Mercurial > repos > devteam > picard1106

view fastq2sam_wrapper.sh @ 14:ad8b197f7d3a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author devteam
date Sat, 01 Feb 2014 20:20:49 -0500
parents 86e7e072c4c9
children
line wrap: on
line source

#!/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