This file is indexed.

/usr/bin/fill-ref-md5 is in vcftools 0.1.12+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}`;
}