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Port details
seqan C++ sequence analysis template library
2.4.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: h2+fbsdports@fsfe.org search for ports maintained by this maintainer
Port Added: 2012-06-06 17:52:27
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: BSD3CLAUSE
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
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  1. /usr/local/share/licenses/seqan-2.4.0/catalog.mk
  2. /usr/local/share/licenses/seqan-2.4.0/LICENSE
  3. /usr/local/share/licenses/seqan-2.4.0/BSD3CLAUSE
  4. include/seqan/align.h
  5. include/seqan/align/align_base.h
  6. include/seqan/align/align_cols.h
  7. include/seqan/align/align_config.h
  8. include/seqan/align/align_interface_wrapper.h
  9. include/seqan/align/align_iterator_base.h
  10. include/seqan/align/align_metafunctions.h
  11. include/seqan/align/align_traceback.h
  12. include/seqan/align/aligned_sequence_concept.h
  13. include/seqan/align/alignment_algorithm_tags.h
  14. include/seqan/align/alignment_operations.h
  15. include/seqan/align/dp_algorithm_impl.h
  16. include/seqan/align/dp_align_simd_helper.h
  17. include/seqan/align/dp_band.h
  18. include/seqan/align/dp_cell.h
  19. include/seqan/align/dp_cell_affine.h
  20. include/seqan/align/dp_cell_dynamic.h
  21. include/seqan/align/dp_cell_linear.h
  22. include/seqan/align/dp_context.h
  23. include/seqan/align/dp_formula.h
  24. include/seqan/align/dp_formula_affine.h
  25. include/seqan/align/dp_formula_dynamic.h
  26. include/seqan/align/dp_formula_linear.h
  27. include/seqan/align/dp_matrix.h
  28. include/seqan/align/dp_matrix_navigator.h
  29. include/seqan/align/dp_matrix_navigator_score_matrix.h
  30. include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
  31. include/seqan/align/dp_matrix_navigator_trace_matrix.h
  32. include/seqan/align/dp_matrix_sparse.h
  33. include/seqan/align/dp_meta_info.h
  34. include/seqan/align/dp_profile.h
  35. include/seqan/align/dp_scout.h
  36. include/seqan/align/dp_scout_simd.h
  37. include/seqan/align/dp_setup.h
  38. include/seqan/align/dp_trace_segment.h
  39. include/seqan/align/dp_traceback_adaptor.h
  40. include/seqan/align/dp_traceback_impl.h
  41. include/seqan/align/evaluate_alignment.h
  42. include/seqan/align/fragment.h
  43. include/seqan/align/gap_anchor.h
  44. include/seqan/align/gapped_value_type.h
  45. include/seqan/align/gaps_anchor.h
  46. include/seqan/align/gaps_array.h
  47. include/seqan/align/gaps_base.h
  48. include/seqan/align/gaps_iterator_anchor.h
  49. include/seqan/align/gaps_iterator_array.h
  50. include/seqan/align/gaps_iterator_base.h
  51. include/seqan/align/global_alignment_banded.h
  52. include/seqan/align/global_alignment_hirschberg_impl.h
  53. include/seqan/align/global_alignment_myers_hirschberg_impl.h
  54. include/seqan/align/global_alignment_myers_impl.h
  55. include/seqan/align/global_alignment_specialized.h
  56. include/seqan/align/global_alignment_unbanded.h
  57. include/seqan/align/local_alignment_banded.h
  58. include/seqan/align/local_alignment_banded_waterman_eggert_impl.h
  59. include/seqan/align/local_alignment_enumeration.h
  60. include/seqan/align/local_alignment_enumeration_banded.h
  61. include/seqan/align/local_alignment_enumeration_unbanded.h
  62. include/seqan/align/local_alignment_unbanded.h
  63. include/seqan/align/local_alignment_waterman_eggert_impl.h
  64. include/seqan/align/matrix_base.h
  65. include/seqan/align_extend.h
  66. include/seqan/align_extend/align_extend.h
  67. include/seqan/align_extend/align_extend_base.h
  68. include/seqan/align_extend/dp_scout_xdrop.h
  69. include/seqan/align_parallel.h
  70. include/seqan/align_parallel/async_wave_execution_interface.h
  71. include/seqan/align_parallel/dp_kernel_adaptor.h
  72. include/seqan/align_parallel/dp_parallel_execution_policies.h
  73. include/seqan/align_parallel/dp_parallel_scout.h
  74. include/seqan/align_parallel/dp_parallel_scout_simd.h
  75. include/seqan/align_parallel/dp_settings.h
  76. include/seqan/align_parallel/dp_traits.h
  77. include/seqan/align_parallel/parallel_align_interface.h
  78. include/seqan/align_parallel/wavefront_alignment_executor.h
  79. include/seqan/align_parallel/wavefront_alignment_result.h
  80. include/seqan/align_parallel/wavefront_alignment_scheduler.h
  81. include/seqan/align_parallel/wavefront_alignment_task.h
  82. include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h
  83. include/seqan/align_parallel/wavefront_task.h
  84. include/seqan/align_parallel/wavefront_task_event.h
  85. include/seqan/align_parallel/wavefront_task_executor.h
  86. include/seqan/align_parallel/wavefront_task_queue.h
  87. include/seqan/align_parallel/wavefront_task_scheduler.h
  88. include/seqan/align_parallel/wavefront_task_util.h
  89. include/seqan/align_profile.h
  90. include/seqan/align_profile/add_to_profile.h
  91. include/seqan/align_profile/score_profile_seq.h
  92. include/seqan/align_split.h
  93. include/seqan/align_split/align_split_interface.h
  94. include/seqan/align_split/dp_scout_split.h
  95. include/seqan/alignment_free.h
  96. include/seqan/alignment_free/af_d2.h
  97. include/seqan/alignment_free/af_d2star.h
  98. include/seqan/alignment_free/af_d2z.h
