[med-svn] [seqan2] 01/03: Merge branch 'experimental'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 5 16:05:56 UTC 2018
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository seqan2.
commit 26d12351c8b86df7153119dc0fb9b24ba986631c
Merge: 5f32821 7e3cc84
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Mon Feb 5 06:53:27 2018 -0800
Merge branch 'experimental'
CHANGELOG.rst | 57 +-
CMakeLists.txt | 11 +-
README.rst | 15 +-
apps/alf/CMakeLists.txt | 2 +-
apps/alf/README | 8 +-
apps/alf/alf.cpp | 2 +-
apps/bs_tools/CMakeLists.txt | 2 +-
apps/bs_tools/bisar.h | 2 +-
apps/bs_tools/casbar.cpp | 10 +-
apps/bs_tools/casbar.h | 4 +-
apps/bs_tools/casbar_consensus_realign.h | 2 +-
apps/bs_tools/casbar_score.h | 42 +-
apps/dfi/CMakeLists.txt | 2 +-
apps/dfi/README | 14 +-
apps/fiona/CMakeLists.txt | 2 +-
apps/fiona/compute_gain.cpp | 11 +-
apps/fiona/fiona.cpp | 36 +-
apps/fx_tools/CMakeLists.txt | 2 +-
apps/gustaf/CMakeLists.txt | 2 +-
apps/gustaf/README | 6 +-
apps/gustaf/create_stellarmatches_from_file.h | 6 +-
apps/gustaf/msplazer.h | 42 +-
apps/gustaf/msplazer_algorithms.h | 10 +-
apps/gustaf/msplazer_out.h | 39 +-
apps/insegt/CMakeLists.txt | 2 +-
apps/insegt/README | 14 +-
apps/insegt/base.h | 6 +-
apps/insegt/create_gff.h | 4 +-
apps/insegt/fusion.h | 46 +-
apps/insegt/overlap_module.h | 32 +-
apps/mason2/CMakeLists.txt | 2 +-
apps/mason2/external_split_merge.cpp | 6 +-
apps/mason2/external_split_merge.h | 6 +-
apps/mason2/fragment_generation.h | 2 +
apps/mason2/genomic_variants.cpp | 18 +-
apps/mason2/mason_genome.cpp | 2 +-
apps/mason2/mason_materializer.cpp | 2 +-
apps/mason2/mason_options.cpp | 38 +-
apps/mason2/mason_options.h | 4 +
apps/mason2/mason_simulator.cpp | 4 +-
apps/mason2/mason_splicing.cpp | 18 +-
apps/mason2/mason_variator.cpp | 38 +-
apps/mason2/vcf_materialization.cpp | 7 +-
apps/micro_razers/CMakeLists.txt | 2 +-
apps/micro_razers/README | 14 +-
apps/micro_razers/micro_razers.cpp | 1 +
apps/ngs_roi/CMakeLists.txt | 9 +-
apps/ngs_roi/project_spliced.cpp | 6 +-
apps/ngs_roi/roi_feature_projection.cpp | 2 +-
apps/pair_align/CMakeLists.txt | 7 +-
apps/pair_align/lib/pair_align_lib.cpp | 2 +-
apps/param_chooser/CMakeLists.txt | 2 +-
apps/rabema/CMakeLists.txt | 4 +-
apps/rabema/rabema_build_gold_standard.cpp | 14 +-
apps/rabema/rabema_evaluate.cpp | 28 +-
apps/rabema/ref_id_mapping.h | 6 +-
apps/razers/CMakeLists.txt | 7 +-
apps/razers/README | 14 +-
apps/razers/outputFormat.h | 8 +-
apps/razers/razers.h | 10 +-
apps/razers/razers_matepairs.h | 10 +-
apps/razers/razers_spliced.h | 12 +-
apps/razers/readSimulator.h | 2 +-
apps/razers/tests/run_tests.py | 7 +
apps/razers3/CMakeLists.txt | 2 +-
apps/razers3/README | 16 +-
apps/razers3/razers.h | 30 +-
apps/razers3/razers_match_filter.h | 4 +-
apps/razers3/razers_matepairs.h | 10 +-
apps/razers3/razers_matepairs_parallel.h | 10 +-
apps/razers3/razers_paired_match_filter.h | 4 +-
apps/razers3/razers_parallel.h | 14 +-
apps/razers3/readSimulator.h | 2 +-
apps/rep_sep/CMakeLists.txt | 2 +-
apps/sak/CMakeLists.txt | 4 +-
apps/sak/sak.cpp | 12 +-
apps/sam2matrix/CMakeLists.txt | 2 +-
apps/samcat/CMakeLists.txt | 7 +-
apps/searchjoin/CMakeLists.txt | 16 +-
apps/searchjoin/db.h | 18 +-
apps/searchjoin/tests/run_tests.py | 6 +
apps/seqan_tcoffee/CMakeLists.txt | 2 +-
apps/seqan_tcoffee/README | 22 +-
apps/seqan_tcoffee/seqan_tcoffee.cpp | 37 +-
apps/seqan_tcoffee/tests/run_tests.py | 6 +
