Mercurial > repos > devteam > picard1106

diff fastq2sam_wrapper.sh @ 101:7d0d25eabacb draft

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author devteam
date Mon, 24 Feb 2014 22:56:46 -0500
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--- /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