  99. include/seqan/alignment_free/af_n2.h
  100. include/seqan/alignment_free/alignment_free_base.h
  101. include/seqan/alignment_free/alignment_free_comparison.h
  102. include/seqan/alignment_free/kmer_functions.h
  103. include/seqan/arg_parse.h
  104. include/seqan/arg_parse/arg_parse_argument.h
  105. include/seqan/arg_parse/arg_parse_ctd_support.h
  106. include/seqan/arg_parse/arg_parse_doc.h
  107. include/seqan/arg_parse/arg_parse_exceptions.h
  108. include/seqan/arg_parse/arg_parse_option.h
  109. include/seqan/arg_parse/arg_parse_parse.h
  110. include/seqan/arg_parse/arg_parse_type_support.h
  111. include/seqan/arg_parse/arg_parse_version_check.h
  112. include/seqan/arg_parse/argument_parser.h
  113. include/seqan/arg_parse/tool_doc.h
  114. include/seqan/arg_parse/xml_support.h
  115. include/seqan/bam_io.h
  116. include/seqan/bam_io/bam_alignment_record.h
  117. include/seqan/bam_io/bam_alignment_record_util.h
  118. include/seqan/bam_io/bam_file.h
  119. include/seqan/bam_io/bam_header_record.h
  120. include/seqan/bam_io/bam_index_bai.h
  121. include/seqan/bam_io/bam_io_context.h
  122. include/seqan/bam_io/bam_sam_conversion.h
  123. include/seqan/bam_io/bam_scanner_cache.h
  124. include/seqan/bam_io/bam_tags_dict.h
  125. include/seqan/bam_io/cigar.h
  126. include/seqan/bam_io/read_bam.h
  127. include/seqan/bam_io/read_sam.h
  128. include/seqan/bam_io/write_bam.h
  129. include/seqan/bam_io/write_sam.h
  130. include/seqan/basic.h
  131. include/seqan/basic/aggregate_concept.h
  132. include/seqan/basic/allocator_chunkpool.h
  133. include/seqan/basic/allocator_interface.h
  134. include/seqan/basic/allocator_multipool.h
  135. include/seqan/basic/allocator_simple.h
  136. include/seqan/basic/allocator_singlepool.h
  137. include/seqan/basic/allocator_to_std.h
  138. include/seqan/basic/alphabet_adapt_builtins.h
  139. include/seqan/basic/alphabet_bio.h
  140. include/seqan/basic/alphabet_concept.h
  141. include/seqan/basic/alphabet_math.h
  142. include/seqan/basic/alphabet_profile.h
  143. include/seqan/basic/alphabet_qualities.h
  144. include/seqan/basic/alphabet_residue.h
  145. include/seqan/basic/alphabet_residue_funcs.h
  146. include/seqan/basic/alphabet_residue_tabs.h
  147. include/seqan/basic/alphabet_simple_type.h
  148. include/seqan/basic/alphabet_storage.h
  149. include/seqan/basic/array_construct_destruct.h
  150. include/seqan/basic/basic_aggregate.h
  151. include/seqan/basic/basic_allocator.h
  152. include/seqan/basic/basic_alphabet.h
  153. include/seqan/basic/basic_concept.h
  154. include/seqan/basic/basic_container.h
  155. include/seqan/basic/basic_debug.h
  156. include/seqan/basic/basic_device.h
  157. include/seqan/basic/basic_exception.h
  158. include/seqan/basic/basic_functors.h
  159. include/seqan/basic/basic_fundamental.h
  160. include/seqan/basic/basic_iterator.h
  161. include/seqan/basic/basic_math.h
  162. include/seqan/basic/basic_metaprogramming.h
  163. include/seqan/basic/basic_parallelism.h
  164. include/seqan/basic/basic_proxy.h
  165. include/seqan/basic/basic_smart_pointer.h
  166. include/seqan/basic/basic_stream.h
  167. include/seqan/basic/basic_tangle.h
  168. include/seqan/basic/basic_type.h
  169. include/seqan/basic/basic_view.h
  170. include/seqan/basic/boost_preprocessor_subset.h
  171. include/seqan/basic/builtin_functions.h
  172. include/seqan/basic/concept_checking.h
  173. include/seqan/basic/container_concept.h
  174. include/seqan/basic/debug_helper.h
  175. include/seqan/basic/debug_test_system.h
  176. include/seqan/basic/fundamental_chunking.h
  177. include/seqan/basic/fundamental_comparison.h
  178. include/seqan/basic/fundamental_concepts.h
  179. include/seqan/basic/fundamental_conversion.h
  180. include/seqan/basic/fundamental_metafunctions.h
  181. include/seqan/basic/fundamental_tags.h
  182. include/seqan/basic/fundamental_transport.h
  183. include/seqan/basic/holder_base.h
  184. include/seqan/basic/holder_simple.h
  185. include/seqan/basic/holder_tristate.h
  186. include/seqan/basic/hosted_type_interface.h
  187. include/seqan/basic/iterator_adapt_pointer.h
  188. include/seqan/basic/iterator_adapt_std.h
  189. include/seqan/basic/iterator_adaptor.h
  190. include/seqan/basic/iterator_base.h
  191. include/seqan/basic/iterator_concept.h
  192. include/seqan/basic/iterator_counting.h
  193. include/seqan/basic/iterator_interface.h
  194. include/seqan/basic/iterator_position.h
  195. include/seqan/basic/iterator_range.h
  196. include/seqan/basic/iterator_zip.h
  197. include/seqan/basic/macro_deprecated.h
  198. include/seqan/basic/math_functions.h
  199. include/seqan/basic/math_log_space_value.h
  200. include/seqan/basic/metaprogramming_control.h
  201. include/seqan/basic/metaprogramming_enable_if.h
  202. include/seqan/basic/metaprogramming_logic.h
  203. include/seqan/basic/metaprogramming_math.h
  204. include/seqan/basic/metaprogramming_type.h
  205. include/seqan/basic/metaprogramming_type_algebra.h
  206. include/seqan/basic/pair_base.h
  207. include/seqan/basic/pair_bit_compressed.h
  208. include/seqan/basic/pair_packed.h
  209. include/seqan/basic/profiling.h
  210. include/seqan/basic/property_map_concept.h
  211. include/seqan/basic/proxy_base.h
  212. include/seqan/basic/proxy_iterator.h
