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[UTIL] inspect
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‎.clang-format‎

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@@ -127,27 +127,31 @@ IncludeCategories:
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Priority: 2
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SortPriority: 0
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CaseSensitive: false
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- Regex: '<sharg/'
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- Regex: '<fmt/'
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Priority: 3
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SortPriority: 0
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CaseSensitive: false
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- Regex: '<seqan3/'
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- Regex: '<sharg/'
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Priority: 4
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SortPriority: 0
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CaseSensitive: false
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- Regex: '<seqan3/'
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Priority: 5
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SortPriority: 0
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CaseSensitive: false
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- Regex: '<hibf/'
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Priority: 6
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Priority: 7
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SortPriority: 0
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CaseSensitive: false
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- Regex: '<.*>'
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Priority: 5
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Priority: 6
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SortPriority: 0
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CaseSensitive: false
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- Regex: '.*'
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Priority: 7
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Priority: 8
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SortPriority: 0
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CaseSensitive: false
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IncludeIsMainRegex: '(Test)?$'
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IncludeIsMainRegex: 'x$'
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IncludeIsMainSourceRegex: ''
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IndentAccessModifiers: false
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IndentCaseBlocks: false

‎include/hibf/interleaved_bloom_filter.hpp‎

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@@ -39,6 +39,11 @@ namespace seqan::hibf
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// config.hpp -> misc/insert_iterator.hpp (Needs interleaved_bloom_filter to be a complete class)
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struct config;
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/*!\brief For testing: An accessor used to inspect private members of seqan::hibf::interleaved_bloom_filter.
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* \ingroup ibf
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*/
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struct inspector;
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/*!\brief A strong type that represents the number of bins for the seqan::hibf::interleaved_bloom_filter.
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* \ingroup ibf
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* \qualifier strong
@@ -148,6 +153,9 @@ class interleaved_bloom_filter : private seqan::hibf::bit_vector
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template <typename t>
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friend struct cereal::base_class;
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//!\brief Allow access to private members. Used for util/inspect.
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friend struct seqan::hibf::inspector;
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//!\brief The number of bins specified by the user.
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size_t bins{};
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//!\brief The number of bins stored in the IBF (next multiple of 64 of `bins`).

‎util/CMakeLists.txt‎

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@@ -12,6 +12,7 @@ add_subdirectory ("${HIBF_ROOT_DIR}" "${CMAKE_CURRENT_BINARY_DIR}/hibf_lib")
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# Dependency: Sharg
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CPMAddPackage (URI "gh:seqan/sharg-parser#main"
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SYSTEM TRUE
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OPTIONS "INSTALL_SHARG OFF" "INSTALL_TDL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING" "BUILD_TESTING OFF"
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"SHARG_NO_TDL ON")
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@@ -20,3 +21,19 @@ target_link_libraries (fpr_correction_check seqan::hibf sharg::sharg)
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add_executable (hash_collisions hash_collisions.cpp)
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target_link_libraries (hash_collisions seqan::hibf sharg::sharg)
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set (CMAKE_REQUIRED_QUIET 1)
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check_cxx_source_runs ("#include <generator>\nint main(){}" HIBF_HAS_COROUTINE_GENERATOR)
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if (HIBF_HAS_COROUTINE_GENERATOR)
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# Dependency: fmt
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CPMAddPackage (URI "gh:fmtlib/fmt#11.2.0"
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SYSTEM TRUE
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OPTIONS "FMT_INSTALL OFF" "CMAKE_MESSAGE_LOG_LEVEL WARNING")
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add_executable (inspect inspect/inspect.cpp)
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target_link_libraries (inspect seqan::hibf sharg::sharg fmt::fmt)
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else ()
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# Available starting with GCC 14.
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# Clang's libc++ does not support std::generator yet (Clang-20).
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message (STATUS " Not building inspect because std::generator is not available.")
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endif ()

