Changelog

Table of Contents

• 3.1.0
  • New features
  • Notable Bug-fixes
  • API changes
• 3.0.3
  • New features
  • Notable Bug-fixes
  • API changes
• 3.0.2
  • New features
  • API changes
  • Notable Bug-fixes
• 3.0.1
  • New features
  • API changes
  • Notable Bug-fixes
• 3.0.0 ("Escala")

This changelog contains a top-level entry for each release with sections on new features, API changes and notable bug-fixes (not all bug-fixes will be listed).

Get to know SeqAn3 with our tutorials.

Please see the release announcement: https://www.seqan.de/announcing-seqan3/

See the porting guide for some help on porting: https://docs.seqan.de/seqan/3-master-user/howto_porting.html

See the documentation on API stability to learn about when API changes are allowed.

3.1.0

New features

Build system

• We now use Doxygen version 1.9.2 to build our documentation (#2765).

Notable Bug-fixes

Argument Parser

• Fixed an issue that led to the wrong option type being printed on errors (#2836).

Search

• Resolved an issue that prevented the FM-Index from being constructed correctly for inputs larger than 4 GiB (#2756).

API changes

The files deprecated in 3.0.3 (denoted by [deleted without replacement]) have been removed.

3.0.3

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

• Check out our updated SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.
• SeqAn 3.0.3 is known to compile with GCC 7.5, 8.4, 9.3, 10.3, and 11.1. Future versions (e.g. GCC 11.2 and 12) might work, but were not yet available at the time of this release.

New features

Alphabet

• Added seqan3::phred94, a quality type that represents the full Phred Score range (Sanger format) and is used for PacBio Phred scores of HiFi reads (#2290).

Argument Parser

• The seqan3::argument_parser constructor was changed to accept a strong-type seqan3::update_notifications::(on|off) instead of a simple bool (which was subject to unexpected implicit conversion) (#2180).
• We expanded the seqan3::output_file_validator, with a parameter seqan3::output_file_open_options to allow overwriting output files (#2009).
• The seqan3::argument_parser has a new member function seqan3::argument_parser::is_option_set that checks whether an option, identified by its long or short name, was set on the command line by the user (#1859).
• The subcommand of the seqan3::argument_parser may contain a dash (#2306).

Build system

• We now use Doxygen version 1.9.1 to build our documentation (#2327).

I/O

• Explicit record-classes with explicit member accessor for our file implementations. We added seqan3::sequence_record for seqan3::sequence_file_(in|out)put, seqan3::sam_record for seqan3::sam_file_(in|out)put and seqan3::structure_record for seqan3::structure_file_(in|out)put. You can now access the id in a sequence file (e.g. fasta file) record via record.id() instead of seqan3::get<seqan3::field::id>(record). This will allow us to add convenient functions that compute information based on the record itself and to provide better documentation. (#2340, #2380, #2389)

Search

• The seqan3::fm_index_cursor and seqan3::bi_fm_index_cursor can be serialised (#2048).
• The seqan3::fm_index_cursor exposes its suffix array interval (#2076).
• The seqan3::interleaved_bloom_filter supports counting occurrences of a range of values (#2373).
• The seqan3::interleaved_bloom_filter supports clearing of bins (#2428).

Notable Bug-fixes

Argument Parser

• Argument parsing with subcommands: If the user forgets or misspells the subcommand, the error is thrown when calling seqan3::argument_parser::parse() and not on construction of the seqan3::argument_parser (#2179).
• The seqan3::regex_validator parses std::filesystem::path's correctly now (#2216).
• The seqan3::input_file_validator and seqan3::input_file_validator support extensions containing a dot (#2363).
• The Argument Parser accepts containers of all values it is able to parse, e.g. a std::vector of enums or bool (#2381).
• The Argument Parser's help pages now contain author and email information (#2374).
• The Argument Parser is able to process defaults for list arguments (#2394).

Range

• The seqan3::views::kmer_hash does not return wrong values when combined with std::views::reverse on a text of the same size as the kmer (#2416).

I/O

• The SAM/BAM format reads the quality field (or any other text field) that starts with an asterisk (*) but is not empty correctly now (#2184).
• Requesting the alignment without also requesting the sequence for BAM files containing empty CIGAR strings does now not result in erroneous parsing (#2418).
• BAM files with 64 references are now parsed correctly (#2423).
• BAM files not containing a plain text header are now accepted (#2536).
• Writing gz-compressed output no longer results in bgzf-compressed output. This change may have following effects (#2458):
  • A noticeable slowdown when writing gz-compressed content since, in contrast to bgzf, gz does not feature parallelisation (magnitude depends on the application and level of parallelisation).
  • A reduced output size when writing gz-compressed content due to gz storing less metadata than bgzf (up to 20% smaller file size).
  • The processed data should experience no negative effects since gz and bgzf are fully compatible.
  • This bug may also cause unexpected parallelisation when reading gz-compressed input. This is the case when the gz-compressed input was also generated with SeqAn.
• The following requirements of parsing a SAM/BAM header where relaxed as they were in violation of the specification (#2605):
  • The order of tags within the header may be arbitrary. Before, necessary tags where required to be first.
  • Unknown tags will emit a warning. Before, a error was raised.

