[med-svn] [Git][med-team/seqan2][master] 8 commits: New upstream version
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Fri Jan 9 14:03:07 GMT 2026
Michael R. Crusoe pushed to branch master at Debian Med / seqan2
Commits:
6701441a by Michael R. Crusoe at 2026-01-09T08:59:41+01:00
New upstream version
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cc29e529 by Michael R. Crusoe at 2026-01-09T08:59:46+01:00
New upstream version 2.5.2
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60581431 by Michael R. Crusoe at 2026-01-09T09:00:33+01:00
Update upstream source from tag 'upstream/2.5.2'
Update to upstream version '2.5.2'
with Debian dir b2133591599164e4e1669477d4f81e9199d4534a
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bef8b7f7 by Michael R. Crusoe at 2026-01-09T09:00:54+01:00
Remove duplicate line from changelog.
Changes-By: lintian-brush
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043d8d9d by Michael R. Crusoe at 2026-01-09T09:39:42+01:00
d/patches: Dropped skip-some-apps-on-some-archs
We don't even build for these archs anymore (not a current Debian port, or not
64-bit.
Restore missing architecture-is-64-bit in d/control; was lost in a
previous commit by accident
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09376402 by Michael R. Crusoe at 2026-01-09T09:44:57+01:00
Restore demos/tutorial/file_io_overview/example.sam after running the tests, instead of deleting it via d/clean.
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5ecec9cd by Michael R. Crusoe at 2026-01-09T09:45:32+01:00
Remove patch skip-some-apps-on-some-archs that is missing from debian/patches/series.
Changes-By: lintian-brush
Fixes: lintian: patch-file-present-but-not-mentioned-in-series
See-also: https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html
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90ae566a by Michael R. Crusoe at 2026-01-09T11:25:11+01:00
routine-update: Ready to upload to unstable
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1313 changed files:
- CHANGELOG.md
- LICENSE
- README.md
- apps/alf/CMakeLists.txt
- apps/alf/LICENSE
- apps/alf/alf.cpp
- apps/bs_tools/CMakeLists.txt
- apps/bs_tools/LICENSE
- apps/bs_tools/bisar.cpp
- apps/bs_tools/casbar.cpp
- apps/bs_tools/four2three.cpp
- apps/dfi/CMakeLists.txt
- apps/fiona/CMakeLists.txt
- apps/fiona/index_qgram_parallel.h
- apps/fx_tools/CMakeLists.txt
- apps/fx_tools/LICENSE
- apps/fx_tools/fx_bam_coverage.cpp
- apps/fx_tools/fx_fastq_stats.cpp
- apps/gustaf/CMakeLists.txt
- apps/gustaf/LICENSE
- apps/gustaf/create_stellarmatches_from_file.h
- apps/gustaf/gustaf.cpp
- apps/gustaf/gustaf_matepairs.h
- apps/gustaf/join_mates.cpp
- apps/gustaf/msplazer.h
- apps/gustaf/msplazer_algorithms.h
- apps/gustaf/msplazer_main.h
- apps/gustaf/msplazer_out.h
- apps/gustaf/msplazer_parse_options.h
- apps/gustaf/stellar_routines.h
- apps/insegt/CMakeLists.txt
- apps/insegt/LICENSE
- apps/mason2/CMakeLists.txt
- apps/mason2/LICENSE
- apps/mason2/TODO
- apps/mason2/external_split_merge.cpp
- apps/mason2/external_split_merge.h
- apps/mason2/fragment_generation.h
- apps/mason2/genomic_variants.cpp
- apps/mason2/genomic_variants.h
- apps/mason2/individual_genome.h
- apps/mason2/mason_frag_sequencing.cpp
- apps/mason2/mason_genome.cpp
- apps/mason2/mason_materializer.cpp
- apps/mason2/mason_methylation.cpp
- apps/mason2/mason_options.cpp
- apps/mason2/mason_options.h
- apps/mason2/mason_simulator.cpp
- apps/mason2/mason_splicing.cpp
- apps/mason2/mason_tests.cpp
- apps/mason2/mason_types.h
- apps/mason2/mason_variator.cpp
- apps/mason2/methylation_levels.cpp
- apps/mason2/methylation_levels.h
- apps/mason2/omp_wrapper.h
- apps/mason2/sequencing.h
- apps/mason2/simulate_454.cpp
- apps/mason2/simulate_base.cpp
- apps/mason2/simulate_genome.cpp
- apps/mason2/simulate_genome.h
- apps/mason2/simulate_illumina.cpp
- apps/mason2/simulate_sanger.cpp
- apps/mason2/tests/libc++/random_var1.vcf
- apps/mason2/tests/libc++/random_var10.vcf
- apps/mason2/tests/libc++/random_var2.vcf
- apps/mason2/tests/libc++/random_var3.vcf
- apps/mason2/tests/libc++/random_var9.vcf
- apps/mason2/tests/libc++/simulator.left1.fq
- apps/mason2/tests/libc++/simulator.left2.fq
- apps/mason2/tests/libc++/simulator.left3.fa
- apps/mason2/tests/libc++/simulator.left4.fa
- apps/mason2/tests/libc++/simulator.left5.fq
- apps/mason2/tests/libc++/simulator.left6.fq
- apps/mason2/tests/libc++/simulator.left7.fa
- apps/mason2/tests/libc++/simulator.left8.fq
- apps/mason2/tests/libc++/simulator.out1.sam
- apps/mason2/tests/libc++/simulator.out1.stderr
- apps/mason2/tests/libc++/simulator.out2.sam