  213. include/seqan/basic/test_system.h
  214. include/seqan/basic/triple_base.h
  215. include/seqan/basic/triple_packed.h
  216. include/seqan/basic/tuple_base.h
  217. include/seqan/basic/tuple_bit_compressed.h
  218. include/seqan/basic/volatile_ptr.h
  219. include/seqan/bed_io.h
  220. include/seqan/bed_io/bed_file.h
  221. include/seqan/bed_io/bed_record.h
  222. include/seqan/bed_io/read_bed.h
  223. include/seqan/bed_io/write_bed.h
  224. include/seqan/blast.h
  225. include/seqan/blast/blast_base.h
  226. include/seqan/blast/blast_io_context.h
  227. include/seqan/blast/blast_record.h
  228. include/seqan/blast/blast_report_out.h
  229. include/seqan/blast/blast_statistics.h
  230. include/seqan/blast/blast_tabular.h
  231. include/seqan/blast/blast_tabular_in.h
  232. include/seqan/blast/blast_tabular_lowlevel.h
  233. include/seqan/blast/blast_tabular_out.h
  234. include/seqan/consensus.h
  235. include/seqan/consensus/consensus_aligner.h
  236. include/seqan/consensus/consensus_aligner_interface.h
  237. include/seqan/consensus/consensus_alignment_options.h
  238. include/seqan/consensus/consensus_base.h
  239. include/seqan/consensus/consensus_builder.h
  240. include/seqan/consensus/consensus_library.h
  241. include/seqan/consensus/consensus_realign.h
  242. include/seqan/consensus/consensus_score.h
  243. include/seqan/consensus/overlap_info_computation.h
  244. include/seqan/consensus/overlapper.h
  245. include/seqan/file.h
  246. include/seqan/file/file_base.h
  247. include/seqan/file/file_cstyle.h
  248. include/seqan/file/file_forwards.h
  249. include/seqan/file/file_interface.h
  250. include/seqan/file/file_mapping.h
  251. include/seqan/file/file_page.h
  252. include/seqan/file/string_external.h
  253. include/seqan/file/string_mmap.h
  254. include/seqan/find.h
  255. include/seqan/find/find_abndm.h
  256. include/seqan/find/find_ahocorasick.h
  257. include/seqan/find/find_base.h
  258. include/seqan/find/find_begin.h
  259. include/seqan/find/find_bndm.h
  260. include/seqan/find/find_bom.h
  261. include/seqan/find/find_hamming_simple.h
  262. include/seqan/find/find_horspool.h
  263. include/seqan/find/find_lambda.h
  264. include/seqan/find/find_multi.h
  265. include/seqan/find/find_multiple_bfam.h
  266. include/seqan/find/find_multiple_shiftand.h
  267. include/seqan/find/find_myers_ukkonen.h
  268. include/seqan/find/find_pattern_base.h
  269. include/seqan/find/find_pex.h
  270. include/seqan/find/find_score.h
  271. include/seqan/find/find_set_horspool.h
  272. include/seqan/find/find_shiftand.h
  273. include/seqan/find/find_shiftor.h
  274. include/seqan/find/find_simple.h
  275. include/seqan/find/find_wild_shiftand.h
  276. include/seqan/find/find_wumanber.h
  277. include/seqan/gff_io.h
  278. include/seqan/gff_io/gff_file.h
  279. include/seqan/gff_io/gff_io_base.h
  280. include/seqan/graph_algorithms.h
  281. include/seqan/graph_algorithms/all_pairs_shortest_path.h
  282. include/seqan/graph_algorithms/bellman_ford.h
  283. include/seqan/graph_algorithms/bipartite_matching.h
  284. include/seqan/graph_algorithms/breadth_first_search.h
  285. include/seqan/graph_algorithms/connected_components.h
  286. include/seqan/graph_algorithms/depth_first_search.h
  287. include/seqan/graph_algorithms/dijkstra.h
  288. include/seqan/graph_algorithms/floyd_warshall.h
  289. include/seqan/graph_algorithms/ford_fulkerson.h
  290. include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
  291. include/seqan/graph_algorithms/graph_algorithm_hmm.h
  292. include/seqan/graph_algorithms/graph_algorithm_lis_his.h
  293. include/seqan/graph_algorithms/kruskal.h
  294. include/seqan/graph_algorithms/maximum_weighted_matching.h
  295. include/seqan/graph_algorithms/path_growing.h
  296. include/seqan/graph_algorithms/prim.h
  297. include/seqan/graph_algorithms/single_source_shortest_path.h
  298. include/seqan/graph_algorithms/strongly_connected_compnents.h
  299. include/seqan/graph_algorithms/topological_sort.h
  300. include/seqan/graph_algorithms/transitive_closure.h
  301. include/seqan/graph_algorithms/weakly_connected_components.h
  302. include/seqan/graph_algorithms/weighted_bipartite_matching.h
  303. include/seqan/graph_align.h
  304. include/seqan/graph_align/graph_algorithm_refine_align.h
  305. include/seqan/graph_align/graph_algorithm_refine_aligngraph.h
  306. include/seqan/graph_align/graph_algorithm_refine_annotation.h
  307. include/seqan/graph_align/graph_algorithm_refine_exact.h
  308. include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
  309. include/seqan/graph_align/graph_algorithm_refine_fragment.h
  310. include/seqan/graph_align/graph_algorithm_refine_inexact.h
  311. include/seqan/graph_align/graph_algorithm_refine_scoring.h
  312. include/seqan/graph_align/graph_impl_align.h
  313. include/seqan/graph_align/graph_impl_align_adapt.h
  314. include/seqan/graph_msa.h
  315. include/seqan/graph_msa/graph_align_tcoffee_base.h
  316. include/seqan/graph_msa/graph_align_tcoffee_distance.h
  317. include/seqan/graph_msa/graph_align_tcoffee_guidetree.h
  318. include/seqan/graph_msa/graph_align_tcoffee_io.h
  319. include/seqan/graph_msa/graph_align_tcoffee_kmer.h
  320. include/seqan/graph_msa/graph_align_tcoffee_library.h
  321. include/seqan/graph_msa/graph_align_tcoffee_msa.h
