/usr/bin/fill-ref-md5 is in vcftools 0.1.11+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 | #!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use IPC::Open2;
use Vcf;
my $opts = parse_params();
fill_ref_md5($opts);
exit;
#--------------------------------
sub error
{
my (@msg) = @_;
if ( scalar @msg ) { confess @msg; }
die
"About: The script computes MD5 sum of the reference sequence and inserts\n",
" 'reference' and 'contig' tags into header as recommended by VCFv4.1.\n",
" The VCF file must be compressed and tabix indexed, as it takes advantage\n",
" of the lightning fast tabix reheader functionality.\n",
"Usage: fill-ref-md5 [OPTIONS] in.vcf.gz out.vcf.gz\n",
"Options:\n",
" -d, --dictionary <file> Where to read/write computed MD5s. Opened in append mode, existing records are not touched.\n",
" -i, --info <AS:xx,SP:xx,TX:xx> Optional info on reference assembly (AS), species (SP), taxonomy (TX)\n",
" -r, --refseq <file> The reference sequence in fasta format indexed by samtools faidx\n",
" -h, -?, --help This help message.\n",
"Examples:\n",
" fill-ref-md5 -i AS:NCBIM37,SP:\"Mus\\ Musculus\" -r NCBIM37_um.fa -d NCBIM37_um.fa.dict in.vcf.gz out.vcf.gz\n",
"\n";
}
sub parse_params
{
my $opts = {};
while (my $arg=shift(@ARGV))
{
if ( $arg eq '-i' || $arg eq '--info' ) { $$opts{info}=shift(@ARGV); next; }
if ( $arg eq '-r' || $arg eq '--refseq' ) { $$opts{refseq}=shift(@ARGV); next; }
if ( $arg eq '-d' || $arg eq '--dictionary' ) { $$opts{dictionary}=shift(@ARGV); next; }
if ( -e $arg && !exists($$opts{file}) ) { $$opts{file} = $arg; next }
if ( exists($$opts{file}) && !exists($$opts{outfile}) ) { $$opts{outfile} = $arg; next }
if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
error("Unknown parameter \"$arg\" or non-existent file. Run -h for help.\n");
}
if ( !exists($$opts{refseq}) && !exists($$opts{dictionary}) ) { error("Expected one of -d or -r options\n"); }
if ( !exists($$opts{file}) ) { error("No input VCF file given.\n"); }
if ( !exists($$opts{outfile}) ) { error("No output VCF file given.\n"); }
return $opts;
}
sub read_dict
{
my ($dict) = @_;
my $out = {};
if ( !$dict or !-e $dict ) { return $out }
open(my $fh,'<',$dict) or error("$dict: $!");
my $line=<$fh>;
if ( $line ne "\@HD\tVN:1.0\tSO:unsorted\n" ) { error("Could not parse $dict: $line"); }
while (my $line=<$fh>)
{
chomp($line);
# @SQ SN:5 LN:152537259 UR:file:/lustre/scratch102/projects/mouse/ref/NCBIM37_um.fa M5:f90804fb8fe9cb06076d51a710fb4563
my @items = split(/\t/,$line);
if ( @items != 5 ) { error("Could not parse $dict: $line"); }
my $item = shift(@items);
if ( $item ne '@SQ' ) { next; }
my $rec = {};
for my $item (@items)
{
if ( !($item=~/^([^:]+):(.+)$/) ) { error("Could not parse $dict: [$item] [$line]"); }
$$rec{$1} = $2;
}
if ( !exists($$rec{SN}) ) { error("No SN in [$dict] [$line]?"); }
$$out{$$rec{SN}} = $rec;
}
close($fh);
return $out;
}
sub add_to_dictionary
{
my ($opts,$dict,$chr) = @_;
if ( !exists($$opts{refseq}) ) { error("The chromosome [$chr] not present in the dictionary and no reference sequence given.\n"); }
my($md5_in,$md5_out,$ok,$len);
eval { open2($md5_out,$md5_in,'md5sum'); $ok=1; };
if ( !$ok ) { error("md5sum: $!"); }
my $cmd = "samtools faidx $$opts{refseq} $chr";
open(my $refseq,"$cmd |") or error("$cmd: $!");
# get rid of the first ">$chr" line.
<$refseq>;
while (my $line=<$refseq>)
{
chomp($line);
print $md5_in $line;
$len += length($line);
}
close($refseq);
close($md5_in);
my @md5 = <$md5_out>;
close($md5_out);
$md5[0] =~ s/\s+.*$//;
chomp($md5[0]);
if ( !$len ) { error("The sequence [$chr] not present in $$opts{refseq}\n"); }
$$dict{$chr} = { dirty=>1, SN=>$chr, LN=>$len, UR=>'file://'.$$opts{refseq}, M5=>$md5[0] };
$$dict{dirty} = 1;
}
sub write_dictionary
{
my ($opts,$dict) = @_;
if ( !$$dict{dirty} or !exists($$opts{dictionary}) ) { return }
my $needs_header = !-e $$opts{dictionary} ? 1 : 0;
open(my $fh,'>>',$$opts{dictionary}) or error("$$opts{dictionary}: $!");
print $fh "\@HD\tVN:1.0\tSO:unsorted\n" unless !$needs_header;
for my $key (sort keys %$dict)
{
if ( ref($$dict{$key}) ne 'HASH' or !$$dict{$key}{dirty} ) { next; }
my $sn = $$dict{$key}{SN};
my $ln = $$dict{$key}{LN};
my $ur = $$dict{$key}{UR};
my $m5 = $$dict{$key}{M5};
print $fh "\@SQ\tSN:$sn\tLN:$ln\tUR:$ur\tM5:$m5\n";
}
close($fh);
}
sub write_header
{
my ($opts,$dict,$chroms) = @_;
my %info;
if ( exists($$opts{info}) )
{
$$opts{info} =~ s/AS:/assembly:/;
$$opts{info} =~ s/SP:/species:/;
$$opts{info} =~ s/TX:/taxonomy:/;
for my $item (split(/,/,$$opts{info}))
{
my ($key,$value) = split(/:/,$item);
if ( !defined $value ) { error("Could not parse the info: [$item] [$$opts{info}]"); }
$info{$key} = $value;
}
}
my $vcf = Vcf->new(file=>$$opts{file});
$vcf->parse_header();
my $uri = $$opts{refseq}=~m{^[^/:]+:} ? '' : 'file:';
$vcf->add_header_line({key=>'reference', value=>"$uri$$opts{refseq}"});
for my $chrom (@$chroms)
{
my %line =
(
key => 'contig',
ID => $$dict{$chrom}{SN},
length => $$dict{$chrom}{LN},
md5 => $$dict{$chrom}{M5},
%info
);
$vcf->add_header_line(\%line);
}
open(my $out,'>',"$$opts{outfile}.header") or error("$$opts{outfile}.header: $!");
print $out $vcf->format_header();
close($out);
}
sub fill_ref_md5
{
my ($opts) = @_;
# List chromosomes
my @chroms = `tabix -l $$opts{file}`;
if ( $? ) { error("The command failed: tabix -l $$opts{file}\n"); }
# Read dictionary
my $dict = read_dict($$opts{dictionary},\@chroms);
for my $chr (@chroms)
{
chomp($chr);
if ( !exists($$dict{$chr}) ) { add_to_dictionary($opts,$dict,$chr); }
}
write_dictionary($opts,$dict);
write_header($opts,$dict,\@chroms);
`tabix -r $$opts{outfile}.header $$opts{file} > $$opts{outfile}`;
}
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