[med-svn] [Git][med-team/diamond-aligner][upstream] New upstream version 2.1.11

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / diamond-aligner


Commits:
e28f2c3b by Étienne Mollier at 2025-03-06T20:39:51+01:00
New upstream version 2.1.11
- - - - -


368 changed files:

- .cirrus.yml
- .github/workflows/cmake.yml
- + .github/workflows/codeql.yml
- − .travis.yml
- CITATION.cff
- CMakeLists.txt
- Dockerfile
- − FindLAPACKE.cmake
- − FindLAPACKEXT.cmake
- README.md
- − azure-pipelines.yml
- src/ChangeLog
- src/align/align.cpp
- src/align/align.h
- src/align/alt_hsp.cpp
- src/align/culling.cpp
- src/align/culling.h
- src/align/def.h
- src/align/extend.cpp
- src/align/extend.h
- src/align/extend_chunk.h
- src/align/full_db.cpp
- src/align/gapped_filter.cpp
- src/align/gapped_final.cpp
- src/align/gapped_score.cpp
- src/align/global_ranking/extend.cpp
- src/align/global_ranking/global_ranking.cpp
- src/align/global_ranking/global_ranking.h
- src/align/global_ranking/table.cpp
- src/align/legacy/banded_swipe_pipeline.cpp
- src/align/legacy/pipeline.h
- src/align/legacy/query_mapper.cpp
- src/align/legacy/query_mapper.h
- src/align/load_hits.h
- src/align/output.cpp
- src/align/short.cpp
- src/align/target.h
- src/align/ungapped.cpp
- src/basic/basic.cpp
- src/basic/config.cpp
- src/basic/config.h
- src/basic/const.h
- src/basic/hssp.cpp
- src/basic/match.h
- src/basic/packed_loc.h
- src/basic/packed_sequence.h
- src/basic/packed_transcript.h
- src/basic/reduction.h
- src/basic/seed.h
- src/basic/seed_iterator.h
- src/basic/sequence.h
- src/basic/shape.h
- src/basic/shape_config.h
- src/basic/statistics.h
- src/basic/translated_position.h
- src/basic/value.cpp
- src/basic/value.h
- src/chaining/aligner.h
- src/chaining/backtrace.cpp
- src/chaining/chaining.h
- src/chaining/diag_graph.h
- src/chaining/greedy_align.cpp
- src/chaining/hamming_ext.cpp
- src/chaining/smith_waterman.cpp
- src/cluster/cascaded/cascaded.cpp
- src/cluster/cascaded/cascaded.h
- src/cluster/cascaded/helpers.cpp
- src/cluster/cascaded/recluster.cpp
- src/cluster/cascaded/wrapper.cpp
- src/cluster/cluster.h
- + src/cluster/external/make_seed_table.cpp
- src/cluster/helpers.cpp
- src/cluster/output.cpp
- src/cluster/realign.cpp
- src/cluster/reassign.cpp
- + src/contrib/dna/alignment.cpp
- + src/contrib/dna/alignment.h
- src/stats/dna_scoring/build_score.cpp → src/contrib/dna/build_score.cpp
- src/stats/dna_scoring/build_score.h → src/contrib/dna/build_score.h
- + src/contrib/dna/chain.cpp
- src/dna/chain.h → src/contrib/dna/chain.h
- src/dna/dna_index.cpp → src/contrib/dna/dna_index.cpp
- src/dna/dna_index.h → src/contrib/dna/dna_index.h
- src/dna/extension.cpp → src/contrib/dna/extension.cpp
- src/dna/extension.h → src/contrib/dna/extension.h
- + src/contrib/dna/extension_chain.cpp
- src/dna/extension_chain.h → src/contrib/dna/extension_chain.h
- + src/contrib/dna/extension_seed_matches.cpp
