Mercurial > repos > devteam > picard1106
changeset 101:7d0d25eabacb draft
Uploaded
| author | devteam |
|---|---|
| date | Mon, 24 Feb 2014 22:56:46 -0500 |
| parents | bd86ab3d004c |
| children | cd321dcb66d5 |
| files | fastq2sam_wrapper.sh |
| diffstat | 1 files changed, 15 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq2sam_wrapper.sh Mon Feb 24 22:56:46 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} 2>&1 + +if [ "$1" == "sam" ] +then + mv $2.sam $2 +fi