API changes

Most of our API or header file changes will trigger a deprecation warning to let you know if something changed and, if applicable, when it will be removed. We recommend upgrading version-by-version to check whether you need to change code. You can either directly check the reported code or verify with our documentation how the new API should be used.

For a complete list of behavioural changes in our public and internal API, you can consult our API stability regression test suite and patches at https://github.com/seqan/seqan3/tree/master/test/api_stability/3.0.2.

Alignment

• The member constants of seqan3::aminoacid_similarity_matrix were changed to lower case (#2599):
  • seqan3::aminoacid_similarity_matrix::BLOSUM30 is replaced by seqan3::aminoacid_similarity_matrix::blosum30.
  • seqan3::aminoacid_similarity_matrix::BLOSUM45 is replaced by seqan3::aminoacid_similarity_matrix::blosum45.
  • seqan3::aminoacid_similarity_matrix::BLOSUM62 is replaced by seqan3::aminoacid_similarity_matrix::blosum62.
  • seqan3::aminoacid_similarity_matrix::BLOSUM80 is replaced by seqan3::aminoacid_similarity_matrix::blosum80.
• Deprecated seqan3::alignment_coordinate and it will be removed in 3.1.0 (#2602).

Header Changes:

#include <seqan3/alignment/band/static_band.hpp> [deleted without replacement]
#include <seqan3/alignment/matrix/advanceable_alignment_coordinate.hpp> [deleted without replacement]
#include <seqan3/alignment/scoring/gap_scheme.hpp> [deleted without replacement]

Alphabet

• We relaxed some requirements of seqan3::alphabet_base<alphabet_t> (#2427):

  • Old requirements: alphabet_t::rank_to_char and alphabet_t::char_to_rank must be lookup tables.
  • New requirements: alphabet_t::rank_to_char and alphabet_t::char_to_rank must be static member functions.

  This allows for more flexible rank <-> char conversion implementations. Lookup tables are still possible within those static member functions. However, alphabets that do not need a lookup table can now use easier and/or more efficient implementations. For example, seqan3::gap always returns rank 0 or char -, or seqan3::phred42 where the rank and char representations are offset by a fixed value.

• We relaxed a requirement of seqan3::nucleotide_base<alphabet_t> (#2584):
  • Old requirement: alphabet_t::complement_table must be a lookup table.
  • New requirement: alphabet_t::rank_complement must be a static member function.
• Removed seqan3::char_is_valid_for requirement from seqan3::writable_alphabet and seqan3::detail::writable_constexpr_alphabet (#2337).
• Removed seqan3::cigar_op, please use seqan3::cigar::operation instead (#2388).
• The literal 'M'_cigar_op was renamed to 'M'_cigar_operation (#2388).
• Renamed seqan3::phred68legacy to seqan3::phred68solexa (#2522).
• Renamed seqan3::sam_dna16 to seqan3::dna16sam (#2521).
• Removed phred constructors (#2537):
  • Use seqan3::phred42::assign_phred() or seqan3::operator""_phred42 instead of seqan3::phred42(phred_type).
  • Use seqan3::phred63::assign_phred() or seqan3::operator""_phred63 instead of seqan3::phred63(phred_type).
  • Use seqan3::phred94::assign_phred() or seqan3::operator""_phred94 instead of seqan3::phred94(phred_type).
  • Use seqan3::phred68legacy::assign_phred() or seqan3::operator""_phred68legacy instead of seqan3::phred68legacy(phred_type).
• Renamed seqan3::quality_base to seqan3::phred_base (#2539).
• Added the seqan3::literals namespace containing all literals. This adds the option to use using namespace seqan3::literals to import literal operators. The old way of explicitly importing specific operators via using seqan3::operator""_{dna4, rna4, ...} is not affected by this change (#2568).
  • Breaking change: Swapped the meaning of seqan3::alphabet_variant::is_alternative and seqan3::alphabet_variant::holds_alternative (#2596).

Header Changes:

#include <seqan3/alphabet/cigar/{cigar_op => cigar}.hpp>
#include <seqan3/alphabet/nucleotide/{sam_dna16 => dna16sam}.hpp}>
#include <seqan3/alphabet/quality/{phred68legacy => phred68solexa}.hpp>
#include <seqan3/alphabet/quality/{quality_base => phred_base}.hpp>

Argument Parser

• seqan3::output_file_validator cannot be constructed with the extension list alone anymore, you need to specify one of the seqan3::output_file_open_options options. (#2009).
• The enum names of seqan3::option_spec were changed to lower case (#2285):
  • seqan3::option_spec::DEFAULT is replaced by seqan3::option_spec::standard.
  • seqan3::option_spec::REQUIRED is replaced by seqan3::option_spec::required.
  • seqan3::option_spec::ADVANCED is replaced by seqan3::option_spec::advanced.
  • seqan3::option_spec::HIDDEN is replaced by seqan3::option_spec::hidden.

Core

• Deprecated seqan3::range_compatible_concept and it will be removed in 3.1.0 (#2265).

