Mercurial > repos > devteam > picard1106
comparison mergebamalignment_wrapper.sh @ 119:a85055d20937 draft
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author | devteam |
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date | Tue, 25 Feb 2014 18:55:41 -0500 |
parents | 11e69ba20b85 |
children |
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118:21bf2afb895c | 119:a85055d20937 |
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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 |