  322. include/seqan/graph_msa/graph_align_tcoffee_progressive.h
  323. include/seqan/graph_msa/graph_align_tcoffee_refinement.h
  324. include/seqan/graph_types.h
  325. include/seqan/graph_types/graph_base.h
  326. include/seqan/graph_types/graph_drawing.h
  327. include/seqan/graph_types/graph_edgestump.h
  328. include/seqan/graph_types/graph_idmanager.h
  329. include/seqan/graph_types/graph_impl_automaton.h
  330. include/seqan/graph_types/graph_impl_directed.h
  331. include/seqan/graph_types/graph_impl_hmm.h
  332. include/seqan/graph_types/graph_impl_oracle.h
  333. include/seqan/graph_types/graph_impl_tree.h
  334. include/seqan/graph_types/graph_impl_trie.h
  335. include/seqan/graph_types/graph_impl_undirected.h
  336. include/seqan/graph_types/graph_impl_wordgraph.h
  337. include/seqan/graph_types/graph_interface.h
  338. include/seqan/graph_types/graph_iterator.h
  339. include/seqan/graph_types/graph_iterator_adjacency.h
  340. include/seqan/graph_types/graph_iterator_bfs.h
  341. include/seqan/graph_types/graph_iterator_dfs.h
  342. include/seqan/graph_types/graph_iterator_edge.h
  343. include/seqan/graph_types/graph_iterator_outedge.h
  344. include/seqan/graph_types/graph_iterator_vertex.h
  345. include/seqan/graph_types/graph_utility_parsing.h
  346. include/seqan/graph_types/property_map_generic.h
  347. include/seqan/graph_types/property_map_internal.h
  348. include/seqan/graph_types/property_map_internal_pointer.h
  349. include/seqan/index.h
  350. include/seqan/index/find2_backtracking.h
  351. include/seqan/index/find2_base.h
  352. include/seqan/index/find2_functors.h
  353. include/seqan/index/find2_index.h
  354. include/seqan/index/find2_index_approx.h
  355. include/seqan/index/find2_index_multi.h
  356. include/seqan/index/find2_vstree_factory.h
  357. include/seqan/index/find_backtracking.h
  358. include/seqan/index/find_index.h
  359. include/seqan/index/find_index_approx.h
  360. include/seqan/index/find_index_binary.h
  361. include/seqan/index/find_index_esa.h
  362. include/seqan/index/find_index_lambda.h
  363. include/seqan/index/find_index_qgram.h
  364. include/seqan/index/find_pigeonhole.h
  365. include/seqan/index/find_quasar.h
  366. include/seqan/index/find_swift.h
  367. include/seqan/index/index_base.h
  368. include/seqan/index/index_bidirectional.h
  369. include/seqan/index/index_bidirectional_stree.h
  370. include/seqan/index/index_bifm.h
  371. include/seqan/index/index_bifm_stree.h
  372. include/seqan/index/index_bwt.h
  373. include/seqan/index/index_childtab.h
  374. include/seqan/index/index_device.h
  375. include/seqan/index/index_dfi.h
  376. include/seqan/index/index_esa_algs.h
  377. include/seqan/index/index_esa_algs_multi.h
  378. include/seqan/index/index_esa_base.h
  379. include/seqan/index/index_esa_drawing.h
  380. include/seqan/index/index_esa_stree.h
  381. include/seqan/index/index_fm.h
  382. include/seqan/index/index_fm_compressed_sa.h
  383. include/seqan/index/index_fm_compressed_sa_iterator.h
  384. include/seqan/index/index_fm_dox.h
  385. include/seqan/index/index_fm_lf_table.h
  386. include/seqan/index/index_fm_rank_dictionary_base.h
  387. include/seqan/index/index_fm_rank_dictionary_levels.h
  388. include/seqan/index/index_fm_rank_dictionary_naive.h
  389. include/seqan/index/index_fm_rank_dictionary_wt.h
  390. include/seqan/index/index_fm_right_array_binary_tree.h
  391. include/seqan/index/index_fm_right_array_binary_tree_iterator.h
  392. include/seqan/index/index_fm_sparse_string.h
  393. include/seqan/index/index_fm_stree.h
  394. include/seqan/index/index_forwards.h
  395. include/seqan/index/index_lcp.h
  396. include/seqan/index/index_lcp_tree.h
  397. include/seqan/index/index_pizzachili.h
  398. include/seqan/index/index_pizzachili_find.h
  399. include/seqan/index/index_pizzachili_string.h
  400. include/seqan/index/index_qgram.h
  401. include/seqan/index/index_qgram_bucketrefinement.h
  402. include/seqan/index/index_qgram_openaddressing.h
  403. include/seqan/index/index_qgram_stree.h
  404. include/seqan/index/index_sa_btree.h
  405. include/seqan/index/index_sa_bwtwalk.h
  406. include/seqan/index/index_sa_lss.h
  407. include/seqan/index/index_sa_mm.h
  408. include/seqan/index/index_sa_qsort.h
  409. include/seqan/index/index_sa_stree.h
  410. include/seqan/index/index_sa_truncated.h
  411. include/seqan/index/index_shawarma.h
  412. include/seqan/index/index_shims.h
  413. include/seqan/index/index_skew3.h
  414. include/seqan/index/index_skew7.h
  415. include/seqan/index/index_skew7_multi.h
  416. include/seqan/index/index_view.h
  417. include/seqan/index/index_wotd.h
  418. include/seqan/index/pipe_merger3.h
  419. include/seqan/index/pipe_merger7.h
  420. include/seqan/index/pizzachili_api.h
  421. include/seqan/index/pump_extender3.h
  422. include/seqan/index/pump_extender7.h
  423. include/seqan/index/pump_lcp_core.h
  424. include/seqan/index/pump_separator7.h
  425. include/seqan/index/radix.h
  426. include/seqan/index/repeat_base.h
  427. include/seqan/index/shape_base.h
  428. include/seqan/index/shape_gapped.h
  429. include/seqan/index/shape_minimizer.h
  430. include/seqan/index/shape_onegapped.h
  431. include/seqan/index/shape_predefined.h
  432. include/seqan/index/shape_threshold.h
