[med-svn] [seqan2] branch upstream updated (5f34962 -> 1fe74e5)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Mon Feb 5 16:06:04 UTC 2018
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository seqan2.
from 5f34962 New upstream version 2.3.2+dfsg2
adds 1fe74e5 New upstream version 2.4.0+dfsg
No new revisions were added by this update.
Summary of changes:
CHANGELOG.rst | 57 +-
CMakeLists.txt | 11 +-
LICENSE | 3 +-
README.rst | 15 +-
apps/alf/CMakeLists.txt | 4 +-
apps/alf/LICENSE | 2 +-
apps/alf/README | 8 +-
apps/alf/alf.cpp | 4 +-
apps/bs_tools/CMakeLists.txt | 4 +-
apps/bs_tools/LICENSE | 2 +-
apps/bs_tools/bisar.cpp | 2 +-
apps/bs_tools/bisar.h | 2 +-
apps/bs_tools/casbar.cpp | 12 +-
apps/bs_tools/casbar.h | 4 +-
apps/bs_tools/casbar_consensus_realign.h | 2 +-
apps/bs_tools/casbar_score.h | 42 +-
apps/bs_tools/four2three.cpp | 2 +-
apps/dfi/CMakeLists.txt | 4 +-
apps/dfi/README | 14 +-
apps/fiona/CMakeLists.txt | 4 +-
apps/fiona/compute_gain.cpp | 11 +-
apps/fiona/fiona.cpp | 36 +-
apps/fiona/index_qgram_parallel.h | 2 +-
apps/fx_tools/CMakeLists.txt | 4 +-
apps/fx_tools/LICENSE | 4 +-
apps/fx_tools/fx_bam_coverage.cpp | 2 +-
apps/fx_tools/fx_fastq_stats.cpp | 2 +-
apps/gustaf/CMakeLists.txt | 4 +-
apps/gustaf/LICENSE | 2 +-
apps/gustaf/README | 6 +-
apps/gustaf/create_stellarmatches_from_file.h | 8 +-
apps/gustaf/gustaf.cpp | 2 +-
apps/gustaf/gustaf_matepairs.h | 2 +-
apps/gustaf/join_mates.cpp | 2 +-
apps/gustaf/msplazer.h | 44 +-
apps/gustaf/msplazer_algorithms.h | 12 +-
apps/gustaf/msplazer_main.h | 2 +-
apps/gustaf/msplazer_out.h | 41 +-
apps/gustaf/msplazer_parse_options.h | 2 +-
apps/gustaf/stellar_routines.h | 2 +-
apps/insegt/CMakeLists.txt | 4 +-
apps/insegt/LICENSE | 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 | 4 +-
apps/mason2/LICENSE | 2 +-
apps/mason2/external_split_merge.cpp | 8 +-
apps/mason2/external_split_merge.h | 10 +-
apps/mason2/fragment_generation.h | 4 +-
apps/mason2/genomic_variants.cpp | 20 +-
apps/mason2/genomic_variants.h | 2 +-
apps/mason2/individual_genome.h | 2 +-
apps/mason2/mason_frag_sequencing.cpp | 2 +-
apps/mason2/mason_genome.cpp | 4 +-
apps/mason2/mason_materializer.cpp | 4 +-
apps/mason2/mason_methylation.cpp | 2 +-
apps/mason2/mason_options.cpp | 40 +-
apps/mason2/mason_options.h | 6 +-
apps/mason2/mason_simulator.cpp | 6 +-
apps/mason2/mason_splicing.cpp | 20 +-
apps/mason2/mason_tests.cpp | 2 +-
apps/mason2/mason_types.h | 2 +-
apps/mason2/mason_variator.cpp | 40 +-
apps/mason2/methylation_levels.cpp | 2 +-
apps/mason2/methylation_levels.h | 2 +-
apps/mason2/omp_wrapper.h | 2 +-
apps/mason2/sequencing.h | 2 +-
apps/mason2/simulate_454.cpp | 2 +-
apps/mason2/simulate_base.cpp | 2 +-
apps/mason2/simulate_genome.cpp | 2 +-
apps/mason2/simulate_genome.h | 2 +-
apps/mason2/simulate_illumina.cpp | 2 +-
apps/mason2/simulate_sanger.cpp | 2 +-
apps/mason2/variation_size_tsv.h | 2 +-
apps/mason2/vcf_materialization.cpp | 9 +-
apps/mason2/vcf_materialization.h | 2 +-
apps/micro_razers/CMakeLists.txt | 4 +-
apps/micro_razers/README | 14 +-
apps/micro_razers/micro_razers.cpp | 1 +
apps/ngs_roi/CMakeLists.txt | 11 +-
apps/ngs_roi/LICENSE | 2 +-
apps/ngs_roi/bam2roi.cpp | 2 +-
apps/ngs_roi/bam2roi.h | 2 +-
apps/ngs_roi/png_canvas.h | 2 +-
apps/ngs_roi/project_interval.cpp | 2 +-
apps/ngs_roi/project_interval.h | 2 +-
apps/ngs_roi/project_spliced.cpp | 8 +-
apps/ngs_roi/project_spliced.h | 2 +-
apps/ngs_roi/record_ext.h | 2 +-
apps/ngs_roi/roi_builder.cpp | 2 +-
apps/ngs_roi/roi_builder.h | 2 +-
apps/ngs_roi/roi_feature_projection.cpp | 4 +-
apps/ngs_roi/roi_plot_thumbnails.cpp | 2 +-
apps/pair_align/CMakeLists.txt | 9 +-
apps/pair_align/lib/pair_align_global.cpp | 2 +-
apps/pair_align/lib/pair_align_lcs.cpp | 2 +-
apps/pair_align/lib/pair_align_lib.cpp | 4 +-
apps/pair_align/lib/pair_align_lib.h | 2 +-
apps/pair_align/lib/pair_align_local.cpp | 2 +-
apps/param_chooser/CMakeLists.txt | 4 +-
apps/param_chooser/test_param_chooser.cpp | 2 +-
apps/rabema/CMakeLists.txt | 6 +-
apps/rabema/rabema_build_gold_standard.cpp | 14 +-
apps/rabema/rabema_evaluate.cpp | 28 +-
apps/rabema/ref_id_mapping.h | 6 +-
apps/rabema/sorting.h | 2 +-
apps/razers/CMakeLists.txt | 9 +-
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 | 4 +-
apps/razers3/README | 16 +-
apps/razers3/profile_timeline.h | 2 +-
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 | 4 +-
apps/sak/CMakeLists.txt | 6 +-
apps/sak/sak.cpp | 14 +-
apps/sam2matrix/CMakeLists.txt | 4 +-
apps/sam2matrix/LICENSE | 2 +-
apps/sam2matrix/sam2matrix.cpp | 2 +-
apps/samcat/CMakeLists.txt | 9 +-
apps/samcat/samcat.cpp | 2 +-
apps/searchjoin/CMakeLists.txt | 18 +-
apps/searchjoin/LICENSE | 2 +-
apps/searchjoin/db.h | 20 +-
apps/searchjoin/finder.h | 2 +-
apps/searchjoin/join.cpp | 2 +-
apps/searchjoin/search.cpp | 2 +-
apps/searchjoin/tests/run_tests.py | 6 +
apps/searchjoin/verifier.h | 2 +-
apps/searchjoin/writer.h | 2 +-
apps/seqan_tcoffee/CMakeLists.txt | 4 +-
apps/seqan_tcoffee/README | 22 +-
apps/seqan_tcoffee/seqan_tcoffee.cpp | 37 +-
apps/seqan_tcoffee/tests/run_tests.py | 6 +
apps/seqcons2/CMakeLists.txt | 4 +-
apps/seqcons2/LICENSE | 2 +-
apps/seqcons2/seqcons.cpp | 2 +-
apps/seqcons2/seqcons_app.cpp | 2 +-
apps/seqcons2/seqcons_app.h | 2 +-
apps/seqcons2/seqcons_options.cpp | 2 +-
apps/seqcons2/seqcons_options.h | 2 +-
apps/sgip/CMakeLists.txt | 4 +-
apps/sgip/sgip.cpp | 2 +-
apps/sgip/sgip_base.h | 4 +-
apps/snp_store/CMakeLists.txt | 4 +-
apps/snp_store/README | 12 +-
apps/snp_store/snp_store.cpp | 10 +-
apps/snp_store/snp_store.h | 6 +-
apps/splazers/CMakeLists.txt | 4 +-
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 | 4 +-
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 | 4 +-
apps/yara/CMakeLists.txt | 4 +-
apps/yara/LICENSE | 4 +-
apps/yara/README.rst | 2 +-
apps/yara/basic_alphabet.h | 2 +-
apps/yara/bits_bucket.h | 2 +-
apps/yara/bits_context.h | 4 +-
apps/yara/bits_hits.h | 2 +-
apps/yara/bits_matches.h | 6 +-
apps/yara/bits_reads.h | 2 +-
apps/yara/bits_seeds.h | 2 +-
apps/yara/file_pair.h | 2 +-
apps/yara/file_prefetched.h | 2 +-
apps/yara/find_extender.h | 2 +-
apps/yara/find_verifier.h | 20 +-
apps/yara/index_fm.h | 2 +-
apps/yara/indexer.cpp | 10 +-
apps/yara/mapper.cpp | 10 +-
