#!/bin/bash
# snpEff executable shell script, adapted from VarScan shell script
jar_name="snpEff.jar"

set -eu -o pipefail

set -o pipefail
export LC_ALL=en_US.UTF-8

# Find original directory of bash script, resolving symlinks
# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
SOURCE="${BASH_SOURCE[0]}"
while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
    SOURCE="$(readlink "$SOURCE")"
    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
done
DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"

JAR_DIR=$DIR

java=java

if [ -n "${JAVA_HOME:=}" ]; then
  if [ -e "$JAVA_HOME/bin/java" ]; then
      java="$JAVA_HOME/bin/java"
  fi
fi

# extract memory and system property Java arguments from the list of provided arguments
# http://java.dzone.com/articles/better-java-shell-script
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 $jvm_prop_opts -cp "$JAR_DIR/$jar_name" $pass_args
else
    eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/$jar_name" $pass_args
fi
exit
