FreeBSD Bugzilla – Attachment 190337 Details for
Bug 225682
[maintainer-update] biology/seqan and biology/seqan-apps
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[patch]
update for biology/seqan
update_biology_seqan.patch (text/plain), 28.56 KB, created by
Hannes Hauswedell
on 2018-02-05 13:58:10 UTC
(
hide
)
Description:
update for biology/seqan
Filename:
MIME Type:
Creator:
Hannes Hauswedell
Created:
2018-02-05 13:58:10 UTC
Size:
28.56 KB
patch
obsolete
>diff -ru seqanOld/distinfo seqan/distinfo >--- seqanOld/distinfo 2016-09-14 21:38:58.000000000 +0200 >+++ seqan/distinfo 2018-02-05 13:08:12.092107000 +0100 >@@ -1,3 +1,3 @@ >-TIMESTAMP = 1473846790 >-SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd >-SIZE (seqan-library-2.2.0.tar.xz) = 5223004 >+TIMESTAMP = 1517832492 >+SHA256 (seqan-library-2.4.0.tar.xz) = dd97b1514ab83acb7d7be911b157979e188e8ca72cc61c430c1e0fd03bcd41a5 >+SIZE (seqan-library-2.4.0.tar.xz) = 4868868 >diff -ru seqanOld/Makefile seqan/Makefile >--- seqanOld/Makefile 2016-09-14 21:38:58.000000000 +0200 >+++ seqan/Makefile 2018-02-05 13:11:27.973901000 +0100 >@@ -2,7 +2,7 @@ > # $FreeBSD: head/biology/seqan/Makefile 422156 2016-09-14 19:38:58Z pawel $ > > PORTNAME= seqan >-PORTVERSION= 2.2.0 >+PORTVERSION= 2.4.0 > CATEGORIES= biology > MASTER_SITES= http://packages.seqan.de/seqan-library/ > DISTNAME= ${PORTNAME}-library-${PORTVERSION} >@@ -23,8 +23,8 @@ > > do-install: > cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include >- ${MKDIR} ${STAGEDIR}/${PREFIX}/share/cmake/Modules >- ${INSTALL_DATA} ${WRKSRC}/share/cmake/Modules/FindSeqAn.cmake ${STAGEDIR}/${PREFIX}/share/cmake/Modules/ >+ ${MKDIR} ${STAGEDIR}/${PREFIX}/lib/cmake/seqan/ >+ ${INSTALL_DATA} ${WRKSRC}/share/cmake/seqan/seqan-config.cmake ${STAGEDIR}/${PREFIX}/lib/cmake/seqan/ > ${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig > ${INSTALL_DATA} ${WRKSRC}/share/pkgconfig/seqan-2.pc ${STAGEDIR}/${PREFIX}/libdata/pkgconfig/ > >diff -ru seqanOld/pkg-plist seqan/pkg-plist >--- seqanOld/pkg-plist 2016-09-14 21:38:58.000000000 +0200 >+++ seqan/pkg-plist 2018-02-05 13:11:55.498440000 +0100 >@@ -6,6 +6,7 @@ > include/seqan/align/align_iterator_base.h > include/seqan/align/align_metafunctions.h > include/seqan/align/align_traceback.h >+include/seqan/align/aligned_sequence_concept.h > include/seqan/align/alignment_algorithm_tags.h > include/seqan/align/alignment_operations.h > include/seqan/align/dp_algorithm_impl.h >@@ -62,6 +63,26 @@ > include/seqan/align_extend/align_extend.h > include/seqan/align_extend/align_extend_base.h > include/seqan/align_extend/dp_scout_xdrop.h >+include/seqan/align_parallel.h >+include/seqan/align_parallel/async_wave_execution_interface.h >+include/seqan/align_parallel/dp_kernel_adaptor.h >+include/seqan/align_parallel/dp_parallel_execution_policies.h >+include/seqan/align_parallel/dp_parallel_scout.h >+include/seqan/align_parallel/dp_parallel_scout_simd.h >+include/seqan/align_parallel/dp_settings.h >+include/seqan/align_parallel/dp_traits.h >+include/seqan/align_parallel/parallel_align_interface.h >+include/seqan/align_parallel/wavefront_alignment_executor.h >+include/seqan/align_parallel/wavefront_alignment_result.h >+include/seqan/align_parallel/wavefront_alignment_scheduler.h >+include/seqan/align_parallel/wavefront_alignment_task.h >+include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h >+include/seqan/align_parallel/wavefront_task.h >+include/seqan/align_parallel/wavefront_task_event.h >+include/seqan/align_parallel/wavefront_task_executor.h >+include/seqan/align_parallel/wavefront_task_queue.h >+include/seqan/align_parallel/wavefront_task_scheduler.h >+include/seqan/align_parallel/wavefront_task_util.h > include/seqan/align_profile.h > include/seqan/align_profile/add_to_profile.h > include/seqan/align_profile/score_profile_seq.h >@@ -84,6 +105,7 @@ > include/seqan/arg_parse/arg_parse_option.h > include/seqan/arg_parse/arg_parse_parse.h > include/seqan/arg_parse/arg_parse_type_support.h >+include/seqan/arg_parse/arg_parse_version_check.h > include/seqan/arg_parse/argument_parser.h > include/seqan/arg_parse/tool_doc.h > include/seqan/arg_parse/xml_support.h >@@ -137,7 +159,6 @@ > include/seqan/basic/basic_metaprogramming.h > include/seqan/basic/basic_parallelism.h > include/seqan/basic/basic_proxy.h >-include/seqan/basic/basic_simd_vector.h > include/seqan/basic/basic_smart_pointer.h > include/seqan/basic/basic_stream.h > include/seqan/basic/basic_tangle.h >@@ -267,6 +288,7 @@ > include/seqan/graph_algorithms/graph_algorithm_hmm.h > include/seqan/graph_algorithms/graph_algorithm_lis_his.h > include/seqan/graph_algorithms/kruskal.h >+include/seqan/graph_algorithms/maximum_weighted_matching.h > include/seqan/graph_algorithms/path_growing.h > include/seqan/graph_algorithms/prim.h > include/seqan/graph_algorithms/single_source_shortest_path.h >@@ -326,6 +348,7 @@ > include/seqan/index/find2_base.h > include/seqan/index/find2_functors.h > include/seqan/index/find2_index.h >+include/seqan/index/find2_index_approx.h > include/seqan/index/find2_index_multi.h > include/seqan/index/find2_vstree_factory.h > include/seqan/index/find_backtracking.h >@@ -476,6 +499,8 @@ > include/seqan/modifier/modifier_string.h > include/seqan/modifier/modifier_view.h > include/seqan/parallel.h >+include/seqan/parallel/enumerable_thread_local.h >+include/seqan/parallel/enumerable_thread_local_iterator.h > include/seqan/parallel/parallel_algorithms.h > include/seqan/parallel/parallel_atomic_misc.h > include/seqan/parallel/parallel_atomic_primitives.h >@@ -488,6 +513,7 @@ > include/seqan/parallel/parallel_serializer.h > include/seqan/parallel/parallel_splitting.h > include/seqan/parallel/parallel_tags.h >+include/seqan/parallel/parallel_thread_pool.h > include/seqan/parse_lm.h > include/seqan/parse_lm/local_match_store.h > include/seqan/parse_lm/parse_blastn_tabular.h >@@ -521,12 +547,33 @@ > include/seqan/reduced_aminoacid.h > include/seqan/reduced_aminoacid/reduced_aminoacid_base.h > include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h > include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_li10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h > include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h > include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_base.h >+include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h >+include/seqan/rna_io.h >+include/seqan/rna_io/bpseq_read_write.h >+include/seqan/rna_io/connect_read_write.h >+include/seqan/rna_io/dot_bracket_read_write.h >+include/seqan/rna_io/ebpseq_read_write.h >+include/seqan/rna_io/rna_header.h >+include/seqan/rna_io/rna_io_context.h >+include/seqan/rna_io/rna_record.h >+include/seqan/rna_io/rna_struct_file.h >+include/seqan/rna_io/stockholm_read_write.h >+include/seqan/rna_io/vienna_read_write.h > include/seqan/roi_io.h > include/seqan/roi_io/read_roi.h > include/seqan/roi_io/roi_file.h >@@ -564,6 +611,7 @@ > include/seqan/seeds/seeds_seed_set_unordered.h > include/seqan/seeds/seeds_seed_simple.h > include/seqan/seq_io.h >+include/seqan/seq_io/bam_sam.h > include/seqan/seq_io/fai_index.h > include/seqan/seq_io/fasta_fastq.h > include/seqan/seq_io/genomic_region.h >@@ -606,6 +654,14 @@ > include/seqan/sequence_journaled/sequence_journaled.h > include/seqan/sequence_journaled/sequence_journaled_iterator.h > include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h >+include/seqan/simd.h >+include/seqan/simd/simd_base.h >+include/seqan/simd/simd_base_seqan_impl.h >+include/seqan/simd/simd_base_seqan_impl_avx2.h >+include/seqan/simd/simd_base_seqan_impl_avx512.h >+include/seqan/simd/simd_base_seqan_impl_sse4.2.h >+include/seqan/simd/simd_base_seqan_interface.h >+include/seqan/simd/simd_base_umesimd_impl.h > include/seqan/simple_intervals_io.h > include/seqan/simple_intervals_io/simple_intervals_file.h > include/seqan/simple_intervals_io/simple_intervals_io.h >@@ -671,8 +727,8 @@ > include/seqan/vcf_io/vcf_record.h > include/seqan/vcf_io/write_vcf.h > include/seqan/version.h >+lib/cmake/seqan/seqan-config.cmake > libdata/pkgconfig/seqan-2.pc >-share/cmake/Modules/FindSeqAn.cmake > %%PORTDOCS%%%%DOCSDIR%%/CHANGELOG.rst > %%PORTDOCS%%%%DOCSDIR%%/LICENSE > %%PORTDOCS%%%%DOCSDIR%%/README.rst >@@ -728,6 +784,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/class_ContainerView.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ContigFile.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ContigStoreElement.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_CountingThreadLocalManager.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_CyclicShape.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_DPBandConfig.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_DefaultJstConfig.html >@@ -735,12 +792,15 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/class_DeltaMap.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Deque.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_EdgeStump.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_EnumerableThreadLocal.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Exception.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_ExecutionPolicy.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ExternalConfig.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ExternalConfigLarge.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ExternalConfigSize.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_FMIndexConfig.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_FaiIndex.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_FastFMIndexConfig.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_File.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_FileMapping.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Finder.html >@@ -771,6 +831,8 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/class_JoinConfig.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_JournaledStringTree.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_LF.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_LevelsPrefixRDConfig.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_LevelsRDConfig.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Lexical.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_LibraryStoreElement.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_LocalAlignmentEnumerator.html >@@ -806,6 +868,11 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/class_Repeat.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_RevTextFibre.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_RightArrayBinaryTree.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_RnaHeader.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_RnaIOContext.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_RnaRecord.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_RnaStructContents.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_RnaStructureGraph.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_RuntimeError.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Score.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Seed.html >@@ -816,6 +883,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/class_SequenceOutputOptions.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Shape.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_SimpleIntervalsIOContext.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_SimpleThreadLocalManager.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_SimpleType.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_SparseString.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Splitter.html >@@ -828,6 +896,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/class_Tag.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_TagList.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_TagSelector.html >+%%PORTDOCS%%%%DOCSDIR%%/html/class_ThreadPool.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ToStdAllocator.