--- /dev/null
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+use Carp;
+
+my $opts = parse_params();
+bcf_fix();
+
+exit;
+
+#--------------------------------
+
+sub error
+{
+ my (@msg) = @_;
+ if ( scalar @msg ) { confess @msg; }
+ die
+ "Usage: bcftools view test.bcf | bcf-fix.pl > test.vcf\n",
+ "Options:\n",
+ " -h, -?, --help This help message.\n",
+ "\n";
+}
+
+
+sub parse_params
+{
+ my $opts = {};
+ while (my $arg=shift(@ARGV))
+ {
+ if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
+ error("Unknown parameter \"$arg\". Run -h for help.\n");
+ }
+ return $opts;
+}
+
+sub bcf_fix
+{
+ while (my $line=<STDIN>)
+ {
+ if ( $line=~/^#CHROM/ )
+ {
+ print
+qq[##INFO=<ID=DP4,Number=4,Type=Integer,Description="Read depth for 1) forward reference bases; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for 1) strand bias (exact test); 2) baseQ bias (t-test); 3) mapQ bias (t); 4) tail distance bias (t)">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="EM estimate of site allele frequency without prior">
+##INFO=<ID=AFE,Number=1,Type=Float,Description="Posterior expectation of site allele frequency (with prior)">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="P-value for Hardy-Weinberg equillibrium (chi-square test)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Descriptin="RMS mapping quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+];
+ print $line;
+ }
+ elsif ( $line=~/^#/ )
+ {
+ print $line;
+ }
+ else
+ {
+ my @items = split(/\t/,$line);
+ my @tags = split(/:/,$items[8]); # FORMAT tags
+
+ my $nidx=2;
+ my @idxs; # Mapping which defines new ordering: $idxs[$inew]=$iold; GT comes first, PL second
+ for (my $i=0; $i<@tags; $i++)
+ {
+ if ( $tags[$i] eq 'GT' ) { $idxs[0]=$i; }
+ elsif ( $tags[$i] eq 'PL' ) { $idxs[1]=$i; }
+ else { $idxs[$nidx++]=$i; }
+ }
+ if ( !exists($tags[0]) or !exists($tags[1]) ) { error("FIXME: expected GT and PL in the format field.\n"); }
+
+ # First fix the FORMAT column
+ $items[8] = 'GT:GL';
+ for (my $i=2; $i<@tags; $i++)
+ {
+ $items[8] .= ':'.$tags[$idxs[$i]];
+ }
+
+ # Now all the genotype columns
+ for (my $iitem=9; $iitem<@items; $iitem++)
+ {
+ @tags = split(/:/,$items[$iitem]);
+ $items[$iitem] = $tags[$idxs[0]] .':';
+
+ # GL=-PL/10
+ my ($a,$b,$c) = split(/,/,$tags[$idxs[1]]);
+ $items[$iitem] .= sprintf "%.2f,%.2f,%.2f",-$a/10.,-$b/10.,-$c/10.;
+
+ for (my $itag=2; $itag<@tags; $itag++)
+ {
+ $items[$iitem] .= ':'.$tags[$idxs[$itag]];
+ }
+ }
+ print join("\t",@items);
+ }
+ }
+}
+