diff options
Diffstat (limited to 'biology')
27 files changed, 84 insertions, 160 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/gatk/Makefile b/biology/gatk/Makefile index 41df894298f4..49a990d3f216 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -1,6 +1,5 @@ PORTNAME= gatk -DISTVERSION= 4.6.1.0 -PORTREVISION= 1 +DISTVERSION= 4.6.2.0 CATEGORIES= biology java EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} @@ -31,7 +30,7 @@ NO_ARCH= yes DEPS_CACHE_DIR= ${WRKDIR} TEST_ENV= ${MAKE_ENV} \ - JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so" \ + JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=${PREFIX}/lib/libfml.so -DLIBFML_PATH=${PREFIX}/lib/libfml.so" \ GATK_LOCAL_JAR=${STAGEDIR}${JAVAJARDIR}/GenomeAnalysisTK-${PORTVERSION}.jar PLIST_FILES= bin/${PORTNAME} \ @@ -117,9 +116,10 @@ do-install: do-test: # tests require WITH_LARGE_FILES=ON, and they use a lot of disk space @cd ${WRKSRC} && \ - ${SETENV} ${TEST_ENV} gradle8 -DLIBBWA_PATH=${PREFIX}/lib/libfml.so test + ${SETENV} ${TEST_ENV} gradle8 test -# tests results as of version 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.1.0: 288552 tests, 301 failures, 37 ignored, 1h55m5.63s duration, 99% successful, see https://github.com/broadinstitute/gatk/issues/8940 +# tests as of 4.6.2.0: 288719 tests completed, 300 failed, 37 skipped # see https://github.com/broadinstitute/gatk/issues/8939: Tests fail to find libgkl libraries in /usr/local/lib .include <bsd.port.mk> diff --git a/biology/gatk/distinfo b/biology/gatk/distinfo index 2494dc43dd72..42fbad5e8a91 100644 --- a/biology/gatk/distinfo +++ b/biology/gatk/distinfo @@ -1,5 +1,5 @@ -TIMESTAMP = 1730356703 -SHA256 (gatk-4.6.1.0-deps.tar.gz) = ea0205776f26bbe51bcdea6dd10df975a2e4861a772901523ff7ab123119b8ad -SIZE (gatk-4.6.1.0-deps.tar.gz) = 922113997 -SHA256 (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 6f840406ce226e202421464e2ae044f3c0bc63da63f245568f8ca1bc7769d378 -SIZE (broadinstitute-gatk-4.6.1.0_GH0.tar.gz) = 4317548196 +TIMESTAMP = 1756227460 +SHA256 (gatk-4.6.2.0-deps.tar.gz) = c956ec3b6a209b4eaf9c20cb312635498b360aa372f824b33d392aa0ac594a77 +SIZE (gatk-4.6.2.0-deps.tar.gz) = 903933113 +SHA256 (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = c76b61a549f49004a54ae86e88cd8b7a180a3bd2e4a56b1c9185f30971c79866 +SIZE (broadinstitute-gatk-4.6.2.0_GH0.tar.gz) = 4318674606 diff --git a/biology/gatk/files/gatk.sh.in b/biology/gatk/files/gatk.sh.in index d3d5c0f7bf5a..20c6c16d5164 100644 --- a/biology/gatk/files/gatk.sh.in +++ b/biology/gatk/files/gatk.sh.in @@ -23,5 +23,5 @@ fi # execute the command # add the LIBBWA_PATH system parameter (not sure whether the env. var or argument alone are sufficient) -JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so" \ -%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" +JAVA_TOOL_OPTIONS="-DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so" \ +%%JAVA%% $MEM_OPTS -DLIBBWA_PATH=%%PREFIX%%/lib/libfml.so -DLIBFML_PATH=%%PREFIX%%/lib/libfml.so -jar %%JAVAJARDIR%%/GenomeAnalysisTK-%%PORTVERSION%%.jar "$@" 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/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-bx-python/Makefile b/biology/py-bx-python/Makefile index 6b66a17d1250..309fa98df6ca 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -1,6 +1,5 @@ PORTNAME= bx-python -DISTVERSION= 0.13.0 -PORTREVISION= 1 +DISTVERSION= 0.14.0 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -14,11 +13,18 @@ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE PY_DEPENDS= ${PYNUMPY} -BUILD_DEPENDS= ${PY_DEPENDS} -RUN_DEPENDS= ${PY_DEPENDS} +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PY_DEPENDS} \ + ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} USES= compiler python -USE_PYTHON= autoplist cython3 distutils +USE_PYTHON= pep517 cython3 autoplist + +post-patch: + # force cythonization, compilation fails otherwise for some reason + @${TOUCH} `${FIND} ${WRKSRC} -name "*.pyx" -o -name "*.pxd"` post-install: @${FIND} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/bx -name "*.so" | ${XARGS} ${STRIP_CMD} diff --git a/biology/py-bx-python/distinfo b/biology/py-bx-python/distinfo index 56d00203a687..85e09edf789a 100644 --- a/biology/py-bx-python/distinfo +++ b/biology/py-bx-python/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1734273029 -SHA256 (bx_python-0.13.0.tar.gz) = ce04696543367efc6b7995d9463efeda691b9a58f6f55a7bd831e642159b0644 -SIZE (bx_python-0.13.0.tar.gz) = 1899129 +TIMESTAMP = 1756062999 +SHA256 (bx_python-0.14.0.tar.gz) = c46eef1006d6107e31d2ff42f1ca27c34ddb080151309a909b4d2e53ca812cc6 +SIZE (bx_python-0.14.0.tar.gz) = 2085934 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 |