- apps/mason2/tests/libc++/simulator.out2.stderr
- apps/mason2/tests/libc++/simulator.out3.stderr
- apps/mason2/tests/libc++/simulator.out4.sam
- apps/mason2/tests/libc++/simulator.out4.stderr
- apps/mason2/tests/libc++/simulator.out5.stderr
- apps/mason2/tests/libc++/simulator.out6.stderr
- apps/mason2/tests/libc++/simulator.out7.sam
- apps/mason2/tests/libc++/simulator.out7.stderr
- apps/mason2/tests/libc++/simulator.out8.sam
- apps/mason2/tests/libc++/simulator.out8.stderr
- apps/mason2/tests/libc++/simulator.right1.fq
- apps/mason2/tests/libc++/simulator.right2.fq
- apps/mason2/tests/libc++/simulator.right3.fa
- apps/mason2/tests/libc++/simulator.right5.fq
- apps/mason2/tests/libc++/simulator.right6.fq
- apps/mason2/tests/libstdc++/random_var1.vcf
- apps/mason2/tests/libstdc++/random_var10.vcf
- apps/mason2/tests/libstdc++/random_var2.vcf
- apps/mason2/tests/libstdc++/random_var3.vcf
- apps/mason2/tests/libstdc++/random_var9.vcf
- apps/mason2/tests/libstdc++/simulator.left1.fq
- apps/mason2/tests/libstdc++/simulator.left2.fq
- apps/mason2/tests/libstdc++/simulator.left3.fa
- apps/mason2/tests/libstdc++/simulator.left4.fa
- apps/mason2/tests/libstdc++/simulator.left5.fq
- apps/mason2/tests/libstdc++/simulator.left6.fq
- apps/mason2/tests/libstdc++/simulator.left7.fa
- apps/mason2/tests/libstdc++/simulator.left8.fq
- apps/mason2/tests/libstdc++/simulator.out1.sam
- apps/mason2/tests/libstdc++/simulator.out1.stderr
- apps/mason2/tests/libstdc++/simulator.out2.sam
- apps/mason2/tests/libstdc++/simulator.out2.stderr
- apps/mason2/tests/libstdc++/simulator.out3.stderr
- apps/mason2/tests/libstdc++/simulator.out4.sam
- apps/mason2/tests/libstdc++/simulator.out4.stderr
- apps/mason2/tests/libstdc++/simulator.out5.stderr
- apps/mason2/tests/libstdc++/simulator.out6.stderr
- apps/mason2/tests/libstdc++/simulator.out7.sam
- apps/mason2/tests/libstdc++/simulator.out7.stderr
- apps/mason2/tests/libstdc++/simulator.out8.sam
- apps/mason2/tests/libstdc++/simulator.out8.stderr
- apps/mason2/tests/libstdc++/simulator.right1.fq
- apps/mason2/tests/libstdc++/simulator.right2.fq
- apps/mason2/tests/libstdc++/simulator.right3.fa
- apps/mason2/tests/libstdc++/simulator.right5.fq
- apps/mason2/tests/libstdc++/simulator.right6.fq
- apps/mason2/variation_size_tsv.h
- apps/mason2/vcf_materialization.cpp
- apps/mason2/vcf_materialization.h
- apps/micro_razers/CMakeLists.txt
- apps/ngs_roi/CMakeLists.txt
- apps/ngs_roi/bam2roi.cpp
- apps/ngs_roi/bam2roi.h
- apps/ngs_roi/png_canvas.h
- apps/ngs_roi/project_interval.cpp
- apps/ngs_roi/project_interval.h
- apps/ngs_roi/project_spliced.cpp
- apps/ngs_roi/project_spliced.h
- apps/ngs_roi/record_ext.h
- apps/ngs_roi/roi_builder.cpp
- apps/ngs_roi/roi_builder.h
- apps/ngs_roi/roi_feature_projection.cpp
- apps/ngs_roi/roi_plot_thumbnails.cpp
- apps/pair_align/CMakeLists.txt
- apps/pair_align/LICENSE
- apps/pair_align/lib/pair_align_global.cpp
- apps/pair_align/lib/pair_align_lcs.cpp
- apps/pair_align/lib/pair_align_lib.cpp
- apps/pair_align/lib/pair_align_lib.h
- apps/pair_align/lib/pair_align_local.cpp
- apps/pair_align/pair_align.cpp
- apps/param_chooser/CMakeLists.txt
- apps/param_chooser/test_param_chooser.cpp
- apps/rabema/CMakeLists.txt
- apps/rabema/rabema_build_gold_standard.cpp
- apps/rabema/sorting.h
- apps/razers/CMakeLists.txt
- apps/razers3/CMakeLists.txt
- apps/razers3/profile_timeline.h
- apps/razers3/razers.cpp
- apps/razers3/razers.h
- apps/rep_sep/CMakeLists.txt
- apps/sak/CMakeLists.txt
- apps/sak/LICENSE
- apps/sak/sak.cpp
- apps/sam2matrix/CMakeLists.txt
- apps/sam2matrix/LICENSE
- apps/sam2matrix/sam2matrix.cpp
- apps/samcat/CMakeLists.txt
- apps/samcat/samcat.cpp
- apps/searchjoin/CMakeLists.txt
- apps/searchjoin/LICENSE
- apps/searchjoin/db.h
- apps/searchjoin/finder.h
- apps/searchjoin/join.cpp
- apps/searchjoin/search.cpp
- apps/searchjoin/verifier.h
- apps/searchjoin/writer.h
- apps/seqan_tcoffee/CMakeLists.txt
- apps/seqcons2/CMakeLists.txt
- apps/seqcons2/LICENSE
- apps/seqcons2/seqcons.cpp
- apps/seqcons2/seqcons_app.cpp
- apps/seqcons2/seqcons_app.h
- apps/seqcons2/seqcons_options.cpp
- apps/seqcons2/seqcons_options.h
- apps/sgip/CMakeLists.txt
- apps/snp_store/CMakeLists.txt
- apps/splazers/CMakeLists.txt
- apps/stellar/CMakeLists.txt
- apps/stellar/LICENSE
- apps/stellar/stellar.cpp
- apps/stellar/stellar.h
- apps/stellar/stellar_extension.h
- apps/stellar/stellar_output.h
- apps/stellar/stellar_types.h
- apps/tree_recon/CMakeLists.txt
- apps/yara/CMakeLists.txt
- apps/yara/LICENSE
- apps/yara/basic_alphabet.h
- apps/yara/bits_bucket.h
- apps/yara/bits_context.h
- apps/yara/bits_hits.h
- apps/yara/bits_matches.h
