#!/usr/bin/perl 
#migrate_db.pl

my $headerfile = shift @ARGV;
my @vcffiles = @ARGV;

open HEADER, "<$headerfile" or die $!;
open OUT, ">int.vcf" or die $!;
while (my $line = <HEADER>) {
    chomp($line);
    print OUT $line,"\n";;
}
close HEADER;
my @sampleorder;

my %headerlines;
foreach $vcf (@vcffiles) {
    $caller = (split(/\./,$vcf))[1];
    open VCF, "gunzip -c $vcf|" or die $!;
    my @sampleids;
    while (my $line = <VCF>) {
	chomp($line);
	if ($line =~ m/#/) {
	    if ($line =~ m/#CHROM/) {
		($chromhd, $posd,$idhd,$refhd,$althd,$scorehd,
		 $filterhd,$annothd,$formathd,@sampleids) = split(/\t/, $line);
		foreach $j (0..$#sampleids) {
		    $sampleids[$j] =~ s/\.final//g;
		}
		unless (@sampleorder) {
		    @sampleorder = @sampleids;
		    print OUT $line,"\n";
		}
		next;
	    }
	    next;
	}
	my ($chrom, $pos,$id,$ref,$alt,$score,
	    $filter,$annot,$format,@gts) = split(/\t/, $line);
	my %hash = ();
	foreach $a (split(/;/,$annot)) {
	    my ($key,$val) = split(/=/,$a);
	    $hash{$key} = $val;
	}
	my @deschead = split(/:/,$format);
	my $newformat = 'GT:DP:AD:AO:RO';
	my %newgts;
	my $missingGT = 0;
      FG:foreach my $i (0..$#gts) {
	  my $allele_info = $gts[$i];
	  my $sid = $sampleids[$i];
	  my @gtinfo = split(/:/,$allele_info);
	  my %gtdata;
	  if ($allele_info eq '.') {
	      $newgts{$sid} = '.:.:.:.:.';
	      $missingGT ++;
	      next FG;
	  }
	  foreach my $i (0..$#deschead) {
	      $gtdata{$deschead[$i]} = $gtinfo[$i];
	  }
	  if ($gtdata{GT} eq './.') {
	      $newgts{$sid} = '.:.:.:.:.';
	      $missingGT ++;
	      next FG;
	  }
	  if ($gtdata{AD}){
	      ($gtdata{RO},@alts) = split(/,/,$gtdata{AD});
	      $gtdata{AO} = join(",",@alts);
	      $gtdata{DP} = $gtdata{RO};
	      foreach (@alts) {
		  $gtdata{DP} += $_;
	      }
	  } elsif (exists $gtdata{NR} && exists $gtdata{NV}) {
	      $gtdata{DP} = $gtdata{NR}; 	
	      $gtdata{AO} = $gtdata{NV};
	      $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
	      $gtdata{AD} = join(",",$gtdata{RO},$gtdata{AO})
	  } elsif (exists $gtdata{AO} && exists $gtdata{RO}) {
	      $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
	      $gtdata{DP} = $gtdata{RO};
	      foreach (split(',',$gtdata{AO})) {
		  $gtdata{DP} += $_;
	      }
	  }
	  if ($gtdata{DP} && $gtdata{DP} < 3) {
	      $missingGT ++;
	  }
	  $newgts{$sid} =  join(":",$gtdata{GT},$gtdata{DP},$gtdata{AD},$gtdata{AO},$gtdata{RO});
      }
	next if ($missingGT == scalar(@gts));
	my @newgts;
	foreach $id (@sampleorder) {
	    push @newgts, $newgts{$id};
	}
	$lines{$chrom}{$pos}{$caller} = join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
    }
    close VCF;
}
my @callers = ('ssvar','platypus','sam','gatk','hotspot');
 F1:foreach $chr (sort {$a cmp $b} keys %lines) {
   F2:foreach $pos (sort {$a <=> $b} keys %{$lines{$chr}}) {
       my $callset = join(",",keys %{$lines{$chr}{$pos}});
     F3:foreach $caller (@callers) {
	 if ($lines{$chr}{$pos}{$caller}) {
	     my ($chrom, $pos,$id,$ref,$alt,$score,$filter,$annot,
		 $format,@gts) = split(/\t/,$lines{$chr}{$pos}{$caller});
	     $annot = $annot.";CallSet=".$callset;
	     print OUT join("\t",$chrom,$pos,$id,$ref,$alt,$score,
			    $filter,$annot,$format,@gts),"\n";
	     last F3;
	 }
     }
   }
}
close OUT;