for i in *1.sam.bam
 do
 echo $i
 /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mapkap1.fa > foo.bam;samtools view -h foo.bam | awk -f /data/images/proton/DKlab/mr/parclip/shrimp/sam2tc1.awk | samtools view -Sb -  > $i.tc.bam;cp foo.bam $i.md.bam
 samtools index $i.md.bam
 samtools index $i.tc.bam
done