apps/seqcons2/CMakeLists.txt | 2 +-
apps/sgip/CMakeLists.txt | 2 +-
apps/sgip/sgip.cpp | 2 +-
apps/sgip/sgip_base.h | 4 +-
apps/snp_store/CMakeLists.txt | 2 +-
apps/snp_store/README | 12 +-
apps/snp_store/snp_store.cpp | 10 +-
apps/snp_store/snp_store.h | 6 +-
apps/splazers/CMakeLists.txt | 2 +-
apps/splazers/README | 15 +-
apps/splazers/outputFormat.h | 8 +-
apps/splazers/razers.h | 10 +-
apps/splazers/razers_matepairs.h | 8 +-
apps/splazers/razers_spliced.h | 24 +-
apps/splazers/readSimulator.h | 2 +-
apps/splazers/splazers.cpp | 1 +
apps/stellar/CMakeLists.txt | 2 +-
apps/stellar/README | 8 +-
apps/stellar/stellar.cpp | 6 +-
apps/stellar/stellar.h | 8 +-
apps/stellar/stellar_extension.h | 6 +-
apps/stellar/stellar_types.h | 4 +-
apps/tree_recon/CMakeLists.txt | 2 +-
apps/yara/CMakeLists.txt | 2 +-
apps/yara/bits_context.h | 2 +-
apps/yara/bits_matches.h | 4 +-
apps/yara/find_verifier.h | 18 +-
apps/yara/indexer.cpp | 8 +-
apps/yara/mapper.cpp | 8 +-
apps/yara/tests/run_tests.py | 6 +
debian/README.Debian | 24 +
debian/changelog | 155 ++
debian/clean | 1 +
debian/control | 6 +-
debian/generate_manpages | 11 +-
debian/patches/series | 2 +-
debian/patches/short-description | 34 -
debian/patches/skip-seqan-revision | 2 +-
debian/patches/skip-some-apps-on-some-archs | 84 +
debian/patches/spelling | 36 +-
debian/rules | 64 +-
debian/source/lintian-overrides | 8 +-
demos/blast/blast_in_lowlevel.cpp | 4 +-
demos/dox/bam_io/bam_file_in.cpp | 2 +-
demos/dox/index/find_repeats.cpp | 2 +-
demos/dox/statistics/build_markov_model.cpp | 3 +-
demos/dox/statistics/load_markov_model.cpp | 3 +-
demos/dox/store/store_example.cpp | 4 +-
demos/howto/custom_file_ending.fa.dat | 4 +
demos/howto/custom_file_endings.cpp | 76 +
demos/howto/custom_file_endings.cpp.stdout | 2 +
demos/tutorial/a_first_example/final_result.cpp | 22 +-
.../a_first_example/final_result.cpp.stdout | 13 +-
demos/tutorial/a_first_example/solution_1.cpp | 4 -
demos/tutorial/a_first_example/solution_2.cpp | 6 +-
.../tutorial/a_first_example/solution_2.cpp.stdout | 2 +-
demos/tutorial/a_first_example/solution_3.cpp | 6 +-
.../tutorial/a_first_example/solution_3.cpp.stdout | 2 +-
demos/tutorial/a_first_example/solution_4.cpp | 4 +-
.../tutorial/a_first_example/solution_4.cpp.stdout | 3 +-
.../solution_4_templateSubclassing.cpp | 2 -
demos/tutorial/a_first_example/solution_5.cpp | 10 +-
.../tutorial/a_first_example/solution_5.cpp.stdout | 4 +-
demos/tutorial/a_first_example/solution_6.cpp | 20 +-
.../tutorial/a_first_example/solution_6.cpp.stdout | 12 +-
demos/tutorial/blast_io/write_assignment.cpp | 3 +-
.../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/iterators/assignment_1_solution.cpp | 4 +-
demos/tutorial/sam_and_bam_io/base.cpp | 6 +-
demos/tutorial/sam_and_bam_io/example7.cpp.stdout | 6 +-
demos/tutorial/sequences/base.cpp | 2 +-
demos/tutorial/string_sets/example_iterators.cpp | 2 +-
demos/unassigned_or_unused/filter_sam.cpp | 2 +-
demos/unassigned_or_unused/sam2svg.cpp | 8 +-
.../tutorial_file_io/solution2.cpp | 61 -
.../tutorial_file_io/solution3.cpp | 72 -
.../stream_compression_formats.cpp | 12 +-
dox/CMakeLists.txt | 56 +-
include/seqan/align.h | 3 +
include/seqan/align/align_base.h | 13 +-
include/seqan/align/align_interface_wrapper.h | 55 +-
.../aligned_sequence_concept.h} | 49 +-
include/seqan/align/dp_algorithm_impl.h | 726 ++++-----