- apps/yara/bits_reads.h
- apps/yara/bits_seeds.h
- apps/yara/file_pair.h
- apps/yara/file_prefetched.h
- apps/yara/find_extender.h
- apps/yara/find_verifier.h
- apps/yara/index_fm.h
- apps/yara/indexer.cpp
- apps/yara/mapper.cpp
- apps/yara/mapper.h
- apps/yara/mapper_aligner.h
- apps/yara/mapper_classifier.h
- apps/yara/mapper_collector.h
- apps/yara/mapper_extender.h
- apps/yara/mapper_filter.h
- apps/yara/mapper_ranker.h
- apps/yara/mapper_verifier.h
- apps/yara/mapper_writer.h
- apps/yara/misc_options.h
- apps/yara/misc_tags.h
- apps/yara/misc_timer.h
- apps/yara/misc_types.h
- apps/yara/store_seqs.h
- debian/changelog
- debian/clean
- debian/control
- debian/patches/series
- − debian/patches/skip-some-apps-on-some-archs
- debian/rules
- demos/LICENSE
- demos/dox/basic/enable_if.cpp
- demos/dox/basic/metaprogramming_control.cpp
- demos/dox/basic/metaprogramming_logic.cpp
- demos/dox/basic/metaprogramming_math.cpp
- demos/dox/basic/metaprogramming_switch.cpp
- demos/dox/sequence/segment.cpp
- demos/dox/sequence/string.cpp
- demos/howto/using_zip_iterator.cpp
- + demos/tutorial/file_io_overview/example.sam
- demos/tutorial/generic_programming/template_subclassing.cpp
- demos/unassigned_or_unused/bam_library_size.cpp
- demos/unassigned_or_unused/bam_print_alignments.cpp
- demos/unassigned_or_unused/bamutil.cpp
- demos/unassigned_or_unused/benchmark_stream.cpp
- demos/unassigned_or_unused/benchmark_stream_write.cpp
- demos/unassigned_or_unused/parse_lm_stellar.cpp
- demos/unassigned_or_unused/sample_seqs.cpp
- demos/unassigned_or_unused/soft_to_hard_masking.cpp
- include/seqan/LICENSE
- include/seqan/align.h
- include/seqan/align/align_base.h
- include/seqan/align/align_cols.h
- include/seqan/align/align_config.h
- include/seqan/align/align_interface_wrapper.h
- include/seqan/align/align_iterator_base.h
- include/seqan/align/align_metafunctions.h
- include/seqan/align/align_traceback.h
- include/seqan/align/aligned_sequence_concept.h
- include/seqan/align/alignment_algorithm_tags.h
- include/seqan/align/alignment_operations.h
- include/seqan/align/dp_algorithm_impl.h
- include/seqan/align/dp_align_simd_helper.h
- include/seqan/align/dp_band.h
- include/seqan/align/dp_cell.h
- include/seqan/align/dp_cell_affine.h
- include/seqan/align/dp_cell_dynamic.h
- include/seqan/align/dp_cell_linear.h
- include/seqan/align/dp_context.h
- include/seqan/align/dp_formula.h
- include/seqan/align/dp_formula_affine.h
- include/seqan/align/dp_formula_dynamic.h
- include/seqan/align/dp_formula_linear.h
- include/seqan/align/dp_matrix.h
- include/seqan/align/dp_matrix_navigator.h
- include/seqan/align/dp_matrix_navigator_score_matrix.h
- include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
- include/seqan/align/dp_matrix_navigator_trace_matrix.h
- include/seqan/align/dp_matrix_sparse.h
- include/seqan/align/dp_meta_info.h
- include/seqan/align/dp_profile.h
- include/seqan/align/dp_scout.h
- include/seqan/align/dp_scout_simd.h
- include/seqan/align/dp_setup.h
- include/seqan/align/dp_trace_segment.h
- include/seqan/align/dp_traceback_adaptor.h
- include/seqan/align/dp_traceback_impl.h
- include/seqan/align/evaluate_alignment.h
- include/seqan/align/fragment.h
- include/seqan/align/gap_anchor.h
- include/seqan/align/gapped_value_type.h
- include/seqan/align/gaps_anchor.h
- include/seqan/align/gaps_array.h
- include/seqan/align/gaps_base.h
- include/seqan/align/gaps_iterator_anchor.h
- include/seqan/align/gaps_iterator_array.h
- include/seqan/align/gaps_iterator_base.h
- include/seqan/align/global_alignment_banded.h
- include/seqan/align/global_alignment_hirschberg_impl.h
- include/seqan/align/global_alignment_myers_hirschberg_impl.h
- include/seqan/align/global_alignment_myers_impl.h
- include/seqan/align/global_alignment_specialized.h
- include/seqan/align/global_alignment_unbanded.h
- include/seqan/align/local_alignment_banded.h
- include/seqan/align/local_alignment_banded_waterman_eggert_impl.h
- include/seqan/align/local_alignment_enumeration.h
- include/seqan/align/local_alignment_enumeration_banded.h
- include/seqan/align/local_alignment_enumeration_unbanded.h
- include/seqan/align/local_alignment_unbanded.h
- include/seqan/align/local_alignment_waterman_eggert_impl.h
- include/seqan/align/matrix_base.h
- include/seqan/align_extend.h
- include/seqan/align_extend/align_extend.h
- include/seqan/align_extend/align_extend_base.h
- include/seqan/align_extend/dp_scout_xdrop.h
- include/seqan/align_parallel.h
- include/seqan/align_parallel/async_wave_execution_interface.h
- include/seqan/align_parallel/dp_kernel_adaptor.h
