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comparison mergebamalignment_wrapper.sh @ 127:4f83d10e2179 draft

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author devteam
date Wed, 26 Feb 2014 00:32:57 -0500
parents 11e69ba20b85
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126:0c7d738f5c44 127:4f83d10e2179
1 #!/bin/bash
2 reference_without_extension=${3%.*}
3 java -jar $JAVA_JAR_PATH/CreateSequenceDictionary.jar R=$3 O=$reference_without_extension.dict
4 eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeBamAlignment.jar O=$1.$2 R=$3 ${*:4}
5 mv $1.$2 $1