apps/yara/mapper.h | 2 +-
apps/yara/mapper_aligner.h | 2 +-
apps/yara/mapper_classifier.h | 2 +-
apps/yara/mapper_collector.h | 2 +-
apps/yara/mapper_extender.h | 2 +-
apps/yara/mapper_filter.h | 2 +-
apps/yara/mapper_ranker.h | 2 +-
apps/yara/mapper_verifier.h | 2 +-
apps/yara/mapper_writer.h | 2 +-
apps/yara/misc_options.h | 2 +-
apps/yara/misc_tags.h | 2 +-
apps/yara/misc_timer.h | 2 +-
apps/yara/misc_types.h | 2 +-
apps/yara/store_seqs.h | 2 +-
apps/yara/tests/run_tests.py | 6 +
demos/LICENSE | 2 +-
demos/blast/blast_in_lowlevel.cpp | 4 +-
demos/dox/bam_io/bam_file_in.cpp | 2 +-
demos/dox/basic/enable_if.cpp | 2 +-
demos/dox/basic/metaprogramming_control.cpp | 2 +-
demos/dox/basic/metaprogramming_logic.cpp | 2 +-
demos/dox/basic/metaprogramming_math.cpp | 2 +-
demos/dox/basic/metaprogramming_switch.cpp | 2 +-
demos/dox/index/find_repeats.cpp | 2 +-
demos/dox/sequence/segment.cpp | 2 +-
demos/dox/sequence/string.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/howto/using_zip_iterator.cpp | 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 +-
.../generic_programming/template_subclassing.cpp | 2 +-
demos/tutorial/genome_annotations/base.cpp | 2 +-
demos/tutorial/indices/find2_index_approx.cpp | 57 +
demos/tutorial/indices/find2_index_approx.stdout | 23 +
demos/tutorial/iterators/assignment_1_solution.cpp | 4 +-
.../journaled_string_tree_base.cpp | 2 +-
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 +-
.../simple_rna_seq/genequant_assignment4.cpp | 2 +-
demos/tutorial/string_sets/example_iterators.cpp | 2 +-
demos/unassigned_or_unused/bam_library_size.cpp | 2 +-
.../unassigned_or_unused/bam_print_alignments.cpp | 2 +-
demos/unassigned_or_unused/bamutil.cpp | 2 +-
demos/unassigned_or_unused/benchmark_stream.cpp | 2 +-
.../benchmark_stream_write.cpp | 2 +-
demos/unassigned_or_unused/filter_sam.cpp | 2 +-
demos/unassigned_or_unused/parse_lm_stellar.cpp | 2 +-
demos/unassigned_or_unused/sam2svg.cpp | 8 +-
demos/unassigned_or_unused/sample_seqs.cpp | 2 +-
.../unassigned_or_unused/soft_to_hard_masking.cpp | 2 +-
.../tutorial_file_io/solution2.cpp | 61 -
.../tutorial_file_io/solution3.cpp | 72 -
.../stream_compression_formats.cpp | 12 +-
dox/CMakeLists.txt | 56 +-
include/seqan/LICENSE | 2 +-
include/seqan/align.h | 5 +-
include/seqan/align/align_base.h | 15 +-
include/seqan/align/align_cols.h | 2 +-
include/seqan/align/align_config.h | 2 +-
include/seqan/align/align_interface_wrapper.h | 57 +-
include/seqan/align/align_iterator_base.h | 2 +-
include/seqan/align/align_metafunctions.h | 2 +-
include/seqan/align/align_traceback.h | 2 +-
.../seqan/align/aligned_sequence_concept.h | 21 +-
include/seqan/align/alignment_algorithm_tags.h | 2 +-
include/seqan/align/alignment_operations.h | 2 +-
include/seqan/align/dp_algorithm_impl.h | 728 ++++-----
include/seqan/align/dp_align_simd_helper.h | 265 ++-
include/seqan/align/dp_band.h | 2 +-
include/seqan/align/dp_cell.h | 116 +-
include/seqan/align/dp_cell_affine.h | 37 +-
include/seqan/align/dp_cell_dynamic.h | 14 +-
include/seqan/align/dp_cell_linear.h | 2 +-
include/seqan/align/dp_context.h | 89 +-
include/seqan/align/dp_formula.h | 253 +--
include/seqan/align/dp_formula_affine.h | 765 +++------
include/seqan/align/dp_formula_dynamic.h | 379 +++--
include/seqan/align/dp_formula_linear.h | 350 ++--
include/seqan/align/dp_matrix.h | 324 ++--
include/seqan/align/dp_matrix_navigator.h | 40 +-
.../seqan/align/dp_matrix_navigator_score_matrix.h | 395 ++---
.../dp_matrix_navigator_score_matrix_sparse.h | 353 ++--
.../seqan/align/dp_matrix_navigator_trace_matrix.h | 381 +++--
include/seqan/align/dp_matrix_sparse.h | 40 +-
include/seqan/align/dp_meta_info.h | 4 +-
include/seqan/align/dp_profile.h | 299 ++--
include/seqan/align/dp_scout.h | 26 +-
include/seqan/align/dp_scout_simd.h | 574 +++++--
include/seqan/align/dp_setup.h | 88 +-
include/seqan/align/dp_trace_segment.h | 10 +-
include/seqan/align/dp_traceback_adaptor.h | 2 +-
include/seqan/align/dp_traceback_impl.h | 167 +-
include/seqan/align/evaluate_alignment.h | 4 +-
include/seqan/align/fragment.h | 2 +-
include/seqan/align/gap_anchor.h | 2 +-
include/seqan/align/gapped_value_type.h | 2 +-
include/seqan/align/gaps_anchor.h | 12 +-
include/seqan/align/gaps_array.h | 2 +-
include/seqan/align/gaps_base.h | 10 +-
include/seqan/align/gaps_iterator_anchor.h | 6 +-
include/seqan/align/gaps_iterator_array.h | 2 +-
include/seqan/align/gaps_iterator_base.h | 2 +-
include/seqan/align/global_alignment_banded.h | 120 +-
.../seqan/align/global_alignment_hirschberg_impl.h | 2 +-
.../align/global_alignment_myers_hirschberg_impl.h | 8 +-
include/seqan/align/global_alignment_myers_impl.h | 4 +-
include/seqan/align/global_alignment_specialized.h | 2 +-
include/seqan/align/global_alignment_unbanded.h | 136 +-
include/seqan/align/local_alignment_banded.h | 75 +-
.../local_alignment_banded_waterman_eggert_impl.h | 6 +-
include/seqan/align/local_alignment_enumeration.h | 2 +-
.../align/local_alignment_enumeration_banded.h | 2 +-
.../align/local_alignment_enumeration_unbanded.h | 2 +-
include/seqan/align/local_alignment_unbanded.h | 111 +-
.../align/local_alignment_waterman_eggert_impl.h | 49 +-
include/seqan/align/matrix_base.h | 335 ++--
include/seqan/align_extend.h | 2 +-
include/seqan/align_extend/align_extend.h | 16 +-
include/seqan/align_extend/align_extend_base.h | 18 +-
include/seqan/align_extend/dp_scout_xdrop.h | 29 +-
include/seqan/{bam_io.h => align_parallel.h} | 106 +-
.../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} | 92 +-
.../dp_traits.h} | 105 +-
.../align_parallel/parallel_align_interface.h | 366 +++++
.../wavefront_alignment_executor.h} | 63 +-
.../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} | 112 +-
include/seqan/align_parallel/wavefront_task.h | 365 +++++
.../wavefront_task_event.h} | 69 +-
.../seqan/align_parallel/wavefront_task_executor.h | 146 ++
.../wavefront_task_queue.h} | 126 +-
.../align_parallel/wavefront_task_scheduler.h | 218 +++
include/seqan/align_parallel/wavefront_task_util.h | 557 +++++++
include/seqan/align_profile.h | 2 +-
include/seqan/align_profile/add_to_profile.h | 8 +-
include/seqan/align_profile/score_profile_seq.h | 2 +-
include/seqan/align_split.h | 2 +-