- include/seqan/align_parallel/dp_parallel_execution_policies.h
- include/seqan/align_parallel/dp_parallel_scout.h
- include/seqan/align_parallel/dp_parallel_scout_simd.h
- include/seqan/align_parallel/dp_settings.h
- include/seqan/align_parallel/dp_traits.h
- include/seqan/align_parallel/parallel_align_interface.h
- include/seqan/align_parallel/wavefront_alignment_executor.h
- include/seqan/align_parallel/wavefront_alignment_result.h
- include/seqan/align_parallel/wavefront_alignment_scheduler.h
- include/seqan/align_parallel/wavefront_alignment_task.h
- include/seqan/align_parallel/wavefront_alignment_thread_local_storage.h
- include/seqan/align_parallel/wavefront_task.h
- include/seqan/align_parallel/wavefront_task_event.h
- include/seqan/align_parallel/wavefront_task_executor.h
- include/seqan/align_parallel/wavefront_task_queue.h
- include/seqan/align_parallel/wavefront_task_scheduler.h
- include/seqan/align_parallel/wavefront_task_util.h
- include/seqan/align_profile.h
- include/seqan/align_profile/add_to_profile.h
- include/seqan/align_profile/score_profile_seq.h
- include/seqan/align_split.h
- include/seqan/align_split/align_split_interface.h
- include/seqan/align_split/dp_scout_split.h
- include/seqan/alignment_free.h
- include/seqan/alignment_free/af_d2.h
- include/seqan/alignment_free/af_d2star.h
- include/seqan/alignment_free/af_d2z.h
- include/seqan/alignment_free/af_n2.h
- include/seqan/alignment_free/alignment_free_base.h
- include/seqan/alignment_free/alignment_free_comparison.h
- include/seqan/alignment_free/kmer_functions.h
- include/seqan/arg_parse.h
- include/seqan/arg_parse/arg_parse_argument.h
- include/seqan/arg_parse/arg_parse_ctd_support.h
- include/seqan/arg_parse/arg_parse_doc.h
- include/seqan/arg_parse/arg_parse_exceptions.h
- include/seqan/arg_parse/arg_parse_option.h
- include/seqan/arg_parse/arg_parse_parse.h
- include/seqan/arg_parse/arg_parse_type_support.h
- include/seqan/arg_parse/arg_parse_version_check.h
- include/seqan/arg_parse/argument_parser.h
- include/seqan/arg_parse/tool_doc.h
- include/seqan/arg_parse/xml_support.h
- include/seqan/bam_io.h
- include/seqan/bam_io/bam_alignment_record.h
- include/seqan/bam_io/bam_alignment_record_util.h
- include/seqan/bam_io/bam_file.h
- include/seqan/bam_io/bam_header_record.h
- include/seqan/bam_io/bam_index_bai.h
- include/seqan/bam_io/bam_io_context.h
- include/seqan/bam_io/bam_sam_conversion.h
- include/seqan/bam_io/bam_scanner_cache.h
- include/seqan/bam_io/bam_tags_dict.h
- include/seqan/bam_io/cigar.h
- include/seqan/bam_io/read_bam.h
- include/seqan/bam_io/read_sam.h
- include/seqan/bam_io/write_bam.h
- include/seqan/bam_io/write_sam.h
- include/seqan/basic.h
- include/seqan/basic/aggregate_concept.h
- include/seqan/basic/allocator_chunkpool.h
- include/seqan/basic/allocator_interface.h
- include/seqan/basic/allocator_multipool.h
- include/seqan/basic/allocator_simple.h
- include/seqan/basic/allocator_singlepool.h
- include/seqan/basic/allocator_to_std.h
- include/seqan/basic/alphabet_adapt_builtins.h
- include/seqan/basic/alphabet_bio.h
- include/seqan/basic/alphabet_concept.h
- include/seqan/basic/alphabet_math.h
- include/seqan/basic/alphabet_profile.h
- include/seqan/basic/alphabet_qualities.h
- include/seqan/basic/alphabet_residue.h
- include/seqan/basic/alphabet_residue_tabs.h
- include/seqan/basic/alphabet_simple_type.h
- include/seqan/basic/alphabet_storage.h
- include/seqan/basic/array_construct_destruct.h
- include/seqan/basic/basic_aggregate.h
- include/seqan/basic/basic_allocator.h
- include/seqan/basic/basic_alphabet.h
- include/seqan/basic/basic_concept.h
- include/seqan/basic/basic_container.h
- include/seqan/basic/basic_debug.h
- include/seqan/basic/basic_exception.h
- include/seqan/basic/basic_functors.h
- include/seqan/basic/basic_fundamental.h
- include/seqan/basic/basic_iterator.h
- include/seqan/basic/basic_math.h
- include/seqan/basic/basic_metaprogramming.h
- include/seqan/basic/basic_parallelism.h
- include/seqan/basic/basic_proxy.h
- include/seqan/basic/basic_smart_pointer.h
- include/seqan/basic/basic_stream.h
- include/seqan/basic/basic_tangle.h
- include/seqan/basic/basic_type.h
- include/seqan/basic/boost_preprocessor_subset.h
- include/seqan/basic/builtin_functions.h
- include/seqan/basic/concept_checking.h
- include/seqan/basic/container_concept.h
- include/seqan/basic/debug_helper.h
- include/seqan/basic/debug_test_system.h
- include/seqan/basic/fundamental_chunking.h
- include/seqan/basic/fundamental_comparison.h
- include/seqan/basic/fundamental_concepts.h
- include/seqan/basic/fundamental_conversion.h
- include/seqan/basic/fundamental_metafunctions.h
