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changeset 96:55b6cd128a41 draft

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Uploaded
author devteam
date Mon, 24 Feb 2014 16:56:09 -0500
parents 6ad4014eddd7
children 7aa4e1ac9d99
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 16:56:09 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