- src/data/reference.h → src/contrib/dna/extension_seed_matches.h
- src/dna/seed_set_dna.cpp → src/contrib/dna/seed_set_dna.cpp
- src/dna/seed_set_dna.h → src/contrib/dna/seed_set_dna.h
- + src/contrib/dna/setup.cpp
- src/dna/smith_watermann.cpp → src/contrib/dna/smith_watermann.cpp
- src/dna/smith_watermann.h → src/contrib/dna/smith_watermann.h
- src/dna/timer.h → src/contrib/dna/timer.h
- src/output/clustering_format.cpp → src/contrib/mcl/clustering_format.cpp
- src/output/clustering_variables.cpp → src/contrib/mcl/clustering_variables.cpp
- src/output/clustering_variables.h → src/contrib/mcl/clustering_variables.h
- src/util/data_structures/lazy_disjoint_set.h → src/contrib/mcl/lazy_disjoint_set.h
- src/contrib/mcl/mcl.cpp
- src/contrib/mcl/mcl.h
- src/output/recursive_parser.h → src/contrib/mcl/recursive_parser.h
- src/contrib/mcl/sparse_matrix_stream.h
- src/data/blastdb/blastdb.cpp
- src/data/blastdb/blastdb.h
- src/data/block/block.cpp
- src/data/block/block.h
- src/data/block/block_wrapper.cpp
- src/data/block/block_wrapper.h
- src/data/dmnd/dmnd.cpp
- src/data/dmnd/dmnd.h
- src/data/enum_seeds.h
- src/data/fasta/fasta_file.cpp
- src/data/fasta/fasta_file.h
- src/data/flags.h
- src/data/frequent_seeds.cpp
- src/data/frequent_seeds.h
- src/data/index.cpp
- src/data/queries.cpp
- src/data/queries.h
- src/data/seed_array.cpp
- src/data/seed_array.h
- src/data/seed_histogram.cpp
- src/data/seed_histogram.h
- src/data/seed_set.cpp
- src/data/seed_set.h
- src/data/sequence_file.cpp
- src/data/sequence_file.h
- src/data/sequence_set.cpp
- src/data/sequence_set.h
- src/data/string_set.h
- src/data/taxon_list.cpp
- src/data/taxon_list.h
- src/data/taxonomy.cpp
- src/data/taxonomy.h
- src/data/taxonomy_nodes.cpp
- src/data/taxonomy_nodes.h
- − src/dna/chain.cpp
- − src/dna/extension_chain.cpp
- src/dp/dp.h
- src/dp/flags.h
- − src/dp/pfscan/pfscan.cpp
- − src/dp/pfscan/pfscan.h
- − src/dp/pfscan/simd.h
- − src/dp/pfscan/smith_waterman.h
- src/dp/needleman_wunsch.h → src/dp/scalar/needleman_wunsch.h
- src/dp/scalar/smith_waterman.cpp
- src/dp/scalar/traceback.h
- src/dp/scan_diags.cpp
- src/dp/score_profile.cpp
- src/dp/score_profile.h
- src/dp/score_vector.h
- src/dp/score_vector_int16.h
- src/dp/score_vector_int8.h
- src/dp/swipe/anchored.h
- src/dp/swipe/anchored_wrapper.cpp
- src/dp/swipe/banded_3frame_swipe.cpp
- src/dp/swipe/banded_matrix.h
- src/dp/swipe/banded_swipe.h
- src/dp/swipe/cell_update.h
- src/dp/swipe/config.h
- src/dp/swipe/full_matrix.h
- src/dp/swipe/full_swipe.h
- src/dp/swipe/stat_cell.h
- src/dp/swipe/swipe.h
- src/dp/swipe/swipe_wrapper.cpp
- src/dp/swipe/target_iterator.h
- src/dp/ungapped.h
- src/dp/ungapped_align.cpp
- src/dp/ungapped_simd.cpp
- src/dp/ungapped_simd.h
- src/util/data_structures/compact_array.h → src/legacy/dmnd/compact_array.h
- + src/legacy/dmnd/io.h
- src/util/io/record_reader.h → src/legacy/dmnd/record_reader.h
