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-rw-r--r--biology/atac-seq/Makefile1
-rw-r--r--biology/biostar-tools/Makefile1
-rw-r--r--biology/chip-seq/Makefile1
-rw-r--r--biology/coverm/Makefile2
-rw-r--r--biology/fasda-utils/Makefile1
-rw-r--r--biology/groopm/Makefile2
-rw-r--r--biology/linux-foldingathome/Makefile6
-rw-r--r--biology/peak-classifier/Makefile2
-rw-r--r--biology/prodigy-lig/Makefile1
-rw-r--r--biology/py-PySCeS/Makefile1
-rw-r--r--biology/py-biopython/Makefile2
-rw-r--r--biology/py-deeptools/Makefile2
-rw-r--r--biology/py-dna-features-viewer/Makefile2
-rw-r--r--biology/py-gtfparse/Makefile1
-rw-r--r--biology/py-htseq/Makefile2
-rw-r--r--biology/py-multiqc/Makefile2
-rw-r--r--biology/py-pydeseq2/Makefile1
-rw-r--r--biology/py-scikit-bio/Makefile1
-rw-r--r--biology/rna-seq/Makefile1
-rw-r--r--biology/seqan3/Makefile17
-rw-r--r--biology/seqan3/distinfo12
-rw-r--r--biology/seqan3/files/patch-cmake_CPM.cmake11
-rw-r--r--biology/seqan3/pkg-plist132
23 files changed, 61 insertions, 143 deletions
diff --git a/biology/atac-seq/Makefile b/biology/atac-seq/Makefile
index d55ab7d3d40d..d24e8007fcf1 100644
--- a/biology/atac-seq/Makefile
+++ b/biology/atac-seq/Makefile
@@ -1,5 +1,6 @@
PORTNAME= atac-seq
DISTVERSION= 0.2.0
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= # empty
diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile
index 6002cae2fc71..2be07b115d09 100644
--- a/biology/biostar-tools/Makefile
+++ b/biology/biostar-tools/Makefile
@@ -1,5 +1,6 @@
PORTNAME= biostar-tools
PORTVERSION= 2.0
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= # empty
diff --git a/biology/chip-seq/Makefile b/biology/chip-seq/Makefile
index 5714a40951dd..6218595cd628 100644
--- a/biology/chip-seq/Makefile
+++ b/biology/chip-seq/Makefile
@@ -1,5 +1,6 @@
PORTNAME= chip-seq
DISTVERSION= 0.1.2
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= # empty
diff --git a/biology/coverm/Makefile b/biology/coverm/Makefile
index 366b6787dce1..9256b1dfe0c8 100644
--- a/biology/coverm/Makefile
+++ b/biology/coverm/Makefile
@@ -1,7 +1,7 @@
PORTNAME= coverm
DISTVERSIONPREFIX= v
DISTVERSION= 0.7.0
-PORTREVISION= 7
+PORTREVISION= 8
CATEGORIES= biology
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/fasda-utils/Makefile b/biology/fasda-utils/Makefile
index 854b7f13b7e0..510bc0a8309d 100644
--- a/biology/fasda-utils/Makefile
+++ b/biology/fasda-utils/Makefile
@@ -1,6 +1,7 @@
PORTNAME= fasda-utils
DISTVERSION= 0.1.0-2
DISTVERSIONSUFFIX= -gf9217f0
+PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/groopm/Makefile b/biology/groopm/Makefile
index e4327194012a..e4767e0271e2 100644
--- a/biology/groopm/Makefile
+++ b/biology/groopm/Makefile
@@ -1,6 +1,6 @@
PORTNAME= GroopM
DISTVERSION= 0.3.4
-PORTREVISION= 5
+PORTREVISION= 6
CATEGORIES= biology python
MASTER_SITES= PYPI
diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile
index 7df5db1a03c8..6b8c70ff3e5d 100644
--- a/biology/linux-foldingathome/Makefile
+++ b/biology/linux-foldingathome/Makefile
@@ -12,7 +12,7 @@ WWW= https://foldingathome.org/
# Distribution without permission is prohibited
LICENSE= FAHSL
LICENSE_NAME= Folding@home Software License
-LICENSE_FILE= ${WRKSRC}/${DISTNAME}/LICENSE
+LICENSE_FILE= ${WRKSRC}/${DISTNAME:T}/LICENSE
LICENSE_PERMS= no-dist-mirror no-dist-sell no-pkg-mirror no-pkg-sell \
auto-accept
@@ -55,7 +55,7 @@ DISTFILES= ${ONLY_FOR_ARCHS:@.ARCH.@${_DISTNAME_${.ARCH.}}${EXTRACT_SUFX}@}
.endif
do-install:
- ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME}/fah-client ${STAGEDIR}${PREFIX}/bin/
+ ${INSTALL_PROGRAM} ${WRKSRC}/${DISTNAME:T}/fah-client ${STAGEDIR}${PREFIX}/bin/
@${MKDIR} ${STAGEDIR}${ETCDIR}
${INSTALL_DATA} ${FILESDIR}/config.xml.sample \
${STAGEDIR}${_FAHCLIENT_CONFIG_XML}.sample
@@ -63,7 +63,7 @@ do-install:
post-install-DOCS-on:
@${MKDIR} ${STAGEDIR}${DOCSDIR}
- ${INSTALL_MAN} ${PORTDOCS:S|^|${WRKSRC}/${DISTNAME}/|} \
+ ${INSTALL_MAN} ${PORTDOCS:S|^|${WRKSRC}/${DISTNAME:T}/|} \
