prod_reproduction/202307-IDTWES/script/plot/run_plot_IDTWES.sh

set -e
ps_dir=/cgdata/guocq/script/idtwes-hg19-cnv/plot_CR
rscript=/cgdata/guocq/soft/R-3.6.0/bin/Rscript
sample=$1
test -s $sample.ptn.tsv || cp ../cnv/${sample}_cnv/$sample.ptn.tsv . || cp ../cnv/${sample}_nscnv/$sample.ptn.tsv .
test -s $sample.tn.tsv || cp ../cnv/${sample}_cnv/$sample.tn.tsv . || cp ../cnv/${sample}_nscnv/$sample.tn.tsv .
test -s $sample.seg || cp ../cnv/${sample}_cnv/$sample.seg . || cp ../cnv/${sample}_nscnv/$sample.seg .
test -s ${sample}.ps.tab || cp ../conest/${sample}.ps.tab .
test -s ${sample}_ROHTableCall.bed || cp ../roh/${sample}_ROHTableCall.bed .
#perl $ps_dir/pre_plot.pl ${sample}
perl $ps_dir/pre_plot.pl ${sample} 0.1
perl $ps_dir/get_roh.pl ${sample} 
$rscript $ps_dir/plot_IDTWES_CR.r ${sample}
convert -density 300 $sample.CR_VAF.pdf $sample.CR_VAF.png
rm -r $sample.ptn.tsv $sample.tn.tsv $sample.seg ${sample}.ps.tab* $sample.CR_VAF.pdf ${sample}_plot.tsv ${sample}_ROHTableCall.bed