644
--- a/Code_v1.5.1/python.scoreCNV.py
+++ b/Code_v1.5.1/python.scoreCNV.py
@@ -260,7 +260,7 @@ def filterOutSmallCNVs(outVDic, sampleCNVDic):
           if(score1>=score2 and cnvType1==cnvType2 and sample1==sample2 and chr1==chr2 and start1<=start2 and end1>=end2):
             if (score1==score2 and cnvType1==cnvType2 and sample1==sample2 and chr1==chr2 and start1==start2 and end1==end2):
               if(idx1<idx2):
-		FalseIDList.append(ID2)
+                FalseIDList.append(ID2)
 
   outVsList=[]
   for ID in outVDic.keys():