set -e

function usage() {
    echo "Usage: $0 [ -r <Result_dir> ] [ -o <out_dir> ] [ -l <sam_list> ] [ -x <script_dir> ] [ -c <WES_CNV_outdir> ]"
    echo "-r Final result dir"
    echo "-o Output dir"
    echo "-l sample list"
    echo "-x script_dir"
    echo "-c WES CNV outdir"
}

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

. $script_dir/conf/conf.cfg 
echo "Result Dir:" $res_dir
echo "CNV analysis Dir:" $cnv_dir
echo "Output outDir:" $out_dir

## keyan-Male
echo -e "\n"
echo "Male:"
test -d $res_dir/keyan || mkdir $res_dir/keyan
test -d $out_dir/keyan || mkdir $out_dir/keyan
cd $out_dir/keyan
for sample in `cut -f1 $sam_list`
do
cp $out_dir/${sample}/${sample}.gatk.hg19_multianno.txt .
cp $cnv_dir/${sample}.CNV.xls .
done
perl $keyan_dir/filter_loop_v5.pl $MKY_genelist
chmod g-w Lib*.xls
rm *.hg19_multianno.txt *.CNV.xls

for sample in  `cut -f1 $sam_list`
do
    lib=`echo $sample|cut -d- -f2`
    cp $lib.filter_raw.xls $res_dir/keyan/$lib.filter_raw.xls
    cp $lib.filter_recessive.xls $res_dir/keyan/$lib.filter_recessive.xls
done

## keyan-Female
echo -e "\n"
echo "Female:"
test -d $res_dir/keyan-F || mkdir $res_dir/keyan-F
test -d $out_dir/keyan-F || mkdir $out_dir/keyan-F
cd $out_dir/keyan-F
for sample in `cut -f1 $sam_list`
do
cp $out_dir/${sample}/${sample}.gatk.hg19_multianno.txt .
cp $cnv_dir/${sample}.CNV.xls .
done
perl $keyan_dir/filter_loop_female_V1.pl $FKY_genelist
chmod g-w Lib*.xls
rm *.hg19_multianno.txt *.CNV.xls

for sample in  `cut -f1 $sam_list`
do
    lib=`echo $sample|cut -d- -f2`
    cp $lib.filter_raw.xls $res_dir/keyan-F/$lib.filter_raw.xls
    cp $lib.filter_recessive.xls $res_dir/keyan-F/$lib.filter_recessive.xls
done