include/seqan/align_split/align_split_interface.h | 63 +-
include/seqan/align_split/dp_scout_split.h | 2 +-
include/seqan/alignment_free.h | 2 +-
include/seqan/alignment_free/af_d2.h | 2 +-
include/seqan/alignment_free/af_d2star.h | 2 +-
include/seqan/alignment_free/af_d2z.h | 2 +-
include/seqan/alignment_free/af_n2.h | 2 +-
include/seqan/alignment_free/alignment_free_base.h | 2 +-
.../alignment_free/alignment_free_comparison.h | 2 +-
include/seqan/alignment_free/kmer_functions.h | 2 +-
include/seqan/arg_parse.h | 2 +-
include/seqan/arg_parse/arg_parse_argument.h | 38 +-
include/seqan/arg_parse/arg_parse_ctd_support.h | 2 +-
include/seqan/arg_parse/arg_parse_doc.h | 4 +-
include/seqan/arg_parse/arg_parse_exceptions.h | 2 +-
include/seqan/arg_parse/arg_parse_option.h | 2 +-
include/seqan/arg_parse/arg_parse_parse.h | 2 +-
include/seqan/arg_parse/arg_parse_type_support.h | 2 +-
include/seqan/arg_parse/arg_parse_version_check.h | 18 +-
include/seqan/arg_parse/argument_parser.h | 2 +-
include/seqan/arg_parse/tool_doc.h | 9 +-
include/seqan/arg_parse/xml_support.h | 2 +-
include/seqan/bam_io.h | 3 +-
include/seqan/bam_io/bam_alignment_record.h | 61 +-
include/seqan/bam_io/bam_alignment_record_util.h | 4 +-
include/seqan/bam_io/bam_file.h | 4 +-
include/seqan/bam_io/bam_header_record.h | 6 +-
include/seqan/bam_io/bam_index_bai.h | 133 +-
include/seqan/bam_io/bam_io_context.h | 2 +-
include/seqan/bam_io/bam_sam_conversion.h | 15 +-
include/seqan/bam_io/bam_scanner_cache.h | 2 +-
include/seqan/bam_io/bam_tags_dict.h | 5 +-
include/seqan/bam_io/cigar.h | 2 +-
include/seqan/bam_io/read_bam.h | 11 +-
include/seqan/bam_io/read_sam.h | 4 +-
include/seqan/bam_io/write_bam.h | 2 +-
include/seqan/bam_io/write_sam.h | 2 +-
include/seqan/basic.h | 5 +-
include/seqan/basic/aggregate_concept.h | 2 +-
include/seqan/basic/allocator_chunkpool.h | 2 +-
include/seqan/basic/allocator_interface.h | 42 +-
include/seqan/basic/allocator_multipool.h | 2 +-
include/seqan/basic/allocator_simple.h | 2 +-
include/seqan/basic/allocator_singlepool.h | 2 +-
include/seqan/basic/allocator_to_std.h | 2 +-
include/seqan/basic/alphabet_adapt_builtins.h | 15 +-
include/seqan/basic/alphabet_bio.h | 2 +-
include/seqan/basic/alphabet_concept.h | 26 +-
include/seqan/basic/alphabet_math.h | 30 +-
include/seqan/basic/alphabet_profile.h | 2 +-
include/seqan/basic/alphabet_qualities.h | 2 +-
include/seqan/basic/alphabet_residue.h | 13 +-
include/seqan/basic/alphabet_residue_tabs.h | 2 +-
include/seqan/basic/alphabet_simple_type.h | 92 +-
include/seqan/basic/alphabet_storage.h | 2 +-
include/seqan/basic/array_construct_destruct.h | 6 +-
include/seqan/basic/basic_aggregate.h | 2 +-
include/seqan/basic/basic_allocator.h | 2 +-
include/seqan/basic/basic_alphabet.h | 2 +-
include/seqan/basic/basic_concept.h | 2 +-
include/seqan/basic/basic_container.h | 2 +-
include/seqan/basic/basic_debug.h | 2 +-
include/seqan/basic/basic_exception.h | 4 +-
include/seqan/basic/basic_functors.h | 2 +-
include/seqan/basic/basic_fundamental.h | 2 +-
include/seqan/basic/basic_iterator.h | 2 +-
include/seqan/basic/basic_math.h | 2 +-
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include/seqan/basic/basic_parallelism.h | 2 +-
include/seqan/basic/basic_proxy.h | 2 +-
include/seqan/basic/basic_simd_vector.h | 1671 -------------------
include/seqan/basic/basic_smart_pointer.h | 2 +-
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include/seqan/graph_algorithms/kruskal.h | 2 +-
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include/seqan/graph_algorithms/path_growing.h | 2 +-
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include/seqan/graph_align.h | 2 +-
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include/seqan/graph_align/graph_impl_align.h | 10 +-
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include/seqan/graph_types.h | 2 +-
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include/seqan/graph_types/graph_interface.h | 5 +-
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include/seqan/index/find2_index.h | 2 +-
include/seqan/index/find2_index_approx.h | 642 ++++++++
include/seqan/index/find_backtracking.h | 4 +-
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include/seqan/index/index_fm_rank_dictionary_wt.h | 59 +-
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include/seqan/index/index_fm_sparse_string.h | 2 +-
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include/seqan/index/index_sa_bwtwalk.h | 22 +-
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include/seqan/index/index_shawarma.h | 2 +-
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include/seqan/index/index_skew3.h | 2 +-
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include/seqan/index/index_wotd.h | 10 +-
include/seqan/index/pipe_merger3.h | 2 +-
include/seqan/index/pipe_merger7.h | 2 +-
include/seqan/index/pizzachili_api.h | 2 +-
include/seqan/index/pump_extender3.h | 2 +-
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include/seqan/journaled_set/score_biaffine.h | 2 +-
include/seqan/journaled_string_tree.h | 2 +-
include/seqan/journaled_string_tree/delta_map.h | 6 +-
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include/seqan/journaled_string_tree/observable.h | 2 +-
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include/seqan/map.h | 2 +-
include/seqan/map/map_adapter_stl.h | 2 +-
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include/seqan/math/math_common_factor.h | 2 +-
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include/seqan/misc/memset.h | 2 +-
include/seqan/misc/name_store_cache.h | 27 +-
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include/seqan/modifier/modifier_alphabet.h | 2 +-
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include/seqan/modifier/modifier_cyclic_shape.h | 2 +-
include/seqan/modifier/modifier_functors.h | 2 +-
include/seqan/modifier/modifier_iterator.h | 2 +-
include/seqan/modifier/modifier_padding.h | 69 +-
include/seqan/modifier/modifier_position.h | 2 +-
include/seqan/modifier/modifier_reverse.h | 2 +-
include/seqan/modifier/modifier_shortcuts.h | 2 +-
include/seqan/modifier/modifier_string.h | 2 +-
include/seqan/modifier/modifier_view.h | 6 +-
