#!/bin/sh
set -eu
PRG="$(basename -- "$0")"

JavOpt=""
PicardProg=""
PicardOpts=""

for i in $@
do
	if [ ! -n "$PicardProg" ]; then
		if echo $i|egrep "^-X"; then
			JavOpt="$JavOpt $i"
		else
			PicardProg="$i"
		fi
	else
		PicardOpts="$PicardOpts $i"
	fi
done
echo JavOpt: $JavOpt
echo PicardProg: $PicardProg
echo PicardOpts: $PicardOpts

case "$PRG" in
picard)
	echo 1>&2 'Warning: picard is not official and should be replaced by PicardCommandLine, only accepting this temporarily to help development of bcbio package.'
	;;
picard-tools)
	echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine'
	;;
PicardCommandLine)
	;;
*)
	PicardProg=$PRG
	PicardsOpts="$PicardProg $PicardOpts"
	;;
esac
export USE_LIBRARY_PATH=USE_LIBRARY_PATH
export PICARD_CLASSPATH=/usr/share/java/picard.jar:/usr/share/java/htsjdk.jar:/usr/share/java/guava.jar:/usr/lib/jvm/default-java/lib/tools.jar:/usr/share/java/commons-lang3.jar:/usr/share/java/gkl.jar:/usr/share/java/gatk-native-bindings.jar:/usr/share/java/barclay.jar

exec java ${JAVA_OPTIONS-} $JavOpt -cp $PICARD_CLASSPATH picard.cmdline.PicardCommandLine $PicardProg $PicardOpts
