Mercurial > repos > devteam > picard1106
annotate fastq2sam_wrapper.sh @ 23:0688aff54e92 draft
Uploaded
author | devteam |
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date | Wed, 12 Feb 2014 18:02:38 -0500 |
parents | 86e7e072c4c9 |
children |
rev | line source |
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1 | 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 |