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comparison fastq2sam_wrapper.sh @ 96:55b6cd128a41 draft

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author devteam
date Mon, 24 Feb 2014 16:56:09 -0500
parents 86e7e072c4c9
children
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95:6ad4014eddd7 96:55b6cd128a41
1 #!/bin/bash
2
3 if [ "$1" == "sam" ]
4 then
5 output=$2.sam
6 else
7 output=$2
8 fi
9
10 java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "$JAVA_JAR_PATH/FastqToSam.jar" SAMPLE_NAME="$3" READ_GROUP_NAME="$4" OUTPUT=$output ${*:5}
11
12 if [ "$1" == "sam" ]
13 then
14 mv $2.sam $2
15 fi