prod_reproduction/202307-FeBY2/run_FeBY2_cnv_call_L2.sh

set -e

function usage() {
    echo "Usage: $0 [ -s <sample> ] [ -o <out_dir> ] [ -l <sam_list> ] [ -x <script_dir> ] [ -c <FeBY2_CNV_outdir> ]"
    echo "-s Sample Name"
    echo "-o Output dir"
    echo "-l sample list"
    echo "-x script_dir"
    echo "-c FeBY2 CNV outdir"
}

if [ $# -eq 0  ]
then
    usage
    exit
fi
while getopts ":s:o:l:x:c:h" opt; do
    case $opt in
        s)
            sample=$OPTARG
            ;;
        o)
            out_dir=$OPTARG
            ;;
        l)
            sam_list=$OPTARG
            ;;
        c)
            cnv_dir=$OPTARG
            ;;
        x)
            feby2_script=$OPTARG
            ;;
        h)
            usage
            exit
            ;;
        \?)
            echo "Invalid option: -$OPTARG" > /dev/stderr
            usage
            exit
            ;;
    esac
done

if [ ! -f $cnv_dir/ref.list ]
then
    echo "Referenc Sample List:$cnv_dir/ref.list does NOT exist!"
    echo "Please Check."
    cp $sam_list ref.list
fi
if [ -d $cnv_dir ]
then
    echo $cnv_dir.
else
    echo $cnv_dir " NOT exist!"
    exit
fi
cd $cnv_dir
echo "out_dir:" $out_dir
. $feby2_script/conf/feby2.cfg 

## CNV call
sh $module/run_CNV_call.sh -s $sample -o $out_dir -x $feby2_script -c $cnv_dir 
## Merge,Filter,Annotation,Plot
sh $module/run_CNV_trim.sh -s $sample -o $out_dir -x $feby2_script -c $cnv_dir