- include/seqan/basic/fundamental_tags.h
- include/seqan/basic/fundamental_transport.h
- include/seqan/basic/holder_base.h
- include/seqan/basic/holder_simple.h
- include/seqan/basic/holder_tristate.h
- include/seqan/basic/hosted_type_interface.h
- include/seqan/basic/iterator_adapt_pointer.h
- include/seqan/basic/iterator_adapt_std.h
- include/seqan/basic/iterator_adaptor.h
- include/seqan/basic/iterator_base.h
- include/seqan/basic/iterator_concept.h
- include/seqan/basic/iterator_counting.h
- include/seqan/basic/iterator_interface.h
- include/seqan/basic/iterator_position.h
- include/seqan/basic/iterator_zip.h
- include/seqan/basic/macro_deprecated.h
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- include/seqan/sequence_journaled/sequence_journaled.h
- include/seqan/sequence_journaled/sequence_journaled_iterator.h
- include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
- include/seqan/simd.h
- include/seqan/simd/simd_base.h
- include/seqan/simd/simd_base_seqan_impl.h
- include/seqan/simd/simd_base_seqan_impl_avx2.h
- include/seqan/simd/simd_base_seqan_impl_avx512.h
- include/seqan/simd/simd_base_seqan_impl_sse4.2.h
- include/seqan/simd/simd_base_seqan_interface.h
- include/seqan/simd/simd_base_umesimd_impl.h
- include/seqan/simple_intervals_io.h
- include/seqan/simple_intervals_io/simple_intervals_file.h
- include/seqan/simple_intervals_io/simple_intervals_io.h
- include/seqan/statistics.h
- include/seqan/statistics/statistics_base.h
- include/seqan/statistics/statistics_markov_model.h
- include/seqan/store.h
- include/seqan/store/store_align.h
- include/seqan/store/store_align_intervals.h
- include/seqan/store/store_all.h
- include/seqan/store/store_annotation.h
- include/seqan/store/store_base.h
- include/seqan/store/store_contig.h
- include/seqan/store/store_intervaltree.h
- include/seqan/store/store_io.h
- include/seqan/store/store_io_gff.h
- include/seqan/store/store_io_sam.h
- include/seqan/store/store_io_ucsc.h
- include/seqan/store/store_library.h
- include/seqan/store/store_matepair.h
- include/seqan/store/store_read.h
- include/seqan/stream.h
- include/seqan/stream/adapt_ios.h
- include/seqan/stream/buffered_stream.h
- include/seqan/stream/file_stream.h
- include/seqan/stream/formatted_file.h
- include/seqan/stream/guess_format.h
- include/seqan/stream/iter_stream.h
- include/seqan/stream/lexical_cast.h
- include/seqan/stream/stream_base.h
- include/seqan/stream/stream_compressor.h
- include/seqan/stream/tokenization.h
- include/seqan/stream/virtual_stream.h
- include/seqan/system.h
- include/seqan/system/file_async.h
- include/seqan/system/file_directory.h
- include/seqan/system/file_forwards.h
- include/seqan/system/file_sync.h
- include/seqan/system/system_base.h
- include/seqan/system/system_event_win.h
- include/seqan/system/system_forwards.h
- include/seqan/tabix_io.h
- include/seqan/tabix_io/tabix_index_tbi.h
- include/seqan/translation.h
- include/seqan/translation/translation.h
- include/seqan/translation/translation_tables.h
- include/seqan/ucsc_io.h
- include/seqan/ucsc_io/ucsc_file.h
- include/seqan/ucsc_io/ucsc_io.h
- include/seqan/ucsc_io/ucsc_record.h
- include/seqan/vcf_io.h
- include/seqan/vcf_io/read_vcf.h
- include/seqan/vcf_io/vcf_file.h
- include/seqan/vcf_io/vcf_header.h
- include/seqan/vcf_io/vcf_header_record.h
- include/seqan/vcf_io/vcf_io_context.h
- include/seqan/vcf_io/vcf_record.h
- include/seqan/vcf_io/write_vcf.h
- include/seqan/version.h
- manual/attic/HowTo/GenerateSeqAnKnimeNodes/knime_node.rst
- manual/source/Infrastructure/Contribute/StyleCpp.rst
- manual/source/Infrastructure/Manage/Releases.rst
- manual/source/Infrastructure/Use/Install.rst
- manual/source/Infrastructure/Use/InstallDependencies.rst
- tests/align/test_align.cpp
- tests/align/test_align_align.h
- tests/align/test_align_alignment_operations.h
- tests/align/test_align_bugs.cpp
- tests/align/test_align_fragment.h
- tests/align/test_align_gaps.h
- tests/align/test_align_gaps_iterator.h
- tests/align/test_align_global_alignment.h
- tests/align/test_align_global_alignment_banded.h
- tests/align/test_align_global_alignment_score.h
- tests/align/test_align_global_alignment_specialized.h
- tests/align/test_align_local_alignment.h
- tests/align/test_align_matrix.h
- tests/align/test_align_myers.h
- tests/align/test_align_simd_base.h
- tests/align/test_align_simd_global.h
- tests/align/test_align_simd_global_equal_length.cpp
- tests/align/test_align_simd_global_variable_length.cpp
- tests/align/test_align_simd_local.h
- tests/align/test_align_simd_local_equal_length.cpp
- tests/align/test_align_simd_local_variable_length.cpp
