for i in 2h*Mm2.bam	 
do
    echo $i
    # add MD flags for bowtie format
    /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-stranded/Mus_musculus.NCBIM37.64-toMM9.fa  >& /dev/null > foo.bam2
 samtools view -h foo.bam2  | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk  > $i.md.bt
    mv foo.bam2 $i.md.bam
done