This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to tag debian/2.4.0_rc0+dfsg-1 in repository seqan2.
commit dc253289cf8287ce2b5b785a3ead4fe84304e772 Merge: 06b4aa4 194b7d5 Author: Michael R. Crusoe <[email protected]> Date: Fri Jan 26 09:44:44 2018 -0800 Update upstream source from tag 'upstream/2.4.0_rc0+dfsg' Update to upstream version '2.4.0~rc0+dfsg' with Debian dir 78da67cef37a7be02c018a184a43ff58be6f70b8 CHANGELOG.rst | 57 +- README.rst | 15 +- apps/alf/CMakeLists.txt | 2 +- apps/alf/alf.cpp | 2 +- apps/bs_tools/CMakeLists.txt | 2 +- apps/bs_tools/casbar_score.h | 42 +- apps/dfi/CMakeLists.txt | 2 +- apps/fiona/CMakeLists.txt | 2 +- apps/fiona/compute_gain.cpp | 6 +- apps/fx_tools/CMakeLists.txt | 2 +- apps/gustaf/CMakeLists.txt | 2 +- apps/insegt/CMakeLists.txt | 2 +- apps/mason2/CMakeLists.txt | 2 +- apps/mason2/mason_genome.cpp | 2 +- apps/mason2/mason_variator.cpp | 10 +- apps/micro_razers/CMakeLists.txt | 2 +- apps/ngs_roi/CMakeLists.txt | 4 +- apps/pair_align/CMakeLists.txt | 7 +- apps/param_chooser/CMakeLists.txt | 2 +- apps/rabema/CMakeLists.txt | 4 +- apps/rabema/rabema_build_gold_standard.cpp | 2 +- apps/rabema/rabema_evaluate.cpp | 4 +- apps/razers/CMakeLists.txt | 7 +- apps/razers3/CMakeLists.txt | 2 +- apps/rep_sep/CMakeLists.txt | 2 +- apps/sak/CMakeLists.txt | 4 +- apps/sam2matrix/CMakeLists.txt | 2 +- apps/samcat/CMakeLists.txt | 2 +- apps/searchjoin/CMakeLists.txt | 16 +- apps/searchjoin/db.h | 8 +- apps/seqan_tcoffee/CMakeLists.txt | 2 +- apps/seqan_tcoffee/tests/run_tests.py | 6 + apps/seqcons2/CMakeLists.txt | 2 +- apps/sgip/CMakeLists.txt | 2 +- apps/snp_store/CMakeLists.txt | 2 +- apps/splazers/CMakeLists.txt | 2 +- apps/stellar/CMakeLists.txt | 2 +- apps/stellar/stellar.cpp | 2 +- apps/tree_recon/CMakeLists.txt | 2 +- apps/yara/CMakeLists.txt | 2 +- apps/yara/find_verifier.h | 18 +- .../tutorial/file_io_overview/solution3.cpp.stdout | 12 +- demos/tutorial/indices/find2_index_approx.cpp | 57 + demos/tutorial/indices/find2_index_approx.stdout | 23 + demos/tutorial/sam_and_bam_io/example7.cpp.stdout | 6 +- dox/CMakeLists.txt | 2 +- include/seqan/align.h | 2 + include/seqan/align/align_interface_wrapper.h | 52 +- .../aligned_sequence_concept.h} | 49 +- include/seqan/align/dp_algorithm_impl.h | 725 ++++----- include/seqan/align/dp_align_simd_helper.h | 163 +- include/seqan/align/dp_cell.h | 110 +- include/seqan/align/dp_cell_affine.h | 35 +- include/seqan/align/dp_cell_dynamic.h | 12 +- include/seqan/align/dp_context.h | 87 +- include/seqan/align/dp_formula.h | 251 ++- include/seqan/align/dp_formula_affine.h | 763 +++------ include/seqan/align/dp_formula_dynamic.h | 377 +++-- include/seqan/align/dp_formula_linear.h | 348 ++-- include/seqan/align/dp_matrix.h | 322 ++-- include/seqan/align/dp_matrix_navigator.h | 36 + .../seqan/align/dp_matrix_navigator_score_matrix.h | 393 ++--- .../dp_matrix_navigator_score_matrix_sparse.h | 351 ++-- .../seqan/align/dp_matrix_navigator_trace_matrix.h | 377 +++-- include/seqan/align/dp_matrix_sparse.h | 38 +- include/seqan/align/dp_profile.h | 307 ++-- include/seqan/align/dp_scout.h | 24 +- include/seqan/align/dp_scout_simd.h | 332 +++- include/seqan/align/dp_setup.h | 86 +- include/seqan/align/dp_trace_segment.h | 8 +- include/seqan/align/dp_traceback_impl.h | 161 +- include/seqan/align/gaps_anchor.h | 2 +- include/seqan/align/gaps_base.h | 6 + include/seqan/align/global_alignment_banded.h | 118 +- include/seqan/align/global_alignment_unbanded.h | 134 +- include/seqan/align/local_alignment_banded.h | 73 +- include/seqan/align/local_alignment_unbanded.h | 109 +- .../align/local_alignment_waterman_eggert_impl.h | 39 +- include/seqan/align/matrix_base.h | 333 ++-- include/seqan/align_extend/align_extend.h | 4 +- include/seqan/align_extend/align_extend_base.h | 16 +- include/seqan/align_extend/dp_scout_xdrop.h | 19 +- .../{parallel/parallel_tags.h => align_parallel.h} | 88 +- .../async_wave_execution_interface.h | 252 +++ include/seqan/align_parallel/dp_kernel_adaptor.h | 343 ++++ .../dp_parallel_execution_policies.h | 174 ++ include/seqan/align_parallel/dp_parallel_scout.h | 263 +++ .../seqan/align_parallel/dp_parallel_scout_simd.h | 362 +++++ .../dp_settings.h} | 95 +- .../parallel_tags.h => align_parallel/dp_traits.h} | 106 +- .../align_parallel/parallel_align_interface.h | 366 +++++ .../wavefront_alignment_executor.h} | 76 +- .../align_parallel/wavefront_alignment_result.h | 165 ++ .../align_parallel/wavefront_alignment_scheduler.h | 347 ++++ .../align_parallel/wavefront_alignment_task.h | 404 +++++ .../wavefront_alignment_thread_local_storage.h | 130 ++ include/seqan/align_parallel/wavefront_task.h | 365 +++++ .../wavefront_task_event.h} | 82 +- .../seqan/align_parallel/wavefront_task_executor.h | 146 ++ .../wavefront_task_queue.h} | 121 +- .../align_parallel/wavefront_task_scheduler.h | 218 +++ include/seqan/align_parallel/wavefront_task_util.h | 557 +++++++ include/seqan/align_split/align_split_interface.h | 51 +- include/seqan/arg_parse/arg_parse_argument.h | 36 +- include/seqan/arg_parse/tool_doc.h | 7 + include/seqan/bam_io/bam_alignment_record_util.h | 2 +- include/seqan/bam_io/bam_index_bai.h | 66 +- include/seqan/bam_io/read_bam.h | 2 +- include/seqan/basic/basic_exception.h | 2 +- include/seqan/basic/fundamental_metafunctions.h | 20 +- include/seqan/basic/fundamental_tags.h | 2 +- include/seqan/basic/iterator_range.h | 30 +- include/seqan/basic/pair_packed.h | 21 +- include/seqan/basic/profiling.h | 42 +- include/seqan/bed_io/bed_record.h | 4 +- include/seqan/find/find_myers_ukkonen.h | 20 +- include/seqan/find/find_score.h | 15 +- include/seqan/index.h | 1 + include/seqan/index/find2_backtracking.h | 4 +- include/seqan/index/find2_index_approx.h | 642 ++++++++ include/seqan/index/find_index_lambda.h | 4 +- include/seqan/index/find_index_qgram.h | 2 +- include/seqan/index/index_base.h | 2 +- include/seqan/index/index_esa_stree.h | 4 +- include/seqan/index/index_fm_compressed_sa.h | 6 +- include/seqan/index/index_fm_lf_table.h | 59 +- .../seqan/index/index_fm_rank_dictionary_base.h | 88 +- .../seqan/index/index_fm_rank_dictionary_levels.h | 6 +- .../seqan/index/index_fm_rank_dictionary_naive.h | 2 +- include/seqan/index/index_fm_rank_dictionary_wt.h | 55 + include/seqan/index/index_qgram.h | 2 +- include/seqan/journaled_string_tree/delta_map.h | 2 +- .../journaled_string_tree_impl.h | 2 +- .../journaled_string_tree_traverser_util.h | 2 +- include/seqan/modifier/modifier_padding.h | 53 +- include/seqan/parallel.h | 6 + include/seqan/parallel/enumerable_thread_local.h | 476 ++++++ .../parallel/enumerable_thread_local_iterator.h | 186 +++ include/seqan/parallel/parallel_algorithms.h | 7 +- include/seqan/parallel/parallel_queue.h | 24 +- .../seqan/parallel/parallel_queue_suspendable.h | 16 +- include/seqan/parallel/parallel_tags.h | 172 ++ include/seqan/parallel/parallel_thread_pool.h | 219 +++ include/seqan/pipe/pipe_sampler.h | 2 +- include/seqan/platform.h | 30 +- include/seqan/score/score_matrix.h | 8 + include/seqan/score/score_matrix_data.h | 72 +- include/seqan/score/score_matrix_dyn.h | 19 + include/seqan/score/score_simd_wrapper.h | 36 +- include/seqan/seeds/banded_chain_alignment_impl.h | 294 ++-- .../seqan/seeds/banded_chain_alignment_profile.h | 24 +- .../seqan/seeds/banded_chain_alignment_traceback.h | 34 +- include/seqan/seeds/seeds_global_chaining.h | 162 +- include/seqan/sequence/string_alloc.h | 22 +- include/seqan/sequence/string_base.h | 24 + include/seqan/sequence/string_set_concat_direct.h | 6 +- include/seqan/sequence/string_set_owner.h | 4 +- include/seqan/simd.h | 19 +- include/seqan/simd/simd_base.h | 99 +- include/seqan/simd/simd_base_seqan_impl.h | 15 +- include/seqan/simd/simd_base_seqan_impl_avx2.h | 11 - include/seqan/simd/simd_base_seqan_impl_avx512.h | 284 ++++ include/seqan/simd/simd_base_seqan_impl_sse4.2.h | 8 +- include/seqan/simd/simd_base_seqan_interface.h | 33 +- include/seqan/simd/simd_base_umesimd_impl.h | 90 +- include/seqan/store/store_all.h | 4 +- include/seqan/store/store_io_sam.h | 2 +- include/seqan/stream/file_stream.h | 8 +- include/seqan/stream/iter_stream.h | 184 ++- include/seqan/stream/virtual_stream.h | 13 +- include/seqan/translation/translation.h | 12 +- include/seqan/vcf_io/read_vcf.h | 126 +- manual/source/Infrastructure/Use/Install.rst | 42 +- .../PatternMatching/OptimalSearchSchemes.rst | 72 + .../Tutorial/Algorithms/PatternMatching/index.rst | 2 + .../Tutorial/GettingStarted/AFirstExample.rst | 1 + .../GettingStarted/BackgroundAndMotivation.rst | 4 +- tests/align/CMakeLists.txt | 46 +- tests/align/test_align.cpp | 14 +- tests/align/test_align_simd.h | 559 ------- tests/align/test_align_simd_base.h | 265 +++ tests/align/test_align_simd_global.h | 122 ++ ...cpp => test_align_simd_global_equal_length.cpp} | 26 +- ... => test_align_simd_global_variable_length.cpp} | 21 +- tests/align/test_align_simd_local.h | 122 ++ ....cpp => test_align_simd_local_equal_length.cpp} | 19 +- ...p => test_align_simd_local_variable_length.cpp} | 18 +- .../test_alignment_algorithms_band_position.h | 62 +- tests/align/test_alignment_algorithms_local.h | 47 + .../align/test_alignment_algorithms_local_banded.h | 32 + .../align/test_alignment_dp_adapt_tracesegments.h | 80 +- tests/align/test_alignment_dp_formula.h | 1326 +++++++++------ tests/align/test_alignment_dp_matrix.h | 2 +- tests/align/test_alignment_dp_matrix_navigator.h | 1704 ++++---------------- tests/align/test_alignment_dp_trace_segment.h | 52 +- tests/align/test_alignment_dp_traceback.h | 395 +++-- tests/align/test_mock.h | 240 +++ tests/align_parallel/CMakeLists.txt | 78 + .../test_align_parallel_algorithm.cpp} | 20 +- .../test_align_parallel_data_structures.cpp} | 83 +- .../test_align_parallel_interface.cpp} | 2 +- .../align_parallel/test_align_parallel_interface.h | 168 ++ .../test_align_parallel_wavefront_alignment.h | 183 +++ .../test_align_wavefront_alignment_scheduler.h | 267 +++ .../test_align_wavefront_alignment_thread_local.h | 93 +- .../test_align_wavefront_intermediate_dp_result.h | 121 ++ .../test_align_wavefront_task_scheduler.h} | 111 +- tests/arg_parse/test_arg_parse.cpp | 1 + tests/arg_parse/test_arg_parse_argument.h | 28 + tests/basic/test_basic_aggregate.h | 5 +- tests/index/CMakeLists.txt | 6 +- .../test_find2_index_approx.cpp} | 21 +- tests/index/test_find2_index_approx.h | 489 ++++++ tests/index/test_index_bifm.cpp | 14 +- tests/modifier/test_modifier.cpp | 3 +- tests/modifier/test_modifier_string_padding.h | 24 + .../test_multiple_translation_units.cpp | 1 + .../test_multiple_translation_units_2.cpp | 1 + tests/parallel/CMakeLists.txt | 4 +- tests/parallel/test_parallel.cpp | 21 + .../test_parallel_enumerable_thread_local.h | 217 +++ tests/parallel/test_parallel_thread_pool.h | 151 ++ tests/seeds/test_seeds_global_chaining.cpp | 26 + tests/simd/test_simd_vector.h | 9 +- tests/translation/test_translation.h | 36 + tests/vcf_io/example_records_with_errors.vcf | 5 +- tests/vcf_io/test_vcf_io.h | 30 +- util/cmake/SeqAnBuildSystem.cmake | 33 +- util/cmake/SeqAnSimdUtility.cmake | 42 +- util/cmake/seqan-config.cmake | 17 +- util/pkgconfig/seqan.pc.in | 4 +- util/skel/app_template/CMakeLists.txt | 2 +- util/travis/linux-cibuild.cmake | 1 - util/travis/linux-cibuild.sh | 5 + 234 files changed, 15786 insertions(+), 7098 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