include/seqan/parallel.h | 8 +-
include/seqan/parallel/enumerable_thread_local.h | 476 ++++++
.../parallel/enumerable_thread_local_iterator.h | 186 +++
include/seqan/parallel/parallel_algorithms.h | 9 +-
include/seqan/parallel/parallel_atomic_misc.h | 2 +-
.../seqan/parallel/parallel_atomic_primitives.h | 2 +-
include/seqan/parallel/parallel_lock.h | 4 +-
include/seqan/parallel/parallel_macros.h | 2 +-
include/seqan/parallel/parallel_queue.h | 26 +-
.../seqan/parallel/parallel_queue_suspendable.h | 18 +-
include/seqan/parallel/parallel_resource_pool.h | 2 +-
include/seqan/parallel/parallel_sequence.h | 2 +-
include/seqan/parallel/parallel_serializer.h | 2 +-
include/seqan/parallel/parallel_splitting.h | 2 +-
include/seqan/parallel/parallel_tags.h | 174 +-
include/seqan/parallel/parallel_thread_pool.h | 219 +++
include/seqan/parse_lm.h | 2 +-
include/seqan/parse_lm/local_match_store.h | 24 +-
include/seqan/parse_lm/parse_blastn_tabular.h | 2 +-
include/seqan/parse_lm/parse_lastz_general.h | 2 +-
include/seqan/parse_lm/parse_stellar_gff.h | 2 +-
include/seqan/pipe.h | 2 +-
include/seqan/pipe/pipe_base.h | 2 +-
include/seqan/pipe/pipe_caster.h | 2 +-
include/seqan/pipe/pipe_counter.h | 2 +-
include/seqan/pipe/pipe_echoer.h | 2 +-
include/seqan/pipe/pipe_edit_environment.h | 2 +-
include/seqan/pipe/pipe_filter.h | 2 +-
include/seqan/pipe/pipe_iterator.h | 2 +-
include/seqan/pipe/pipe_joiner.h | 2 +-
include/seqan/pipe/pipe_namer.h | 2 +-
include/seqan/pipe/pipe_sampler.h | 4 +-
include/seqan/pipe/pipe_shifter.h | 2 +-
include/seqan/pipe/pipe_source.h | 4 +-
include/seqan/pipe/pipe_tupler.h | 2 +-
include/seqan/pipe/pool_base.h | 10 +-
include/seqan/pipe/pool_mapper.h | 2 +-
include/seqan/pipe/pool_sorter.h | 2 +-
include/seqan/platform.h | 114 +-
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include/seqan/random/random_base.h | 2 +-
include/seqan/random/random_beta.h | 2 +-
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include/seqan/realign/realign_base.h | 12 +-
include/seqan/realign/realign_helper_functions.h | 2 +-
include/seqan/reduced_aminoacid.h | 17 +-
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..._base.h => reduced_aminoacid_buchfink11_base.h} | 49 +-
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.../reduced_aminoacid_cluster_red_base.h | 2 +-
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.../reduced_aminoacid_murphy10_base.h | 2 +-
.../reduced_aminoacid_murphy10_tables.h | 2 +-
...y10_base.h => reduced_aminoacid_murphy5_base.h} | 45 +-
...tables.h => reduced_aminoacid_murphy5_tables.h} | 57 +-
...y10_base.h => reduced_aminoacid_solis10_base.h} | 50 +-
...tables.h => reduced_aminoacid_solis10_tables.h} | 56 +-
include/seqan/rna_io.h | 2 +-
include/seqan/rna_io/bpseq_read_write.h | 2 +-
include/seqan/rna_io/connect_read_write.h | 2 +-
include/seqan/rna_io/dot_bracket_read_write.h | 2 +-
include/seqan/rna_io/ebpseq_read_write.h | 2 +-
include/seqan/rna_io/rna_header.h | 2 +-
include/seqan/rna_io/rna_io_context.h | 2 +-
include/seqan/rna_io/rna_record.h | 17 +-
include/seqan/rna_io/rna_struct_file.h | 2 +-
include/seqan/rna_io/stockholm_read_write.h | 2 +-
include/seqan/rna_io/vienna_read_write.h | 2 +-
include/seqan/roi_io.h | 2 +-
include/seqan/roi_io/read_roi.h | 2 +-
include/seqan/roi_io/roi_file.h | 2 +-
include/seqan/roi_io/roi_io_context.h | 2 +-
include/seqan/roi_io/roi_record.h | 2 +-
include/seqan/roi_io/write_roi.h | 2 +-
include/seqan/score.h | 3 +-
include/seqan/score/score_base.h | 2 +-
include/seqan/score/score_edit.h | 2 +-
include/seqan/score/score_matrix.h | 10 +-
include/seqan/score/score_matrix_data.h | 74 +-
include/seqan/score/score_matrix_dyn.h | 21 +-
include/seqan/score/score_matrix_io.h | 2 +-
include/seqan/score/score_simd_wrapper.h | 77 +-
include/seqan/score/score_simple.h | 2 +-
include/seqan/seeds.h | 2 +-
include/seqan/seeds/banded_chain_alignment.h | 2 +-
include/seqan/seeds/banded_chain_alignment_impl.h | 306 ++--
.../seqan/seeds/banded_chain_alignment_profile.h | 26 +-
include/seqan/seeds/banded_chain_alignment_scout.h | 2 +-
.../seqan/seeds/banded_chain_alignment_traceback.h | 36 +-
include/seqan/seeds/basic_iter_indirect.h | 2 +-
include/seqan/seeds/seeds_base.h | 2 +-
include/seqan/seeds/seeds_combination.h | 2 +-
include/seqan/seeds/seeds_extension.h | 6 +-
include/seqan/seeds/seeds_global_chaining.h | 168 +-
include/seqan/seeds/seeds_global_chaining_base.h | 2 +-
.../seqan/seeds/seeds_global_chaining_gusfield.h | 2 +-
include/seqan/seeds/seeds_seed_base.h | 2 +-
include/seqan/seeds/seeds_seed_chained.h | 2 +-
include/seqan/seeds/seeds_seed_diagonal.h | 2 +-
include/seqan/seeds/seeds_seed_set_base.h | 2 +-
include/seqan/seeds/seeds_seed_set_non_scored.h | 2 +-
include/seqan/seeds/seeds_seed_set_scored.h | 2 +-
include/seqan/seeds/seeds_seed_set_unordered.h | 2 +-
include/seqan/seeds/seeds_seed_simple.h | 2 +-
include/seqan/seq_io.h | 2 +-
include/seqan/seq_io/bam_sam.h | 7 +-
include/seqan/seq_io/fai_index.h | 2 +-
include/seqan/seq_io/fasta_fastq.h | 14 +-
include/seqan/seq_io/genomic_region.h | 2 +-
include/seqan/seq_io/read_embl.h | 8 +-
include/seqan/seq_io/read_genbank.h | 8 +-
include/seqan/seq_io/sequence_file.h | 8 +-
include/seqan/sequence.h | 2 +-
include/seqan/sequence/adapt_array_pointer.h | 2 +-
include/seqan/sequence/adapt_stl_container.h | 5 +-
include/seqan/sequence/container_view_zip.h | 2 +-
include/seqan/sequence/iter_concat_virtual.h | 2 +-
include/seqan/sequence/segment_base.h | 2 +-
include/seqan/sequence/segment_infix.h | 2 +-
include/seqan/sequence/segment_prefix.h | 2 +-
include/seqan/sequence/segment_suffix.h | 2 +-
include/seqan/sequence/segment_utils.h | 2 +-
include/seqan/sequence/sequence_concatenator.h | 2 +-
include/seqan/sequence/sequence_forwards.h | 5 +-
include/seqan/sequence/sequence_interface.h | 2 +-
include/seqan/sequence/sequence_lexical.h | 2 +-
include/seqan/sequence/sequence_shortcuts.h | 2 +-
include/seqan/sequence/string_alloc.h | 24 +-
include/seqan/sequence/string_array.h | 2 +-
include/seqan/sequence/string_base.h | 26 +-
include/seqan/sequence/string_block.h | 2 +-
include/seqan/sequence/string_cstyle.h | 5 +-
include/seqan/sequence/string_packed.h | 14 +-