${STAGEDIR}${DOCSDIR}
.include <bsd.port.mk>
diff --git a/biology/peak-classifier/Makefile b/biology/peak-classifier/Makefile
index fc7ddb9226a8..68494512fcc6 100644
--- a/biology/peak-classifier/Makefile
+++ b/biology/peak-classifier/Makefile
@@ -1,7 +1,7 @@
PORTNAME= peak-classifier
DISTVERSION= 0.1.4-13
DISTVERSIONSUFFIX= -gfb89af3
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/prodigy-lig/Makefile b/biology/prodigy-lig/Makefile
index ec7ceaea67be..37913457187b 100644
--- a/biology/prodigy-lig/Makefile
+++ b/biology/prodigy-lig/Makefile
@@ -1,6 +1,7 @@
PORTNAME= prodigy-lig
DISTVERSIONPREFIX= v
DISTVERSION= 1.1.3
+PORTREVISION= 1
CATEGORIES= biology python
MAINTAINER= yuri@FreeBSD.org
diff --git a/biology/py-PySCeS/Makefile b/biology/py-PySCeS/Makefile
index 5d0d40274f5a..7291292a9a83 100644
--- a/biology/py-PySCeS/Makefile
+++ b/biology/py-PySCeS/Makefile
@@ -1,5 +1,6 @@
PORTNAME= pysces
DISTVERSION= 1.2.2
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 2bfba7847829..4a6221924aac 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -1,6 +1,6 @@
PORTNAME= biopython
DISTVERSION= 1.85
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology python
MASTER_SITES= http://www.biopython.org/DIST/
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-deeptools/Makefile b/biology/py-deeptools/Makefile
index fcf917e832ff..383412b04c15 100644
--- a/biology/py-deeptools/Makefile
+++ b/biology/py-deeptools/Makefile
@@ -1,6 +1,6 @@
PORTNAME= deepTools
DISTVERSION= 3.5.2
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-dna-features-viewer/Makefile b/biology/py-dna-features-viewer/Makefile
index d29f8e043694..ebfa72d4bdb7 100644
--- a/biology/py-dna-features-viewer/Makefile
+++ b/biology/py-dna-features-viewer/Makefile
@@ -1,6 +1,6 @@
PORTNAME= dna-features-viewer
DISTVERSION= 3.1.3
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-gtfparse/Makefile b/biology/py-gtfparse/Makefile
index 584f7935729f..00b52550618d 100644
--- a/biology/py-gtfparse/Makefile
+++ b/biology/py-gtfparse/Makefile
@@ -1,5 +1,6 @@
PORTNAME= gtfparse
DISTVERSION= 2.5.0
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-htseq/Makefile b/biology/py-htseq/Makefile
index 68a608f3c79c..311252464790 100644
--- a/biology/py-htseq/Makefile
+++ b/biology/py-htseq/Makefile
@@ -1,6 +1,6 @@
PORTNAME= HTSeq
DISTVERSION= 2.0.9
-PORTREVISION= 1
+PORTREVISION= 2
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-multiqc/Makefile b/biology/py-multiqc/Makefile
index 8d8beda640a8..c03e6022d862 100644
--- a/biology/py-multiqc/Makefile
+++ b/biology/py-multiqc/Makefile
@@ -1,6 +1,6 @@
PORTNAME= multiqc
DISTVERSION= 1.25.2
-PORTREVISION= 2
+PORTREVISION= 3
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-pydeseq2/Makefile b/biology/py-pydeseq2/Makefile
index 79df1d1ad48c..d117262003fc 100644
--- a/biology/py-pydeseq2/Makefile
+++ b/biology/py-pydeseq2/Makefile
@@ -1,5 +1,6 @@
PORTNAME= pydeseq2
DISTVERSION= 0.5.2
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile
index f3451e54a4bf..cf6465dcf46e 100644
--- a/biology/py-scikit-bio/Makefile
+++ b/biology/py-scikit-bio/Makefile
@@ -1,5 +1,6 @@
PORTNAME= scikit-bio
DISTVERSION= 0.6.3
+PORTREVISION= 1
CATEGORIES= biology education python
MASTER_SITES= PYPI
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
diff --git a/biology/rna-seq/Makefile b/biology/rna-seq/Makefile
index 61a68e7a6c0c..2a35c927e991 100644
--- a/biology/rna-seq/Makefile
+++ b/biology/rna-seq/Makefile
@@ -1,5 +1,6 @@
PORTNAME= rna-seq
DISTVERSION= 0.1.4
+PORTREVISION= 1
CATEGORIES= biology python
MASTER_SITES= # empty
diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile
index 9c8fc69ba93e..c1675008fd19 100644
--- a/biology/seqan3/Makefile
+++ b/biology/seqan3/Makefile
@@ -1,10 +1,16 @@
PORTNAME= seqan3
-DISTVERSION= 3.3.0
+DISTVERSION= 3.4.0
CATEGORIES= biology devel math
+MASTER_SITES= https://github.com/cpm-cmake/CPM.cmake/releases/download/v0.42.0/:cpm
