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view fastq2sam_wrapper.sh @ 22:b0585923decc draft

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author devteam
date Tue, 11 Feb 2014 18:43:11 -0500
parents 86e7e072c4c9
children
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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}

if [ "$1" == "sam" ]
then
    mv $2.sam $2
fi