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#!/bin/bash
set -eou pipefail
default_jvm_mem_opts="-Xms512m -Xmx1g"
jvm_mem_opts=""
jvm_prop_opts=""
pass_args=""
for arg in "$@"; do
case $arg in
'-D'*)
jvm_prop_opts="$jvm_prop_opts $arg"
;;
'-XX'*)
jvm_prop_opts="$jvm_prop_opts $arg"
;;
'-Xm'*)
jvm_mem_opts="$jvm_mem_opts $arg"
;;
*)
pass_args="$pass_args $arg"
;;
esac
done
if [ "$jvm_mem_opts" == "" ]; then
jvm_mem_opts="$default_jvm_mem_opts"
fi
pass_arr=($pass_args)
if [[ ${pass_arr[0]:=} == org* ]]
then
eval java $jvm_mem_opts $jvm_prop_opts -cp '/usr/share/java/gatk/GenomeAnalysisTK.jar' $pass_args
else
eval java $jvm_mem_opts $jvm_prop_opts -jar '/usr/share/java/gatk/GenomeAnalysisTK.jar' $pass_args
fi
exit
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