- tests/align/test_align_stream.h
- tests/align/test_alignment_algorithms_band_position.h
- tests/align/test_alignment_algorithms_dynamic_gap.h
- tests/align/test_alignment_algorithms_global.h
- tests/align/test_alignment_algorithms_global_banded.h
- tests/align/test_alignment_algorithms_local.h
- tests/align/test_alignment_algorithms_local_banded.h
- tests/align/test_alignment_dp_adapt_tracesegments.h
- tests/align/test_alignment_dp_band.h
- tests/align/test_alignment_dp_cell.h
- tests/align/test_alignment_dp_formula.h
- tests/align/test_alignment_dp_matrix.h
- tests/align/test_alignment_dp_matrix_navigator.h
- tests/align/test_alignment_dp_profile.h
- tests/align/test_alignment_dp_trace_segment.h
- tests/align/test_alignment_dp_traceback.h
- tests/align/test_evaluate_alignment.h
- tests/align/test_local_align.h
- tests/align/test_mock.h
- tests/align_extend/test_align_extend.cpp
- tests/align_extend/test_align_extend.h
- tests/align_parallel/test_align_parallel_algorithm.cpp
- tests/align_parallel/test_align_parallel_data_structures.cpp
- tests/align_parallel/test_align_parallel_interface.cpp
- tests/align_parallel/test_align_parallel_interface.h
- tests/align_parallel/test_align_parallel_wavefront_alignment.h
- tests/align_parallel/test_align_wavefront_alignment_scheduler.h
- tests/align_parallel/test_align_wavefront_alignment_thread_local.h
- tests/align_parallel/test_align_wavefront_intermediate_dp_result.h
- tests/align_parallel/test_align_wavefront_task_scheduler.h
- tests/align_profile/test_align_profile.cpp
- tests/align_split/test_align_split.cpp
- tests/align_split/test_align_split.h
- tests/alignment_free/test_alignment_free.cpp
- tests/arg_parse/test_arg_parse.cpp
- tests/arg_parse/test_arg_parse.h
- tests/arg_parse/test_arg_parse_argument.h
- tests/arg_parse/test_arg_parse_ctd_support.h
- tests/arg_parse/test_arg_parse_option.h
- tests/arg_parse/test_arg_parse_version_check.cpp
- tests/arg_parse/test_arg_parse_version_check.h
- tests/arg_parse/test_argument_parser.h
- tests/arg_parse/test_extensions.h
- tests/bam_io/test_bam_alignment_record.h
- tests/bam_io/test_bam_file.h
- tests/bam_io/test_bam_header_record.h
- tests/bam_io/test_bam_index.h
- tests/bam_io/test_bam_io.cpp
- tests/bam_io/test_bam_io_context.h
- tests/bam_io/test_bam_sam_conversion.h
- tests/bam_io/test_bam_tags_dict.h
- tests/bam_io/test_read_bam.h
- tests/bam_io/test_read_sam.h
- tests/bam_io/test_write_bam.h
- tests/bam_io/test_write_sam.h
- tests/basic/test_basic.cpp
- tests/basic/test_basic_aggregate.cpp
- tests/basic/test_basic_aggregate.h
- tests/basic/test_basic_allocator.cpp
- tests/basic/test_basic_allocator.h
- tests/basic/test_basic_alphabet.cpp
- tests/basic/test_basic_alphabet.h
- tests/basic/test_basic_alphabet_adapt_builtins.h
- tests/basic/test_basic_alphabet_bio.h
- tests/basic/test_basic_alphabet_concepts.h
- tests/basic/test_basic_alphabet_math.h
- tests/basic/test_basic_alphabet_profile.h
- tests/basic/test_basic_alphabet_qualities.h
- tests/basic/test_basic_alphabet_residue.h
- tests/basic/test_basic_alphabet_simple_type.h
- tests/basic/test_basic_alphabet_storage.h
- tests/basic/test_basic_array_construct_destruct.h
- tests/basic/test_basic_array_constructor_destruct.h
- tests/basic/test_basic_concept.cpp
- tests/basic/test_basic_concepts.h
- tests/basic/test_basic_construct_destruct.h
- tests/basic/test_basic_container.cpp
- tests/basic/test_basic_container_proxy.h
- tests/basic/test_basic_exception.cpp
- tests/basic/test_basic_exception.h
- tests/basic/test_basic_fundamental.cpp
- tests/basic/test_basic_fundamental_comparison.h
- tests/basic/test_basic_fundamental_concepts.h
- tests/basic/test_basic_fundamental_conversion.h
- tests/basic/test_basic_fundamental_helpers.h
- tests/basic/test_basic_fundamental_metafunctions.h
- tests/basic/test_basic_fundamental_tags.h
- tests/basic/test_basic_fundamental_transport.h
- tests/basic/test_basic_hosted_type_interface.h
- tests/basic/test_basic_iterator.cpp
- tests/basic/test_basic_iterator.h
- tests/basic/test_basic_iterator_concepts.h
- tests/basic/test_basic_iterator_zip.h
- tests/basic/test_basic_math.cpp
- tests/basic/test_basic_math.h
- tests/basic/test_basic_metaprogramming.cpp
- tests/basic/test_basic_metaprogramming.h
- tests/basic/test_basic_metaprogramming_control.h
- tests/basic/test_basic_metaprogramming_enable_if.h
- tests/basic/test_basic_metaprogramming_logic.h
- tests/basic/test_basic_metaprogramming_math.h
- tests/basic/test_basic_metaprogramming_type.h
- tests/basic/test_basic_parallelism.cpp
- tests/basic/test_basic_parallelism.h
- tests/basic/test_basic_proxy.cpp