Header Changes:

#include <seqan3/core/algorithm/bound.hpp> [Functionality included in alignment/configuration/align_config_band.hpp]
#include <seqan3/core/{algorithm => configuration}/configuration.hpp>
#include <seqan3/core/{algorithm => configuration}/pipeable_config_element.hpp>
 
#include <seqan3/{core => utility}/char_operations/predicate.hpp>
#include <seqan3/{core => utility}/char_operations/transform.hpp>
 
#include <seqan3/{core => utility/tuple}/common_tuple.hpp>
 
#include <seqan3/{core/concept/tuple => utility/tuple/concept}.hpp>
 
#include <seqan3/{core => utility}/math.hpp>
 
#include <seqan3/{core => utility/tuple}/pod_tuple.hpp>
 
#include <seqan3/{core => utility}/simd/concept.hpp>
#include <seqan3/{core => utility}/simd/{simd_algorithm => algorithm}.hpp>
#include <seqan3/{core => utility}/simd/simd.hpp>
#include <seqan3/{core => utility}/simd/simd_traits.hpp>
#include <seqan3/{core => utility}/simd/{view_iota_simd => views/iota_simd}.hpp>
#include <seqan3/{core => utility}/simd/{view_to_simd => views/to_simd}.hpp>
 
#include <seqan3/{core/tuple_utility => utility/tuple/pop_front}.hpp>
#include <seqan3/{core/tuple_utility => utility/tuple/split}.hpp>
 
#include <seqan3/{core => utility}/type_list/traits.hpp>
#include <seqan3/{core => utility}/type_list/type_list.hpp>
 
#include <seqan3/{core => utility}/type_traits/basic.hpp>
#include <seqan3/{core => utility}/type_traits/concept.hpp>
#include <seqan3/{core => utility}/type_traits/function{ =>_traits}.hpp>
#include <seqan3/{core => utility}/type_traits/{lazy => lazy_conditional.hpp>
#include <seqan3/{core/type_traits/pack => utility/type_pack/traits}.hpp>
#include <seqan3/{core => utility}/type_traits/pre.hpp>  [deleted without replacement]
#include <seqan3/core/{type_traits/range => range/type_traits}.hpp>

I/O

• Deprecated seqan3::field::seq_qual. Use seqan3::field::seq and seqan3::field::qual instead. (#2379). Check out SeqAn3 Cookbook - Write Record for usage.
• Renamed seqan3::alignment_file* to seqan3::sam_file* (#2459):
  • seqan3::alignment_file_header is replaced by seqan3::sam_file_header.
  • seqan3::alignment_file_input_default_traits is replaced by seqan3::sam_file_input_default_traits.
  • seqan3::alignment_file_input is replaced by seqan3::sam_file_input.
  • seqan3::alignment_file_input_format is replaced by seqan3::sam_file_input_format.
  • seqan3::alignment_file_input_options is replaced by seqan3::sam_file_input_options.
  • seqan3::alignment_file_output is replaced by seqan3::sam_file_output.
  • seqan3::alignment_file_output_format is replaced by seqan3::sam_file_output_format.
  • seqan3::alignment_file_output_options is replaced by seqan3::sam_file_output_options.
• seqan3::sam_file_input and seqan3::sam_file_output do not accept seqan3::field::ref_seq, seqan3::field::evalue and seqan3::field::bit_score anymore. (#2658).
• The seqan3::get accessor for I/O records, e.g. seqan3::get<seqan3::field::id>(record), is deprecated, please use the corresponding member accessor (#2420):
  • If you used files as views with seqan3::views::get<seqan3::field::id> to project a single field, e.g.
    • seqan3::views::get<seqan3::field::id>(fin) => std::views::transform(fin, [](auto && record){ return record.id(); })
    • fin | seqan3::views::get<seqan3::field::id>() => fin | std::views::transform([](auto && record){ return record.id(); })
    • or per projection: fin | std::views::transform(&decltype(fin)::record_type::id)
  • seqan3::sequence_record:
    • seqan3::get<seqan3::field::id>(record) => record.id()
    • seqan3::get<seqan3::field::seq>(record) => record.sequence()
    • seqan3::get<seqan3::field::qual>(record) => record.base_qualities()
  • seqan3::structure_record:
    • seqan3::get<seqan3::field::id>(record) => record.id()
    • seqan3::get<seqan3::field::seq>(record) => record.sequence()
    • seqan3::get<seqan3::field::structure>(record) => record.sequence_structure()
    • seqan3::get<seqan3::field::energy>(record) => record.energy()
    • seqan3::get<seqan3::field::bpp>(record) => record.base_pair_probability_matrix()
  • seqan3::sam_record:
    • seqan3::get<seqan3::field::id>(record) => record.id()
    • seqan3::get<seqan3::field::seq>(record) => record.sequence()
    • seqan3::get<seqan3::field::qual>(record) => record.base_qualities()
    • seqan3::get<seqan3::field::offset>(record) => record.sequence_position()
    • seqan3::get<seqan3::field::alignment>(record) => record.alignment()
    • seqan3::get<seqan3::field::ref_id>(record) => record.reference_id()
    • seqan3::get<seqan3::field::ref_offset>(record) => record.reference_position()
    • seqan3::get<seqan3::field::header_ptr>(record) => record.header_ptr()
    • seqan3::get<seqan3::field::flag>(record) => record.flag()
    • std::get<0>(seqan3::get<seqan3::field::mate>(record)) => record.mate_reference_id()
    • std::get<1>(seqan3::get<seqan3::field::mate>(record)) => record.mate_position()
    • std::get<2>(seqan3::get<seqan3::field::mate>(record)) => record.template_length()
    • seqan3::get<seqan3::field::mapq>(record) => record.mapping_quality()
    • seqan3::get<seqan3::field::cigar>(record) => record.cigar_sequence()
    • seqan3::get<seqan3::field::tags>(record) => record.tags()