include/seqan/align/dp_align_simd_helper.h | 263 ++-
include/seqan/align/dp_cell.h | 114 +-
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 | 38 +-
.../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 | 379 +++--
include/seqan/align/dp_matrix_sparse.h | 38 +-
include/seqan/align/dp_meta_info.h | 2 +-
include/seqan/align/dp_profile.h | 297 +++-
include/seqan/align/dp_scout.h | 24 +-
include/seqan/align/dp_scout_simd.h | 572 +++++--
include/seqan/align/dp_setup.h | 86 +-
include/seqan/align/dp_trace_segment.h | 8 +-
include/seqan/align/dp_traceback_impl.h | 165 +-
include/seqan/align/evaluate_alignment.h | 2 +-
include/seqan/align/gaps_anchor.h | 10 +-
include/seqan/align/gaps_base.h | 8 +-
include/seqan/align/gaps_iterator_anchor.h | 4 +-
include/seqan/align/global_alignment_banded.h | 118 +-
.../align/global_alignment_myers_hirschberg_impl.h | 6 +-
include/seqan/align/global_alignment_myers_impl.h | 2 +-
include/seqan/align/global_alignment_unbanded.h | 134 +-
include/seqan/align/local_alignment_banded.h | 73 +-
.../local_alignment_banded_waterman_eggert_impl.h | 4 +-
include/seqan/align/local_alignment_unbanded.h | 109 +-
.../align/local_alignment_waterman_eggert_impl.h | 47 +-
include/seqan/align/matrix_base.h | 333 ++--
include/seqan/align_extend/align_extend.h | 14 +-
include/seqan/align_extend/align_extend_base.h | 16 +-
include/seqan/align_extend/dp_scout_xdrop.h | 27 +-
include/seqan/{bam_io.h => align_parallel.h} | 104 +-
.../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_profile/add_to_profile.h | 6 +-
include/seqan/align_split/align_split_interface.h | 61 +-
include/seqan/arg_parse/arg_parse_argument.h | 36 +-
include/seqan/arg_parse/arg_parse_version_check.h | 16 +-
include/seqan/arg_parse/tool_doc.h | 7 +
include/seqan/bam_io.h | 1 +
include/seqan/bam_io/bam_alignment_record.h | 59 +-
include/seqan/bam_io/bam_alignment_record_util.h | 2 +-
include/seqan/bam_io/bam_file.h | 2 +-
include/seqan/bam_io/bam_header_record.h | 4 +-
include/seqan/bam_io/bam_index_bai.h | 129 +-
include/seqan/bam_io/bam_sam_conversion.h | 13 +-
include/seqan/bam_io/bam_tags_dict.h | 3 +
include/seqan/bam_io/read_bam.h | 9 +-
include/seqan/bam_io/read_sam.h | 2 +-
include/seqan/basic.h | 3 -
include/seqan/basic/allocator_interface.h | 40 +-
include/seqan/basic/alphabet_adapt_builtins.h | 13 +-
include/seqan/basic/alphabet_concept.h | 24 +-
include/seqan/basic/alphabet_math.h | 28 +-
include/seqan/basic/alphabet_residue.h | 11 +
include/seqan/basic/alphabet_simple_type.h | 90 +-
include/seqan/basic/array_construct_destruct.h | 4 +-
include/seqan/basic/basic_exception.h | 2 +-
include/seqan/basic/basic_simd_vector.h | 1671 -------------------
include/seqan/basic/basic_stream.h | 29 +-
include/seqan/basic/debug_test_system.h | 15 +-
include/seqan/basic/fundamental_concepts.h | 32 +-
include/seqan/basic/fundamental_metafunctions.h | 20 +-
include/seqan/basic/fundamental_tags.h | 2 +-
include/seqan/basic/fundamental_transport.h | 4 +-
include/seqan/basic/holder_tristate.h | 6 +-
include/seqan/basic/iterator_adaptor.h | 12 +-
include/seqan/basic/iterator_interface.h | 14 +-
include/seqan/basic/iterator_range.h | 30 +-
include/seqan/basic/math_log_space_value.h | 2 +-
include/seqan/basic/pair_bit_compressed.h | 17 +-
include/seqan/basic/pair_packed.h | 35 +-
include/seqan/basic/profiling.h | 42 +-
include/seqan/basic/proxy_base.h | 4 +-
include/seqan/bed_io/bed_record.h | 4 +-
