Imported Upstream version 0.1.9

[samtools.git] / bcftools / bcf-fix.pl

diff --git a/bcftools/bcf-fix.pl b/bcftools/bcf-fix.pl
new file mode 100755 (executable)
index 0000000..61c6136
--- /dev/null
+++ b/bcftools/bcf-fix.pl
@@ -0,0 +1,101 @@
+#!/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);
+        }
+    }
+}
+