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1 #!/bin/bash
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2
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3 CONTROLFILE=""
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4
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5 while getopts "f:c:t:o:s:q:p:" optionName; do
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6 case "$optionName" in
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7
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8 f) CHIPFILE="$OPTARG";;
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9 c) CONTROLFILE="$OPTARG";;
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10 t) TYPE="$OPTARG";;
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11 s) CHIPOUTPUT="$OPTARG";;
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12 o) CONTROLOUTPUT="$OPTARG";;
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13 q) IFPROCSAMPLE="$OPTARG";;
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14 p) IFOUTSAM="$OPTARG";;
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15
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16 esac
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17 done
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18
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19 local_path=/usr/bin/controlsubset
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20
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21 LOGTMP=$IFOUTSAM.log.tmp
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22
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23 if [[ $IFPROCSAMPLE == "Yes" ]]
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24 then
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25 perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -s $CHIPOUTPUT -o $CONTROLOUTPUT >$LOGTMP 2>>$LOGTMP
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26 else
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27 perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -o $CONTROLOUTPUT >>$LOGTMP 2>>$LOGTMP
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28 fi
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29
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30 if [[ $TYPE == "bam" && $IFOUTSAM == "No" ]]
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31 then
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32
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33 samtools view -S -b $CONTROLOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CONTROLOUTPUT 2>>$LOGTMP
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34 rm $CONTROLOUTPUT
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35 mv $CONTROLOUTPUT.bam $CONTROLOUTPUT
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36
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37 if [[ $IFPROCSAMPLE == "Yes" ]]
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38 then
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39 samtools view -S -b $CHIPOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CHIPOUTPUT 2>>$LOGTMP
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40 rm $CHIPOUTPUT
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41 mv $CHIPOUTPUT.bam $CHIPOUTPUT
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42 fi
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43 fi
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44
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45 head -2 $LOGTMP
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46 if [ -r $LOGTMP ]; then
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47 rm $LOGTMP
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48 fi
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