[med-svn] [seqan2] 01/02: Update upstream source from tag 'upstream/2.4.0_rc0+dfsg'

Michael Crusoe misterc-guest at moszumanska.debian.org
Tue Jan 30 10:59:55 UTC 2018


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 <michael.crusoe at gmail.com>
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(-)

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