Header Changes:

#include <seqan3/io/{alignment_file=> sam_file}/format_bam.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/format_sam.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/header.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/input.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/input_format_concept.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/input_options.hpp>
#include <seqan3/io/{alignment_file/misc => sam_file/sam_flag}.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/output.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/output_format_concept.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/output_options.hpp>
#include <seqan3/io/{alignment_file=> sam_file}/sam_tag_dictionary.hpp>

Range

• We made seqan3::views::convert NOAPI and moved it to seqan3/utility/views/convert.hpp. You can still use seqan3::views::convert in the meantime, but we encourage using std::views::transform instead as shown in our Cookbook (#2524).
• Deprecated seqan3::views::as_const, there is no alternative other than reimplementing it yourself (#2567).
• Deprecated seqan3::views::drop, use std::views::drop or seqan3::views::type_reduce | std::views::drop. (#2540)
• Deprecated seqan3::views::join. Please use std::views::join or seqan3::views::join_with instead (#2526).
• Deprecated seqan3::views::move, use the std::ranges::move algorithm, std::[cpp20::]move_iterator or an explicit for loop where you move the value. (#2563)
• Deprecated seqan3::views::take and it will be removed in 3.1.0. Use std::views::take instead (#2541).
• Deprecated seqan3::views::take_line and it will be removed in 3.1.0 (#2525).
• Deprecated seqan3::views::take_exactly. Please use std::views::take or std::views::counted instead (#2601).
• Deprecated seqan3::views::take_until and it will be removed in 3.1.0. Use std::views::take_while(std::not_fn(predicate)) instead (#2604).
• Deprecated seqan3::views::take_until_and_consume and it will be removed in 3.1.0. There is no alternative other than reimplementing it yourself (#2604).
• Deprecated seqan3::views::to_upper and it will be removed in 3.1.0, use std::views::transform([](auto && chr){return std::toupper(chr)}). (#2538)
• Deprecated seqan3::views::to_lower and it will be removed in 3.1.0, use std::views::transform([](auto && chr){return std::tolower(chr)}). (#2556)
• Deprecated seqan3::views::persist. There is no replacement, use lvalues instead of rvalues (#2553).
• Renamed seqan3::gap_decorator::unaligned_seq_type to seqan3::gap_decorator::unaligned_sequence_type (#2564).
• Renamed seqan3::views::get to seqan3::views::elements (#2554).
• Renamed seqan3::translation_frames::*FRAME* (#2565):
  • seqan3::translation_frames::FWD_FRAME_0 is replaced by seqan3::translation_frames::forward_frame0.
  • seqan3::translation_frames::FWD_FRAME_1 is replaced by seqan3::translation_frames::forward_frame1.
  • seqan3::translation_frames::FWD_FRAME_2 is replaced by seqan3::translation_frames::forward_frame2.
  • seqan3::translation_frames::REV_FRAME_0 is replaced by seqan3::translation_frames::reverse_frame0.
  • seqan3::translation_frames::REV_FRAME_1 is replaced by seqan3::translation_frames::reverse_frame1.
  • seqan3::translation_frames::REV_FRAME_2 is replaced by seqan3::translation_frames::reverse_frame2.
  • seqan3::translation_frames::FWD_REV_0 is replaced by seqan3::translation_frames::forward_reverse0.
  • seqan3::translation_frames::FWD_REV_1 is replaced by seqan3::translation_frames::forward_reverse1.
  • seqan3::translation_frames::FWD_REV_2 is replaced by seqan3::translation_frames::forward_reverse2.
  • seqan3::translation_frames::FWD is replaced by seqan3::translation_frames::forward_frames.
  • seqan3::translation_frames::REV is replaced by seqan3::translation_frames::reverse_frames.
  • seqan3::translation_frames::SIX_FRAME is replaced by seqan3::translation_frames::six_frames.
• Renamed seqan3::type_reduce_view to seqan3::type_reduce_t (#2587).

Header Changes:

#include <seqan3/{range/concept => alphabet/range/sequence}.hpp>
#include <seqan3/{range/concept => alphabet/range/concept}.hpp>
 
#include <seqan3/{range => utility}/container/aligned_allocator.hpp>
#include <seqan3/{range => alphabet}/container/{bitcompressed_vector => bitpacked_sequence}.hpp>
#include <seqan3/{range => alphabet}/container/concatenated_sequences.hpp>
#include <seqan3/{range => utility}/container/concept.hpp>
#include <seqan3/{range => utility}/container/dynamic_bitset.hpp>
#include <seqan3/{range => utility}/container/small_string.hpp>
#include <seqan3/{range => utility}/container/small_vector.hpp>
 