include/seqan/sequence/string_packed_old.h | 4 +-
include/seqan/sequence/string_set_base.h | 7 +-
include/seqan/sequence/string_set_concat_direct.h | 8 +-
.../seqan/sequence/string_set_dependent_generous.h | 2 +-
.../seqan/sequence/string_set_dependent_tight.h | 2 +-
include/seqan/sequence/string_set_owner.h | 12 +-
include/seqan/sequence/string_set_segment.h | 2 +-
include/seqan/sequence_journaled.h | 2 +-
.../journal_entries_sorted_array.h | 2 +-
include/seqan/sequence_journaled/journal_entry.h | 2 +-
.../seqan/sequence_journaled/sequence_journaled.h | 2 +-
.../sequence_journaled_iterator.h | 2 +-
.../sequence_journaled_iterator_fast.h | 2 +-
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/simple_intervals_io.h | 2 +-
.../simple_intervals_io/simple_intervals_file.h | 2 +-
.../simple_intervals_io/simple_intervals_io.h | 2 +-
include/seqan/statistics.h | 2 +-
include/seqan/statistics/statistics_base.h | 2 +-
include/seqan/statistics/statistics_markov_model.h | 4 +-
include/seqan/store.h | 2 +-
include/seqan/store/store_align.h | 6 +-
include/seqan/store/store_align_intervals.h | 2 +-
include/seqan/store/store_all.h | 56 +-
include/seqan/store/store_annotation.h | 6 +-
include/seqan/store/store_base.h | 2 +-
include/seqan/store/store_contig.h | 8 +-
include/seqan/store/store_intervaltree.h | 2 +-
include/seqan/store/store_io.h | 2 +-
include/seqan/store/store_io_gff.h | 2 +-
include/seqan/store/store_io_sam.h | 10 +-
include/seqan/store/store_io_ucsc.h | 4 +-
include/seqan/store/store_library.h | 2 +-
include/seqan/store/store_matepair.h | 4 +-
include/seqan/store/store_read.h | 4 +-
include/seqan/stream.h | 8 +-
include/seqan/stream/adapt_ios.h | 2 +-
include/seqan/stream/buffered_stream.h | 2 +-
include/seqan/stream/file_stream.h | 12 +-
include/seqan/stream/formatted_file.h | 26 +-
include/seqan/stream/guess_format.h | 2 +-
include/seqan/stream/iostream_bgzf.h | 31 +-
include/seqan/stream/iter_stream.h | 186 ++-
include/seqan/stream/lexical_cast.h | 10 +-
include/seqan/stream/stream_base.h | 2 +-
include/seqan/stream/stream_compressor.h | 34 +-
include/seqan/stream/tokenization.h | 32 +-
include/seqan/stream/virtual_stream.h | 15 +-
include/seqan/system.h | 2 +-
include/seqan/system/file_async.h | 15 +-
include/seqan/system/file_directory.h | 2 +-
include/seqan/system/file_forwards.h | 2 +-
include/seqan/system/file_sync.h | 2 +-
include/seqan/system/system_base.h | 2 +-
include/seqan/system/system_event_win.h | 2 +-
include/seqan/system/system_forwards.h | 2 +-
include/seqan/tabix_io.h | 2 +-
include/seqan/tabix_io/tabix_index_tbi.h | 12 +-
include/seqan/translation.h | 2 +-
include/seqan/translation/translation.h | 14 +-
include/seqan/translation/translation_tables.h | 2 +-
include/seqan/ucsc_io.h | 2 +-
include/seqan/ucsc_io/ucsc_file.h | 2 +-
include/seqan/ucsc_io/ucsc_io.h | 2 +-
include/seqan/ucsc_io/ucsc_record.h | 2 +-
include/seqan/vcf_io.h | 2 +-
include/seqan/vcf_io/read_vcf.h | 128 +-
include/seqan/vcf_io/vcf_file.h | 2 +-
include/seqan/vcf_io/vcf_header.h | 2 +-
include/seqan/vcf_io/vcf_header_record.h | 2 +-
include/seqan/vcf_io/vcf_io_context.h | 2 +-
include/seqan/vcf_io/vcf_record.h | 2 +-
include/seqan/vcf_io/write_vcf.h | 2 +-
include/seqan/version.h | 6 +-
.../HowTo/GenerateSeqAnKnimeNodes/knime_node.rst | 2 +-
.../source/Infrastructure/Contribute/StyleCpp.rst | 6 +-
.../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 +-
.../GettingStarted/ParsingCommandLineArguments.rst | 2 +-
.../Tutorial/HowTo/Recipes/CustomFileEndings.rst | 89 +
manual/source/seqan.bib | 11 -
tests/align/CMakeLists.txt | 51 +-
tests/align/test_align.cpp | 16 +-
tests/align/test_align_align.h | 2 +-
tests/align/test_align_alignment_operations.h | 2 +-
tests/align/test_align_fragment.h | 2 +-
tests/align/test_align_gaps.h | 2 +-
tests/align/test_align_gaps_iterator.h | 2 +-
tests/align/test_align_global_alignment.h | 2 +-
tests/align/test_align_global_alignment_banded.h | 2 +-
tests/align/test_align_global_alignment_score.h | 2 +-
.../test_align_global_alignment_specialized.h | 2 +-
tests/align/test_align_local_alignment.h | 2 +-
tests/align/test_align_matrix.h | 2 +-
tests/align/test_align_myers.h | 2 +-
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} | 28 +-
... => test_align_simd_global_variable_length.cpp} | 23 +-
tests/align/test_align_simd_local.h | 122 ++
....cpp => test_align_simd_local_equal_length.cpp} | 21 +-
...p => test_align_simd_local_variable_length.cpp} | 20 +-
tests/align/test_align_stream.h | 2 +-
.../test_alignment_algorithms_band_position.h | 98 +-
.../align/test_alignment_algorithms_dynamic_gap.h | 2 +-
tests/align/test_alignment_algorithms_global.h | 2 +-
.../test_alignment_algorithms_global_banded.h | 2 +-
tests/align/test_alignment_algorithms_local.h | 49 +-
.../align/test_alignment_algorithms_local_banded.h | 34 +-
.../align/test_alignment_dp_adapt_tracesegments.h | 82 +-
tests/align/test_alignment_dp_band.h | 2 +-
tests/align/test_alignment_dp_cell.h | 4 +-
tests/align/test_alignment_dp_formula.h | 1328 +++++++++------
tests/align/test_alignment_dp_matrix.h | 4 +-
tests/align/test_alignment_dp_matrix_navigator.h | 1706 ++++----------------
tests/align/test_alignment_dp_profile.h | 2 +-
tests/align/test_alignment_dp_trace_segment.h | 54 +-
tests/align/test_alignment_dp_traceback.h | 397 +++--
tests/align/test_evaluate_alignment.h | 2 +-
tests/align/test_local_align.h | 2 +-
tests/align/test_mock.h | 240 +++
tests/align_extend/test_align_extend.cpp | 2 +-
tests/align_extend/test_align_extend.h | 2 +-
tests/align_parallel/CMakeLists.txt | 78 +
.../test_align_parallel_algorithm.cpp} | 24 +-
.../test_align_parallel_data_structures.cpp} | 51 +-
.../test_align_parallel_interface.cpp} | 4 +-
.../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} | 91 +-
.../test_align_wavefront_intermediate_dp_result.h | 121 ++
.../test_align_wavefront_task_scheduler.h | 83 +-
tests/align_profile/test_align_profile.cpp | 2 +-
tests/align_split/test_align_split.cpp | 2 +-
tests/align_split/test_align_split.h | 2 +-
tests/alignment_free/test_alignment_free.cpp | 2 +-
tests/arg_parse/test_arg_parse.cpp | 3 +-
tests/arg_parse/test_arg_parse.h | 2 +-
tests/arg_parse/test_arg_parse_argument.h | 30 +-
