#!/usr/bin/env bash
#PBS -N FMBY2_cnv_prep
#PBS -j oe
#PBS -l ncpus=8
#PBS -l nodes=1
#PBS -l mem=30G
## AZFc_u3==0 
. $script_dir/conf/conf.cfg
cd $cnv_dir

ls *_F_QC_plot.pdf |sed 's/_F_QC_plot.pdf//' > F.sam.list
ls *_M_QC_plot.pdf |sed 's/_M_QC_plot.pdf//' > M.sam.list
perl $exe_dir/com_cov_norm.pl FMBY2.exon.cov.xls

if [ -s F.sam.list ]
then
    nFsam=`cat F.sam.list |wc -l `
    echo $nFsam
    if [ $nFsam -lt 10 ]
    then
        cp $dat_dir/F_CNV/*.pcov .
        cat F.sam.list $dat_dir/F_CNV/F.ref.list |head -n 10 > F.ref.list
    else
        cp F.sam.list F.ref.list
    fi
else
    rm F.sam.list
fi

# for male CNV REF sample list
if [ -s M.sam.list ]
then
    perl $exe_dir/prep_cnv_Mref.pl FMBY2.M.XY.sam.xls . M.sam.list
    grep REF $dat_dir/M_CNV/FMBY2.chr.cov.xls |cat FMBY2.M.XY.sam.xls - > FMBY2.chr.cov.xls
    nMsam=`cat FMBY2.M.XY.sam.xls |wc -l `
    if [ $nMsam -lt 16 ]
    then
        grep -v REF $dat_dir/M_CNV/FMBY2.chr.cov.xls |cat FMBY2.chr.cov.xls - |head -n 16 > FMBY2.chr.cov.xls.1
        mv FMBY2.chr.cov.xls.1 FMBY2.chr.cov.xls
        for sam in `cut -f1 FMBY2.chr.cov.xls|grep Control `
        do
            echo $sam
            cp $dat_dir/M_CNV/$sam.pcov .
        done
    fi
    test -f M.ref.list || Rscript $exe_dir/get_mby2_ref.r FMBY2.chr.cov.xls 6
    awk '$4>0.1{print $1}' FMBY2.chr.cov.xls |cat - M.ref.list |sort |uniq -c |awk '$1==2{print $2}' > M.ref.list.1
    perl $exe_dir/com_cov_norm.pl FMBY2.AZF.cov2.xls . M.ref.list.1
    Rscript $exe_dir/get_AZF_ref.r FMBY2.AZF.cov2.xls M.ref.list.2 20 && rm FMBY2.AZF.cov2.xls
    mv M.ref.list M.ref.list.cluster
    sort M.ref.list.2 |head -n 15 > M.ref.list
else
    rm M.sam.list
fi
exit
perl $exe_dir/com_cov_norm.pl FMBY2.exon.cov.xls
perl $exe_dir/prep_cnv_Mref.pl FMBY2.chr.cov.xls
#cat $dat_dir/FMBY2.chr.cov.xls >> FMBY2.chr.cov.xls
test -f ref.list || Rscript $exe_dir/get_mby2_ref.r FMBY2.chr.cov.xls 6
#grep -v 'REFDEL' ref.list > ref.list.1
awk '$4>0.1{print $1}' FMBY2.chr.cov.xls |cat - ref.list |sort |uniq -c |awk '$1==2{print $2}' > ref.list.1
#cp $dat_dir/FMBY2Control*.pcov .
perl $exe_dir/com_cov_norm.pl FMBY2.AZF.cov2.xls . ref.list.1
Rscript $exe_dir/get_AZF_ref.r FMBY2.AZF.cov2.xls ref.list.2 20 && rm FMBY2.AZF.cov2.xls
perl $exe_dir/com_cov_norm.pl FMBY2.AZF.cov.xls . ref.list.2
mv ref.list ref.list.cluster
sort ref.list.2 |head -n 15 > ref.list