#include <seqan3/{range => alignment}/decorator/gap_decorator.hpp>
 
#include <seqan3/{range => alphabet/range}/hash.hpp>
 
#include <seqan3/{range => io}/views/async_input_buffer.hpp>
#include <seqan3/{range => alphabet}/views/char_to.hpp>
#include <seqan3/{range => utility}/views/chunk.hpp>
#include <seqan3/{range => alphabet}/views/complement.hpp>
#include <seqan3/{range => utility}/views/convert.hpp>
#include <seqan3/{range => utility}/views/deep.hpp>
#include <seqan3/{range => utility}/views/enforce_random_access.hpp>
#include <seqan3/{range => utility}/views/{get => elements}.hpp>
#include <seqan3/{range => utility}/views/interleave.hpp>
#include <seqan3/range/views/istreambuf.hpp> [deleted without replacement]
#include <seqan3/{range => utility}/views/{join => join_with}.hpp>
#include <seqan3/{range => search}/views/kmer_hash.hpp>
#include <seqan3/{range => search}/views/minimiser.hpp>
#include <seqan3/{range => search}/views/minimiser_hash.hpp>
#include <seqan3/{range => utility}/views/pairwise_combine.hpp>
#include <seqan3/range/views/persist> [deleted without replacement]
#include <seqan3/{range => alphabet}/views/rank_to.hpp>
#include <seqan3/{range => utility}/views/repeat.hpp>
#include <seqan3/{range => utility}/views/repeat_n.hpp>
#include <seqan3/{range => utility}/views/single_pass_input.hpp>
#include <seqan3/{range => utility}/views/slice.hpp>
#include <seqan3/range/views/take.hpp> [deleted without replacement]
#include <seqan3/range/views/take_exactly.hpp> [deleted without replacement]
#include <seqan3/range/views/take_line.hpp> [deleted without replacement]
#include <seqan3/range/views/take_until.hpp> [deleted without replacement]
#include <seqan3/{range => utility}/views/to.hpp>
#include <seqan3/{range => alphabet}/views/to_char.hpp>
#include <seqan3/{range => alphabet}/views/to_rank.hpp>
#include <seqan3/{range => alphabet}/views/translate.hpp>
#include <seqan3/{range => alphabet}/views/translate_join.hpp>
#include <seqan3/{range => alphabet}/views/trim_quality.hpp>
#include <seqan3/{range => utility}/views/type_reduce.hpp>
#include <seqan3/{range => utility}/views/zip.hpp>

Search

• We removed the concepts seqan3::[bi_]fm_index[_cursor]_specialisation. We did this because we currently have only one implementation modelling each concept and are not completely sure if the current definition of the concepts is the right one. If you used those concepts, you can check whether the cursor type is seqan3::[bi_]fm_index_cursor as a substitute. (#2348)

3.0.2

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

• Check out our new SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.
• SeqAn 3.0.2 is known to compile with GCC 7.5, 8.4, 9.3 and 10.2. Future versions (e.g. GCC 10.3 and 11) might work, but were not yet available at the time of this release.

New features

Alignment

• The alignment algorithm can now be invoked with a user defined callback function using the alignment configuration seqan3::align_cfg::on_result (#1876).
• The function seqan3::align_pairwise accepts a std::pair of sequences as input (#1913).
• We lowered the requirements of the seqan3::aligned_sequence concept by removing everything that needs write access to the object. We then added a new seqan3::writable_aligned_sequence concept which extends seqan3::aligned_sequence with the requirements that need write access (e.g. insert_gap) (#1933).

Argument Parser

• The following functions accept a seqan3::argument_parser::option_spec::ADVANCED to control what is displayed on the (advanced) help page:
  • seqan3::argument_parser::add_section
  • seqan3::argument_parser::add_subsection
  • seqan3::argument_parser::add_line
  • seqan3::argument_parser::add_list_item Note that other seqan3::argument_parser::option_specs like REQUIRED are ignored (#1652).

I/O

• The seqan3::format_fasta accepts the file extension .fas as a valid extension for the FASTA format (#1599).

Build system

• Add top-level CMakeLists.txt (#1475).
• We now use Doxygen version 1.8.20 to build our documentation (#2081).

Range

• The seqan3::views::minimiser has been added. This is a view that computes the minimum in a window shifted over a range of comparable values (#1654).
• The seqan3::views::minimiser_hash has been added. This is a view that computes the minimisers of a range of type seqan3::semialphabet (#1721).

Search

• Added seqan3::interleaved_bloom_filter, a data structure that efficiently answers set-membership queries for multiple bins (#920).
• Added seqan3::search_cfg::hit, which allows dynamic configuration of the hit strategy. (#1853).
• Added seqan3::search_cfg::on_result, which allows providing a custom callback for the search algorithm (#2019).

API changes

• The required version of the ranges-v3 library has increased: We now support the versions >= 0.11.0 and < 0.12.0, increasing the previous requirement of >= 0.10.0 and < 0.11.0 (#2014).

