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lib/App/SimulateReads/Read.pm  view on Meta::CPAN

	default    => 0
);

has '_base' => (
	is         => 'rw',
	isa        => 'Int',
	builder    => '_build_base',
	lazy_build => 1
);

has '_not_base' => (
	is         => 'ro',
	isa        => 'HashRef',
	builder    => '_build_not_base',
	lazy_build => 1
);

sub _build_not_base {
	my %not_base = (
		A => ['T', 'C', 'G'],
		a => ['t', 'c', 'g'],
		T => ['A', 'C', 'G'],
		t => ['a', 'c', 'g'],
		C => ['A', 'T', 'G'],
		c => ['a', 't', 'g'],
		G => ['A', 'T', 'C'],
		g => ['a', 't', 'c']
	);
	return \%not_base;
}

sub _build_base {
	my $self = shift;
	# If sequencing_error equal to zero, set _base to zero
	return $self->sequencing_error && int(1 / $self->sequencing_error);
}

sub subseq {
	my ($self, $seq_ref, $seq_len, $slice_len, $pos) = @_;

lib/App/SimulateReads/Read.pm  view on Meta::CPAN

}

sub reverse_complement {
	my ($self, $seq_ref) = @_;
	$$seq_ref = reverse $$seq_ref;
	$$seq_ref =~ tr/atcgATCG/tagcTAGC/;
}

sub _randb {
	my ($self, $base) = @_;
	return $self->_not_base->{$base}[int(rand(3))] || $base;
}

__END__

=pod

=encoding UTF-8

=head1 NAME