- Module alignment
- Write detailed landing page.
- Module alignment_file
- document at a later point in time
- Module concept
- write me.
- Module configuration
- Write detailed landing page.
- Module core_view
- write me.
- Module io
- write me!
- Module search
Elaborate on that (space consumption for growing k, maybe a rule of thumb).
k-mer indices are coming soon. Stay tuned!
- Module search_configuration
- Write detailed landing page.
- Class seqan3::alignment_file_output< selected_field_ids_, valid_formats_, stream_type_ >
TODO introduce snippet once seqan3:;alignment_file_in is implemented.
TODO introduce snippet once seqan3:;alignment_file_in is implemented.
- Member seqan3::alignment_file_output< selected_field_ids_, valid_formats_, stream_type_ >::operator| (rng_t &&range, alignment_file_output &f)
- TODO Implement the snippet once seqan3::alignment_file_in is implemented
- Class seqan3::bi_fm_index< text_t, index_traits_t >
- write me
- Member seqan3::bi_fm_index< text_t, index_traits_t >::bi_fm_index (text_t const &text)
- At least linear.
- Member seqan3::bi_fm_index< text_t, index_traits_t >::construct (text_t const &text)
This has to be better implemented with regard to the memory peak due to not matching interfaces with the SDSL.
At least linear.
Ensure strong exception guarantee.
- Member seqan3::bi_fm_index< text_t, index_traits_t >::load (filesystem::path const &path)
- cereal
- Member seqan3::bi_fm_index< text_t, index_traits_t >::store (filesystem::path const &path) const
- cereal
- Member seqan3::bi_fm_index_concept::rev_iterator_type
- Write me!
- Class seqan3::bi_fm_index_default_traits
- write me
- Member seqan3::bi_fm_index_iterator_concept::size_type
- Write me!
- Class seqan3::debug_stream_type
- implement.
- Member seqan3::field
- Table which files take which fields
- Class seqan3::fm_index< text_t, fm_index_traits >
seqan3::search that encapsulates the use of iterators.
The underlying implementation of the FM Index (Rank data structure, sampling rates, etc.) can be specified ...
- Member seqan3::fm_index< text_t, fm_index_traits >::construct (text_t const &text)
This has to be better implemented with regard to the memory peak due to not matching interfaces with the SDSL.
At least linear.
- Member seqan3::fm_index< text_t, fm_index_traits >::fm_index (text_t const &text)
- At least linear.
- Member seqan3::fm_index< text_t, fm_index_traits >::load (filesystem::path const &path)
- cereal
- Member seqan3::fm_index< text_t, fm_index_traits >::store (filesystem::path const &path) const
- cereal
- Member seqan3::fm_index_concept::iterator_type
- Write me!
- Class seqan3::fm_index_default_traits
- Asymptotic space consumption:
- Member seqan3::fm_index_iterator_concept::size_type
- Write me!
- Member seqan3::search (index_t const &index, queries_t &&queries, configuration_t const &cfg)
- Update concepts and documentation of
configuration_t
everywhere once it has been refactored by rrahn.
- Class seqan3::sequence_file_format_fastq
- link).
- Namespace seqan3::simd
- more details.
- Module sequence
- document at a later point in time
- Page Serialisation in SeqAn3
- write me!
- Module stream
- write me!
- Module submodule_fm_index
- (between a factor of X and Y depending on the configuration).
- Module submodule_search_algorithm
- Rewrite landing page.