Alignment

• The alignment configuration elements have been refactored:
  • All options are now classes and must be constructed explicitly even if they don’t take any arguments, e.g. seqan3::align_cfg::vectorise -> seqan3::align_cfg::vectorised{}.
  • The configuration seqan3::align_cfg::band has been replaced by seqan3::align_cfg::band_fixed_size, and will directly be initialised with a seqan3::align_cfg::lower_diagonal and seqan3::align_cfg::upper_diagonal instead of a seqan3::static_band class. It also directly exposes the lower_diagonal and upper_diagonal as public members (#1873).
  • The configuration seqan3::align_cfg::mode has been replaced by two separate configuration elements seqan3::align_cfg::method_global and seqan3::align_cfg::method_local (#1918).
  • The configuration seqan3::align_cfg::aligned_ends has been replaced by seqan3::align_cfg::method_global. The free end-gaps are now initialised via constructor arguments to the seqan3::align_cfg::method_global configuration (#2119).
  • The configuration seqan3::align_cfg::vectorise has been replaced by seqan3::align_cfg::vectorised (#2026).
  • The configuration seqan3::align_cfg::scoring has been replaced by seqan3::align_cfg::scoring_scheme (#2027).
  • The configuration seqan3::align_cfg::result has been replaced by seqan3::align_cfg::output_* options. When no output configuration was configured, the default behaviour changed from computing only the score to all possible outputs. Please read the linked documentation above carefully to understand all implied changes (#2024 & #2035).
  • The configuration seqan3::align_cfg::gap has been replaced by seqan3::align_cfg::gap_cost_affine, which is directly initialised with the relevant gap scores (#2037).
  • The configuration seqan3::align_cfg::max_error has been replaced by seqan3::align_cfg::min_score, and thus prepares it for non-edit scoring schemes in the future as well (#2021).

Header Changes:

#include <seqan3/alignment/configuration/{align_config_max_error.hpp => align_config_min_score.hpp}>
#include <seqan3/alignment/configuration/{align_config_scoring.hpp => align_config_scoring_scheme.hpp}>
#include <seqan3/alignment/configuration/{align_config_vectorise.hpp => align_config_vectorised.hpp}>
#include <seqan3/alignment/configuration/{align_config_gap.hpp => align_config_gap_cost_affine.hpp}>
#include <seqan3/alignment/configuration/{align_config_mode.hpp => align_config_method.hpp}>
#include <seqan3/alignment/configuration/{align_config_result.hpp => align_config_score_type.hpp}>
 
#include <seqan3/alignment/configuration/align_config_aligned_ends.hpp> [deleted without replacement; is now part of seqan3::align_cfg::method_global]
 
#include <seqan3/{alignment/pairwise => core/algorithm}/alignment_range.hpp>

Core

• In accordance with the standard, the following concepts have been renamed:
  • std::default_constructible to std::default_initializable
  • std::readable to std::indirectly_readable
  • std::writable to std::indirectly_writable (#1860).
• The seqan3::remove_cvref_t has been replaced by std::remove_cvref_t (#2079).

Range

• The seqan3::begin(), seqan3::end(), seqan3::cbegin(), seqan3::cend(), seqan3::size(), seqan3::empty() functions have been deprecated. Use std::ranges::{begin|end|cbegin|cend|size|empty}() instead (#1663).
• The seqan3::forward_range has been removed. Use std::ranges::borrowed_range instead (#2038).
• The seqan3::views:trim has been renamed to seqan3::views:trim_quality (#2025).

Header Changes:

#include <seqan3/range/views/{trim.hpp => trim_quality.hpp}>

Search

• Moved seqan3::search from search/algorithm/ to search/ (#1696).
• The seqan3::search_result_range returns now a seqan3::search_result which unifies the interface for all the search instances, e.g. using an index over a single text or a text collection (#1706).
• Configuration refactoring:
  • The configuration seqan3::search_cfg::max_error has been replaced by individual configuration elements:
    • seqan3::search_cfg::max_error{seqan3::search_cfg::total} to seqan3::search_cfg::max_error_total{}
    • seqan3::search_cfg::max_error{seqan3::search_cfg::insertion} to seqan3::search_cfg::max_error_insertion{}
    • seqan3::search_cfg::max_error{seqan3::search_cfg::deletion} to seqan3::search_cfg::max_error_deletion{}
    • seqan3::search_cfg::max_error{seqan3::search_cfg::substitution} to seqan3::search_cfg::max_error_substitution{} (#1861).
  • The max error configurations can be initialised with either a seqan3::search_cfg::error_rate or seqan3::search_cfg::error_count, and can be reassigned (#1861).
  • The configuration seqan3::search_cfg::mode has been replaced by individual configuration elements (#1639):
    • seqan3::search_cfg::mode{seqan3::search_cfg::all} to seqan3::search_cfg::hit_all{}
    • seqan3::search_cfg::mode{seqan3::search_cfg::best} to seqan3::search_cfg::hit_single_best{}
    • seqan3::search_cfg::mode{seqan3::search_cfg::all_best} to seqan3::search_cfg::hit_all_best{}
    • seqan3::search_cfg::mode{seqan3::search_cfg::strata{5}} to seqan3::search_cfg::hit_strata{5}
    • The seqan3::search_cfg::hit_strata member variable value has been replaced to stratum
  • The configurationseqan3::search_cfg::output has been replaced by individual configuration elements (#1862):
    • seqan3::search_cfg::output{seqan3::search_cfg::text_position} to seqan3::search_cfg::output_reference_begin_position{}
    • seqan3::search_cfg::output{seqan3::search_cfg::text_position} to seqan3::search_cfg::output_index_cursor
    • seqan3::search_cfg::output_query_id{} has been added
    • seqan3::search_cfg::output_reference_id{} has been added
• Removed seqan3::bi_fm_index_cursor::to_rev_cursor() and seqan3::bi_fm_index::rev_cursor() (#1892).

