Mercurial > repos > devteam > picard1106

diff mergebamalignment_wrapper.sh @ 13:11e69ba20b85 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author devteam
date Sat, 01 Feb 2014 20:20:26 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergebamalignment_wrapper.sh	Sat Feb 01 20:20:26 2014 -0500
@@ -0,0 +1,5 @@
+#!/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