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annotate mergebamalignment_wrapper.sh @ 119:a85055d20937 draft

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author devteam
date Tue, 25 Feb 2014 18:55:41 -0500
parents 11e69ba20b85
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/bin/bash
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2 reference_without_extension=${3%.*}
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3 java -jar $JAVA_JAR_PATH/CreateSequenceDictionary.jar R=$3 O=$reference_without_extension.dict
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4 eval java -Xmx2G -jar $JAVA_JAR_PATH/MergeBamAlignment.jar O=$1.$2 R=$3 ${*:4}
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5 mv $1.$2 $1