mv IL4-15mMm.bam.md.bam IL4-15mMm.bam.md.bam2
for i in *md.bam
do
    echo $i
    # add MD flags for bowtie format
    samtools view -h $i  | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk2  > $i.bt2
done
IL4-15mMm.bam.md.bam2 IL4-15mMm.bam.md.bam