- tests/basic/test_basic_proxy.h
- tests/basic/test_basic_smart_pointer.cpp
- tests/basic/test_basic_smart_pointer_holder.h
- tests/basic/test_basic_tag.h
- tests/basic/test_basic_transport.h
- tests/basic/test_basic_type.h
- tests/bed_io/test_bed_io.cpp
- tests/blast/test_blast.cpp
- tests/blast/test_blast_input.h
- tests/blast/test_blast_misc.h
- tests/blast/test_blast_output.h
- tests/blast/test_blast_statistics.h
- tests/consensus/test_consensus.cpp
- tests/consensus/test_consensus.h
- tests/consensus/test_consensus_realign.h
- tests/consensus_v2/test_consensus_v2.cpp
- tests/find/test_find.cpp
- tests/find/test_find_hamming.h
- tests/find/test_find_myers_banded.h
- tests/gff_io/test_gff_io.cpp
- tests/gff_io/test_gff_io.h
- tests/graph_algorithms/test_graph_algorithms.cpp
- tests/graph_algorithms/test_graph_algorithms.h
- tests/graph_align/test_graph_align.cpp
- tests/graph_align/test_graph_impl_align.h
- tests/graph_align/test_graph_match_refinement.h
- tests/graph_msa/test_graph_msa.cpp
- tests/graph_msa/test_graph_msa_guide_tree.h
- tests/graph_msa/test_graph_tcoffee.h
- tests/graph_types/test_graph_types_basic.cpp
- tests/graph_types/test_graph_types_derived.cpp
- tests/graph_types/test_graph_types_iterators.cpp
- tests/graph_types/test_graph_types_property_map.cpp
- tests/graph_types/test_graph_types_types.cpp
- tests/graph_types/test_graph_types_utils.cpp
- tests/index/test_crosscompare.h
- tests/index/test_find2_index_approx.cpp
- tests/index/test_find2_index_approx.h
- tests/index/test_index_base.cpp
- tests/index/test_index_bifm.cpp
- tests/index/test_index_creation.cpp
- tests/index/test_index_creation.h
- tests/index/test_index_crosscompare_char.cpp
- tests/index/test_index_crosscompare_char_dfi.cpp
- tests/index/test_index_crosscompare_dna.cpp
- tests/index/test_index_crosscompare_dna_dfi.cpp
- tests/index/test_index_drawing.cpp
- tests/index/test_index_finder.cpp
- tests/index/test_index_fm.cpp
- tests/index/test_index_fm_rank_dictionary.cpp
- tests/index/test_index_fm_right_array_binary_tree.cpp
- tests/index/test_index_fm_right_array_binary_tree.h
- tests/index/test_index_fm_right_array_binary_tree_iterator.h
- tests/index/test_index_fm_sparse_string.cpp
- tests/index/test_index_fm_stree.h
- tests/index/test_index_helpers.h
- tests/index/test_index_qgram.cpp
- tests/index/test_index_repeats.cpp
- tests/index/test_index_repeats.h
- tests/index/test_index_sa_bwtwalk.cpp
- tests/index/test_index_shapes.cpp
- tests/index/test_index_stree_iterators.cpp
- tests/index/test_index_vstree.cpp
- tests/index/test_qgram_index.h
- tests/index/test_sa_bwtwalk.h
- tests/index/test_shapes.h
- tests/index/test_stree_iterators.h
- tests/journaled_set/test_journaled_set.cpp
- tests/journaled_set/test_journaled_set.h
- tests/journaled_string_tree/test_basic_observable.cpp
- tests/journaled_string_tree/test_basic_observable.h
- tests/journaled_string_tree/test_delta_map.cpp
- tests/journaled_string_tree/test_delta_map.h
- tests/journaled_string_tree/test_delta_store.h
- tests/journaled_string_tree/test_journaled_string_tree.cpp
- tests/journaled_string_tree/test_journaled_string_tree.h
- tests/journaled_string_tree/test_journaled_string_tree_find.cpp
- tests/journaled_string_tree/test_journaled_string_tree_find.h
- tests/journaled_string_tree/test_journaled_string_tree_mock.h
- tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp
- tests/journaled_string_tree/test_journaled_string_tree_traverser.h
- tests/map/test_map.cpp
- tests/map/test_map_map.h
- tests/map/test_map_sumlist.h
- tests/misc/test_misc.cpp
- tests/misc/test_misc_accumulators.h
- tests/misc/test_misc_bit_twiddling.h
- tests/misc/test_misc_edit_environment.h
- tests/misc/test_misc_interval_tree.h
- tests/modifier/helpers.h
- tests/modifier/test_modifier.cpp
- tests/modifier/test_modifier_alphabet.h
- tests/modifier/test_modifier_functors.h
- tests/modifier/test_modifier_shortcuts.h
- tests/modifier/test_modifier_string.h
- tests/modifier/test_modifier_string_padding.h
- tests/modifier/test_modifier_view.h
- tests/modifier_cyclic_shape/test_cyclic_shape.h
- tests/modifier_cyclic_shape/test_modifier_cyclic_shape.cpp
- tests/modifier_cyclic_shape/test_modifier_cyclic_shape.h
- tests/multiple_translation_units/test_multiple_translation_units.cpp
- tests/multiple_translation_units/test_multiple_translation_units_2.cpp
- tests/parallel/test_parallel.cpp
- tests/parallel/test_parallel_algorithms.h
- tests/parallel/test_parallel_atomic_misc.h
- tests/parallel/test_parallel_atomic_primitives.h
- tests/parallel/test_parallel_enumerable_thread_local.h
- tests/parallel/test_parallel_queue.h