  433. include/seqan/journaled_set.h
  434. include/seqan/journaled_set/journal_alignment_interface.h
  435. include/seqan/journaled_set/journal_alignment_traceback_adaptor.h
  436. include/seqan/journaled_set/journaled_set_base.h
  437. include/seqan/journaled_set/journaled_set_impl.h
  438. include/seqan/journaled_set/journaled_set_join.h
  439. include/seqan/journaled_set/journaled_set_join_config.h
  440. include/seqan/journaled_set/journaled_set_join_global_align_compact.h
  441. include/seqan/journaled_set/journaled_set_join_global_align_manhatten.h
  442. include/seqan/journaled_set/journaled_set_journal_trace_descriptor.h
  443. include/seqan/journaled_set/score_biaffine.h
  444. include/seqan/journaled_string_tree.h
  445. include/seqan/journaled_string_tree/delta_map.h
  446. include/seqan/journaled_string_tree/delta_map_entry.h
  447. include/seqan/journaled_string_tree/delta_map_iterator.h
  448. include/seqan/journaled_string_tree/delta_store.h
  449. include/seqan/journaled_string_tree/journaled_string_tree_base.h
  450. include/seqan/journaled_string_tree/journaled_string_tree_impl.h
  451. include/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h
  452. include/seqan/journaled_string_tree/journaled_string_tree_traverser.h
  453. include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h
  454. include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h
  455. include/seqan/journaled_string_tree/jst_extension_base.h
  456. include/seqan/journaled_string_tree/jst_extension_horspool.h
  457. include/seqan/journaled_string_tree/jst_extension_myers_ukkonen.h
  458. include/seqan/journaled_string_tree/jst_extension_shiftand.h
  459. include/seqan/journaled_string_tree/jst_extension_shiftor.h
  460. include/seqan/journaled_string_tree/observable.h
  461. include/seqan/journaled_string_tree/stack_observer.h
  462. include/seqan/map.h
  463. include/seqan/map/map_adapter_stl.h
  464. include/seqan/map/map_base.h
  465. include/seqan/map/map_chooser.h
  466. include/seqan/map/map_skiplist.h
  467. include/seqan/map/map_vector.h
  468. include/seqan/map/sumlist.h
  469. include/seqan/map/sumlist_mini.h
  470. include/seqan/map/sumlist_skip.h
  471. include/seqan/math.h
  472. include/seqan/math/math_common_factor.h
  473. include/seqan/math/math_operators.h
  474. include/seqan/math/math_rational.h
  475. include/seqan/misc/accumulators.h
  476. include/seqan/misc/base.h
  477. include/seqan/misc/bit_twiddling.h
  478. include/seqan/misc/bit_twiddling_functors.h
  479. include/seqan/misc/dequeue.h
  480. include/seqan/misc/edit_environment.h
  481. include/seqan/misc/interval_tree.h
  482. include/seqan/misc/map.h
  483. include/seqan/misc/memset.h
  484. include/seqan/misc/name_store_cache.h
  485. include/seqan/misc/priority_type_base.h
  486. include/seqan/misc/priority_type_heap.h
  487. include/seqan/misc/set.h
  488. include/seqan/misc/svg.h
  489. include/seqan/misc/terminal.h
  490. include/seqan/misc/union_find.h
  491. include/seqan/modifier.h
  492. include/seqan/modifier/cyclic_shape.h
  493. include/seqan/modifier/modifier_alphabet.h
  494. include/seqan/modifier/modifier_alphabet_expansion.h
  495. include/seqan/modifier/modifier_cyclic_shape.h
  496. include/seqan/modifier/modifier_functors.h
  497. include/seqan/modifier/modifier_iterator.h
  498. include/seqan/modifier/modifier_padding.h
  499. include/seqan/modifier/modifier_position.h
  500. include/seqan/modifier/modifier_reverse.h
  501. include/seqan/modifier/modifier_shortcuts.h
  502. include/seqan/modifier/modifier_string.h
  503. include/seqan/modifier/modifier_view.h
  504. include/seqan/parallel.h
  505. include/seqan/parallel/enumerable_thread_local.h
  506. include/seqan/parallel/enumerable_thread_local_iterator.h
  507. include/seqan/parallel/parallel_algorithms.h
  508. include/seqan/parallel/parallel_atomic_misc.h
  509. include/seqan/parallel/parallel_atomic_primitives.h
  510. include/seqan/parallel/parallel_lock.h
  511. include/seqan/parallel/parallel_macros.h
  512. include/seqan/parallel/parallel_queue.h
  513. include/seqan/parallel/parallel_queue_suspendable.h
  514. include/seqan/parallel/parallel_resource_pool.h
  515. include/seqan/parallel/parallel_sequence.h
  516. include/seqan/parallel/parallel_serializer.h
  517. include/seqan/parallel/parallel_splitting.h
  518. include/seqan/parallel/parallel_tags.h
  519. include/seqan/parallel/parallel_thread_pool.h
  520. include/seqan/parse_lm.h
  521. include/seqan/parse_lm/local_match_store.h
  522. include/seqan/parse_lm/parse_blastn_tabular.h
  523. include/seqan/parse_lm/parse_lastz_general.h
  524. include/seqan/parse_lm/parse_stellar_gff.h
  525. include/seqan/pipe.h
  526. include/seqan/pipe/pipe_base.h
  527. include/seqan/pipe/pipe_caster.h
  528. include/seqan/pipe/pipe_counter.h
  529. include/seqan/pipe/pipe_echoer.h
  530. include/seqan/pipe/pipe_edit_environment.h
  531. include/seqan/pipe/pipe_filter.h
  532. include/seqan/pipe/pipe_iterator.h
  533. include/seqan/pipe/pipe_joiner.h
  534. include/seqan/pipe/pipe_namer.h
  535. include/seqan/pipe/pipe_sampler.h
  536. include/seqan/pipe/pipe_shifter.h
  537. include/seqan/pipe/pipe_source.h
  538. include/seqan/pipe/pipe_tupler.h
  539. include/seqan/pipe/pool_base.h
  540. include/seqan/pipe/pool_mapper.h