tests/arg_parse/test_arg_parse_ctd_support.h | 5 +-
tests/arg_parse/test_arg_parse_option.h | 2 +-
tests/arg_parse/test_arg_parse_version_check.cpp | 2 +-
tests/arg_parse/test_arg_parse_version_check.h | 2 +-
tests/arg_parse/test_argument_parser.h | 2 +-
tests/arg_parse/test_extensions.h | 2 +-
tests/bam_io/test_bam_alignment_record.h | 2 +-
tests/bam_io/test_bam_file.h | 28 +-
tests/bam_io/test_bam_header_record.h | 2 +-
tests/bam_io/test_bam_index.h | 19 +-
tests/bam_io/test_bam_io.cpp | 4 +-
tests/bam_io/test_bam_io_context.h | 2 +-
tests/bam_io/test_bam_sam_conversion.h | 13 +-
tests/bam_io/test_bam_tags_dict.h | 2 +-
tests/bam_io/test_read_bam.h | 12 +-
tests/bam_io/test_read_sam.h | 2 +-
tests/bam_io/test_write_bam.h | 8 +-
tests/bam_io/test_write_sam.h | 2 +-
tests/basic/CMakeLists.txt | 7 -
tests/basic/test_basic.cpp | 3 +-
tests/basic/test_basic_aggregate.cpp | 2 +-
tests/basic/test_basic_aggregate.h | 7 +-
tests/basic/test_basic_allocator.cpp | 2 +-
tests/basic/test_basic_allocator.h | 2 +-
tests/basic/test_basic_alphabet.cpp | 8 +-
tests/basic/test_basic_alphabet.h | 52 +-
tests/basic/test_basic_alphabet_adapt_builtins.h | 201 +--
tests/basic/test_basic_alphabet_bio.h | 2 +-
tests/basic/test_basic_alphabet_concepts.h | 2 +-
tests/basic/test_basic_alphabet_math.h | 31 +-
tests/basic/test_basic_alphabet_profile.h | 2 +-
tests/basic/test_basic_alphabet_qualities.h | 2 +-
tests/basic/test_basic_alphabet_residue.h | 76 +-
tests/basic/test_basic_alphabet_simple_type.h | 2 +-
tests/basic/test_basic_alphabet_storage.h | 2 +-
tests/basic/test_basic_array_construct_destruct.h | 2 +-
.../basic/test_basic_array_constructor_destruct.h | 2 +-
tests/basic/test_basic_concept.cpp | 6 +-
tests/basic/test_basic_concepts.h | 41 +-
tests/basic/test_basic_construct_destruct.h | 2 +-
tests/basic/test_basic_container.cpp | 2 +-
tests/basic/test_basic_container_proxy.h | 2 +-
tests/basic/test_basic_exception.cpp | 2 +-
tests/basic/test_basic_exception.h | 8 +-
tests/basic/test_basic_fundamental.cpp | 2 +-
tests/basic/test_basic_fundamental_comparison.h | 2 +-
tests/basic/test_basic_fundamental_concepts.h | 2 +-
tests/basic/test_basic_fundamental_conversion.h | 2 +-
tests/basic/test_basic_fundamental_helpers.h | 2 +-
tests/basic/test_basic_fundamental_metafunctions.h | 2 +-
tests/basic/test_basic_fundamental_tags.h | 2 +-
tests/basic/test_basic_fundamental_transport.h | 2 +-
tests/basic/test_basic_hosted_type_interface.h | 2 +-
tests/basic/test_basic_iterator.cpp | 2 +-
tests/basic/test_basic_iterator.h | 4 +-
tests/basic/test_basic_iterator_concepts.h | 2 +-
tests/basic/test_basic_iterator_zip.h | 2 +-
tests/basic/test_basic_math.cpp | 2 +-
tests/basic/test_basic_math.h | 2 +-
tests/basic/test_basic_metaprogramming.cpp | 2 +-
tests/basic/test_basic_metaprogramming.h | 2 +-
tests/basic/test_basic_metaprogramming_control.h | 2 +-
tests/basic/test_basic_metaprogramming_enable_if.h | 2 +-
tests/basic/test_basic_metaprogramming_logic.h | 2 +-
tests/basic/test_basic_metaprogramming_math.h | 2 +-
tests/basic/test_basic_metaprogramming_type.h | 2 +-
tests/basic/test_basic_parallelism.cpp | 2 +-
tests/basic/test_basic_parallelism.h | 2 +-
tests/basic/test_basic_proxy.cpp | 2 +-
tests/basic/test_basic_proxy.h | 2 +-
tests/basic/test_basic_simd_vector.h | 155 --
tests/basic/test_basic_smart_pointer.cpp | 2 +-
tests/basic/test_basic_smart_pointer_holder.h | 2 +-
tests/basic/test_basic_tag.h | 2 +-
tests/basic/test_basic_transport.h | 2 +-
tests/basic/test_basic_type.h | 2 +-
tests/bed_io/test_bed_io.cpp | 10 +-
tests/blast/test_blast.cpp | 2 +-
tests/blast/test_blast_input.h | 10 +-
tests/blast/test_blast_misc.h | 2 +-
tests/blast/test_blast_output.h | 4 +-
tests/blast/test_blast_statistics.h | 2 +-
tests/consensus/test_consensus.cpp | 2 +-
tests/consensus/test_consensus.h | 29 +-
tests/consensus/test_consensus_realign.h | 7 +-
tests/consensus_v2/test_consensus_v2.cpp | 2 +-
tests/find/test_find.cpp | 2 +-
tests/find/test_find_hamming.h | 2 +-
tests/find/test_find_myers_banded.h | 2 +-
tests/gff_io/test_gff_io.cpp | 2 +-
tests/gff_io/test_gff_io.h | 39 +-
tests/graph_algorithms/test_graph_algorithms.cpp | 2 +-
tests/graph_algorithms/test_graph_algorithms.h | 2 +-
tests/graph_align/test_graph_align.cpp | 2 +-
tests/graph_align/test_graph_impl_align.h | 2 +-
tests/graph_align/test_graph_match_refinement.h | 2 +-
tests/graph_msa/test_graph_msa.cpp | 2 +-
tests/graph_msa/test_graph_msa_guide_tree.h | 2 +-
tests/graph_msa/test_graph_tcoffee.h | 2 +-
tests/graph_types/test_graph_types_basic.cpp | 2 +-
tests/graph_types/test_graph_types_derived.cpp | 2 +-
tests/graph_types/test_graph_types_iterators.cpp | 2 +-
.../graph_types/test_graph_types_property_map.cpp | 2 +-
tests/graph_types/test_graph_types_types.cpp | 2 +-
tests/graph_types/test_graph_types_utils.cpp | 2 +-
tests/index/CMakeLists.txt | 6 +-
tests/index/test_crosscompare.h | 2 +-
.../test_find2_index_approx.cpp} | 19 +-
tests/index/test_find2_index_approx.h | 489 ++++++
tests/index/test_index_base.cpp | 2 +-
tests/index/test_index_bifm.cpp | 18 +-
tests/index/test_index_creation.cpp | 2 +-
tests/index/test_index_creation.h | 8 +-
tests/index/test_index_crosscompare_char.cpp | 2 +-
tests/index/test_index_crosscompare_char_dfi.cpp | 2 +-
tests/index/test_index_crosscompare_dna.cpp | 2 +-
tests/index/test_index_crosscompare_dna_dfi.cpp | 2 +-
tests/index/test_index_drawing.cpp | 2 +-
tests/index/test_index_finder.cpp | 2 +-
tests/index/test_index_fm.cpp | 2 +-
tests/index/test_index_fm_rank_dictionary.cpp | 9 +-
.../test_index_fm_right_array_binary_tree.cpp | 2 +-
.../index/test_index_fm_right_array_binary_tree.h | 2 +-
...est_index_fm_right_array_binary_tree_iterator.h | 2 +-
tests/index/test_index_fm_sparse_string.cpp | 2 +-
tests/index/test_index_fm_stree.h | 2 +-
tests/index/test_index_helpers.h | 10 +-
tests/index/test_index_qgram.cpp | 2 +-
tests/index/test_index_repeats.cpp | 2 +-
tests/index/test_index_repeats.h | 2 +-
tests/index/test_index_sa_bwtwalk.cpp | 2 +-
tests/index/test_index_shapes.cpp | 2 +-
tests/index/test_index_stree_iterators.cpp | 3 +-
tests/index/test_index_vstree.cpp | 2 +-
tests/index/test_qgram_index.h | 25 +-
