Mask

Provides the mask alphabet and functionality for creating masked composites. More...

Collaboration diagram for Mask:

Classes
class	seqan3::mask
	Implementation of a masked alphabet to be used for tuple composites. More...
struct	seqan3::mask_printer< mask_t >
	The printer used for formatted output of seqan3::mask alphabet. More...
class	seqan3::masked< sequence_alphabet_t >
	Implementation of a masked composite, which extends a given alphabet with a mask. More...

Detailed Descriptionno-api

Provides the mask alphabet and functionality for creating masked composites.

See also

Alphabet

Introduction

Masks are useful in cases where an alphabet needs to be augmented with additional information. A common use case is the introduction of don't-care positions (masking) in nucleotide or aminoacid sequences without using 'N' or 'X', respectively. Instead, the original alphabet is combined with seqan3::mask to create a seqan3::masked composite. When printed via the seqan3::debug_stream, masked characters are displayed in lowercase.

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/mask/masked.hpp>
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::masked<seqan3::dna4> dna4_masked{};
    seqan3::masked<seqan3::dna4> dna4_another_masked{'A'_dna4, seqan3::mask::unmasked};
    // create a dna4 masked alphabet with an unmasked A
 
    dna4_masked.assign_char('a'); // assigns a masked 'A'_dna4
 
    if (dna4_masked.to_char() != dna4_another_masked.to_char())
    {
        seqan3::debug_stream << dna4_masked.to_char() << " is not the same as " << dna4_another_masked.to_char()
                             << "\n";
    }
}

Types of masking

There are two types of masking:

• hard-masking, which converts masked characters to the ambiguous/unknown character ('N' or 'X')
• soft-masking, which uses lowercase for masked characters

Repeat masking

The use of soft-masking was popularised by RepeatMasker. Interspersed repeats (transposons, retrotransposons and processed pseudogenes) and low complexity sequences are denoted by lowercase characters. Note that larger repeats, such as segmental duplications, large tandem repeats and whole gene duplications are generally not masked.