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view mergebamalignment_wrapper.sh @ 149:1f83354245da draft

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author rayan
date Mon, 21 Jul 2014 16:17:32 -0400
parents 11e69ba20b85
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#!/bin/bash
reference_without_extension=${3%.*}
java -jar $JAVA_JAR_PATH/CreateSequenceDictionary.jar R=$3 O=$reference_without_extension.dict
eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeBamAlignment.jar O=$1.$2 R=$3 ${*:4}
mv $1.$2 $1