Mercurial > repos > devteam > picard1106
comparison fastq2sam_wrapper.sh @ 101:7d0d25eabacb draft
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author | devteam |
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date | Mon, 24 Feb 2014 22:56:46 -0500 |
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100:bd86ab3d004c | 101:7d0d25eabacb |
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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} 2>&1 | |
11 | |
12 if [ "$1" == "sam" ] | |
13 then | |
14 mv $2.sam $2 | |
15 fi |