- tests/parallel/test_parallel_splitting.h
- tests/parallel/test_parallel_thread_pool.h
- tests/parse_lm/test_parse_lm.cpp
- tests/parse_lm/test_parse_lm.h
- tests/pipe/test_pipe.cpp
- tests/pipe/test_pipe.h
- tests/platform/test_platform.cpp
- tests/platform/test_platform_range_based_for_loops.h
- tests/random/test_random.cpp
- tests/random/test_random_basic.h
- tests/random/test_random_beta.h
- tests/random/test_random_util.h
- tests/realign/test_realign.cpp
- tests/reduced_aminoacid/test_reduced_aminoacid.cpp
- tests/reduced_aminoacid/test_reduced_aminoacid.h
- tests/rna_io/test_rna_io.cpp
- tests/rna_io/test_rna_io.h
- tests/roi_io/test_roi_io.cpp
- tests/score/test_score.cpp
- tests/seeds/seed_set_test_helpers.h
- tests/seeds/test_align_banded_chain_impl.cpp
- tests/seeds/test_align_banded_chain_issue_2540.cpp
- tests/seeds/test_banded_chain_alignment_interface.cpp
- tests/seeds/test_seeds_combination.cpp
- tests/seeds/test_seeds_extension.cpp
- tests/seeds/test_seeds_global_chaining.cpp
- tests/seeds/test_seeds_seed_base.cpp
- tests/seeds/test_seeds_seed_chained.cpp
- tests/seeds/test_seeds_seed_diagonal.cpp
- tests/seeds/test_seeds_seed_set_base.cpp
- tests/seeds/test_seeds_seed_set_unordered.cpp
- tests/seeds/test_seeds_seed_simple.cpp
- tests/seq_io/test_fai_index.h
- tests/seq_io/test_genomic_region.h
- tests/seq_io/test_read_bam.h
- tests/seq_io/test_seq_io.cpp
- tests/seq_io/test_seq_io_generic.h
- tests/seq_io/test_sequence_file.h
- tests/seq_io/test_stream_read_embl.h
- tests/seq_io/test_stream_read_genbank.h
- tests/seq_io/test_stream_record_reader_fasta.h
- tests/seq_io/test_stream_write_fasta.h
- tests/seq_io/test_tag_select_intersect.h
- tests/seq_io/test_write_bam.h
- tests/sequence/test_segment.h
- tests/sequence/test_segment_beta.h
- tests/sequence/test_sequence.cpp
- tests/sequence/test_sequence.h
- tests/sequence/test_sequence_std_adaptions.h
- tests/sequence/test_sequence_v2.cpp
- tests/sequence/test_string.h
- tests/sequence/test_string_packed_extension.h
- tests/sequence/test_string_set.h
- tests/sequence/test_stringset.h
- tests/sequence/test_stringset_v2.cpp
- tests/sequence_journaled/test_sequence_journaled.cpp
- tests/sequence_journaled/test_sequence_journaled.h
- tests/sequence_journaled/test_sequence_journaled_iterator.h
- tests/simd/test_simd_vector.cpp
- tests/simd/test_simd_vector.h
- tests/simple_intervals_io/test_simple_intervals_io.cpp
- tests/statistics/test_statistics.cpp
- tests/statistics/test_statistics_base.h
- tests/statistics/test_statistics_markov_model.h
- tests/store/test_store.cpp
- tests/store/test_store_io.h
- tests/store/test_store_io_bam.h
- tests/stream/test_stream.cpp
- tests/stream/test_stream_file_stream.h
- tests/stream/test_stream_generic.h
- tests/stream/test_stream_lexical_cast.h
- tests/stream/test_stream_tokenization.h
- tests/stream/test_stream_virtual_stream.h
- tests/stream/test_stream_write.h
- tests/swift_local/test_find_swift.cpp
- tests/tabix_io/test_tabix_io.cpp
- tests/tabix_io/test_tabix_io.h
- tests/translation/test_translation.cpp
- tests/translation/test_translation.h
- tests/ucsc_io/test_ucsc_io.cpp
- tests/vcf_io/test_vcf_io.cpp
- tests/vcf_io/test_vcf_io.h
- util/bin/link_check.sh
- util/bump_app_versions.sh
- util/cmake/FindGitInfo.cmake
- util/cmake/FindSDE.cmake
- util/cmake/FindUmesimd.cmake
- util/cmake/GetCurrentDate.cmake
- util/cmake/GetCurrentDate.cpp
- util/cmake/SeqAnBuildSystem.cmake
- util/cmake/SeqAnConsistentFPFlags.cmake
- util/cmake/SeqAnContribs.cmake
- util/cmake/SeqAnCtdSetup.cmake
- + util/cmake/SeqAnMSVCccache.cmake
- util/cmake/SeqAnSimdUtility.cmake
- util/cmake/SeqAnUsabilityAnalyzer.cmake
- util/cmake/SetCPackSystemName.cmake
- util/cmake/ctd/COPYRIGHT
- util/cmake/ctd/LICENSE
- util/cmake/package.cmake
- util/cmake/seqan-config.cmake
- util/headers/header_bsd.txt
- util/linux_binary_tests.sh
- util/py_lib/seqan/LICENSE
- util/skel/app_template/LICENSE
- util/skel/app_template/app.cpp
- util/skel/demo_template/demo.cpp
- util/skel/header_template/header.h
- util/skel/header_template/library_header.h
- util/skel/module_template/header.h
- util/skel/module_template/module.h
- util/skel/test_template/test.cpp
- util/skel/test_template/test.h
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/seqan2/-/compare/f5d29b0235262d65271a5570f1fe6474bdbfeb93...90ae566a8ff6d638e815f46622461401cea37a1e
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View it on GitLab: https://salsa.debian.org/med-team/seqan2/-/compare/f5d29b0235262d65271a5570f1fe6474bdbfeb93...90ae566a8ff6d638e815f46622461401cea37a1e
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