‎util/inspect/example.md‎

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<!--
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SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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SPDX-License-Identifier: CC-BY-4.0
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-->
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# Nomenclature
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For an IBF, `User bins` and `Active bins` are the same.
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In an HIBF,
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* `User bins`: Bins that actually contain the data of a user bin.
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* `Active bins`: Merged or deleted bins (see `seqan::hibf::bin_kind`).
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# Format
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* The data for each IBF is printed in a block.
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* The children of an IBF are printed after the parent.
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* Intendation levels are used to indicate the hierarchy of IBFs, e.g., the children of an IBF are indented by one level.
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* A level of indentation is four spaces.
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* The data for an IBF in the HIBF is indented by two spaces.
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* The [HIBF with Format Annotations](#hibf-with-format-annotations) section shows an output with explanations/annotations.
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# Miscellaneous
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* The output is colored on the terminal.
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* The output is not colored when redirected/piped.
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* Test data may not be up-to-date if IBF/HIBF implementations have changed.
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* Test data added: 2025-07-29
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# IBF
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**Example data:** https://ftp.seqan.de/hibf/util.test.ibf \
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**Command:** `./inspect --input util.test.ibf`
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```text
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User bins: 128
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Technical bins: 128
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Empty bins: 0
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Bin words: 2
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Bin size: 1,024
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Total size: 131,072
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Hash functions: 3
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Hash shift: 53
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```
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# Simple HIBF
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**Example data:** https://ftp.seqan.de/hibf/util.test.simple.hibf \
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**Command:** `./inspect --input util.test.simple.hibf --hibf`
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```text
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User bins: 2
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Empty bins: 0
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IBFs: 1
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Total size: 4,112
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ID: 0 Level: 0 Children: 0
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User bins: 2
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Active bins: 64
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Technical bins: 64
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Empty bins: 0
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Bin words: 1
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Bin size: 48
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Total size: 3,072
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Hash functions: 2
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Hash shift: 58
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```
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# HIBF
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**Example data:** https://ftp.seqan.de/hibf/util.test.hibf \
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**Command:** `./inspect --input util.test.hibf --hibf`
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```text
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User bins: 4,097
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Empty bins: 0
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IBFs: 66
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Total size: 5,362,464
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ID: 0 Level: 0 Children: 64
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User bins: 0
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Active bins: 64
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Technical bins: 64
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Empty bins: 0
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Bin words: 1
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Bin size: 2,642
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Total size: 169,088
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Hash functions: 2
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Hash shift: 52
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ID: 3 Level: 1 Children: 0
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User bins: 64
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Active bins: 64
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Technical bins: 64
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Empty bins: 0
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Bin words: 1
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Bin size: 1,245
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Total size: 79,680
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Hash functions: 2
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Hash shift: 53
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[...]
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ID: 1 Level: 1 Children: 1
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User bins: 63
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Active bins: 64
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Technical bins: 64
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Empty bins: 0
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Bin words: 1
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Bin size: 1,245
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Total size: 79,680
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Hash functions: 2
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Hash shift: 53
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ID: 2 Level: 2 Children: 0
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User bins: 2
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Active bins: 64
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Technical bins: 64
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Empty bins: 0
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Bin words: 1
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Bin size: 394
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Total size: 25,216
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Hash functions: 2
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Hash shift: 55
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```
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# HIBF with Format Annotations
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```text
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User bins: 4,097 ──────┐
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Empty bins: 0 ├ HIBF Metadata
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IBFs: 66 │
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Total size: 5,362,464 ─┘
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ID: 0 Level: 0 Children: 64 ─┬── Root IBF
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User bins: 0 │
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Active bins: 64 │
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Technical bins: 64 │
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Empty bins: 0 │
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Bin words: 1 ├ Root IBF Metadata
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Bin size: 2,642 │
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Total size: 169,088 │
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Hash functions: 2 │
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Hash shift: 52 ─────────────┘
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ID: 3 Level: 1 Children: 0 ──────┐
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User bins: 64 │
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Active bins: 64 │
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Technical bins: 64 │
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Empty bins: 0 │
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Bin words: 1 │
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Bin size: 1,245 │
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Total size: 79,680 │
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Hash functions: 2 │
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Hash shift: 53 │
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[...] ├ Direct Children if the Root IBF
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ID: 1 Level: 1 Children: 1 │
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User bins: 63 │
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Active bins: 64 │
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Technical bins: 64 │
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Empty bins: 0 │
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Bin words: 1 │
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Bin size: 1,245 │
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Total size: 79,680 │
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Hash functions: 2 │
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Hash shift: 53 ─────────────────┘
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ID: 2 Level: 2 Children: 0 ─┐
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User bins: 2 │
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Active bins: 64 │
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Technical bins: 64 │
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Empty bins: 0 │
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Bin words: 1 ├ Child of IBF with ID=1
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Bin size: 394 │
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Total size: 25,216 │
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Hash functions: 2 │
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Hash shift: 55 ────────────┘
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```

