SeqAn3
Todo List
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.