  541. include/seqan/pipe/pool_sorter.h
  542. include/seqan/platform.h
  543. include/seqan/random.h
  544. include/seqan/random/random_base.h
  545. include/seqan/random/random_beta.h
  546. include/seqan/random/random_util.h
  547. include/seqan/realign.h
  548. include/seqan/realign/realign_base.h
  549. include/seqan/realign/realign_helper_functions.h
  550. include/seqan/reduced_aminoacid.h
  551. include/seqan/reduced_aminoacid/reduced_aminoacid_base.h
  552. include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h
  553. include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_base.h
  554. include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h
  555. include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_base.h
  556. include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h
  557. include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h
  558. include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h
  559. include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h
  560. include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h
  561. include/seqan/reduced_aminoacid/reduced_aminoacid_li10_base.h
  562. include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h
  563. include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h
  564. include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h
  565. include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_base.h
  566. include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h
  567. include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_base.h
  568. include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h
  569. include/seqan/rna_io.h
  570. include/seqan/rna_io/bpseq_read_write.h
  571. include/seqan/rna_io/connect_read_write.h
  572. include/seqan/rna_io/dot_bracket_read_write.h
  573. include/seqan/rna_io/ebpseq_read_write.h
  574. include/seqan/rna_io/rna_header.h
  575. include/seqan/rna_io/rna_io_context.h
  576. include/seqan/rna_io/rna_record.h
  577. include/seqan/rna_io/rna_struct_file.h
  578. include/seqan/rna_io/stockholm_read_write.h
  579. include/seqan/rna_io/vienna_read_write.h
  580. include/seqan/roi_io.h
  581. include/seqan/roi_io/read_roi.h
  582. include/seqan/roi_io/roi_file.h
  583. include/seqan/roi_io/roi_io_context.h
  584. include/seqan/roi_io/roi_record.h
  585. include/seqan/roi_io/write_roi.h
  586. include/seqan/score.h
  587. include/seqan/score/score_base.h
  588. include/seqan/score/score_edit.h
  589. include/seqan/score/score_matrix.h
  590. include/seqan/score/score_matrix_data.h
  591. include/seqan/score/score_matrix_dyn.h
  592. include/seqan/score/score_matrix_io.h
  593. include/seqan/score/score_simd_wrapper.h
  594. include/seqan/score/score_simple.h
  595. include/seqan/seeds.h
  596. include/seqan/seeds/banded_chain_alignment.h
  597. include/seqan/seeds/banded_chain_alignment_impl.h
  598. include/seqan/seeds/banded_chain_alignment_profile.h
  599. include/seqan/seeds/banded_chain_alignment_scout.h
  600. include/seqan/seeds/banded_chain_alignment_traceback.h
  601. include/seqan/seeds/basic_iter_indirect.h
  602. include/seqan/seeds/seeds_base.h
  603. include/seqan/seeds/seeds_combination.h
  604. include/seqan/seeds/seeds_extension.h
  605. include/seqan/seeds/seeds_global_chaining.h
  606. include/seqan/seeds/seeds_global_chaining_base.h
  607. include/seqan/seeds/seeds_global_chaining_gusfield.h
  608. include/seqan/seeds/seeds_seed_base.h
  609. include/seqan/seeds/seeds_seed_chained.h
  610. include/seqan/seeds/seeds_seed_diagonal.h
  611. include/seqan/seeds/seeds_seed_set_base.h
  612. include/seqan/seeds/seeds_seed_set_non_scored.h
  613. include/seqan/seeds/seeds_seed_set_scored.h
  614. include/seqan/seeds/seeds_seed_set_unordered.h
  615. include/seqan/seeds/seeds_seed_simple.h
  616. include/seqan/seq_io.h
  617. include/seqan/seq_io/bam_sam.h
  618. include/seqan/seq_io/fai_index.h
  619. include/seqan/seq_io/fasta_fastq.h
  620. include/seqan/seq_io/genomic_region.h
  621. include/seqan/seq_io/read_embl.h
  622. include/seqan/seq_io/read_genbank.h
  623. include/seqan/seq_io/sequence_file.h
  624. include/seqan/sequence.h
  625. include/seqan/sequence/adapt_array_pointer.h
  626. include/seqan/sequence/adapt_stl_container.h
  627. include/seqan/sequence/container_view.h
  628. include/seqan/sequence/container_view_zip.h
  629. include/seqan/sequence/iter_concat_virtual.h
  630. include/seqan/sequence/segment_base.h
  631. include/seqan/sequence/segment_infix.h
  632. include/seqan/sequence/segment_prefix.h
  633. include/seqan/sequence/segment_suffix.h
  634. include/seqan/sequence/segment_utils.h
  635. include/seqan/sequence/sequence_concatenator.h
  636. include/seqan/sequence/sequence_forwards.h
  637. include/seqan/sequence/sequence_interface.h
  638. include/seqan/sequence/sequence_lexical.h
  639. include/seqan/sequence/sequence_shortcuts.h
  640. include/seqan/sequence/string_alloc.h
  641. include/seqan/sequence/string_array.h
  642. include/seqan/sequence/string_base.h
  643. include/seqan/sequence/string_block.h
  644. include/seqan/sequence/string_cstyle.h
  645. include/seqan/sequence/string_packed.h
  646. include/seqan/sequence/string_packed_old.h
  647. include/seqan/sequence/string_set_base.h
  648. include/seqan/sequence/string_set_concat_direct.h