‎util/inspect/fmt.hpp‎

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// SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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// SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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// SPDX-License-Identifier: BSD-3-Clause
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#pragma once
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#include <fmt/color.h>
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#include <sharg/detail/terminal.hpp>
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namespace seqan::hibf::util
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{
13+
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struct styles
15+
{
16+
static inline bool const cout_is_terminal = sharg::detail::stdout_is_terminal();
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static inline bool const cerr_is_terminal = sharg::detail::stderr_is_terminal();
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static bool use_style(FILE * stream)
20+
{
21+
return (stream == stdout && cout_is_terminal) || (stream == stderr && cerr_is_terminal);
22+
}
23+
24+
static fmt::text_style color(fmt::color const color, FILE * stream = stdout)
25+
{
26+
if (use_style(stream))
27+
return fmt::fg(color);
28+
else
29+
return fmt::text_style{};
30+
}
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static fmt::text_style emphasis(fmt::emphasis const emphasis, FILE * stream = stdout)
33+
{
34+
if (use_style(stream))
35+
return emphasis;
36+
else
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return fmt::text_style{};
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}
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};
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} // namespace seqan::hibf::util

‎util/inspect/inspect.cpp‎

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// SPDX-FileCopyrightText: 2006-2025, Knut Reinert & Freie Universität Berlin
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// SPDX-FileCopyrightText: 2016-2025, Knut Reinert & MPI für molekulare Genetik
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// SPDX-License-Identifier: BSD-3-Clause
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#include <sharg/parser.hpp>
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#include <cereal/archives/binary.hpp>
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#include <hibf/hierarchical_interleaved_bloom_filter.hpp>
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#include "fmt.hpp"
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#include "inspect.hpp"
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struct config
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{
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std::filesystem::path input{};
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bool is_hibf{};
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};
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config parse_arguments(std::vector<std::string> command_line)
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{
22+
sharg::parser parser{"inspect", std::move(command_line), sharg::update_notifications::off};
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config cfg{};
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parser.add_option(cfg.input,
26+
sharg::config{.short_id = '\0',
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.long_id = "input",
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.description = "The index to inspect.",
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.validator = sharg::input_file_validator{}});
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parser.add_flag(cfg.is_hibf,
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sharg::config{.short_id = '\0', .long_id = "hibf", .description = "The index is an HIBF"});
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parser.info.author = "Enrico Seiler";
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parser.info.short_copyright = "BSD 3-Clause License";
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parser.info.short_description = "Inspect an IBF/HIBF.";
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parser.parse();
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return cfg;
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}
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int main(int argc, char ** argv)
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{
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try
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{
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config const config = parse_arguments({argv, argv + argc});
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if (!config.is_hibf)
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{
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seqan::hibf::interleaved_bloom_filter ibf{};
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{
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std::ifstream os{config.input, std::ios::binary};
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cereal::BinaryInputArchive iarchive{os};
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iarchive(ibf);
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}
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seqan::hibf::util::inspect(ibf);
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}
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else
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{
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seqan::hibf::hierarchical_interleaved_bloom_filter hibf{};
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{
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std::ifstream os{config.input, std::ios::binary};
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cereal::BinaryInputArchive iarchive{os};
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iarchive(hibf);
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}
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seqan::hibf::util::inspect(hibf);
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}
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}
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catch (std::exception const & ext)
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{
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fmt::print(stderr, seqan::hibf::util::styles::color(fmt::color::red, stderr), "[Error]");
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fmt::print(stderr, " {}\n", ext.what());
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std::exit(-1);
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}
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return 0;
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}

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