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). See the documentation on API stability to learn about when API changes are allowed.
find_package(SeqAn3)
is now case-insensitive and always populates SEQAN3_*
variables in all upper-case.seqan3::type_list
and type packs.seqan3::custom::
. Please see About Customisation.seqan3::value_list_validator{{1,2,3}}
does not work, use seqan3::value_list_validator{1,2,3}
instead).input_file_validator
to input_file_validator<>
).validator
can validate has been renamed from value_type
to option_value_type
.find_package(SEQAN3 3.0.1)
requires at least seqan3 with a version of >= 3.0.1
and < 4.0.0
).SEQAN3_VERSION_STRING
defined by find_package(SEQAN3)
was renamed to SEQAN3_VERSION
.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>
.field::flag
of SAM/BAM input and output is now an enum instead of a simple integer (see seqan3::sam_flag).field::([A-Z_]+)
replace field::\L$1
.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.seqan3::concatenated_sequences::data()
function has been deprecated: Use seqan3::concatenated_sequences::raw_data()
instead.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}
.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.seqan3::fm_index::char_type
member was renamed to seqan3::fm_index::alphabet_type
The same applies for the seqan3::bi_fm_index
.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
.seqan3::fm_index
and seqan3::bi_fm_index
now work properly.seqan3::fm_index
and seqan3::bi_fm_index
constructed from a text collection containing a single text now return correct result.Initial release of SeqAn3.