Mercurial > repos > jbrayet > controlsubset_1_0_docker
view createControlSubSet_wrapper.sh @ 3:342a53ff1fd6 draft default tip
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author | jbrayet |
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date | Tue, 02 Feb 2016 09:02:51 -0500 |
parents | 3b1e9f048405 |
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#!/bin/bash CONTROLFILE="" while getopts "f:c:t:o:s:q:p:" optionName; do case "$optionName" in f) CHIPFILE="$OPTARG";; c) CONTROLFILE="$OPTARG";; t) TYPE="$OPTARG";; s) CHIPOUTPUT="$OPTARG";; o) CONTROLOUTPUT="$OPTARG";; q) IFPROCSAMPLE="$OPTARG";; p) IFOUTSAM="$OPTARG";; esac done local_path=/usr/bin/controlsubset LOGTMP=$IFOUTSAM.log.tmp if [[ $IFPROCSAMPLE == "Yes" ]] then perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -s $CHIPOUTPUT -o $CONTROLOUTPUT >$LOGTMP 2>>$LOGTMP else perl $local_path/createControlSubSet.pl -f $CHIPFILE -c $CONTROLFILE -t $TYPE -o $CONTROLOUTPUT >>$LOGTMP 2>>$LOGTMP fi if [[ $TYPE == "bam" && $IFOUTSAM == "No" ]] then samtools view -S -b $CONTROLOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CONTROLOUTPUT 2>>$LOGTMP rm $CONTROLOUTPUT mv $CONTROLOUTPUT.bam $CONTROLOUTPUT if [[ $IFPROCSAMPLE == "Yes" ]] then samtools view -S -b $CHIPOUTPUT 2>>$LOGTMP | samtools sort -m 4000000000 - $CHIPOUTPUT 2>>$LOGTMP rm $CHIPOUTPUT mv $CHIPOUTPUT.bam $CHIPOUTPUT fi fi head -2 $LOGTMP if [ -r $LOGTMP ]; then rm $LOGTMP fi