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 -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ImageReferenceTable.nd -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/IndexInfo.nd -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/PreviousMenuState.nd -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/PreviousSettings.nd -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/SymbolTable.nd -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Languages.txt -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Menu.txt -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Topics.txt -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/EventsH.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FilesJ.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsA.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsD.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsE.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsF.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsG.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsH.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsN.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsP.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsQ.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsR.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsS.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralA.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralD.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralE.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralF.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralG.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralH.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralJ.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralK.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralL.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralN.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralP.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralQ.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralR.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralS.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/NoResults.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/PropertiesD.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/PropertiesS.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/styles/1.css -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/styles/2.css -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/styles/main.css -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/config.php -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/deparam/index.php -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/donate.gif -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/bbq.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/burger.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/burger.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/chicken.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/chicken.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/index.php -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kebabs.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kebabs.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kielbasa.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kielbasa.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/ribs.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/ribs.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/steak.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/steak.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/XMLpage.php -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/bbq.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/burger.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/chicken.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/index.php -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/kebabs.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/kielbasa.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/page.php -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/pages.xml -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/ribs.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/steak.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/bbq.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/burger.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/burger.jpg -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/chicken.html -%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/chicken.jpg -%%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