[med-svn] [Git][med-team/diamond-aligner][master] 8 commits: New upstream version

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / diamond-aligner


Commits:
122ef45c by Andreas Tille at 2026-09-03T10:41:46+02:00
New upstream version

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fa5e5581 by Andreas Tille at 2026-09-03T10:41:47+02:00
New upstream version 2.2.6
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5c3c25ef by Andreas Tille at 2026-09-03T10:42:34+02:00
Update upstream source from tag 'upstream/2.2.6'

Update to upstream version '2.2.6'
with Debian dir 0c5a1baa591f0e88c06914db3394d1568b907075
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9533596d by Andreas Tille at 2026-09-03T09:42:47+01:00
Set upstream metadata fields: Bug-Submit, Repository-Browse.

Changes-By: lintian-brush
Fixes: lintian: source: upstream-metadata-missing-bug-tracking [debian/upstream/metadata]
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html

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7d3bc4f0 by Andreas Tille at 2026-09-03T10:46:36+02:00
No patches needed any more for this upstream version

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22558b29 by Andreas Tille at 2026-09-03T10:54:47+02:00
d/copyright: add new Files ;  Add debian/lrc.config

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0134a949 by Andreas Tille at 2026-09-03T11:04:55+02:00
src/lib/atomic_wait was removed from upstream source

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ee616ec0 by Andreas Tille at 2026-09-03T11:12:45+02:00
Upload to unstable

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172 changed files:

- CITATION.cff
- CMakeLists.txt
- README.md
- debian/changelog
- debian/copyright
- + debian/lrc.config
- − debian/patches/compatibility.patch
- − debian/patches/remove-duplicated-traits.patch
- − debian/patches/series
- debian/upstream/metadata
- 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.


View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/6fe0cfa0a516c547ab9ab89f1f908d727d686bdc...ee616ec0e76f3e4d7ba7a8f2b6771e5211ce97a7

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View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/6fe0cfa0a516c547ab9ab89f1f908d727d686bdc...ee616ec0e76f3e4d7ba7a8f2b6771e5211ce97a7
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