# HG changeset patch # User devteam # Date 1390523512 18000 # Node ID 86e7e072c4c9f402753b6e4cf3149bd5f0704cc5 # Parent 8b335563c71a097f177c6cf0cf87ddc847c8e62a Uploaded diff -r 8b335563c71a -r 86e7e072c4c9 fastq2sam_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq2sam_wrapper.sh Thu Jan 23 19:31:52 2014 -0500 @@ -0,0 +1,15 @@ +#!/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