  649. include/seqan/sequence/string_set_dependent_generous.h
  650. include/seqan/sequence/string_set_dependent_tight.h
  651. include/seqan/sequence/string_set_owner.h
  652. include/seqan/sequence/string_set_segment.h
  653. include/seqan/sequence/string_set_view.h
  654. include/seqan/sequence_journaled.h
  655. include/seqan/sequence_journaled/journal_entries_sorted_array.h
  656. include/seqan/sequence_journaled/journal_entry.h
  657. include/seqan/sequence_journaled/sequence_journaled.h
  658. include/seqan/sequence_journaled/sequence_journaled_iterator.h
  659. include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
  660. include/seqan/simd.h
  661. include/seqan/simd/simd_base.h
  662. include/seqan/simd/simd_base_seqan_impl.h
  663. include/seqan/simd/simd_base_seqan_impl_avx2.h
  664. include/seqan/simd/simd_base_seqan_impl_avx512.h
  665. include/seqan/simd/simd_base_seqan_impl_sse4.2.h
  666. include/seqan/simd/simd_base_seqan_interface.h
  667. include/seqan/simd/simd_base_umesimd_impl.h
  668. include/seqan/simple_intervals_io.h
  669. include/seqan/simple_intervals_io/simple_intervals_file.h
  670. include/seqan/simple_intervals_io/simple_intervals_io.h
  671. include/seqan/statistics.h
  672. include/seqan/statistics/statistics_base.h
  673. include/seqan/statistics/statistics_markov_model.h
  674. include/seqan/store.h
  675. include/seqan/store/store_align.h
  676. include/seqan/store/store_align_intervals.h
  677. include/seqan/store/store_all.h
  678. include/seqan/store/store_annotation.h
  679. include/seqan/store/store_base.h
  680. include/seqan/store/store_contig.h
  681. include/seqan/store/store_intervaltree.h
  682. include/seqan/store/store_io.h
  683. include/seqan/store/store_io_gff.h
  684. include/seqan/store/store_io_sam.h
  685. include/seqan/store/store_io_ucsc.h
  686. include/seqan/store/store_library.h
  687. include/seqan/store/store_matepair.h
  688. include/seqan/store/store_read.h
  689. include/seqan/stream.h
  690. include/seqan/stream/adapt_ios.h
  691. include/seqan/stream/buffered_stream.h
  692. include/seqan/stream/file_stream.h
  693. include/seqan/stream/formatted_file.h
  694. include/seqan/stream/guess_format.h
  695. include/seqan/stream/iostream_bgzf.h
  696. include/seqan/stream/iostream_bzip2.h
  697. include/seqan/stream/iostream_bzip2_impl.h
  698. include/seqan/stream/iostream_zip.h
  699. include/seqan/stream/iostream_zip_impl.h
  700. include/seqan/stream/iostream_zutil.h
  701. include/seqan/stream/iter_stream.h
  702. include/seqan/stream/lexical_cast.h
  703. include/seqan/stream/stream_base.h
  704. include/seqan/stream/stream_compressor.h
  705. include/seqan/stream/tokenization.h
  706. include/seqan/stream/virtual_stream.h
  707. include/seqan/system.h
  708. include/seqan/system/file_async.h
  709. include/seqan/system/file_directory.h
  710. include/seqan/system/file_forwards.h
  711. include/seqan/system/file_sync.h
  712. include/seqan/system/system_base.h
  713. include/seqan/system/system_event_win.h
  714. include/seqan/system/system_forwards.h
  715. include/seqan/tabix_io.h
  716. include/seqan/tabix_io/tabix_index_tbi.h
  717. include/seqan/translation.h
  718. include/seqan/translation/translation.h
  719. include/seqan/translation/translation_tables.h
  720. include/seqan/ucsc_io.h
  721. include/seqan/ucsc_io/ucsc_file.h
  722. include/seqan/ucsc_io/ucsc_io.h
  723. include/seqan/ucsc_io/ucsc_record.h
  724. include/seqan/vcf_io.h
  725. include/seqan/vcf_io/read_vcf.h
  726. include/seqan/vcf_io/vcf_file.h
  727. include/seqan/vcf_io/vcf_header.h
  728. include/seqan/vcf_io/vcf_header_record.h
  729. include/seqan/vcf_io/vcf_io_context.h
  730. include/seqan/vcf_io/vcf_record.h
  731. include/seqan/vcf_io/write_vcf.h
  732. include/seqan/version.h
  733. lib/cmake/seqan/seqan-config.cmake
  734. libdata/pkgconfig/seqan-2.pc
  735. @owner
  736. @group
  737. @mode
Collapse this list.
Dependency lines:
  • seqan>0:biology/seqan
Conflicts:
CONFLICTS:
  • seqan1
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/seqan/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/seqan
  • pkg install seqan
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: seqan
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
seqan
ABIlatestquarterly
FreeBSD:11:aarch642.4.02.4.0
FreeBSD:11:amd642.4.02.4.0
FreeBSD:11:armv62.1.1_12.4.0
FreeBSD:11:i3862.4.02.4.0
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips642.1.1_12.4.0
FreeBSD:12:aarch642.4.02.4.0
FreeBSD:12:amd642.4.02.4.0
FreeBSD:12:armv62.4.02.4.0
FreeBSD:12:armv72.4.02.4.0
FreeBSD:12:i3862.4.02.4.0
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips642.4.02.4.0
FreeBSD:12:powerpc64pkg-fallout2.4.0
FreeBSD:13:aarch642.4.02.4.0
FreeBSD:13:amd642.4.02.4.0
FreeBSD:13:armv62.4.02.4.0
FreeBSD:13:armv72.4.02.4.0
FreeBSD:13:i3862.4.02.4.0
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips642.4.02.4.0
FreeBSD:13:powerpc642.4.02.4.0
FreeBSD:13:riscv64pkg-fallout2.4.0
FreeBSD:14:aarch642.4.0pkg-fallout
FreeBSD:14:amd642.4.0pkg-fallout
FreeBSD:14:armv62.4.0pkg-fallout
FreeBSD:14:armv72.4.0pkg-fallout
FreeBSD:14:i3862.4.0pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips642.4.0pkg-fallout
FreeBSD:14:powerpc642.4.0pkg-fallout
FreeBSD:14:riscv642.4.0pkg-fallout
 
