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.
Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.
seqan3::align_cfg::on_result
(#1876).seqan3::align_pairwise
accepts a std::pair
of sequences as input (#1913).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).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_spec
s like REQUIRED
are ignored (#1652).seqan3::format_fasta
accepts the file extension .fas
as a valid extension for the FASTA format (#1599).CMakeLists.txt
(#1475).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).seqan3::views::minimiser_hash
has been added. This is a view that computes the minimisers of a range of type seqan3::semialphabet
(#1721).seqan3::interleaved_bloom_filter
, a data structure that efficiently answers set-membership queries for multiple bins (#920).seqan3::search_cfg::hit
, which allows dynamic configuration of the hit strategy. (#1853).seqan3::search_cfg::on_result
, which allows providing a custom callback for the search algorithm (#2019).seqan3::align_cfg::vectorise
-> seqan3::align_cfg::vectorised{}
.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has been replaced by seqan3::align_cfg::band_fixed_size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).seqan3::align_cfg::mode
has been replaced by two separate configuration elements seqan3::align_cfg::method_global
and seqan3::align_cfg::method_local
(#1918).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).seqan3::align_cfg::vectorise
has been replaced by seqan3::align_cfg::vectorised
(#2026).seqan3::align_cfg::scoring
has been replaced by seqan3::align_cfg::scoring_scheme
(#2027).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).seqan3::align_cfg::gap
has been replaced by seqan3::align_cfg::gap_cost_affine
, which is directly initialised with the relevant gap scores (#2037).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:
std::default_constructible
to std::default_initializable
std::readable
to std::indirectly_readable
std::writable
to std::indirectly_writable
(#1860).seqan3::remove_cvref_t
has been replaced by std::remove_cvref_t
(#2079).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).seqan3::forward_range
has been removed. Use std::ranges::borrowed_range
instead (#2038).seqan3::views:trim
has been renamed to seqan3::views:trim_quality
(#2025).Header Changes:
seqan3::search
from search/algorithm/
to search/
(#1696).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).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).seqan3::search_cfg::error_rate
or seqan3::search_cfg::error_count
, and can be reassigned (#1861).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}
seqan3::search_cfg::hit_strata
member variable value
has been replaced to stratum
seqan3::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 addedseqan3::search_cfg::output_reference_id{}
has been addedseqan3::bi_fm_index_cursor::to_rev_cursor()
and seqan3::bi_fm_index::rev_cursor()
(#1892).Header Changes:
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).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).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
)
seqan3::field::cigar
was added to the default fields for reading and writing alignment files (#1642). This has the following impact:seqan3::alignment_file_output{"foo.sam"} = seqan3::alignment_file_input{"bar.sam"};
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!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).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).Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.
seqan3::semialphabet_any
, a semi-alphabet that type erases all other semi-alphabets of the same size (#981).seqan3::dna3bs
, an alphabet that mimics a bisulfite-treated dna4 sequence (#1191).seqan3::align_cfg::result
configuration (#1340).seqan3::align_pairwise
can be parallelised using theseqan3::align_cfg::parallel
configuration (#1379, #1444).seqan3::input_file_validator
and seqan3::output_file_validator
(#863).seqan3::value_list_validator
is now constructible from a range or a parameter pack (#1298).seqan3::argument_parser::add_option
(and add_positional_option) calls allow enum types when using the seqan3::enumeration_names
customisation point (#1196).find_package(SeqAn3)
is now case-insensitive and always populates SEQAN3_*
variables in all upper-case (#1427).seqan3::lzcnt
, seqan3::tzcnt
, and seqan3::popcount
for bit manipulation (#1141).seqan3::type_list
and type packs (#1204, #1214, #1273).seqan3::upcast
and seqan3::upcast_signed
(#1190).seqan3::field::cigar
into a vector over seqan3::cigar
is supported via seqan3::alignment_file_input
(#1192).seqan3::field::cigar
into a vector over seqan3::cigar
is supported via seqan3::alignment_file_output
(#1192).seqan3::view::async_input_buffer
(#1205).seqan3::views::kmer_hash
, a view that computes hash values of an alphabet sequence given a seqan3::shape
(#946).seqan3::views::to
, a view that returns a container created from a range by copying all elements (#1033).seqan3::dynamic_bitset
, a container that stores single bits and has a dynamic size (#1153).seqan3::views::translate_join
, analogue to seqan3::views::translate
but returns a flattened range (#1171).seqan3::views::to_simd
, a view that transforms a range of ranges into chunks of seqan3::simd
vectors (#1190).seqan3::views::as_const
, a view that provides only const &
to elements of the underlying range (#1410).seqan3::views::move
, a view that turns lvalue-references into rvalue-references (#1410).seqan3::views::all
to seqan3::views::type_reduce
(#1410).std::to_chars
overload for floating point data types in our seqan3/std/from_chars
header (#1160).seqan3::custom::
. Please see About Customisation (#1225).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).seqan3::cigar
alphabet is not an seqan3::alphabet
anymore but only a seqan3::semialphabet
(#1285).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).input_file_validator
to input_file_validator<>
) (#863).validator
can validate has been renamed from value_type
to option_value_type
(#1394).find_package(SEQAN3 3.0.1)
requires at least SeqAn3 with a version of >= 3.0.1
and < 4.0.0
) (#1425).SEQAN3_VERSION_STRING
defined by find_package(SEQAN3)
was renamed to SEQAN3_VERSION
(#1425).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).seqan3::views:zip()
, for input we will implement unzip()
in the future (#1398 #1412).seqan3::field::flag
of SAM/BAM input and output is now an enum instead of an integer, see seqan3::sam_flag
(#1390).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).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).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).seqan3::view
has been renamed to seqan3::views
(#1251).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).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).seqan3::fm_index::char_type
member was renamed to seqan3::fm_index::alphabet_type
The same applies for the seqan3::bi_fm_index
(#1433).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).seqan3::gap_decorator
does not cause assert anymore (#1109).seqan3::argument_parser
is restricted to alpha-numeric characters and _
and -
(#1133).seqan3::fm_index
and seqan3::bi_fm_index
now work properly (#1144).seqan3::fm_index
and seqan3::bi_fm_index
constructed from a text collection containing a single text now returns the correct result (#1316).seqan3::views::take
is sized if the underlying range is sized (#1146).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.