add mapq30 haploid accessibility

    export SHELL=$(type -p bash)

    export junction_rt_string=${junction_rt_string}

    doit () {

            samtools view -@ 2 ${junction_rt_string} -h reads.sorted.bam $1 | awk 'BEGIN{OFS="\t"}{for (i=12; i<=NF; i++) {if ($i ~ /^ip/) {split($i, ip, ":"); locus[ip[3]]++; break}}}END{for (i in locus) {print $3, i-1, i, locus[i]}}' | sort -k2,2n -S6G

            mapq=$2

            samtools view -@ 2 ${junction_rt_string} -q $mapq -h reads.sorted.bam $1 | awk 'BEGIN{OFS="\t"}{for (i=12; i<=NF; i++) {if ($i ~ /^ip/) {split($i, ip, ":"); locus[ip[3]]++; break}}}END{for (i in locus) {print $3, i-1, i, locus[i]}}' | sort -k2,2n -S6G

    }

    export -f doit

    awk '{print $1}' $chrom_sizes | parallel -j $threads --will-cite --joblog temp.log -k doit > tmp.bedgraph

    # mapq1 accessibility track

    awk '{print $1}' $chrom_sizes | parallel -j $threads --will-cite --joblog temp.log -k doit {} 1 > tmp.bedgraph

    exitval=`awk 'NR>1{if($7!=0){c=1; exit}}END{print c+0}' temp.log`

	[ $exitval -eq 0 ] || { echo ":( Pipeline failed at building diploid contact maps. See stderr for more info. Exiting! " | tee -a /dev/stderr && exit 1; }

	rm temp.log

    bedGraphToBigWig tmp.bedgraph $chrom_sizes inter.bw

    rm tmp.bedgraph

    # mapq30 accessibility track

    awk '{print $1}' $chrom_sizes | parallel -j $threads --will-cite --joblog temp.log -k doit {} 30 > tmp.bedgraph

    exitval=`awk 'NR>1{if($7!=0){c=1; exit}}END{print c+0}' temp.log`

	[ $exitval -eq 0 ] || { echo ":( Pipeline failed at building diploid contact maps. See stderr for more info. Exiting! " | tee -a /dev/stderr && exit 1; }

	rm temp.log

    bedGraphToBigWig tmp.bedgraph $chrom_sizes inter_30.bw

    rm tmp.bedgraph

    echo ":) Done building accessibility tracks." >&1

	[ "$last_stage" == "dhs" ] && { echo "Done with the requested workflow. Exiting after building haploid accessibility tracks!"; exit; }

    fi

    # build mnd file

    # build mnd file: can do without sort -n, repeat what was done in hic stage.

    export SHELL=$(type -p bash)

	export psf=${psf}

	export pipeline=${phaser_dir}