Mercurial > repos > devteam > picard1106
diff fastq2sam_wrapper.sh @ 1:86e7e072c4c9 draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 23 Jan 2014 19:31:52 -0500 |
| parents | |
| children |
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--- /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