+DISTFILES= CPM.cmake:cpm
+DIST_SUBDIR= ${PORTNAME}-${DISTVERSION}
+EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} \
+ xxsds-sdsl-lite-d54d389_GH0${EXTRACT_SUFX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= C++ header-only library for biological sequence analysis
-WWW= https://github.com/seqan/seqan3
+WWW= https://www.seqan.de/ \
+ https://github.com/seqan/seqan3
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/LICENSE.md
@@ -15,14 +21,13 @@ BUILD_DEPENDS= ${HPP_DEPENDS}
RUN_DEPENDS= ${HPP_DEPENDS} \
coin-or-lemon>0:math/lemon
-USES= cmake localbase
+USES= cmake compiler:c++23-lang localbase
USE_GITHUB= yes
GH_ACCOUNT= seqan
GH_TUPLE= xxsds:sdsl-lite:d54d389:sdsl_lite/submodules/sdsl-lite
-USE_GCC= yes # tests only pass with gcc, see https://github.com/seqan/seqan3/issues/2643, otherwise gcc isn't needed because this is a header-only library
-# tests fail to compile, see https://github.com/seqan/seqan3/issues/3191
+CMAKE_ARGS= -DCPM_LOCATION=${DISTDIR}/${DIST_SUBDIR}
TEST_WRKSRC= ${WRKSRC}/.test
@@ -33,7 +38,7 @@ post-install:
do-test:
@${MKDIR} ${TEST_WRKSRC} && cd ${TEST_WRKSRC} && \
- ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${WRKSRC}/test/unit && \
+ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFETCHCONTENT_FULLY_DISCONNECTED=OFF ${WRKSRC}/test/unit && \
${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \
ctest
diff --git a/biology/seqan3/distinfo b/biology/seqan3/distinfo
index 8fa5387420f9..9e9fe56de4ee 100644
--- a/biology/seqan3/distinfo
+++ b/biology/seqan3/distinfo
@@ -1,5 +1,7 @@
-TIMESTAMP = 1694368553
-SHA256 (seqan-seqan3-3.3.0_GH0.tar.gz) = 96975406445c8a5974803eefa146ee2f85206f6d2c2bccf45171ee0b1a653fb8
-SIZE (seqan-seqan3-3.3.0_GH0.tar.gz) = 1564852
-SHA256 (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1
-SIZE (xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835
+TIMESTAMP = 1756395731
+SHA256 (seqan3-3.4.0/CPM.cmake) = 2020b4fc42dba44817983e06342e682ecfc3d2f484a581f11cc5731fbe4dce8a
+SIZE (seqan3-3.4.0/CPM.cmake) = 44969
+SHA256 (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 8e000e6788f1e2ada071b36f64231d56f18e2d687ab4122d86cd3aefc6c87743
+SIZE (seqan3-3.4.0/seqan-seqan3-3.4.0_GH0.tar.gz) = 1749810
+SHA256 (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = eaac28144b34a833afb8c03139abbe427d4b95a827bf5b9b6532353f9cff9ec1
+SIZE (seqan3-3.4.0/xxsds-sdsl-lite-d54d389_GH0.tar.gz) = 1183835
diff --git a/biology/seqan3/files/patch-cmake_CPM.cmake b/biology/seqan3/files/patch-cmake_CPM.cmake
new file mode 100644
index 000000000000..c288163d7312
--- /dev/null
+++ b/biology/seqan3/files/patch-cmake_CPM.cmake
@@ -0,0 +1,11 @@
+--- cmake/CPM.cmake.orig 2025-08-28 15:36:29 UTC
++++ cmake/CPM.cmake
+@@ -16,7 +16,7 @@ get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DO
+ # Expand relative path. This is important if the provided path contains a tilde (~)
+ get_filename_component (CPM_DOWNLOAD_LOCATION ${CPM_DOWNLOAD_LOCATION} ABSOLUTE)
+
+-file (DOWNLOAD https://github.com/cpm-cmake/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake
++file (DOWNLOAD file://${CPM_LOCATION}/CPM.cmake
+ ${CPM_DOWNLOAD_LOCATION} EXPECTED_HASH SHA256=${CPM_HASH_SUM})
+
+ include (${CPM_DOWNLOAD_LOCATION})
diff --git a/biology/seqan3/pkg-plist b/biology/seqan3/pkg-plist
index 19d86e63d82e..e727ba232e45 100644
--- a/biology/seqan3/pkg-plist
+++ b/biology/seqan3/pkg-plist
@@ -91,6 +91,7 @@ include/seqan3/alignment/scoring/all.hpp
include/seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp
include/seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp
include/seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp
+include/seqan3/alignment/scoring/hamming_scoring_scheme.hpp
include/seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp
include/seqan3/alignment/scoring/scoring_scheme_base.hpp
include/seqan3/alignment/scoring/scoring_scheme_concept.hpp
@@ -191,11 +192,16 @@ include/seqan3/contrib/README.md