Header Changes:

#include <seqan3/search/{algorithm => }/search.hpp>
#include <seqan3/{search/search_result_range.hpp => core/algorithm/algorithm_result_generator_range.hpp}>
 
#include <seqan3/search/configuration/{mode.hpp => hit.hpp}>
#include <seqan3/search/configuration/{max_error_rate.hpp => max_error.hpp AND max_error_common.hpp}>

Notable Bug-fixes

Alignment

• When invoking the alignment algorithm with a user defined thread count using the seqan3::align_cfg::parallel configuration element, all available threads were used. This is now fixed and only the specified number of threads will be spawned (#1854).
• Using an unsigned score type via the seqan3::align_cfg::score_type configuration is prevented with a static assert, since gaps and mismatches have negative scores and thus need a signed score type (#1891).

Argument Parser

• Long option identifiers and their value must be separated by a space or equal sign =. Applying this restriction resolves an ambiguity that occurs if one long option identifier is the prefix of another (#1792).

  Valid short id value pairs: -iValue, -i=Value, -i Value Valid long id value pairs: --id=Value, --id Value (prohibited now: --idValue)

I/O

• The seqan3::field::cigar was added to the default fields for reading and writing alignment files (#1642). This has the following impact:
  1. Reading and writing in one line is now possible without additional reference information: seqan3::alignment_file_output{"foo.sam"} = seqan3::alignment_file_input{"bar.sam"};
  2. The seqan3::alignment_file_output now accepts seqan3::field::cigar and seqan3::field::alignment although they store redundant information. For the SAM/BAM format this ambiguity is handled by favouring the CIGAR information at all times if present. Note that this breaks your code if you have not selected custom fields and used structural bindings!

Search

• The seqan3::fm_index_cursor::extend_right(), seqan3::bi_fm_index_cursor::extend_right() and seqan3::bi_fm_index_cursor::extend_left() functions handle c-style strings without including the null character (#1588).
• seqan3::fm_index and seqan3::bi_fm_index construct the index correctly if a collection with a single text is passed as input (#1892).

Range

• Added size() function to seqan3::views::kmer_hash (#1722).
• operator[](difference_type const n) of the iterator of the seqan3::views::kmer_hash is declared const and returns value n steps after the current position without jumping to that position (#1756).

3.0.1

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

New features

Alphabet

• Added seqan3::semialphabet_any, a semi-alphabet that type erases all other semi-alphabets of the same size (#981).
• Added seqan3::dna3bs, an alphabet that mimics a bisulfite-treated dna4 sequence (#1191).

Alignment

• The score type used in the alignment score matrix and the result type is configurable through a template argument of the seqan3::align_cfg::result configuration (#1340).
• The functionseqan3::align_pairwise can be parallelised using theseqan3::align_cfg::parallel configuration (#1379, #1444).

Argument parser

• Simplified reading file extensions from formatted files with theseqan3::input_file_validator and seqan3::output_file_validator (#863).
• The seqan3::value_list_validator is now constructible from a range or a parameter pack (#1298).
• Enable subcommand argument parsing, see How-to for an example (#1185).
• The seqan3::argument_parser::add_option (and add_positional_option) calls allow enum types when using the seqan3::enumeration_names customisation point (#1196).

Build system

• find_package(SeqAn3) is now case-insensitive and always populates SEQAN3_* variables in all upper-case (#1427).

Core

• Added seqan3::lzcnt, seqan3::tzcnt, and seqan3::popcount for bit manipulation (#1141).
• Added traits for "metaprogramming" with seqan3::type_list and type packs (#1204, #1214, #1273).
• Added SIMD functions seqan3::upcast and seqan3::upcast_signed (#1190).

I/O

• We increased our input performance using a faster iterator on the stream buffer (#1030).
• Support of padded alignments in the SAM/BAM format was added (#1173).
• Reading seqan3::field::cigar into a vector over seqan3::cigar is supported via seqan3::alignment_file_input (#1192).
• Writing seqan3::field::cigar into a vector over seqan3::cigar is supported via seqan3::alignment_file_output (#1192).
• Asynchronous input (background file reading) supported via seqan3::view::async_input_buffer (#1205).

Range

• Added seqan3::views::kmer_hash, a view that computes hash values of an alphabet sequence given a seqan3::shape (#946).
• Added seqan3::views::to, a view that returns a container created from a range by copying all elements (#1033).
• Added seqan3::dynamic_bitset, a container that stores single bits and has a dynamic size (#1153).
• Added seqan3::views::translate_join, analogue to seqan3::views::translate but returns a flattened range (#1171).
• Added seqan3::views::to_simd, a view that transforms a range of ranges into chunks of seqan3::simd vectors (#1190).
• Added seqan3::views::as_const, a view that provides only const & to elements of the underlying range (#1410).
• Added seqan3::views::move, a view that turns lvalue-references into rvalue-references (#1410).
• Renamed seqan3::views::all to seqan3::views::type_reduce (#1410).

Search

• The memory footprint of FM-indices over text collections was reduced (#1363).

Std

• We provide a std::to_chars overload for floating point data types in our seqan3/std/from_chars header (#1160).

API changes

• The required version of the ranges-v3 library has increased: We now support the versions >= 0.10.0 and < 0.11.0, increasing the previous requirement of >= 0.5.0 and < 0.6.0 (#1471).
• Customising for third party types has changes slightly: You are only affected if you added types to seqan3::custom::. Please see About Customisation (#1225).
• All our concepts are named in the snake_case style (e.g. seqan3::WritableAlphabet -> seqan3::writable_alphabet)! This change was motivated by the decision of the ISO C++ committee to also use snake case everywhere (#1235).

