##Author: guochangquan
##Copyright 202207
##company: NuProbe

function usage() {
    echo "Usage: $0 [ -i <fq_dir> ] [ -l <sample list> ] [ -o <analysis_dir> ] 
                    [ -c <FMBY2_CNV_outdir> ] [ -x <FMBY2_script_dir> ] [ -r <FMBY2_Result_dir> ] "
    echo "-i Input fastq dir.File structure follow:fq_dir/sample/sample_R1/2.fastq.gz"
    echo "-l Sample list, per line for one SampleName and Sample_Panel[MBY2|FeBY2]"
    echo "-o FMBY2 analysis output dir"
    echo "-c FMBY2 CNV analysis outdir.default:analysis_dir/cnv_FMBY2"
    echo "-x FMBY2 scripts dir"
    echo "-r FMBY2 Result dir"
}

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

while getopts ":x:i:l:c:r:o:h" opt; do
    case $opt in
        x)
            script_dir=$OPTARG
            ;;
        i)
            fq_dir=$OPTARG
            ;;
        l)
            sam_list=$OPTARG
            ;;
        o)
            out_dir=$OPTARG
            ;;
        c)
            cnv_dir=$OPTARG
            ;;
        r)
            res_dir=$OPTARG
            ;;
        h)
            usage
            exit
            ;;
        \?)
            echo "Invalid option: -$OPTARG" 
            usage
            exit
            ;;
    esac
done

echo "Input FASTQ dir:$fq_dir"
echo "FMBY2 analysis output dir:$out_dir"
echo "FMBY2 CNV analysis dir:$cnv_dir"
echo "Sample List:$sam_list"
echo "FMBY2 scripts dir:$script_dir"

## 测试输入路径/文件是否正确
if [ ! -d $fq_dir ]
then
    echo "Input fastq dir does NOT exist! "
    echo "Please check $fq_dir."
    exit
fi
if [ ! -f $sam_list ]
then
    echo "Sample List does NOT exist! "
    echo "Please check $sam_list."
    exit
fi
test -d $out_dir || mkdir -p $out_dir
test -d $out_dir/log || mkdir -p $out_dir/log
if [ -d $cnv_dir ]
then
    echo "FMBY2 CNV Outdir exist!"
    echo "Please check!"
    #exit
else
    mkdir -p $cnv_dir
    mkdir -p $cnv_dir/AZF_call/img
fi

for sample in `cut -f1 $sam_list`
do
    echo "Sample Checking: " $sample
    export SAM=$sample
    fq1=` find $fq_dir -name "*${sample}*.gz" |perl -ne 'print if /$ENV{SAM}(_S\d+)?(_L\d+)?(_combined)?_R?1(_\d+)?.f(ast)?q.gz/' `
    fq2=` find $fq_dir -name "*${sample}*.gz" |perl -ne 'print if /$ENV{SAM}(_S\d+)?(_L\d+)?(_combined)?_R?2(_\d+)?.f(ast)?q.gz/' `
    nfq1=`find $fq_dir -name "*${sample}*.gz" |perl -ne 'print if /$ENV{SAM}(_S\d+)?(_L\d+)?(_combined)?_R?1(_\d+)?.f(ast)?q.gz/' |wc -l `
    nfq2=`find $fq_dir -name "*${sample}*.gz" |perl -ne 'print if /$ENV{SAM}(_S\d+)?(_L\d+)?(_combined)?_R?2(_\d+)?.f(ast)?q.gz/' |wc -l `
    echo $sample "FASTQ1:" $fq1
    ## ONLY ONE FASTQ1/FASTQ2 file for SAMPLE
    if [ -z $fq1 ]; then
        echo "Cannot find FASTQ1 file for $sample"
        exit
    elif [ $nfq1 -gt 1 ]; then
        echo "More Than ONE FASTQ1 file for $sample"
        exit
    fi
    if [ -z $fq2 ]; then
        echo "Cannot find FASTQ2 file for $sample"
        exit
    elif [ $nfq2 -gt 1 ]; then
        echo "More Than ONE FASTQ2 file for $sample"
        exit
    fi

    if [ -d $out_dir/${sample} ]
    then
        echo -e "Directory $out_dir/${sample} exists, Please check. Exit!"
        echo -e "${sample} quit!"
        #exit
    else
        mkdir $out_dir/${sample} -p
    fi
done

if [ ! -d $res_dir ]
then
    echo "Result Directory NOT exists, Please check. Exit!"
    exit
else
    test -d $res_dir/MBY2-AZF || mkdir $res_dir/MBY2-AZF
    test -d $res_dir/QC || mkdir $res_dir/QC
    test -d $res_dir/cnv || mkdir $res_dir/cnv 
    test -d $res_dir/yesuan || mkdir $res_dir/yesuan
    test -d $res_dir/CFTR_intron9 || mkdir $res_dir/CFTR_intron9
fi
test -s $out_dir/$sam_list || cp $sam_list $out_dir/
sams=(`cut -f1 $sam_list`)
num=${#sams[@]}
mindx=` expr $num - 1 `
log=$out_dir/log/FMBY2
if [ $num -lt 2 ]
then
    fid1=`qsub -v sample=${sams[0]},fq_dir=$fq_dir,out_dir=$out_dir,cnv_dir=$cnv_dir,script_dir=$script_dir $script_dir/run_FMBY2_single_L1.pbs`
    qsub -W depend=afterok:$fid1 -v out_dir=$out_dir,cnv_dir=$cnv_dir,script_dir=$script_dir,res_dir=$res_dir,sam_list=$sam_list $script_dir/run_FMBY2_Copy_L1.pbs
else
    fid1=`qsub -o $log.S1 -v log=$log.S1,fq_dir=$fq_dir,out_dir=$out_dir,sam_list=$sam_list,cnv_dir=$cnv_dir,script_dir=$script_dir -J 0-$mindx $script_dir/run_FMBY2_prep_L1.pbs`
    fid2=`qsub -W depend=afterok:$fid1 -o $log.S2 -v sam_list=$sam_list,cnv_dir=$cnv_dir,script_dir=$script_dir $script_dir/run_FMBY2_stat_L1.pbs `
    fid3=`qsub -W depend=afterok:$fid2 -o $log.S3 -v log=$log.S3,out_dir=$out_dir,sam_list=$sam_list,cnv_dir=$cnv_dir,script_dir=$script_dir -J 0-$mindx $script_dir/run_FMBY2_cnv_call_L1.pbs`
    qsub -W depend=afterok:$fid3 -o $log.S4 -v out_dir=$out_dir,cnv_dir=$cnv_dir,script_dir=$script_dir,res_dir=$res_dir,sam_list=$sam_list $script_dir/run_FMBY2_Copy_L1.pbs
fi