- − src/lib/MemoryPool/MemoryPool.h
- − src/lib/MemoryPool/MemoryPool.tcc
- src/lib/WFA2-lib.diamond/alignment/cigar.h
- src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp
- src/lib/alp/njn_ioutil.cpp
- src/lib/alp/njn_matrix.hpp
- src/lib/alp/njn_vector.hpp
- src/lib/alp/sls_alignment_evaluer.cpp
- src/lib/alp/sls_alp_data.cpp
- src/lib/alp/sls_basic.hpp
- src/lib/blast/blastn_score.cpp
- src/lib/ips4o/buffers.hpp
- src/util/algo/MurmurHash3.cpp → src/lib/murmurhash/MurmurHash3.cpp
- src/util/algo/MurmurHash3.h → src/lib/murmurhash/MurmurHash3.h
- src/lib/tantan/LambdaCalculator.cc
- src/masking/def.h
- src/masking/masking.cpp
- src/masking/masking.h
- src/masking/tantan.cpp
- src/masking/tantan.h
- src/output/blast_pairwise_format.cpp
- src/output/blast_tab_format.cpp
- src/output/daa/daa_file.h
- src/output/daa/daa_record.cpp
- src/output/daa/daa_record.h
- src/output/daa/daa_write.cpp
- src/output/daa/daa_write.h
- src/output/daa/merge.cpp
- src/output/daa/view.cpp
- src/output/def.h
- src/output/join_blocks.cpp
- src/output/output.h
- src/output/output_format.cpp
- src/output/output_format.h
- src/output/output_sink.cpp
- src/output/paf_format.cpp
- src/output/sam_format.cpp
- src/output/target_culling.h
- src/output/taxon_format.cpp
- src/output/xml_format.cpp
- src/run/config.cpp
- src/run/config.h
- src/run/double_indexed.cpp
- src/run/main.cpp
- src/run/tools.cpp
- src/run/tools.h
- src/run/workflow.h
- src/search/finger_print.h
- src/search/hit.h
- src/search/kmer_ranking.cpp
- src/search/kmer_ranking.h
- src/search/left_most.h
- src/search/search.h
- src/search/seed_complexity.cpp
- src/search/seed_complexity.h
- src/search/setup.cpp
- src/search/sse_dist.h
- src/search/stage0.cpp
- src/search/stage1.h
- src/search/stage2.h
- src/stats/cbs.cpp
- src/stats/cbs.h
- src/stats/comp_based_stats.cpp
- src/stats/hauser_correction.cpp
- src/stats/hauser_correction.h
- src/stats/matrix_adjust.cpp
- src/stats/matrix_adjust_eigen.cpp
- src/stats/score_matrix.cpp
- src/stats/score_matrix.h
- src/stats/standard_matrix.h
- src/stats/stats.cpp
- src/test/data.cpp
- src/test/test.cpp
- src/test/test.h
- src/test/test_cases.cpp
- src/tools/benchmark.cpp
- src/tools/benchmark_io.cpp
- src/tools/benchmark_swipe.cpp
- src/tools/find_shapes.cpp
- src/tools/greedy_vertex_cover.cpp
- − src/tools/join.cpp
- src/tools/roc.cpp
- src/tools/rocid.cpp
- src/tools/tools.cpp
- src/tools/tsv.cpp
- − src/tools/tsv_record.cpp
- − src/tools/tsv_record.h
- − src/tools/view.cpp
- src/util/algo/algo.h
- − src/util/algo/edge_vec.cpp
- − src/util/algo/edge_vec.h
- src/util/algo/external_sort.h
- src/util/algo/greedy_vertex_cover.cpp
- src/util/algo/hash_join.h
- src/util/algo/join_result.h
- src/util/algo/partition.h
- src/util/algo/pattern_matcher.h
- src/util/algo/radix_cluster.h
- src/util/algo/radix_sort.h
- src/util/algo/transform_iterator.h
- src/util/algo/varint.h
- src/util/async_buffer.h