include/seqan/blast/blast_statistics.h | 23 +-
include/seqan/consensus/consensus_base.h | 2 +-
include/seqan/consensus/consensus_library.h | 2 +-
include/seqan/consensus/consensus_realign.h | 2 +-
include/seqan/consensus/overlap_info_computation.h | 4 +-
include/seqan/consensus/overlapper.h | 2 +-
include/seqan/file/file_base.h | 1 +
include/seqan/file/file_page.h | 4 +-
include/seqan/find/find_bom.h | 1 +
include/seqan/find/find_multiple_bfam.h | 1 +
include/seqan/find/find_myers_ukkonen.h | 26 +-
include/seqan/find/find_score.h | 15 +-
include/seqan/find/find_shiftand.h | 4 +-
include/seqan/find/find_shiftor.h | 2 +-
include/seqan/find/find_wumanber.h | 4 +-
include/seqan/gff_io/gff_io_base.h | 15 +-
.../graph_algorithms/maximum_weighted_matching.h | 246 +++
include/seqan/graph_align/graph_impl_align.h | 8 +-
.../graph_msa/graph_align_tcoffee_guidetree.h | 2 +-
include/seqan/graph_types/graph_interface.h | 3 +-
include/seqan/index.h | 1 +
include/seqan/index/find2_backtracking.h | 4 +-
include/seqan/index/find2_index_approx.h | 642 ++++++++
include/seqan/index/find_backtracking.h | 2 +-
include/seqan/index/find_index_lambda.h | 4 +-
include/seqan/index/find_index_qgram.h | 2 +-
include/seqan/index/find_pigeonhole.h | 4 +-
include/seqan/index/index_base.h | 5 +-
include/seqan/index/index_bifm_stree.h | 3 +
include/seqan/index/index_childtab.h | 2 +-
include/seqan/index/index_esa_stree.h | 4 +-
include/seqan/index/index_fm_compressed_sa.h | 4 +-
include/seqan/index/index_fm_lf_table.h | 75 +-
.../seqan/index/index_fm_rank_dictionary_base.h | 88 +-
.../seqan/index/index_fm_rank_dictionary_levels.h | 10 -
include/seqan/index/index_fm_rank_dictionary_wt.h | 57 +-
include/seqan/index/index_fm_stree.h | 17 +-
include/seqan/index/index_pizzachili.h | 4 +
include/seqan/index/index_qgram.h | 12 +-
include/seqan/index/index_sa_bwtwalk.h | 20 +-
include/seqan/index/index_sa_lss.h | 4 +-
include/seqan/index/index_sa_stree.h | 6 +-
include/seqan/index/index_sa_truncated.h | 8 +-
include/seqan/index/index_wotd.h | 8 +-
include/seqan/index/shape_threshold.h | 2 +-
include/seqan/journaled_string_tree/delta_map.h | 4 +-
.../journaled_string_tree/delta_map_iterator.h | 4 +-
.../journaled_string_tree_impl.h | 2 +-
.../journaled_string_tree_traverser.h | 12 +
.../journaled_string_tree_traverser_util.h | 14 +-
include/seqan/math/math_rational.h | 6 +-
include/seqan/misc/interval_tree.h | 12 +-
include/seqan/misc/name_store_cache.h | 25 +-
include/seqan/modifier/modifier_padding.h | 67 +-
include/seqan/modifier/modifier_view.h | 4 +-
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_lock.h | 2 +
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/parse_lm/local_match_store.h | 22 +-
include/seqan/pipe/pipe_sampler.h | 2 +-
include/seqan/pipe/pipe_source.h | 2 +-
include/seqan/pipe/pool_base.h | 8 +-
include/seqan/platform.h | 112 +-
include/seqan/realign/realign_base.h | 10 +-
include/seqan/reduced_aminoacid.h | 17 +-
.../reduced_aminoacid_buchfink11_base.h} | 89 +-
.../reduced_aminoacid_buchfink11_tables.h | 155 ++
.../reduced_aminoacid_cannata10_base.h} | 86 +-
.../reduced_aminoacid_cannata10_tables.h | 154 ++
.../reduced_aminoacid_li10_base.h} | 86 +-
.../reduced_aminoacid_li10_tables.h | 154 ++
.../reduced_aminoacid_murphy5_base.h} | 81 +-
.../reduced_aminoacid_murphy5_tables.h | 149 ++
.../reduced_aminoacid_solis10_base.h} | 86 +-
