@@ -83,18 +83,22 @@ function(bam1,bam2,refFsa,regChr,regStart,regEnd,minBaseQuality = 13,

 			testDf <- data.frame(chr = testTmp2[,1],testMtx,stringsAsFactors=FALSE)

 			## for genotype duplicated positions, trace back

-			countMtxDup <- countMtx[!maxBaseIndex & !allZeroIndex,]

-			countMtxDupDf <- as.data.frame(countMtxDup[duplicated(countMtxDup[,-11]),,drop=FALSE],stringsAsFactors=FALSE)

+			countMtxDup <- countMtx[!maxBaseIndex & !allZeroIndex,,drop=FALSE]

+			countMtxDupDf <- as.data.frame(countMtxDup[duplicated(countMtxDup[,-11,drop=FALSE]),,drop=FALSE],stringsAsFactors=FALSE)

-			if(nrow(countMtxDupDf) > 0){

+			if(nrow(countMtxDupDf) > 0 & nrow(testDf) > 0){

+				

+				countMtxDupDfFull <- cbind(countMtxDupDf,testDf[match(apply(countMtxDupDf[,-11,drop=FALSE],1,paste,collapse=' '),apply(testDf[,3:12],1,paste,collapse=' ')),c('X12','X13')])

+				countMtxDupDfFull <- countMtxDupDfFull[!is.na(countMtxDupDfFull$X12),,drop=FALSE]

+				

+				if(nrow(countMtxDupDfFull) > 0){

+					countMtxDupDfFull[,'X14'] <- unique(testDf$chr)

+					countMtxDupDfFull <- countMtxDupDfFull[,c(14,11,1:10,12,13)]

+					colnames(countMtxDupDfFull) <- colnames(testDf)

+					testDf <- rbind(testDf,countMtxDupDfFull)

+					testDf <- testDf[order(testDf[,'X1']),]

+				}

-				countMtxDupDfFull <- cbind(countMtxDupDf,testDf[match(apply(countMtxDupDf[,-11],1,paste,collapse=' '),apply(testDf[,3:12],1,paste,collapse=' ')),c('X12','X13')])

-				countMtxDupDfFull <- countMtxDupDfFull[!is.na(countMtxDupDfFull$X12),]

-				countMtxDupDfFull[,'X14'] <- unique(testDf$chr)

-				countMtxDupDfFull <- countMtxDupDfFull[,c(14,11,1:10,12,13)]

-				colnames(countMtxDupDfFull) <- colnames(testDf)

-				testDf <- rbind(testDf,countMtxDupDfFull)

-				testDf <- testDf[order(testDf[,'X1']),]

 			}

 			return(testDf)