include/seqan3/contrib/parallel/buffer_queue.hpp
include/seqan3/contrib/parallel/serialised_resource_pool.hpp
include/seqan3/contrib/parallel/suspendable_queue.hpp
+include/seqan3/contrib/sdsl-lite.hpp
include/seqan3/contrib/std/.clang-format
include/seqan3/contrib/std/.gitignore
-include/seqan3/contrib/std/LICENSE
+include/seqan3/contrib/std/LICENSE.md
+include/seqan3/contrib/std/LICENSES/BSD-3-Clause.txt
+include/seqan3/contrib/std/LICENSES/CC-BY-4.0.txt
+include/seqan3/contrib/std/LICENSES/CC0-1.0.txt
include/seqan3/contrib/std/README.md
include/seqan3/contrib/std/all_view.hpp
+include/seqan3/contrib/std/chunk_by_view.hpp
include/seqan3/contrib/std/chunk_view.hpp
include/seqan3/contrib/std/concepts.hpp
include/seqan3/contrib/std/detail/adaptor_base.hpp
@@ -203,7 +209,9 @@ include/seqan3/contrib/std/detail/adaptor_for_view_without_args.hpp
include/seqan3/contrib/std/detail/adaptor_from_functor.hpp
include/seqan3/contrib/std/detail/compiler_definitions.hpp
include/seqan3/contrib/std/detail/exposition_only.hpp
+include/seqan3/contrib/std/detail/movable_box.hpp
include/seqan3/contrib/std/detail/non_propagating_cache.hpp
+include/seqan3/contrib/std/enumerate_view.hpp
include/seqan3/contrib/std/join_with_view.hpp
include/seqan3/contrib/std/pair.hpp
include/seqan3/contrib/std/to.hpp
@@ -239,14 +247,13 @@ include/seqan3/core/debug_stream.hpp
include/seqan3/core/debug_stream/all.hpp
include/seqan3/core/debug_stream/byte.hpp
include/seqan3/core/debug_stream/debug_stream_type.hpp
+include/seqan3/core/debug_stream/default_printer.hpp
include/seqan3/core/debug_stream/detail/to_string.hpp
include/seqan3/core/debug_stream/optional.hpp
include/seqan3/core/debug_stream/range.hpp
include/seqan3/core/debug_stream/tuple.hpp
include/seqan3/core/debug_stream/variant.hpp
include/seqan3/core/detail/all.hpp
-include/seqan3/core/detail/all_view.hpp
-include/seqan3/core/detail/copyable_wrapper.hpp
include/seqan3/core/detail/customisation_point.hpp
include/seqan3/core/detail/deferred_crtp_base.hpp
include/seqan3/core/detail/empty_type.hpp
@@ -364,127 +371,10 @@ include/seqan3/search/views/minimiser.hpp
include/seqan3/search/views/minimiser_hash.hpp
include/seqan3/std/charconv
include/seqan3/std/new
-include/seqan3/submodules/sdsl-lite/include/sdsl/.gitignore
-include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vector_il.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bit_vectors.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bits.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_g.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_gg.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/bp_support_sada.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/cereal.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/coder.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/coder_comma.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_delta.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/coder_fibonacci.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/config.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_bwt.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_config.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_isa.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/construct_sa_se.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sada.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/csa_wt.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/cst_fully.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/cst_iterators.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sada.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/cst_sct3.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/dac_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/divsufsort.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/enc_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/fast_cache.