.../reduced_aminoacid_solis10_tables.h | 154 ++
include/seqan/rna_io/rna_record.h | 15 +-
include/seqan/score.h | 1 +
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 | 75 +-
include/seqan/seeds/banded_chain_alignment_impl.h | 304 ++--
.../seqan/seeds/banded_chain_alignment_profile.h | 24 +-
.../seqan/seeds/banded_chain_alignment_traceback.h | 34 +-
include/seqan/seeds/seeds_extension.h | 4 +-
include/seqan/seeds/seeds_global_chaining.h | 166 +-
include/seqan/seq_io/bam_sam.h | 5 +-
include/seqan/seq_io/fasta_fastq.h | 12 +-
include/seqan/seq_io/read_embl.h | 6 +-
include/seqan/seq_io/read_genbank.h | 6 +-
include/seqan/seq_io/sequence_file.h | 6 +-
include/seqan/sequence/adapt_stl_container.h | 3 +-
include/seqan/sequence/sequence_forwards.h | 3 +
include/seqan/sequence/string_alloc.h | 22 +-
include/seqan/sequence/string_base.h | 24 +
include/seqan/sequence/string_cstyle.h | 3 +-
include/seqan/sequence/string_packed.h | 12 +-
include/seqan/sequence/string_packed_old.h | 2 +-
include/seqan/sequence/string_set_base.h | 5 +-
include/seqan/sequence/string_set_concat_direct.h | 6 +-
include/seqan/sequence/string_set_owner.h | 10 +-
include/seqan/simd.h | 143 ++
include/seqan/simd/simd_base.h | 390 +++++
include/seqan/simd/simd_base_seqan_impl.h | 154 ++
include/seqan/simd/simd_base_seqan_impl_avx2.h | 1492 +++++++++++++++++
include/seqan/simd/simd_base_seqan_impl_avx512.h | 284 ++++
include/seqan/simd/simd_base_seqan_impl_sse4.2.h | 1053 ++++++++++++
include/seqan/simd/simd_base_seqan_interface.h | 392 +++++
include/seqan/simd/simd_base_umesimd_impl.h | 655 ++++++++
include/seqan/statistics/statistics_markov_model.h | 2 +-
include/seqan/store/store_align.h | 4 +-
include/seqan/store/store_all.h | 54 +-
include/seqan/store/store_annotation.h | 4 +-
include/seqan/store/store_contig.h | 6 +-
include/seqan/store/store_io_sam.h | 8 +-
include/seqan/store/store_io_ucsc.h | 2 +-
include/seqan/store/store_matepair.h | 2 +-
include/seqan/store/store_read.h | 2 +-
include/seqan/stream.h | 6 +
include/seqan/stream/file_stream.h | 10 +-
include/seqan/stream/formatted_file.h | 24 +
include/seqan/stream/iostream_bgzf.h | 31 +-
include/seqan/stream/iter_stream.h | 184 ++-
include/seqan/stream/lexical_cast.h | 8 +-
include/seqan/stream/stream_compressor.h | 32 +-
include/seqan/stream/tokenization.h | 30 +-
include/seqan/stream/virtual_stream.h | 13 +-
include/seqan/system/file_async.h | 13 +-
include/seqan/tabix_io/tabix_index_tbi.h | 10 +-
include/seqan/translation/translation.h | 12 +-
include/seqan/vcf_io/read_vcf.h | 126 +-
include/seqan/version.h | 4 +-
.../Infrastructure/Use/CustomBuildSystem.rst | 40 +
.../source/Infrastructure/Use/FindSeqAnCMake.rst | 24 +
manual/source/Infrastructure/Use/Install.rst | 42 +-
.../PatternMatching/OptimalSearchSchemes.rst | 72 +
.../Tutorial/Algorithms/PatternMatching/index.rst | 2 +
.../DataStructures/Indices/StringIndices.rst | 16 +
.../DataStructures/Sequence/StringsAndSegments.rst | 2 +-
.../Tutorial/GettingStarted/AFirstExample.rst | 34 +-
.../GettingStarted/BackgroundAndMotivation.rst | 4 +-
.../Tutorial/HowTo/Recipes/CustomFileEndings.rst | 89 +
manual/source/seqan.bib | 11 -
tests/align/CMakeLists.txt | 51 +-
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 | 96 +-
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_cell.h | 2 +-
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} | 26 +-