Alphabet

• The seqan3::cigar alphabet is not an seqan3::alphabet anymore but only a seqan3::semialphabet (#1285).

Argument parser

• The seqan3::value_list_validator is not constructible from a std::initialiser_list any more (e.g. seqan3::value_list_validator{{1,2,3}} does not work, use seqan3::value_list_validator{1,2,3} instead) (#1298).
• Changed class signature of input/output file validators: Most user code will be unaffected; to fix possible compiler errors you need to add an empty template parameter list to the respective instances (e.g. change input_file_validator to input_file_validator<>) (#863).
• The member type that denotes which arguments a validator can validate has been renamed from value_type to option_value_type (#1394).
• Some exception names were altered and some removed (#1467):
  • The exception seqan3::parser_invalid_argument was renamed to seqan3::argument_parser_error.
  • The exception seqan3::validation_failed was renamed to seqan3::validation_error.
  • The exception seqan3::parser_design_error was renamed to seqan3::design_error and also inherits from seqan3::argument_parser_error.
  • The exception seqan3::type_conversion_failed was deprecated, you can catch seqan3::user_input_error instead.
  • The exception seqan3::overflow_error_on_conversion was deprecated, you can catch seqan3::user_input_error instead.

Build system

• find_package accepts minimum versions (e.g. find_package(SEQAN3 3.0.1) requires at least SeqAn3 with a version of >= 3.0.1 and < 4.0.0) (#1425).
• The variable SEQAN3_VERSION_STRING defined by find_package(SEQAN3) was renamed to SEQAN3_VERSION (#1425).

Core

• The type_list header has moved: If you included <seqan3/core/type_list.hpp> you need to change the path to <seqan3/core/type_list/type_list.hpp> (#1204).

I/O

• Removed the field-based in- and output interface for sequence and structure files through std::get and std::tie: Output can instead be achieved with seqan3::views:zip(), for input we will implement unzip() in the future (#1398 #1412).
• The seqan3::field::flag of SAM/BAM input and output is now an enum instead of an integer, see seqan3::sam_flag (#1390).
• Uppercase seqan3::field names are deprecated. Use the lower case field names instead. You can easily find and replace all occurrences by the following regex: find field::([A-Z_]+) replace field::\L$1 (#1421).
• Removed the char type from the input and output files: Most user code will be unaffected; however, if you have fully specified all templates of any of the input or output files in your code, you need to remove the template parameter to select the char type of the stream, e.g. change seqan3::sequence_file_input<traits_t, fields_t, formats_t, char> to seqan3::sequence_file_input<traits_t, fields_t, formats_t>. Before this change, setting the char type gave the impression that also streams over wide characters are supported which is not the case yet (#1400).

Range

• The seqan3::concatenated_sequences::data() function has been deprecated: Use seqan3::concatenated_sequences::raw_data() instead (#1208).
• seqan3::to_char must always return a built-in character type (#1285).
• seqan3/range/view has be renamed to seqan3/range/views (#1251).
• namespace seqan3::view has been renamed to seqan3::views (#1251).

Search

• Changed class signature of (bi_)fm_index: All code that relies on automatic template deduction will be unaffected. In case you specified the template parameters of a seqan3::fm_index or seqan3::bi_fm_index you will need to add the alphabet type as first parameter and pass a seqan3::text_layout instead of a bool to indicate the text layout (single, collection). For example, fm_index<false> index{text} where text is of type dna4_vector needs to be changed to fm_index<dna4, text_layout::single> index{text} (#1222).
• The construct() method of the (bi_)fm_index is now private: Use the constructor seqan3::fm_index::fm_index(text_t && text) or seqan3::bi_fm_index::bi_fm_index(text_t && text) instead (#1222).
• The seqan3::fm_index::char_type member was renamed to seqan3::fm_index::alphabet_type The same applies for the seqan3::bi_fm_index (#1433).
• The seqan3::fm_index_cursor::index_char_type member was renamed to seqan3::fm_index_cursor::index_alphabet_type The same applies for the seqan3::bi_fm_index_cursor (#1433).

Notable Bug-fixes

• All our headers are self contained (#1085).
• The alignment algorithm with edit distance returns the correct back coordinate (#1093).
• Inserting or deleting gaps into an empty seqan3::gap_decorator does not cause assert anymore (#1109).
• Some fixes to edge cases in BAM file writing (#1110).
• The application name of the seqan3::argument_parser is restricted to alpha-numeric characters and _ and - (#1133).
• Copying and moving the seqan3::fm_index and seqan3::bi_fm_index now work properly (#1144).
• Searching in the seqan3::fm_index and seqan3::bi_fm_index constructed from a text collection containing a single text now returns the correct result (#1316).
• The view seqan3::views::take is sized if the underlying range is sized (#1146).
• The detection of the pthread library works correctly on linux based systems (#1200).
• The translation table for nucleotide to amino acid translation was corrected (#1485).
• The amino acid score matrices were corrected (#1455).

3.0.0 ("Escala")

This is the initial release of SeqAn3. It is an entirely new library so there is no changelog that covers the differences to SeqAn2.

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.