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        }
        if ( scalar @out )
        {
            push @msg, @out;
        }
        $self->throw(@msg);
    }
    return (@out);
}

# Read the first file of the fasta file and make a guess: Are all chromosomes
#   names as 'chr1','chr2',etc or just '1','2',...?
# Future TODO: more robust chromosome name mapping?
sub chromosome_naming
{
    my ($self,$fa_file) = @_;
    open(my $fh,'<',"$fa_file.fai") or $self->throw("$fa_file.fai: $!");
    my $line=<$fh>;
    if ( !($line=~/^(chr)?\S+\t/) ) { chomp($line); $self->throw("FIXME: the sequence names not in '>(chr)?\\S+' format [$line] ... $fa_file.fai\n"); }
    close($fh); 
    $$self{chr_naming} = defined $1 ? $1 : '';