.../test_align_parallel_data_structures.cpp} | 45 +-
.../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} | 85 +-
.../test_align_wavefront_intermediate_dp_result.h | 121 ++
.../test_align_wavefront_task_scheduler.h} | 99 +-
tests/arg_parse/test_arg_parse.cpp | 1 +
tests/arg_parse/test_arg_parse_argument.h | 28 +
tests/arg_parse/test_arg_parse_ctd_support.h | 3 +-
tests/bam_io/test_bam_file.h | 26 +-
tests/bam_io/test_bam_index.h | 17 +-
tests/bam_io/test_bam_io.cpp | 2 +-
tests/bam_io/test_bam_sam_conversion.h | 11 +
tests/bam_io/test_read_bam.h | 10 +-
tests/bam_io/test_write_bam.h | 6 +-
tests/basic/CMakeLists.txt | 7 -
tests/basic/test_basic.cpp | 1 -
tests/basic/test_basic_aggregate.h | 5 +-
tests/basic/test_basic_alphabet.cpp | 6 +-
tests/basic/test_basic_alphabet.h | 50 +-
tests/basic/test_basic_alphabet_adapt_builtins.h | 199 ---
tests/basic/test_basic_alphabet_math.h | 29 +-
tests/basic/test_basic_alphabet_residue.h | 74 +-
tests/basic/test_basic_concept.cpp | 4 +-
tests/basic/test_basic_concepts.h | 39 +
tests/basic/test_basic_exception.h | 6 +-
tests/basic/test_basic_iterator.h | 2 +-
tests/basic/test_basic_simd_vector.h | 155 --
tests/bed_io/test_bed_io.cpp | 8 +-
tests/blast/test_blast_input.h | 8 +-
tests/blast/test_blast_output.h | 2 +-
tests/consensus/test_consensus.h | 27 +-
tests/consensus/test_consensus_realign.h | 5 +-
tests/gff_io/test_gff_io.h | 37 +-
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 | 16 +-
tests/index/test_index_creation.h | 6 +-
tests/index/test_index_fm_rank_dictionary.cpp | 7 +-
tests/index/test_index_helpers.h | 8 +-
tests/index/test_index_stree_iterators.cpp | 1 +
tests/index/test_qgram_index.h | 23 +-
tests/index/test_sa_bwtwalk.h | 2 +-
tests/index/test_stree_iterators.h | 18 +
tests/journaled_string_tree/test_delta_map.h | 14 +-
.../test_journaled_string_tree.h | 2 +-
.../test_journaled_string_tree_traverser.cpp | 1 +
.../test_journaled_string_tree_traverser.h | 16 +
tests/misc/test_misc.cpp | 6 +-
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/parse_lm/test_parse_lm.h | 2 +-
tests/reduced_aminoacid/test_reduced_aminoacid.cpp | 5 +
tests/reduced_aminoacid/test_reduced_aminoacid.h | 95 ++
tests/rna_io/CMakeLists.txt | 4 +-
tests/roi_io/test_roi_io.cpp | 8 +-
tests/score/test_score.cpp | 9 +-
tests/seeds/test_align_banded_chain_impl.cpp | 2 +-
tests/seeds/test_seeds_global_chaining.cpp | 26 +
tests/seq_io/test_fai_index.h | 24 +-
tests/seq_io/test_sequence_file.h | 36 +-
tests/sequence/test_sequence.h | 53 +-
tests/sequence/test_string_packed_extension.h | 4 +-
tests/sequence/test_string_set.h | 67 +-
tests/{rna_io => simd}/CMakeLists.txt | 30 +-
.../test_simd_vector.cpp} | 28 +-
tests/simd/test_simd_vector.h | 979 +++++++++++
tests/statistics/test_statistics_base.h | 3 +-
tests/store/test_store_io.h | 92 +-
tests/store/test_store_io_bam.h | 10 +-
tests/stream/test_stream_lexical_cast.h | 4 +-
tests/stream/test_stream_tokenization.h | 60 +-
tests/stream/test_stream_virtual_stream.h | 15 +-
tests/tabix_io/test_tabix_io.h | 11 +-
tests/translation/test_translation.h | 41 +-
tests/ucsc_io/test_ucsc_io.cpp | 24 +-
tests/vcf_io/example_records_with_errors.vcf | 5 +-
tests/vcf_io/test_vcf_io.h | 46 +-
util/cmake/FindSDE.cmake | 81 +
util/cmake/FindUmesimd.cmake | 65 +
util/cmake/SeqAnBuildSystem.cmake | 101 +-
util/cmake/SeqAnContribs.cmake | 113 +-
util/cmake/SeqAnSimdUtility.cmake | 647 ++++++++
