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lib/BioX/Seq/Fetch.pm  view on Meta::CPAN

sub _load_faidx {
    
    my ($self) = @_;

    my $fn_idx  = $self->{fn} . '.fai';
    $self->write_index if (! -e $fn_idx);

    # make sure FASTA file is not newer than its index; otherwise index file
    # may be out of date and cause silent corruption downstream
    my $mtime_fas = stat($self->{fn})->mtime;
    my $mtime_idx = stat($fn_idx)->mtime;
    if ($mtime_fas > $mtime_idx) {
        die "Index file exists but is older than FASTA file and probably out"
            . " of date. Refresh or remove the existing index before"
            . " proceeding.\n"
    }

    my @ids;

    open my $in, '<', $fn_idx
        or die "Error opening index file: $!\n";