tests/index/test_sa_bwtwalk.h | 4 +-
tests/index/test_shapes.h | 2 +-
tests/index/test_stree_iterators.h | 20 +-
tests/journaled_set/test_journaled_set.cpp | 2 +-
tests/journaled_set/test_journaled_set.h | 2 +-
.../test_basic_observable.cpp | 2 +-
.../journaled_string_tree/test_basic_observable.h | 2 +-
tests/journaled_string_tree/test_delta_map.cpp | 2 +-
tests/journaled_string_tree/test_delta_map.h | 16 +-
tests/journaled_string_tree/test_delta_store.h | 2 +-
.../test_journaled_string_tree.cpp | 2 +-
.../test_journaled_string_tree.h | 4 +-
.../test_journaled_string_tree_find.cpp | 2 +-
.../test_journaled_string_tree_find.h | 2 +-
.../test_journaled_string_tree_mock.h | 2 +-
.../test_journaled_string_tree_traverser.cpp | 3 +-
.../test_journaled_string_tree_traverser.h | 18 +-
tests/map/test_map.cpp | 2 +-
tests/map/test_map_map.h | 2 +-
tests/map/test_map_sumlist.h | 2 +-
tests/misc/test_misc.cpp | 8 +-
tests/misc/test_misc_accumulators.h | 2 +-
tests/misc/test_misc_bit_twiddling.h | 2 +-
tests/misc/test_misc_edit_environment.h | 2 +-
tests/misc/test_misc_interval_tree.h | 2 +-
tests/modifier/helpers.h | 2 +-
tests/modifier/test_modifier.cpp | 5 +-
tests/modifier/test_modifier_alphabet.h | 2 +-
tests/modifier/test_modifier_functors.h | 2 +-
tests/modifier/test_modifier_shortcuts.h | 2 +-
tests/modifier/test_modifier_string.h | 2 +-
tests/modifier/test_modifier_string_padding.h | 26 +-
tests/modifier/test_modifier_view.h | 2 +-
tests/modifier_cyclic_shape/test_cyclic_shape.h | 2 +-
.../test_modifier_cyclic_shape.cpp | 2 +-
.../test_modifier_cyclic_shape.h | 2 +-
.../test_multiple_translation_units.cpp | 3 +-
.../test_multiple_translation_units_2.cpp | 3 +-
tests/parallel/CMakeLists.txt | 4 +-
tests/parallel/test_parallel.cpp | 23 +-
tests/parallel/test_parallel_algorithms.h | 2 +-
tests/parallel/test_parallel_atomic_misc.h | 2 +-
tests/parallel/test_parallel_atomic_primitives.h | 2 +-
.../test_parallel_enumerable_thread_local.h | 217 +++
tests/parallel/test_parallel_queue.h | 2 +-
tests/parallel/test_parallel_splitting.h | 2 +-
tests/parallel/test_parallel_thread_pool.h | 151 ++
tests/parse_lm/test_parse_lm.cpp | 2 +-
tests/parse_lm/test_parse_lm.h | 4 +-
tests/pipe/test_pipe.cpp | 2 +-
tests/pipe/test_pipe.h | 2 +-
tests/platform/test_platform.cpp | 2 +-
.../platform/test_platform_range_based_for_loops.h | 2 +-
tests/random/test_random.cpp | 2 +-
tests/random/test_random_basic.h | 2 +-
tests/random/test_random_beta.h | 2 +-
tests/random/test_random_util.h | 2 +-
tests/realign/test_realign.cpp | 2 +-
tests/reduced_aminoacid/test_reduced_aminoacid.cpp | 7 +-
tests/reduced_aminoacid/test_reduced_aminoacid.h | 97 +-
tests/rna_io/CMakeLists.txt | 4 +-
tests/rna_io/test_rna_io.cpp | 2 +-
tests/rna_io/test_rna_io.h | 2 +-
tests/roi_io/test_roi_io.cpp | 10 +-
tests/score/test_score.cpp | 11 +-
tests/seeds/seed_set_test_helpers.h | 2 +-
tests/seeds/test_align_banded_chain_impl.cpp | 4 +-
.../test_banded_chain_alignment_interface.cpp | 2 +-
tests/seeds/test_seeds_combination.cpp | 2 +-
tests/seeds/test_seeds_extension.cpp | 2 +-
tests/seeds/test_seeds_global_chaining.cpp | 28 +-
tests/seeds/test_seeds_seed_base.cpp | 2 +-
tests/seeds/test_seeds_seed_chained.cpp | 2 +-
tests/seeds/test_seeds_seed_diagonal.cpp | 2 +-
tests/seeds/test_seeds_seed_set_base.cpp | 2 +-
tests/seeds/test_seeds_seed_set_unordered.cpp | 2 +-
tests/seeds/test_seeds_seed_simple.cpp | 2 +-
tests/seq_io/test_fai_index.h | 26 +-
tests/seq_io/test_genomic_region.h | 2 +-
tests/seq_io/test_read_bam.h | 2 +-
tests/seq_io/test_seq_io.cpp | 2 +-
tests/seq_io/test_seq_io_generic.h | 2 +-
tests/seq_io/test_sequence_file.h | 38 +-
tests/seq_io/test_stream_read_embl.h | 2 +-
tests/seq_io/test_stream_read_genbank.h | 2 +-
tests/seq_io/test_stream_record_reader_fasta.h | 2 +-
tests/seq_io/test_stream_write_fasta.h | 2 +-
tests/seq_io/test_tag_select_intersect.h | 2 +-
tests/seq_io/test_write_bam.h | 2 +-
tests/sequence/test_segment.h | 2 +-
tests/sequence/test_segment_beta.h | 2 +-
tests/sequence/test_sequence.cpp | 2 +-
tests/sequence/test_sequence.h | 55 +-
tests/sequence/test_sequence_std_adaptions.h | 2 +-
tests/sequence/test_sequence_v2.cpp | 2 +-
tests/sequence/test_string.h | 2 +-
tests/sequence/test_string_packed_extension.h | 6 +-
tests/sequence/test_string_set.h | 69 +-
tests/sequence/test_stringset.h | 2 +-
tests/sequence/test_stringset_v2.cpp | 2 +-
.../sequence_journaled/test_sequence_journaled.cpp | 2 +-
tests/sequence_journaled/test_sequence_journaled.h | 2 +-
.../test_sequence_journaled_iterator.h | 2 +-
tests/{rna_io => simd}/CMakeLists.txt | 30 +-
.../test_simd_vector.cpp} | 30 +-
tests/simd/test_simd_vector.h | 979 +++++++++++
.../test_simple_intervals_io.cpp | 2 +-
tests/statistics/test_statistics.cpp | 2 +-
tests/statistics/test_statistics_base.h | 5 +-
tests/statistics/test_statistics_markov_model.h | 2 +-
tests/store/test_store.cpp | 2 +-
tests/store/test_store_io.h | 94 +-
tests/store/test_store_io_bam.h | 12 +-
tests/stream/test_stream.cpp | 2 +-
tests/stream/test_stream_file_stream.h | 2 +-
tests/stream/test_stream_generic.h | 2 +-
tests/stream/test_stream_lexical_cast.h | 6 +-
tests/stream/test_stream_tokenization.h | 62 +-
tests/stream/test_stream_virtual_stream.h | 17 +-
tests/stream/test_stream_write.h | 2 +-
tests/swift_local/test_find_swift.cpp | 2 +-
tests/tabix_io/test_tabix_io.cpp | 2 +-
tests/tabix_io/test_tabix_io.h | 13 +-
tests/translation/test_translation.cpp | 2 +-
tests/translation/test_translation.h | 43 +-
tests/ucsc_io/test_ucsc_io.cpp | 26 +-
tests/vcf_io/example_records_with_errors.vcf | 5 +-
tests/vcf_io/test_vcf_io.cpp | 2 +-
tests/vcf_io/test_vcf_io.h | 48 +-
util/bin/adjust_copyright_years.sh | 5 +-
util/cmake/FindGitInfo.cmake | 2 +-
util/cmake/{FindGitInfo.cmake => FindSDE.cmake} | 69 +-
.../cmake/{FindGitInfo.cmake => FindUmesimd.cmake} | 53 +-
util/cmake/GetCurrentDate.cmake | 2 +-
util/cmake/GetCurrentDate.cpp | 2 +-
util/cmake/SeqAnBuildSystem.cmake | 111 +-
util/cmake/SeqAnConsistentFPFlags.cmake | 2 +-
util/cmake/SeqAnContribs.cmake | 115 +-
util/cmake/SeqAnCtdSetup.cmake | 2 +-
util/cmake/SeqAnSimdUtility.cmake | 647 ++++++++
util/cmake/SeqAnUsabilityAnalyzer.cmake | 2 +-
util/cmake/SetCPackSystemName.cmake | 2 +-