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/hyb_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_buffer.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/int_vector_mapper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/inv_perm_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/io.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/iterators.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/k2_treap_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/k2_tree_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_byte.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_dac.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_sada.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_vlc.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/lcp_wt.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/louds_tree.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/memory_management.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/memory_tracking.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/platform.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/qsufsort.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/ram_filebuf.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/ram_fs.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_scan.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_int_v.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_scan.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rank_support_v5.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/rrr_vector_15.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/sd_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/sdsl_concepts.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/select_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_mcl.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/select_support_scan.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/sfstream.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_int_stack.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/sorted_stack_support.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/structure_tree.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_array_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_arrays.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/suffix_trees.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/uint128_t.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/uint256_t.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/uintx_t.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/util.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/vectors.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/version.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/vlc_vector.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wavelet_trees.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wm_int.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_algorithm.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_ap.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_blcd.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_epr.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_gmr.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_helper.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_huff.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_hutu.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_int.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_pc.hpp
-include/seqan3/submodules/sdsl-lite/include/sdsl/wt_rlmn.hpp
include/seqan3/utility/all.hpp
include/seqan3/utility/bloom_filter/all.hpp
include/seqan3/utility/bloom_filter/bloom_filter.hpp
+include/seqan3/utility/bloom_filter/bloom_filter_strong_types.hpp
include/seqan3/utility/char_operations/all.hpp
include/seqan3/utility/char_operations/predicate.hpp
include/seqan3/utility/char_operations/predicate_detail.hpp
generated by cgit v1.2.3 (git 2.25.1) at 2025-09-03 17:50:11 +0000