awk -f /data/results/tools/formats/fastq2fasta.awk IL4-q25-m15.fastq  > IL4-q25-m15.fa

Oct 14 19:39 shrimp-map-genome1.sh
3200000 217856 10892.
Mon Oct 15 10:19:02 EEST 2018 (15h)

 10912770  10912770 270843628 /data/images/proton/DKlab/mr/parclip/raw/IL4-q25-m15.fa
(/ 10912770 2)
5456385
(/ 32 55.0)
0.5818181818181818
(/ 15 0.581)
25.817555938037867



 11380460  11380460 396024346 /data/images/proton/DKlab/mr/parclip/raw/IFN/ugc_604_10_F3.csfasta 
(/ 11380460 2)
5690230
5600000 741221 37061.
        Reads Matched:          5,688,413    (99.9681%)


for i in IL4-q25.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/shrimp/ref/shrimp/mm9.fa  >& /dev/null > foo.bam2
    samtools view -h foo.bam2  | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk2  > $i.md.bt
    mv foo.bam2 $i.md.bam
done