util/cmake/ctd/COPYRIGHT | 2 +-
util/cmake/ctd/LICENSE | 2 +-
util/cmake/package.cmake | 2 +-
util/cmake/seqan-config.cmake | 33 +-
util/pkgconfig/seqan.pc.in | 4 +-
util/py_lib/CMakeLists.txt | 5 +
util/py_lib/seqan/LICENSE | 2 +-
util/skel/app_template/CMakeLists.txt | 2 +-
util/skel/app_template/LICENSE | 2 +-
util/skel/app_template/app.cpp | 2 +-
util/skel/demo_template/demo.cpp | 2 +-
util/skel/header_template/header.h | 2 +-
util/skel/header_template/library_header.h | 2 +-
util/skel/module_template/header.h | 2 +-
util/skel/module_template/module.h | 2 +-
util/skel/test_template/test.cpp | 2 +-
util/skel/test_template/test.h | 2 +-
util/travis/linux-cibuild.cmake | 1 -
util/travis/linux-cibuild.sh | 5 +
1354 files changed, 25764 insertions(+), 12530 deletions(-)
create mode 100644 demos/howto/custom_file_ending.fa.dat
create mode 100644 demos/howto/custom_file_endings.cpp
create mode 100644 demos/howto/custom_file_endings.cpp.stdout
create mode 100644 demos/tutorial/indices/find2_index_approx.cpp
create mode 100644 demos/tutorial/indices/find2_index_approx.stdout
delete mode 100644 demos/unassigned_or_unused/tutorial_file_io/solution2.cpp
delete mode 100644 demos/unassigned_or_unused/tutorial_file_io/solution3.cpp
copy util/skel/header_template/library_header.h => include/seqan/align/aligned_sequence_concept.h (86%)
copy include/seqan/{bam_io.h => align_parallel.h} (58%)
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/{journaled_string_tree/jst_extension_horspool.h => align_parallel/dp_settings.h} (58%)
copy include/seqan/{journaled_string_tree/jst_extension_horspool.h => align_parallel/dp_traits.h} (57%)
create mode 100644 include/seqan/align_parallel/parallel_align_interface.h
copy include/seqan/{journaled_set/journaled_set_join_global_align_manhatten.h => align_parallel/wavefront_alignment_executor.h} (63%)
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
copy include/seqan/{journaled_string_tree/stack_observer.h => align_parallel/wavefront_alignment_thread_local_storage.h} (50%)
create mode 100644 include/seqan/align_parallel/wavefront_task.h
copy include/seqan/{journaled_set/journaled_set_join_global_align_manhatten.h => align_parallel/wavefront_task_event.h} (63%)
create mode 100644 include/seqan/align_parallel/wavefront_task_executor.h
copy include/seqan/{align/dp_cell_linear.h => align_parallel/wavefront_task_queue.h} (55%)
create mode 100644 include/seqan/align_parallel/wavefront_task_scheduler.h
create mode 100644 include/seqan/align_parallel/wavefront_task_util.h
delete mode 100644 include/seqan/basic/basic_simd_vector.h
create mode 100644 include/seqan/graph_algorithms/maximum_weighted_matching.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
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_base.h => reduced_aminoacid_buchfink11_base.h} (80%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_tables.h => reduced_aminoacid_buchfink11_tables.h} (78%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_base.h => reduced_aminoacid_cannata10_base.h} (81%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_tables.h => reduced_aminoacid_cannata10_tables.h} (77%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_base.h => reduced_aminoacid_li10_base.h} (81%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_tables.h => reduced_aminoacid_li10_tables.h} (80%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_base.h => reduced_aminoacid_murphy5_base.h} (83%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_tables.h => reduced_aminoacid_murphy5_tables.h} (77%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_base.h => reduced_aminoacid_solis10_base.h} (80%)
copy include/seqan/reduced_aminoacid/{reduced_aminoacid_murphy10_tables.h => reduced_aminoacid_solis10_tables.h} (81%)
create mode 100644 include/seqan/simd.h
create mode 100644 include/seqan/simd/simd_base.h
create mode 100644 include/seqan/simd/simd_base_seqan_impl.h
create mode 100644 include/seqan/simd/simd_base_seqan_impl_avx2.h
create mode 100644 include/seqan/simd/simd_base_seqan_impl_avx512.h
create mode 100644 include/seqan/simd/simd_base_seqan_impl_sse4.2.h
create mode 100644 include/seqan/simd/simd_base_seqan_interface.h
create mode 100644 include/seqan/simd/simd_base_umesimd_impl.h
create mode 100644 manual/source/Tutorial/Algorithms/PatternMatching/OptimalSearchSchemes.rst
create mode 100644 manual/source/Tutorial/HowTo/Recipes/CustomFileEndings.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} (56%)
copy tests/align/{test_align_simd.cpp => test_align_simd_global_variable_length.cpp} (65%)
create mode 100644 tests/align/test_align_simd_local.h
copy tests/align/{test_align_simd.cpp => test_align_simd_local_equal_length.cpp} (73%)
copy tests/align/{test_align_simd.cpp => test_align_simd_local_variable_length.cpp} (76%)
create mode 100644 tests/align/test_mock.h
create mode 100644 tests/align_parallel/CMakeLists.txt
copy tests/{basic/test_basic_allocator.cpp => align_parallel/test_align_parallel_algorithm.cpp} (78%)
copy tests/{basic/test_basic_smart_pointer.cpp => align_parallel/test_align_parallel_data_structures.cpp} (56%)
rename tests/{align/test_align_simd.cpp => align_parallel/test_align_parallel_interface.cpp} (95%)
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 tests/{basic/test_basic_alphabet_storage.h => align_parallel/test_align_wavefront_alignment_thread_local.h} (53%)
create mode 100644 tests/align_parallel/test_align_wavefront_intermediate_dp_result.h
copy demos/howto/using_zip_iterator.cpp => tests/align_parallel/test_align_wavefront_task_scheduler.h (54%)
delete mode 100644 tests/basic/test_basic_simd_vector.h
copy tests/{tabix_io/test_tabix_io.cpp => index/test_find2_index_approx.cpp} (78%)
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
copy tests/{rna_io => simd}/CMakeLists.txt (68%)
rename tests/{basic/test_basic_simd_vector.cpp => simd/test_simd_vector.cpp} (76%)
create mode 100644 tests/simd/test_simd_vector.h
copy util/cmake/{FindGitInfo.cmake => FindSDE.cmake} (57%)
copy util/cmake/{FindGitInfo.cmake => FindUmesimd.cmake} (61%)
create mode 100644 util/cmake/SeqAnSimdUtility.cmake
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