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_ToolDoc.html > %%PORTDOCS%%%%DOCSDIR%%/html/class_Triple.html >@@ -868,6 +937,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/concept_IntegerConcept.html > %%PORTDOCS%%%%DOCSDIR%%/html/concept_IteratorAssociatedTypesConcept.html > %%PORTDOCS%%%%DOCSDIR%%/html/concept_LessThanComparableConcept.html >+%%PORTDOCS%%%%DOCSDIR%%/html/concept_MoveConstructibleConcept.html > %%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableBidirectionalIteratorConcept.html > %%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableForwardIteratorConcept.html > %%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableRandomAccessIteratorConcept.html >@@ -1143,6 +1213,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/global_function_lexicalCast.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_function_lexicalCastWithException.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_function_localAlignment.html >+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_localAlignmentScore.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_function_log2.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_function_longestCommonSubsequence.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_function_longestIncreasingSubsequence.html >@@ -1287,13 +1358,16 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5StringComplement.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5StringReverse.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5StringReverseComplement.html >+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaAdjacencyIterator.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaIterator.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaString.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringComplement.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringReverse.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringReverseComplement.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_SelectableAminoAcidMatrix.html >+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Sequential.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_SimpleScoreTypedef.html >+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_TSizeRna5String.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_TraceBack.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_UnicodeString.html > %%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Vtml200.html >@@ -1390,7 +1464,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/js/jquery.js > %%PORTDOCS%%%%DOCSDIR%%/html/js/jquery.smooth-scroll.js > %%PORTDOCS%%%%DOCSDIR%%/html/js/lang_entities.js >-%%PORTDOCS%%%%DOCSDIR%%/html/js/less.min.js >+%%PORTDOCS%%%%DOCSDIR%%/html/js/less-1.4.1.js > %%PORTDOCS%%%%DOCSDIR%%/html/js/link.data.js > %%PORTDOCS%%%%DOCSDIR%%/html/js/module_tree.js > %%PORTDOCS%%%%DOCSDIR%%/html/js/rubydoc_custom.js >@@ -1408,10 +1482,8 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/animations/animation5.less > %%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/less.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/README.md >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/ZeroClipboard/ZeroClipboard.min.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/ZeroClipboard/ZeroClipboard.swf > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/README.md >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/bootstrap-3.0.0.min.css >+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/bootstrap-3.0.0.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/bootstrap-multiselect.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/prettify.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/custom.html >@@ -1420,25 +1492,24 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/fonts/glyphicons-halflings-regular.ttf > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/fonts/glyphicons-halflings-regular.woff > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/index.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/bootstrap-3.0.0.min.js >+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/bootstrap-3.0.0.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/bootstrap-multiselect.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/jquery-2.0.3.min.js >+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/jquery-2.0.3.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/knockout-2.3.0.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/prettify.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/knockout-examples.html > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/less/bootstrap-multiselect.less > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/tests.html > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-treeview/css/bootstrap-treeview.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-treeview/js/bootstrap-treeview.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/css/bootstrap.css >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/css/bootstrap.min.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.eot > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.svg > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.ttf > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.woff > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/js/bootstrap.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/js/bootstrap.min.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/bower.json >+%%PORTDOCS%%%%DOCSDIR%%/html/lib/clipboard/clipboard.js >+%%PORTDOCS%%%%DOCSDIR%%/html/lib/clipboard/license.txt > %%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/css/font-awesome.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/css/font-awesome.min.css > %%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/fonts/FontAwesome.otf >@@ -1475,116 +1546,8 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/LICENSE-GPL > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/LICENSE-MIT > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/README.markdown >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/files/jquery-ba-bbq-js.