Étienne Mollier pushed to branch master at Debian Med / diamond-aligner
Commits: e28f2c3b by Étienne Mollier at 2025-03-06T20:39:51+01:00 New upstream version 2.1.11 - - - - - 929b7901 by Étienne Mollier at 2025-03-06T20:39:56+01:00 Update upstream source from tag 'upstream/2.1.11' Update to upstream version '2.1.11' with Debian dir 7cc430daa1ed5775e5a3b7579e91c98f38c71360 - - - - - 50ea1090 by Étienne Mollier at 2025-03-07T22:24:45+01:00 d/copyright: much needed copyright rehaul. - - - - - fdbbd476 by Étienne Mollier at 2025-03-07T22:25:24+01:00 d/control: declare compliance to standards version 4.7.2. - - - - - 228cfb51 by Étienne Mollier at 2025-03-07T22:25:54+01:00 d/control: add myself to uploaders. - - - - - 4d1eb669 by Étienne Mollier at 2025-03-07T22:44:30+01:00 typo.patch: fix typo caught by lintian. - - - - - 63338deb by Étienne Mollier at 2025-03-07T22:45:02+01:00 d/changelog: ready for upload to unstable. - - - - - 373 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 - debian/changelog - debian/control - debian/copyright - + debian/patches/series - + debian/patches/typo.patch - 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/-/compare/c40a04e2d2348643b947bd83f99397385ecdd854...63338deb1c9ee39a8eb618c0675b666c9ebbbb53 -- View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/c40a04e2d2348643b947bd83f99397385ecdd854...63338deb1c9ee39a8eb618c0675b666c9ebbbb53 You're receiving this email because of your account on salsa.debian.org.
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