[med-svn] [seqan2] branch upstream-experimental updated (4955144 -> 6384831)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Jan 30 11:03:24 UTC 2018
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream-experimental
in repository seqan2.
from 4955144 New upstream version 2.3.2.001platform-issues10-6f85721+dfsg
adds 194b7d5 New upstream version 2.4.0~rc0+dfsg
adds 6384831 New upstream version 2.4.0~rc1+dfsg
No new revisions were added by this update.
Summary of changes:
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 | 95 +-
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 | 29 +-
include/seqan/simd/simd_base_umesimd_impl.h | 96 +-
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/iostream_bgzf.h | 23 +-
include/seqan/stream/iter_stream.h | 184 ++-
include/seqan/stream/stream_compressor.h | 10 +
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 | 270 ++++
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 | 266 +++
.../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 | 13 +-
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 | 66 +-
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 +
236 files changed, 15834 insertions(+), 7113 deletions(-)
create mode 100644 demos/tutorial/indices/find2_index_approx.cpp
create mode 100644 demos/tutorial/indices/find2_index_approx.stdout
copy include/seqan/{parallel/parallel_tags.h => align/aligned_sequence_concept.h} (69%)
copy include/seqan/{parallel/parallel_tags.h => align_parallel.h} (54%)
create mode 100644 include/seqan/align_parallel/async_wave_execution_interface.h
create mode 100644 include/seqan/align_parallel/dp_kernel_adaptor.h
create mode 100644 include/seqan/align_parallel/dp_parallel_execution_policies.h
create mode 100644 include/seqan/align_parallel/dp_parallel_scout.h
create mode 100644 include/seqan/align_parallel/dp_parallel_scout_simd.h
copy include/seqan/{parallel/parallel_tags.h => align_parallel/dp_settings.h} (55%)
copy include/seqan/{parallel/parallel_tags.h => align_parallel/dp_traits.h} (54%)
create mode 100644 include/seqan/align_parallel/parallel_align_interface.h
copy include/seqan/{parallel/parallel_tags.h => align_parallel/wavefront_alignment_executor.h} (59%)
create mode 100644 include/seqan/align_parallel/wavefront_alignment_result.h
create mode 100644 include/seqan/align_parallel/wavefront_alignment_scheduler.h
create mode 100644 include/seqan/align_parallel/wavefront_alignment_task.h
create mode 100644 include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h
create mode 100644 include/seqan/align_parallel/wavefront_task.h
copy include/seqan/{parallel/parallel_tags.h => align_parallel/wavefront_task_event.h} (59%)
create mode 100644 include/seqan/align_parallel/wavefront_task_executor.h
copy include/seqan/{parallel/parallel_tags.h => align_parallel/wavefront_task_queue.h} (51%)
create mode 100644 include/seqan/align_parallel/wavefront_task_scheduler.h
create mode 100644 include/seqan/align_parallel/wavefront_task_util.h
create mode 100644 include/seqan/index/find2_index_approx.h
create mode 100644 include/seqan/parallel/enumerable_thread_local.h
create mode 100644 include/seqan/parallel/enumerable_thread_local_iterator.h
create mode 100644 include/seqan/parallel/parallel_thread_pool.h
create mode 100644 include/seqan/simd/simd_base_seqan_impl_avx512.h
create mode 100644 manual/source/Tutorial/Algorithms/PatternMatching/OptimalSearchSchemes.rst
delete mode 100644 tests/align/test_align_simd.h
create mode 100644 tests/align/test_align_simd_base.h
create mode 100644 tests/align/test_align_simd_global.h
copy tests/align/{test_align_simd.cpp => test_align_simd_global_equal_length.cpp} (57%)
copy tests/align/{test_align_simd.cpp => test_align_simd_global_variable_length.cpp} (67%)
create mode 100644 tests/align/test_align_simd_local.h
copy tests/align/{test_align_simd.cpp => test_align_simd_local_equal_length.cpp} (75%)
copy tests/align/{test_align_simd.cpp => test_align_simd_local_variable_length.cpp} (78%)
create mode 100644 tests/align/test_mock.h
create mode 100644 tests/align_parallel/CMakeLists.txt
copy tests/{align/test_align_simd.cpp => align_parallel/test_align_parallel_algorithm.cpp} (75%)
copy tests/{multiple_translation_units/test_multiple_translation_units.cpp => align_parallel/test_align_parallel_data_structures.cpp} (50%)
copy tests/{align/test_align_simd.cpp => align_parallel/test_align_parallel_interface.cpp} (98%)
create mode 100644 tests/align_parallel/test_align_parallel_interface.h
create mode 100644 tests/align_parallel/test_align_parallel_wavefront_alignment.h
create mode 100644 tests/align_parallel/test_align_wavefront_alignment_scheduler.h
copy include/seqan/parallel/parallel_tags.h => tests/align_parallel/test_align_wavefront_alignment_thread_local.h (51%)
create mode 100644 tests/align_parallel/test_align_wavefront_intermediate_dp_result.h
copy tests/{multiple_translation_units/test_multiple_translation_units.cpp => align_parallel/test_align_wavefront_task_scheduler.h} (53%)
rename tests/{align/test_align_simd.cpp => index/test_find2_index_approx.cpp} (77%)
create mode 100644 tests/index/test_find2_index_approx.h
create mode 100644 tests/parallel/test_parallel_enumerable_thread_local.h
create mode 100644 tests/parallel/test_parallel_thread_pool.h
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