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‎LICENSE.md‎

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# Copyright {#about_copyright}
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| Summary | |
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|---------------------------|--------------------------------------------------------------------------------------------|
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| Copyright holders | Knut Reinert, [FU-Berlin](https://fu-berlin.de), [MPI MolGen](https://www.molgen.mpg.de/) |
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| Library source code | ![](doc/about/copyright/bsdl_badge.svg) |
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| Documentation | ![](doc/about/copyright/ccby_badge.svg) |
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| Snippets and examples | ![](doc/about/copyright/cc0_badge.svg) |
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| Dependencies | ![](doc/about/copyright/copyfree_badge.svg) |
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In hibf, we have adopted the use of SPDX identifiers to specify the license under which each file is provided.
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# Source code license
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This approach simplifies the process of license declaration as it replaces the full license text with a single line
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identifier. The SPDX identifier is a globally recognized standard that allows for easy identification and understanding
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of the license. This means that each file in our project will have a license identifier at the top, making it clear
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under which license the file is provided. For more information about the specific licenses, you can refer to the
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[SPDX License List](https://spdx.org/licenses/).
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The contents of this repository/directory, in particular the library
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source code of HIBF, are licensed under the following terms:
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For the purpose of referring to a singular license, hibf is licensed under BSD-3-Clause:
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```
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Copyright (c) 2006-2025, Knut Reinert & Freie Universität Berlin
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OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
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DAMAGE.
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```
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# Documentation
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The API documentation and manual are additionally provided under the
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terms of the [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).
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This includes
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* doxygen-style comments within the library source code;
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* Markdown files and images in the `doc`-subfolder;
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* HTML or other representation produced from the above.
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The source code examples and snippets within the documentation are
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additionally provided under the terms of the
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[Creative Commons Public Domain Dedication 1.0](https://creativecommons.org/publicdomain/zero/1.0/deed).
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This includes:
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* source code files (`*.cpp`, `*.hpp`) in the `doc`-subfolder;
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* the contents of `test/snippet`.
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# Submodules
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This repository/directory may contain other projects' content in the
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`submodules`-subfolder. We try to ensure that all dependencies are
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permissively licensed (BSD/MIT/X11/ISC/Boost…), but please verify the
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respective license files yourself.

‎doc/about/api/index.md‎

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‎doc/about/citing/index.md‎

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# Publications
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HIBF has not yet been published academically, for now cite SeqAn2:
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| Publication | |
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|---------------|---------------------------------------------------------------------------------------------------|
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| Title | The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. |
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| Year | 2017 |
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| Authors | Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., ... & Urgese, G. |
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| Journal | Journal of biotechnology, 261, 157-168 |
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| Links | [original](https://doi.org/10.1016/j.jbiotec.2017.07.017) |
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Certain compontents of SeqAn are published separately. If you make strong use of
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one of those compononts and/or specifically compare to that component, please
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cite the respective publication **additionally**.
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## Alignment module
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| Publication | |
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|---------------|---------------------------------------------------------------------------------------------------|
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| Title | Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. |
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| Year | 2018 |
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| Authors | Rahn, R., Budach, S., Costanza, P., Ehrhardt, M., Hancox, J., & Reinert, K |
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| Journal | Bioinformatics, 34(20), 3437-3445 |
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| Links | [original](https://doi.org/10.1093/bioinformatics/bty380) |
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Cite the above publication when you make strong use of the alignment module, in
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particular if you rely on the high-performance computing capabilities.
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## Search module
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| Publication | |
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|---------------|---------------------------------------------------------------------------------------------------|
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| Title | From theory to practice: Plug and play with succinct data structures. |
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| Year | 2014 |
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| Authors | Gog, S., Beller, T., Moffat, A., & Petri, M. |
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| Journal | International Symposium on Experimental Algorithms (pp. 326-337). Springer, Cham. |
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| Links | [original](https://doi.org/10.1007/978-3-319-07959-2_28) |
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Full text indexing in HIBF makes use of the Succint data structure library (SDSL).
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Version 3 has not yet been published, for now cite SDSL-v2 (above).
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## IBF
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| Publication | |
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|---------------|-----------------------------------------------------------------------------------------------------------|
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| Title | Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences |
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| Year | 2021 |
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| Authors | Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert |
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| Journal | iScience 2021 24 (7): 102782 |
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| Links | https://doi.org/10.1016/j.isci.2021.102782 |
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## HIBF
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| Publication | |
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|---------------|----------------------------------------------------------------------------------------------------------|
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| Title | Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries |
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| Year | 2023 |
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| Authors | Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron, and Knut Reinert |
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| Journal | Genome Biol 24, 131 (2023) |
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| Links | https://doi.org/10.1186/s13059-023-02971-4 |

‎doc/cookbook/index.md‎

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\include test/snippet/hibf/config_number_of_user_bins.cpp
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\include test/snippet/hibf/hibf_construction.cpp
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\include test/snippet/hibf/hierarchical_interleaved_bloom_filter.cpp
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\include test/snippet/ibf/counting_agent.cpp
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\include test/snippet/ibf/containment_agent_bulk_contains.cpp
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\include test/snippet/ibf/containment_agent_construction.cpp
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\include test/snippet/ibf/counting_agent_construction.cpp
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\include test/snippet/ibf/counting_agent.cpp
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\include test/snippet/ibf/counting_vector.cpp
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\include test/snippet/ibf/interleaved_bloom_filter_clear.cpp
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\include test/snippet/ibf/interleaved_bloom_filter_constructor.cpp
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\include test/snippet/ibf/interleaved_bloom_filter_emplace.cpp
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\include test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.cpp
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\include test/snippet/ibf/interleaved_bloom_filter_try_increase_bin_number_to.cpp
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\include test/snippet/ibf/containment_agent_bulk_contains.cpp
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\include test/snippet/ibf/containment_agent_construction.cpp
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\include test/snippet/ibf/membership_agent_construction.cpp
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\include test/snippet/ibf/membership_agent_membership_for.cpp
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\include test/snippet/readme.cpp
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\include test/snippet/snippet_main.cpp
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\include test/snippet/test/tmp_directory.cpp

‎include/hibf/hierarchical_interleaved_bloom_filter.hpp‎

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}
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/*!\brief `membership_for` cannot be called on a temporary, since the object the returned reference points to
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* is immediately destroyed.
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*/
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//!\brief Deleted. Calling this function on a temporary would result in a dangling reference.
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template <std::ranges::range value_range_t>
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[[nodiscard]] std::vector<uint64_t> const & membership_for(value_range_t && values,
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uint16_t const threshold) && noexcept = delete;
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/*!\brief `bulk_count` cannot be called on a temporary, since the object the returned reference points to
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*/
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//!\brief Deleted. Calling this function on a temporary would result in a dangling reference.
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template <std::ranges::range value_range_t>
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[[nodiscard]] counting_vector<value_t> const & bulk_count(value_range_t && values,
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size_t const threshold) && noexcept = delete;

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