- src/util/binary_buffer.h
- src/util/command_line_parser.cpp
- src/util/command_line_parser.h
- src/util/data_structures/array.h
- src/util/data_structures/bit_vector.h
- src/util/data_structures/deque.h
- src/util/data_structures/double_array.h
- src/util/data_structures/flat_array.h
- src/util/data_structures/hash_table.h
- src/util/data_structures/sparse_flat_array.h
- src/util/escape_sequences.h
- src/util/geo/diagonal_segment.h
- src/util/geo/geo.h
- src/util/geo/interval.h
- src/util/geo/interval_partition.h
- src/util/geo/interval_tree.h
- src/util/hsp/approx_hsp.h
- src/util/io/async_file.h
- src/util/io/compressed_stream.cpp
- src/util/io/compressed_stream.h
- src/util/io/deserializer.cpp
- src/util/io/deserializer.h
- src/util/io/exceptions.h
- src/util/io/file_sink.cpp
- src/util/io/file_sink.h
- src/util/io/file_source.cpp
- src/util/io/file_source.h
- src/util/io/input_file.cpp
- src/util/io/input_file.h
- src/util/io/input_stream_buffer.cpp
- src/util/io/input_stream_buffer.h
- src/util/io/output_file.cpp
- src/util/io/output_file.h
- src/util/io/output_stream_buffer.cpp
- src/util/io/serializer.cpp
- src/util/io/serializer.h
- src/util/io/stream_entity.h
- src/util/io/temp_file.cpp
- src/util/io/temp_file.h
- src/util/io/text_input_file.cpp
- src/util/io/text_input_file.h
- src/util/io/zstd_stream.cpp
- src/util/io/zstd_stream.h
- src/util/kmer/kmer.h
- src/util/log_stream.h
- src/util/math/integer.h
- src/util/math/log2_fast.h
- src/util/memory/alignment.h
- src/util/options/option.h
- src/util/parallel/filestack.cpp
- src/util/parallel/filestack.h
- src/util/parallel/multiprocessing.cpp
- src/util/parallel/multiprocessing.h
- src/util/parallel/parallelizer.cpp
- src/util/parallel/parallelizer.h
- src/util/parallel/thread_pool.h
- src/util/ptr_vector.h
- src/util/scores/cutoff_table.h
- src/util/search/seed_table.h
- − src/util/seq_file_format.cpp
- − src/util/seq_file_format.h
- src/util/sequence/sequence.cpp
- src/util/sequence/sequence.h
- src/util/sequence/translate.h
- src/util/simd/vector.h
- − src/util/string/fixed_string.h
- src/util/string/string.cpp
- src/util/string/string.h
- src/util/string/tokenizer.h
- + src/util/string/tokenizer_dyn.h
- src/util/system.h
- src/util/system/endianness.h
- src/util/system/system.cpp
- src/util/system/system.h
- src/util/table.h
- src/util/text_buffer.h
- src/util/tsv/build_helper.h
- src/util/tsv/construct.h
- src/util/tsv/file.cpp
- src/util/tsv/file.h
- src/data/index.h → src/util/tsv/file_read.h
- src/util/tsv/helpers.h
- src/util/tsv/merge.cpp
- src/util/tsv/read_tsv.cpp
- src/util/tsv/record.cpp
- src/util/tsv/record.h
- src/util/tsv/table.cpp
- src/util/tsv/table.h
- src/util/tsv/tsv.cpp
- src/util/tsv/tsv.h
- src/util/util.cpp
- src/util/util.h


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/e28f2c3baebfbaeca3a7621a6d69e97eec883be6

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