Merge branch 'single_dedup' of https://github.com/aidenlab/juicer into single_dedup

    fi

    cat $splitdir/*.res.txt | awk -v ligation=$ligation -v dups=$dups -f ${juiceDir}/scripts/common/stats_sub.awk >> $outputdir/inter.txt

    cp $outputdir/inter.txt $outputdir/inter_30.txt

    if [ $singleend -eq 1 ] 

    then

	for i in {1..5}; do echo $i >> $outputdir/tmp; done 

	echo 0 > $outputdir/tmp2 

	cp $outputdir/tmp2 $outputdir/tmp3   

	for i in {1..29}; do echo $i >> $outputdir/tmp3; done

	echo -ne "Below MAPQ1 (Paired): " >> $outputdir/inter.txt

	samtools view $sthreadstring -F 3852 -D rt:$outputdir/tmp -h $outputdir/merged_dedup.bam | samtools view $sthreadstring -D MQ:$outputdir/tmp2 | awk '{print $1}' | uniq | wc -l >> $outputdir/inter.txt

	echo -ne "Below MAPQ30 (Paired): " >> $outputdir/inter_30.txt

	samtools view $sthreadstring -F 3852 -D rt:$outputdir/tmp -h $outputdir/merged_dedup.bam | samtools view $sthreadstring -D MQ:$outputdir/tmp3 | awk '{print $1}' | uniq | wc -l >> $outputdir/inter_30.txt

	rm $outputdir/tmp*

    fi                                

    if [ $assembly -eq 1 ] 

    then

	${juiceDir}/scripts/common/juicer_tools statistics $site_file $outputdir/inter.txt $outputdir/merged1.txt none

	${juiceDir}/scripts/common/juicer_tools statistics $site_file $outputdir/inter_30.txt $outputdir/merged30.txt none

    else

	${juiceDir}/scripts/common/juicer_tools statistics $site_file $outputdir/inter.txt $outputdir/merged1.txt $genomeID

	${juiceDir}/scripts/common/juicer_tools statistics $site_file $outputdir/inter_30.txt $outputdir/merged30.txt $genomeID

    fi

    # if early exit, we stop here, once the stats are calculated

    if [ ! -z "$earlyexit" ]