#!/usr/bin/env bash
##Author: guochangquan
##Copyright 20210929
##company: NuProbe

set -e

function usage() {
    echo "Usage: $0 [ -s <sample> ] [ -i <fq_dir> ] [ -o <analysis_dir> ] [ -x <script_dir> ] [ -c <FeBY2_CNV_outdir> ]"
    echo "-s sample name"
    echo "-i input fastq dir"
    echo "-x script_dir"
    echo "-o analysis_dir"
    echo "-c FeBY2 CNV outdir"
}

if [ $# -eq 0  ]
then
    usage
    exit
fi
feby2_script=$(cd "$(readlink -f "$0" | xargs dirname)"; pwd)

while getopts ":s:c:x:o:i:h" opt; do
    case $opt in
        i)
            fq_dir=$OPTARG
            ;;
        o)
            out_dir=$OPTARG
            ;;
        s)
            sample=$OPTARG
            ;;
        c)
            cnv_dir=$OPTARG
            ;;
        x)
            feby2_script=$OPTARG
            ;;
        h)
            usage
            exit
            ;;
        \?)
            echo "Invalid option: -$OPTARG" > /dev/stderr
            usage
            exit
            ;;
    esac
done
echo "Input FASTQ dir:" $fq_dir
echo "Output BAM dir:" $out_dir
echo "Sample Name:" $sample
echo "CNV Analysis dir:" $cnv_dir
echo $feby2_script

. $feby2_script/conf/feby2.cfg
test -d $out_dir/${sample} || mkdir ${outdir}/${sample}
cd $out_dir/${sample}

### FASTQ TRIM and Mapping
sh $module/run_FQ2BAM_Speedseq.sh -s $sample -i $fq_dir -o $out_dir -x $feby2_script

### SNV/INDEL CAll and annotation
sh $module/run_BAM2VCF_HC.sh -s $sample -o $out_dir -x $feby2_script

### QC
sh $module/run_QC.sh -s $sample -o $out_dir -x $feby2_script

### yesuan
sh $module/run_yesuan.sh -s $sample -o $out_dir -x $feby2_script

### prepare for CNV
sh $module/run_CNV_prep.sh -s $sample -o $out_dir -x $feby2_script -c $cnv_dir

## for CNV
cd $cnv_dir
cp $feby2_script/dat/*.pcov $cnv_dir/
cp $feby2_script/dat/ref.list $cnv_dir/
perl $exe_dir/stats_chrs.pl FeBY2.chr.cov.xls && rm *.idxstats
perl $exe_dir/com_cov_norm.pl FeBY2.exon.cov.xls

## 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