util/cmake/seqan-config.cmake | 31 +-
util/pkgconfig/seqan.pc.in | 4 +-
util/py_lib/CMakeLists.txt | 5 +
util/skel/app_template/CMakeLists.txt | 2 +-
util/travis/linux-cibuild.cmake | 1 -
util/travis/linux-cibuild.sh | 5 +
539 files changed, 25905 insertions(+), 11231 deletions(-)
diff --cc debian/changelog
index a0976d7,e539765..e646631
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,21 -1,158 +1,176 @@@
+ seqan2 (2.4.0~rc2+dfsg-1) experimental; urgency=medium
+
+ * Testing upstream's 3rd formal release candidate for 2.4.0
+ * debian/rules: use --max-parallel to more cleanly limit parallel building
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 31 Jan 2018 22:23:03 -0800
+
+ seqan2 (2.4.0~rc1+dfsg-2) experimental; urgency=medium
+
+ * debian/rules: Drop amd64, mips, mipsel to -j3 to save memory
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 31 Jan 2018 04:16:59 -0800
+
+ seqan2 (2.4.0~rc1+dfsg-1) experimental; urgency=medium
+
+ * Testing upstream's 2nd formal release candidate for 2.4.0
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 30 Jan 2018 03:00:53 -0800
+
+ seqan2 (2.4.0~rc0+dfsg-1) experimental; urgency=medium
+
+ * Testing upstream's formal release candidate
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 26 Jan 2018 10:14:15 -0800
+
+ seqan2 (2.3.2.001platform-issues10-6f85721+dfsg-2) experimental; urgency=medium
+
+ * enable asyncio on all archs as a test
+ * disable parallel building on powerpcspe
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 04 Jan 2018 05:11:43 -0800
+
+ seqan2 (2.3.2.001platform-issues10-6f85721+dfsg-1) experimental; urgency=medium
+
+ * Hopefully final update from upstream :-)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 03 Jan 2018 09:27:33 -0800
+
+ seqan2 (2.3.2.000platform-issues9-028fd79+dfsg-1) experimental; urgency=medium
+
+ * Another update from upstream
+ * debian/rules: build flags simplification:
+ - use DEB_*_MAINT_APPEND
+ - pass -DNDEBUG -O3 as per upstream
+ - drop -DSEQAN_BUILD_SYSTEM=DEVELOP as that is the default
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 22 Dec 2017 00:03:51 -0800
+
+ seqan2 (2.3.2.000platform-issues8-6f85721+dfsg-2) experimental; urgency=medium
+
+ * Force rebuild
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 14 Dec 2017 01:51:28 -0800
+
+ seqan2 (2.3.2.000platform-issues8-6f85721+dfsg-1) experimental; urgency=medium
+
+ * Another update from upstream
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Fri, 08 Dec 2017 04:41:18 -0800
+
+ seqan2 (2.3.2.000platform-issues7-41f58c3+dfsg-2) experimental; urgency=medium
+
+ [ Andreas Tille ]
+ * Work around missing dir in indep-only builds
+ Closes: #882169
+
+ [ Michael R. Crusoe ]
+ * Cleanup from not pushing my changes
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 06 Dec 2017 05:28:59 -0800
+
+ seqan2 (2.3.2.000platform-issues7-41f58c3+dfsg-1) experimental; urgency=medium
+
+ * Another update from upstream
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 21 Nov 2017 22:19:27 -0800
+
+ seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-3) experimental; urgency=medium
+
+ * Typo fix
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 18 Nov 2017 06:19:44 -0800
+
+ seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-2) experimental; urgency=medium
+
+ * Now try -O3 everywhere
+ * Remove the sparc64 test code
+ * Delete symlinks for apps that are skipped for a particular architecture
