seqan · eseiler · Mar 24, 2025 · Mar 24, 2025 · Mar 24, 2025 · Mar 24, 2025
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,17 +1,14 @@
 # Copyright {#about_copyright}
 
-| Summary                   |                                                                                            |
-|---------------------------|--------------------------------------------------------------------------------------------|
-| Copyright holders         | Knut Reinert, [FU-Berlin](https://fu-berlin.de), [MPI MolGen](https://www.molgen.mpg.de/)  |
-| Library source code       | ![](doc/about/copyright/bsdl_badge.svg)                                                    |
-| Documentation             | ![](doc/about/copyright/ccby_badge.svg)                                                    |
-| Snippets and examples     | ![](doc/about/copyright/cc0_badge.svg)                                                     |
-| Dependencies              | ![](doc/about/copyright/copyfree_badge.svg)                                                |
+In hibf, we have adopted the use of SPDX identifiers to specify the license under which each file is provided.
 
-# Source code license
+This approach simplifies the process of license declaration as it replaces the full license text with a single line
+identifier. The SPDX identifier is a globally recognized standard that allows for easy identification and understanding
+of the license. This means that each file in our project will have a license identifier at the top, making it clear
+under which license the file is provided. For more information about the specific licenses, you can refer to the
+[SPDX License List](https://spdx.org/licenses/).
 
-The contents of this repository/directory, in particular the library
-source code of HIBF, are licensed under the following terms:
+For the purpose of referring to a singular license, hibf is licensed under BSD-3-Clause:
 
 ```
 Copyright (c) 2006-2025, Knut Reinert & Freie Universität Berlin
@@ -42,26 +39,3 @@ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
 OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
 DAMAGE.
 ```
-
-# Documentation
-
-The API documentation and manual are additionally provided under the
-terms of the [Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/).
-This includes
-  * doxygen-style comments within the library source code;
-  * Markdown files and images in the `doc`-subfolder;
-  * HTML or other representation produced from the above.
-
-The source code examples and snippets within the documentation are
-additionally provided under the terms of the
-[Creative Commons Public Domain Dedication 1.0](https://creativecommons.org/publicdomain/zero/1.0/deed).
-This includes:
-  * source code files (`*.cpp`, `*.hpp`) in the `doc`-subfolder;
-  * the contents of `test/snippet`.
-
-# Submodules
-
-This repository/directory may contain other projects' content in the
-`submodules`-subfolder. We try to ensure that all dependencies are
-permissively licensed (BSD/MIT/X11/ISC/Boost…), but please verify the
-respective license files yourself.
diff --git a/doc/about/api/index.md b/doc/about/api/index.md
diff --git a/doc/about/citing/index.md b/doc/about/citing/index.md
@@ -14,43 +14,22 @@ on SeqAn. This will help us continue to acquire funding and improve the library.
 