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Events.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Files.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Functions.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/General.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Properties.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/javascript/main.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/javascript/searchdata.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ClassHierarchy.nd >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ConfigFileInfo.nd >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/FileInfo.nd >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ImageFileInfo.nd 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>-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/index.php >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kebabs.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kebabs.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kielbasa.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kielbasa.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/ribs.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/ribs.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/steak.html >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/steak.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/bbq.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/burger.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/chicken.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/index.php >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/kebabs.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/kielbasa.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/ribs.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/steak.jpg >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/index.css >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/index.php > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/jquery.ba-bbq.js >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/jquery.ba-bbq.min.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/LGPLv3.txt >-%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/clipboard.swf > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushAS3.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushBash.js > %%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushCSharp.js >@@ -1784,6 +1747,7 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_Joiner.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_JournaledSet.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_JournaledString.html >+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Levels.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_LevenshteinStringEnumerator.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_MMapString.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_MapperConfig.html >@@ -1837,6 +1801,8 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_RightArrayBinaryTreeIterator.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna5.html >+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RnaStructFileIn.html >+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RnaStructFileOut.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileIn.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileOut.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_Sampler.html >@@ -1882,7 +1848,6 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_TrieBfamPattern.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_TristateHolder.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tupler.html >-%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TwoLevelRankDictionary.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileIn.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileOut.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_UnbandedLocalAlignmentEnumerator.html >@@ -1894,20 +1859,30 @@ > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileOut.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_VectorSet.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_VertexIterator.html >+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WTRDConfig.html >+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WavefrontExecutionPolicy.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_WaveletTree.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_WildShiftAndPattern.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_WordGraph.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_WuManberPattern.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ZipContainerView.html > %%PORTDOCS%%%%DOCSDIR%%/html/specialization_ZipIterator.html >+%%PORTDOCS%%%%DOCSDIR%%/html/tag_BlockOffsetOptimization.html >+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Buchfink11.html >+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Cannata10.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_Default.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_DotDrawing.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_EditDistance.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_GeneticCode.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_HammingDistance.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_LevenshteinDistance.html >+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Li10.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_Move.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_Murphy10.html >+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Murphy5.html > %%PORTDOCS%%%%DOCSDIR%%/html/tag_Nothing.html >+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Solis10.html > %%PORTDOCS%%%%DOCSDIR%%/html/variable_BAM_95FLAG_95SUPPLEMENTARY_32_61_320x0800.html > %%PORTDOCS%%%%DOCSDIR%%/html/variable_LibraryStoreElementstd.html >+%%PORTDOCS%%@dir %%DOCSDIR%%/html/docs/seqan >+%%PORTDOCS%%@dir %%DOCSDIR%%/html/lists
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