Mercurial > repos > devteam > picard1106
view fastq2sam_wrapper.sh @ 136:aab4fc9d443d draft
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author | devteam |
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date | Wed, 26 Feb 2014 17:30:53 -0500 |
parents | 7d0d25eabacb |
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#!/bin/bash if [ "$1" == "sam" ] then output=$2.sam else output=$2 fi java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "$JAVA_JAR_PATH/FastqToSam.jar" SAMPLE_NAME="$3" READ_GROUP_NAME="$4" OUTPUT=$output ${*:5} 2>&1 if [ "$1" == "sam" ] then mv $2.sam $2 fi