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#!/bin/bash
#---------------------------------------------------------------------------------------------------
#
# Wrapper for HomeBrew-science project
#
# snpSift executable shell script
# https://pcingola.github.io/SnpEff/
# Extracts memory and system property Java arguments from the list of provided arguments
# (ie -Xms 1g -Xmx 4g)
#
# Source https://gist.github.com/chapmanb/8732049
# Created by: Brad Chapman
#---------------------------------------------------------------------------------------------------
jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
java=java
if [ -e "$JAVA_HOME/bin/java" ]
then
java="$JAVA_HOME/bin/java"
fi
default_jvm_mem_opts="-Xms1g -Xmx4g"
jvm_mem_opts=""
jvm_prop_opts=""
pass_args=""
for arg in "$@"; do
case $arg in
'-D'*)
jvm_prop_opts="$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
exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/SnpSift.jar $pass_args
exit
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