adding RG tag for single end, moving the bam job later in thee e sequence

	# RG group; ID derived from paired-end name, sample and library can be user set

	if [ $singleend -eq 1 ]

	then

	    rg="@RG\\tID:${jname%%.fastq*}\\tSM:${sampleName}\\tLB:${libraryName}"

	    rg="@RG\\tID:${jname%%.fastq*}\\tSM:${sampleName}\\tPL:LS454\\tLB:${libraryName}"

	else

	    rg="@RG\\tID:${jname%%.fastq*}\\tSM:${sampleName}\\tPL:ILM\\tLB:${libraryName}"

	fi

    sbatch_wait2="#SBATCH -d afterok:$jid2"

    sbatch_wait0="#SBATCH -d afterok:$jid1:$jid2"

    jid=`sbatch <<- PRESTATS | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH -p $queue

	#SBATCH -o $debugdir/prestats-%j.out

	#SBATCH -e $debugdir/prestats-%j.err

	#SBATCH -t $queue_time

	${sbatch_cpu_alloc} 

	#SBATCH --ntasks=1

	#SBATCH --mem-per-cpu=1G

	#SBATCH -J "${groupname}_prestats"

	${sbatch_wait}

	$userstring

	${load_awk}

        date

        ${load_java}

	${load_samtools}

        export IBM_JAVA_OPTIONS="-Xmx1024m -Xgcthreads1"

        export _JAVA_OPTIONS="-Xmx1024m -Xms1024m"

        tail -n1 $headfile | awk '{printf"%-1000s\n", \\\$0}' > $outputdir/inter.txt

	# count duplicates via samtools view -c

	# for paired end, count only first in pair to avoid double counting

	if [ $singleend -eq 1 ] 

	then 

		if [ -f $outputdir/merged_dedup.bam ]

		then

			samtools view $sthreadstring -f 1024 -F 256 $outputdir/merged_dedup.bam | awk '{if (\\\$0~/rt:A:7/){singdup++}else{dup++}}END{print dup,singdup}' > $outputdir/tmp

		else

			awk 'and(\\\$2,1024)>0 && and(\\\$2,256)==0{if (\\\$0~/rt:A:7/){singdup++}else{dup++}}END{print dup,singdup}' $outputdir/merged_dedup.sam > $outputdir/tmp 

		fi

		cat $splitdir/*.res.txt | awk -v fname=$outputdir/tmp -v ligation=$ligation -v singleend=1 -f ${juiceDir}/scripts/stats_sub.awk >> $outputdir/inter.txt

	else 

		if [ -f $outputdir/merged_dedup.bam ] 

		then

			samtools view $sthreadstring -c -f 1089 -F 256 $outputdir/merged_dedup.bam > $outputdir/tmp

		else

		        awk 'and(\\\$2,1024)>0 && and(\\\$2,1)>0 && and(\\\$2,64)>0 && and(\\\$2,256)==0{dup++}END{print dup}' $outputdir/merged_dedup.sam > $outputdir/tmp

		fi

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

	fi

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

        date

PRESTATS`

    sbatch_wait000="${sbatch_wait1}:$jid"

    jid=`sbatch <<- BAMRM  | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH -p $queue

METH`

    fi

    jid=`sbatch <<- PRESTATS | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH -p $queue

	#SBATCH -o $debugdir/prestats-%j.out

	#SBATCH -e $debugdir/prestats-%j.err

	#SBATCH -t $queue_time

	${sbatch_cpu_alloc} 

	#SBATCH --ntasks=1

	#SBATCH --mem-per-cpu=1G

	#SBATCH -J "${groupname}_prestats"

	${sbatch_wait}

	$userstring

	${load_awk}

        date

        ${load_java}

	${load_samtools}

        export IBM_JAVA_OPTIONS="-Xmx1024m -Xgcthreads1"

        export _JAVA_OPTIONS="-Xmx1024m -Xms1024m"

        tail -n1 $headfile | awk '{printf"%-1000s\n", \\\$0}' > $outputdir/inter.txt

	# count duplicates via samtools view -c

	# for paired end, count only first in pair to avoid double counting

	if [ $singleend -eq 1 ] 

	then 

		samtools view $sthreadstring -c -f 1024 -F 256 $outputdir/merged_dedup.*am > $outputdir/tmp

	else 

		samtools view $sthreadstring -c -f 1089 -F 256 $outputdir/merged_dedup.*am > $outputdir/tmp

	fi

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

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

	rm $outputdir/tmp

	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.*am | 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.*am | samtools view $sthreadstring -D MQ:$outputdir/tmp3 | awk '{print \\\$1}' | uniq | wc -l >> $outputdir/inter_30.txt 

		rm $outputdir/tmp*

	fi

        date

PRESTATS`

    sbatch_wait0="${sbatch_wait1}:$jid"

    sbatch_wait00="${sbatch_wait2}:$jid"

    jid=`sbatch <<- STATS | egrep -o -e "\b[0-9]+$"

	#!/bin/bash -l

	#SBATCH --ntasks=1

	#SBATCH --mem=25G

	#SBATCH -J "${groupname}_stats"

	${sbatch_wait0}

	${sbatch_wait000}

        $userstring			

	date

	samtools view $sthreadstring -O SAM -F 1024 $outputdir/merged_dedup.*am | awk -v mnd=1 -f ${juiceDir}/scripts/sam_to_pre.awk > ${outputdir}/merged_nodups.txt 

	date

MND`

	    sbatch_wait1="afterok:$jid"

	    sbatch_wait1="#SBATCH -d afterok:$jid"

	fi

	jid=`sbatch <<- FINCLN1 | egrep -o -e "\b[0-9]+$"