This port has no dependencies.
This port is required by:
for Build

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. biology/unanimity*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. http://packages.seqan.de/seqan-library/
Collapse this list.
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2016-05-10
    Affects: users of biology/seqan
    Author: junovitch@FreeBSD.org
    Reason: 
      The biology/seqan port has been split into biology/seqan (only the
      library) and biology/seqan-apps for the programs based on SeqAn. Both
      ports are based on version 2.1.1 of the SeqAn repository. There is a new
      biology/seqan1 port with version 1.3 of SeqAn for backwards compatibility,
      but this port will likely be deprecated in the next year so please update
      your software to SeqAn2.
    
    

Number of commits found: 24

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.4.0
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
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2.4.0
20 Jul 2022 14:20:57
commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
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2.4.0
29 Oct 2021 09:50:18
commit hash:819f25b36d45b8ac5593ec8e6f470d9ad454b08acommit hash:819f25b36d45b8ac5593ec8e6f470d9ad454b08acommit hash:819f25b36d45b8ac5593ec8e6f470d9ad454b08acommit hash:819f25b36d45b8ac5593ec8e6f470d9ad454b08a files touched by this commit
Stefan Eßer (se) search for other commits by this committer
*/*: Remove redundant '-[0-9]*' from CONFLICTS

The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").

Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".

Approved by:	portmgr (blanket)
2.4.0
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.4.0
10 Mar 2018 06:21:37
Revision:464043Original commit files touched by this commit
yuri search for other commits by this committer
biology/seqan-apps, biology/seqan: Update to 2.4.0

Port changes for biology/seqan-apps:
* Changed to DISTVERSION
* Updated COMMENT
* Added USES=compiler:openmp
* Removed BROKEN_xx (upstream now claims support for these architectures)
* Removed USE_GCC
* Added SSE4/AVX2/NATIVE SIMD options

Port changes for biology/seqan:
* Changed to DISTVERSION
* Added NO_ARCH
* Added PORTDOCS=*
* Updated do-install

PR:		225682
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Approved by:	tcberner (mentor, implicit)
2.2.0
14 Sep 2016 19:38:58
Revision:422156Original commit files touched by this commit
pawel search for other commits by this committer
- Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]
- Fix spelling in pkg-descr

PR:		212682 [1]
Submitted by:	Hannes Hauswedell (maintainer) [1]
2.1.1_1
27 May 2016 16:10:36
Revision:415945Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Do install cmake and pkgconfig modules
- While here, switch to options helpers

PR:		209710
Submitted by:	h2+fbsdports@fsfe.org (maintainer)
2.1.1
10 May 2016 01:05:23
Revision:414898Original commit files touched by this commit
junovitch search for other commits by this committer
biology/seqan: update 1.3.1 -> 2.1.1
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>
1.3.1_3
21 Mar 2015 11:53:28
Revision:381791Original commit files touched by this commit
marino search for other commits by this committer
biology/segan: Limit GCC to 4.8 while waiting for update

Due to questionable c++, GCC 4.9 and newer cannot build seqan.  An update
has been in the works that will enable clang compilers and all versions
of GCC to build seqan, but it is not quite ready yet.  While waiting for
it, limit the version of GCC used to 4.8.

PR:	196851
1.3.1_3
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
1.3.1_3
19 Oct 2014 07:38:12
Revision:371171Original commit files touched by this commit
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
1.3.1_3
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
1.3.1_2
10 Jul 2014 22:29:52
Revision:361497Original commit files touched by this commit
adamw search for other commits by this committer
Use gcc on all platforms.

PR:		191692
Submitted by:	maintainer
1.3.1_2
01 Jun 2014 11:42:17
Revision:356100Original commit files touched by this commit
ohauer search for other commits by this committer
- add stage support
- adjust BSDn license
1.3.1_2
10 Mar 2014 20:55:22
Revision:347809Original commit files touched by this commit
gerald search for other commits by this committer
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3.  This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.

Part II, Bump PORTREVISIONs.

PR:		182136
Supported by:	Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by:	bdrewery (two -exp runs)
1.3.1_1
07 Mar 2014 15:52:40
Revision:347402Original commit files touched by this commit
bapt search for other commits by this committer
Convert b* to USES=zip
1.3.1_1
26 Oct 2013 00:52:36
Revision:331644Original commit files touched by this commit
gerald search for other commits by this committer
Update to libmpc version 1.0.1 which brings the following fixes:

 - Switched to automake 1.11.6, see CVE-2012-3386.
 - #14669: Fixed extraction of CC from gmp.h.
 - Fixed case of intermediate zero real or imaginary part in mpc_fma,
   found by hydra with GMP_CHECK_RANDOMIZE=1346362345.

This is on top of the following changes from version 1.0

 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
   invariant sections) for the documentation.
 - 100% of all lines are covered by tests
 - Renamed functions
   . mpc_mul_2exp to mpc_mul_2ui
   . mpc_div_2exp to mpc_div_2ui
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1.3.1
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.3.1
17 Aug 2013 16:27:24
Revision:324851Original commit files touched by this commit
gerald search for other commits by this committer
Replace USE_GCC=4.6+ and USE_GCC=4.4+ by USE_GCC=yes.

Right now this is a noop in the former case and a noop in the latter
case unless lang/gcc44 has been installed explicitly.

This puts a bit more emphasis on standardizing on a canonical version
"current" GCC and makes it easier to update that canonical version
by changing the default in Mk/bsd.gcc.mk and updating the lang/gcc port.

That is, USE_GCC=yes means "use a decent/modern version of GCC" without
having to worry about details.

Approved by:	portmgr (bdrewery)
1.3.1
22 Mar 2013 20:06:15
Revision:314960Original commit files touched by this commit
makc search for other commits by this committer
- convert USE_CMAKE to USES
- while here clean up some ports from CMAKE_VERBOSE, which is intended
  for users

Approved by:	portmgr (miwi)
1.3.1
21 Jul 2012 22:20:33
Original commit files touched by this commit
gerald search for other commits by this committer
Replace USE_GCC=4.4+ by USE_GCC=4.6+ since GCC 4.4 is on its way out.

Approved by:	maintainer
1.3.1
07 Jun 2012 13:04:53
Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix maintainer email

Submitted by:   maintainer via private email
1.3.1
06 Jun 2012 17:51:33
Original commit files touched by this commit
amdmi3 search for other commits by this committer
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data. The library is licensed under the
3-clause BSD license except the applications which are GPL.

WWW: http://www.seqan.de/

PR:             167571
Submitted by:   Hannes <h2+fbsdports@fsfe.org>

Number of commits found: 24