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 18 Nov 2017 04:50:55 -0800
+
+ seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-1) experimental; urgency=medium
+
+ * Skip yara on kfreebsd-i386
+ * Try out -O2 on archs that had been previously -O1
+ * Fix typo in bam2roi help text
+ * From upstream: another round of changes for the problems that affect
+ all big endian.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 11 Nov 2017 05:44:36 -0800
+
+ seqan2 (2.3.2.000platform-issues5-86390dc+dfsg-1) experimental; urgency=medium
+
+ * Another update from upstream including a tweak to sparc64
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 08 Nov 2017 07:03:25 -0800
+
+ seqan2 (2.3.2.000platform-issues4-fba8744+dfsg-1) experimental; urgency=medium
+
+ * Another refresh from upstream's branch
+ * Skip yara on armel, as well.
+ * d/control: declare seqan2 can be built without root, R³:no.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 06 Nov 2017 12:15:11 -0800
+
+ seqan2 (2.3.2.000platform-issues3-1d438c8+dfsg-2) experimental; urgency=medium
+
+ * Skip yara on armhf & sh4.
+ * Disable parallel building on armel
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 04 Nov 2017 02:09:12 -0700
+
+ seqan2 (2.3.2.000platform-issues3-1d438c8+dfsg-1) experimental; urgency=medium
+
+ * require tests to pass everywhere
+ * skip the razers{3,} and yara apps on mips{el,}
+ * restore parallel build blocking only for armhf, sh4, and kfreebsd*
+ * Another refresh from upstream, this time focusing on bam files
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 02 Nov 2017 11:41:21 -0700
+
+ seqan2 (2.3.2.000platform-issues2-206d1f7+dfsg-1) experimental; urgency=medium
+
+ * Typo for CXXFLAGS: -O1 instead of -01
+ * Another refresh from upstream in response to errors discovered via the
+ Debian build machines.
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 26 Oct 2017 08:48:11 -0700
+
+ seqan2 (2.3.2.000platform-issues1-66a8baf+dfsg-1) experimental; urgency=medium
+
+ * Refresh from upstream with additional fixes
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Wed, 25 Oct 2017 04:08:29 -0700
+
+ seqan2 (2.3.2.000platform-issues0-8ae7bc0+dfsg1-1) experimental; urgency=medium
+
+ * Patch for mips64el from bunk at debian.org (Closes: #878933)
+ * Temporarily enable all archs again
+ * Upstream source is pre-2.4.0, remove patches that they have merged:
+ short-description, spelling
+ * Cleaned up per-arch settings in debian/rules
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 23 Oct 2017 09:58:43 -0700
+
+seqan2 (2.3.2+dfsg2-4) unstable; urgency=medium
+
+ * Work around missing dir in indep-only builds
+ Closes: #882169
+ * d/rules: drop --parallel which is redundant for debhelper 10
+ * Do not generate manpages in arch indep builds (as done in
+ experimental branch)
+
+ -- Andreas Tille <tille at debian.org> Wed, 06 Dec 2017 11:11:59 +0100
+
+seqan2 (2.3.2+dfsg2-3) unstable; urgency=medium
+
+ * Patch for mips64el from bunk at debian.org (Closes: #878933)
+ * Cleaned up per-arch settings in debian/rules
+ * Disable parallel building on sh4
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Tue, 24 Oct 2017 04:56:12 -0700
+
seqan2 (2.3.2+dfsg2-2) unstable; urgency=medium
* As per upstream, disable async-io for many platforms
--
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