prod_reproduction/202307-FMBY2/run_FMBY2_cnv_call_L2.sh

set -e

function usage() {
    echo "Usage: $0 [ -s <sample> ] [ -o <out_dir> ] [ -x <script_dir> ] 
                    [ -c <WES_CNV_outdir> ] [ -p <pseudo_panel> ]"
    echo "-s Sample Name"
    echo "-o Output dir"
    echo "-p Pseudo Panel[MBY2|FeBY2]"
    echo "-x script_dir"
    echo "-c WES CNV outdir"
}

if [ $# -eq 0  ]
then
    usage
    exit
fi
while getopts ":s:o:p:x:c:h" opt; do
    case $opt in
        s)
            sample=$OPTARG
            ;;
        o)
            out_dir=$OPTARG
            ;;
        c)
            cnv_dir=$OPTARG
            ;;
        p)
            panel=$OPTARG
            ;;
        x)
            script_dir=$OPTARG
            ;;
        h)
            usage
            exit
            ;;
        \?)
            echo "Invalid option: -$OPTARG" 
            usage
            exit
            ;;
    esac
done

if [ -d $cnv_dir ]
then
    echo $cnv_dir.
else
    echo $cnv_dir " NOT exist!"
    exit
fi
cd $cnv_dir
echo "out_dir:" $out_dir
. $script_dir/conf/conf.cfg 

## CNV call
sh $module/run_CNV_call.sh -s $sample -o $out_dir -x $script_dir -c $cnv_dir 
## Merge,Filter,Annotation,Plot
sh $module/run_CNV_trim.sh -s $sample -o $out_dir -x $script_dir -c $cnv_dir 
## CNV plot
#sh $module/run_CNV_plot.sh -s $sample -o $out_dir -x $script_dir -c $cnv_dir 
## AZF
if [ "$panel" = "MBY2" ]
then
. $module/run_MBY2AZF_hg19_200113.sh $sample
fi