#!/usr/bin/perl
use strict;
use warnings;

die "usage:perl $0 germline/somatic tumor_prefix name input_file outputDir" unless @ARGV==5;
my($type,$tumor,$name,$input,$outputDir)=@ARGV;
`filter_vep -i $input  -o ${outputDir}/${name}_${type}_vepanno_filter.vcf --format vcf --force_overwrite --filter "(Consequence != synonymous_variant) and (Consequence != intron_variant) and (Consequence != intergenic_variant) and (Consequence != 3_prime_UTR_variant) and (Consequence != upstream_gene_variant) and (Consequence != downstream_gene_variant) and (Consequence != 5_prime_UTR_variant)"`;

if($type eq "germline"){
	open IN,"${outputDir}/${name}_${type}_vepanno_filter.vcf";
	open OUT,">${outputDir}/${name}_${type}_vepanno_Filter.vcf";
	while(<IN>){
		if (/^##/){
			print OUT;
			next;
		}elsif(/^#CHROM/){
			$_=~s/TUMOR/$tumor/;
			print OUT;
			next;
		}else{
			chomp;
			my @line=split("\t",$_);
			next if $line[6] ne "PASS";
			my $n_af=(split(":",$line[-2]))[-2];
			my $t_af=(split(":",$line[-1]))[-2];
			$n_af=~s/%//;
			$t_af=~s/%//;
			print OUT "$_\n" if ($n_af>=10 and $t_af>=10);
		}
	}
	`rm ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
	`mv ${outputDir}/${name}_${type}_vepanno_Filter.vcf ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
}elsif($type eq "somatic"){
	open IN,"${outputDir}/${name}_${type}_vepanno_filter.vcf";
	open OUT,">${outputDir}/${name}_${type}_vepanno_Filter.vcf";
	while(<IN>){
		if (/^##/){
                        print OUT;
                        next;
                }elsif(/^#CHROM/){
                        $_=~s/TUMOR/$tumor/;
                        print OUT;
                        next;
		}else{
			chomp;
			my @line=split("\t",$_);
			next if $line[6] ne "PASS";
			my $n_af=(split(":",$line[-2]))[-2];
			my $t_af=(split(":",$line[-1]))[-2];
			$n_af=~s/%//;
			$t_af=~s/%//;
			print OUT "$_\n" if ($n_af<2 and $t_af>=5);
		}
	}
	`rm ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
	`mv ${outputDir}/${name}_${type}_vepanno_Filter.vcf ${outputDir}/${name}_${type}_vepanno_filter.vcf`;
}