Mercurial > repos > devteam > picard1106

view fastq2sam_wrapper.sh @ 142:844fa42ad305 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author devteam
date Thu, 27 Feb 2014 13:15:52 -0500
parents 7d0d25eabacb
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} 2>&1

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