Andreas Tille pushed to branch upstream at Debian Med / diamond-aligner
Commits: fa5e5581 by Andreas Tille at 2026-09-03T10:41:47+02:00 New upstream version 2.2.6 - - - - - 165 changed files: - CITATION.cff - CMakeLists.txt - README.md - src/ChangeLog - src/align/align.cpp - src/align/alt_hsp.cpp - src/align/culling.cpp - src/align/def.h - src/align/extend.cpp - src/align/extend.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/table.cpp - src/align/load_hits.h - src/align/output.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/packed_transcript.h - src/basic/sequence.h - src/basic/shape.h - src/basic/statistics.h - src/cluster/cluster.h - + src/cluster/combine_blocks.cpp - + src/cluster/count_seeds.cpp - src/cluster/data.cpp - src/cluster/file_array.h - src/cluster/helpers.cpp - src/cluster/len_sort.cpp - src/cluster/lin_index.cpp - src/cluster/make_blocks.cpp - src/cluster/multinode.cpp - src/cluster/multinode.h - src/cluster/output.cpp - src/cluster/radixed_table.h - src/cluster/realign.cpp - src/cluster/search.cpp - src/cluster/volume.h - src/data/blastdb/phr.cpp - src/data/blastdb/psq.cpp - src/data/fasta/fasta_file.cpp - src/data/fasta/fasta_file.h - src/data/fasta/parser.h - + src/data/fasta/volumed_fasta_file.cpp - + src/data/fasta/volumed_fasta_file.h - src/data/seed_set.cpp - src/data/seed_set.h - src/data/sequence_file.cpp - src/data/sequence_file.h - src/dp/dp.h - src/dp/scalar/traceback.h - src/dp/score_profile.cpp - 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/full_matrix.h - src/dp/swipe/full_swipe.h - src/dp/swipe/swipe.h - src/dp/swipe/swipe_wrapper.cpp - src/dp/swipe/target_iterator.h - src/dp/ungapped_simd.cpp - src/chaining/aligner.h → src/legacy/chaining/aligner.h - src/chaining/backtrace.cpp → src/legacy/chaining/backtrace.cpp - src/chaining/chaining.h → src/legacy/chaining/chaining.h - src/chaining/diag_graph.h → src/legacy/chaining/diag_graph.h - src/chaining/greedy_align.cpp → src/legacy/chaining/greedy_align.cpp - src/chaining/hamming_ext.cpp → src/legacy/chaining/hamming_ext.cpp - src/chaining/smith_waterman.cpp → src/legacy/chaining/smith_waterman.cpp - src/legacy/daa/daa_record.cpp - src/legacy/daa/view.cpp - src/legacy/dmnd/io.h - src/align/legacy/banded_swipe_pipeline.cpp → src/legacy/frameshift/banded_swipe_pipeline.cpp - src/align/legacy/pipeline.h → src/legacy/frameshift/pipeline.h - src/align/legacy/query_mapper.cpp → src/legacy/frameshift/query_mapper.cpp - src/align/legacy/query_mapper.h → src/legacy/frameshift/query_mapper.h - src/run/tools.cpp → src/legacy/tools.cpp - src/legacy/util/task_queue.h - − src/lib/atomic_wait/atomic_wait - − src/lib/atomic_wait/barrier - − src/lib/atomic_wait/latch - − src/lib/atomic_wait/semaphore - − src/lib/interval_tree/interval_tree.hpp - − src/lib/interval_tree/interval_tree_fwd.hpp - − src/lib/interval_tree/interval_types.hpp - − src/masking/lambda.cpp - src/masking/masking.h - src/masking/tantan.cpp - src/masking/tantan.h - src/util/simd/vector8_avx512.h → src/masking/tantan_step.h - + src/masking/tantan_step_avx2.h - + src/masking/tantan_step_avx512.h - src/util/simd/vector_generic.h → src/masking/tantan_step_generic.h - + src/masking/tantan_step_neon.h - + src/masking/tantan_step_sse.h - src/output/blast_pairwise_format.cpp - src/output/blast_tab_format.cpp - src/output/output_format.cpp - src/output/output_format.h - src/output/target_culling.h - src/run/config.cpp - src/run/double_indexed.cpp - src/run/main.cpp - src/run/workflow.h - src/search/hamming/finger_print.h - src/search/hamming/kernel.h - src/search/hamming/kernel_lin.h - src/search/hamming/kernel_mutual_cov.h - src/search/hamming/stage1_2.cpp - src/search/hit_buffer.cpp - src/search/hit_buffer.h - src/search/lin_index/lin_index.cpp - src/search/lin_index/lin_index.h - src/search/lin_index/scan.cpp - src/search/search.h - src/search/seed_array/enum_seeds.h - src/search/seed_array/seed_iterator.h - src/search/setup.cpp - src/search/stage2.h - src/stats/cbs.cpp - src/stats/cbs.h - src/stats/stats.cpp - + src/test/blastx-frameshift.out - src/test/deepclust-multiblock.out - src/test/deepclust.out - src/test/diamond-test-blastp-very-sensitive.out - src/test/hit_buffer_stress.cpp - src/test/linclust.out - src/test/realign.out - src/tools/benchmark.cpp - + src/tools/count_distinct.cpp - src/tools/greedy_vertex_cover.cpp - src/util/algo/hash_join.h - src/util/algo/hyperloglog.h - + src/util/data_structures/bloom_filter.h - src/util/data_structures/mem_buffer.h - src/util/data_structures/reorder_queue.h - src/util/intrin.h - src/util/memory/alignment.h - + src/util/memory/mem_profile.cpp - + src/util/memory/mem_profile.h - src/util/memory/memory_resource.h - src/util/memory/vmbuffer.h - src/util/simd.cpp - src/util/simd.h - src/util/simd/dispatch.h - src/util/simd/transpose.h - − src/util/simd/vector.h - − src/util/simd/vector8_avx2.h - − src/util/simd/vector8_neon.h - − src/util/simd/vector8_sse.h - src/util/system/system.cpp - src/util/system/system.h - src/util/text_buffer.h The diff was not included because it is too large. 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