 # Publications
 
-HIBF has not yet been published academically, for now cite SeqAn2:
-
-| Publication   |                                                                                                   |
-|---------------|---------------------------------------------------------------------------------------------------|
-| Title         | The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.       |
-| Year          | 2017                                                                                              |
-| Authors       | Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., ... & Urgese, G. |
-| Journal       | Journal of biotechnology, 261, 157-168                                                            |
-| Links         | [original](https://doi.org/10.1016/j.jbiotec.2017.07.017)                                         |
-
-Certain compontents of SeqAn are published separately. If you make strong use of
-one of those compononts and/or specifically compare to that component, please
-cite the respective publication **additionally**.
-
-## Alignment module
-
-| Publication   |                                                                                                   |
-|---------------|---------------------------------------------------------------------------------------------------|
-| Title         | Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.          |
-| Year          | 2018                                                                                              |
-| Authors       | Rahn, R., Budach, S., Costanza, P., Ehrhardt, M., Hancox, J., & Reinert, K                        |
-| Journal       | Bioinformatics, 34(20), 3437-3445                                                                 |
-| Links         | [original](https://doi.org/10.1093/bioinformatics/bty380)                                         |
-
-Cite the above publication when you make strong use of the alignment module, in
-particular if you rely on the high-performance computing capabilities.
-
-## Search module
-
-| Publication   |                                                                                                   |
-|---------------|---------------------------------------------------------------------------------------------------|
-| Title         | From theory to practice: Plug and play with succinct data structures.                             |
-| Year          | 2014                                                                                              |
-| Authors       | Gog, S., Beller, T., Moffat, A., & Petri, M.                                                      |
-| Journal       | International Symposium on Experimental Algorithms (pp. 326-337). Springer, Cham.                 |
-| Links         | [original](https://doi.org/10.1007/978-3-319-07959-2_28)                                          |
-
-
-Full text indexing in HIBF makes use of the Succint data structure library (SDSL).
-Version 3 has not yet been published, for now cite SDSL-v2 (above).
+## IBF
+
+| Publication   |                                                                                                           |
+|---------------|-----------------------------------------------------------------------------------------------------------|
+| Title         | Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences |
+| Year          | 2021                                                                                                      |
+| Authors       | Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc, and Knut Reinert                            |
+| Journal       | iScience 2021 24 (7): 102782                                                                              |
+| Links         | https://doi.org/10.1016/j.isci.2021.102782                                                                |
+
+## HIBF
+
+| Publication   |                                                                                                          |
+|---------------|----------------------------------------------------------------------------------------------------------|
+| Title         | Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries                  |
+| Year          | 2023                                                                                                     |
+| Authors       | Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron, and Knut Reinert |
+| Journal       | Genome Biol 24, 131 (2023)                                                                               |
+| Links         | https://doi.org/10.1186/s13059-023-02971-4                                                               |
diff --git a/doc/cookbook/index.md b/doc/cookbook/index.md
@@ -29,16 +29,18 @@ Search for keywords with `Strg + F`.
 \include test/snippet/hibf/config_number_of_user_bins.cpp
 \include test/snippet/hibf/hibf_construction.cpp
 \include test/snippet/hibf/hierarchical_interleaved_bloom_filter.cpp
-\include test/snippet/ibf/counting_agent.cpp
+\include test/snippet/ibf/containment_agent_bulk_contains.cpp
+\include test/snippet/ibf/containment_agent_construction.cpp
 \include test/snippet/ibf/counting_agent_construction.cpp
+\include test/snippet/ibf/counting_agent.cpp
 \include test/snippet/ibf/counting_vector.cpp
 \include test/snippet/ibf/interleaved_bloom_filter_clear.cpp
 \include test/snippet/ibf/interleaved_bloom_filter_constructor.cpp
 \include test/snippet/ibf/interleaved_bloom_filter_emplace.cpp
 \include test/snippet/ibf/interleaved_bloom_filter_increase_bin_number_to.cpp
 \include test/snippet/ibf/interleaved_bloom_filter_try_increase_bin_number_to.cpp
-\include test/snippet/ibf/membership_agent_bulk_contains.cpp
 \include test/snippet/ibf/membership_agent_construction.cpp
+\include test/snippet/ibf/membership_agent_membership_for.cpp
 \include test/snippet/readme.cpp
 \include test/snippet/snippet_main.cpp
 \include test/snippet/test/tmp_directory.cpp

diff --git a/include/hibf/all.hpp b/include/hibf/all.hpp
@@ -8,11 +8,11 @@
  */
 
 /*!\defgroup ibf IBF
- * \brief The Interleaved Bloom Filter.
+ * \brief The Interleaved Bloom Filter: seqan::hibf::interleaved_bloom_filter
  */
 
 /*!\defgroup hibf HIBF
- * \brief The HIBF: seqan::hibf::hierarchical_interleaved_bloom_filter
+ * \brief The Hierarchical Interleaved Bloom Filter: seqan::hibf::hierarchical_interleaved_bloom_filter
  *
  * The Hierarchical Interleaved Bloom Filter is a data structure that provides fast answers to set-membership queries
  * for multiple samples/set/user-bins.

diff --git a/include/hibf/hierarchical_interleaved_bloom_filter.hpp b/include/hibf/hierarchical_interleaved_bloom_filter.hpp
@@ -438,8 +438,7 @@ class hierarchical_interleaved_bloom_filter::membership_agent_type
         return result_buffer;
     }
 
-    // `membership_for` cannot be called on a temporary, since the object the returned reference points to
-    // is immediately destroyed.
+    //!\brief Deleted. Calling this function on a temporary would result in a dangling reference.
     template <std::ranges::range value_range_t>
     [[nodiscard]] std::vector<uint64_t> const & membership_for(value_range_t && values,
                                                                uint16_t const threshold) && noexcept = delete;
@@ -566,8 +565,7 @@ class hierarchical_interleaved_bloom_filter::counting_agent_type
         return result_buffer;
     }
 
-    // `bulk_count` cannot be called on a temporary, since the object the returned reference points to
-    // is immediately destroyed.
+    //!\brief Deleted. Calling this function on a temporary would result in a dangling reference.
     template <std::ranges::range value_range_t>
     [[nodiscard]] counting_vector<value_t> const & bulk_count(value_range_t && values,
                                                               size_t const threshold) && noexcept = delete;