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view fastq2sam_wrapper.sh @ 143:b2ca2d181fb4 draft

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fixed downsample sam in picard1106 (accept bam)
author Rayan Chikhi <chikhi@psu.edu>
date Mon, 16 Jun 2014 17:38:15 -0400
parents 7d0d25eabacb
children
line wrap: on
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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