#!/bin/sh

checkExitCode() {
if [ $? -ne 0 ]; then
	echo "Error"
	exit 1;
fi
}

BASEDIR=`dirname $0`

if [ $# -lt 1 ]; then echo "Error No inputs provided" && exit 1; fi

. $BASEDIR/io.sh 4 3 1 "$@"

# For each FASTA file version, The customProDB annotations should be stored on the server under <path_to_fastafile>/cpdbAnnot/
# Get annotations for the input bam file using the input fasta file as reference to maintain consistent genomics fasta files
ANNDIR=`dirname $INPUTS4`/cpdbAnnot/

echo $R_HOME/bin/Rscript --no-save --no-restore $BASEDIR/calcRPKMByExon.R $INPUTS1 $INPUTS2 $INPUTS3 $ANNDIR $OUTPUTS1 $PARAMS1 $PARAMS2 $PARAMS3
$R_HOME/bin/Rscript --no-save --no-restore $BASEDIR/calcRPKMByExon.R $INPUTS1 $INPUTS2 $INPUTS3 $ANNDIR $OUTPUTS1 $PARAMS1 $PARAMS2 $PARAMS3

checkExitCode