[med-svn] [Git][med-team/diamond-aligner][upstream] New upstream version 2.2.8

[Andreas Tille (@tille)]

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


Commits:
38da2abb by Andreas Tille at 2026-10-19T12:01:37+02:00
New upstream version 2.2.8
- - - - -


61 changed files:

- CITATION.cff
- CMakeLists.txt
- src/ChangeLog
- src/align/align.cpp
- src/align/extend.cpp
- src/align/gapped_score.cpp
- + src/align/new/extension.h
- + src/align/new/extension_pipeline.cpp
- + src/align/new/extension_pipeline.h
- + src/align/new/sw.h
- + src/align/new/thread_pool.h
- 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/statistics.h
- src/cluster/combine_blocks.cpp
- src/cluster/data.cpp
- src/cluster/file_array.h
- src/cluster/input_buffer.h
- src/cluster/len_sort.cpp
- src/cluster/merge.cpp
- src/cluster/multinode.cpp
- src/cluster/multinode.h
- src/cluster/output.cpp
- src/cluster/search.cpp
- src/dp/swipe/anchored.h → src/dp/anchored_swipe/anchored.h
- + src/dp/anchored_swipe/anchored_wrapper.cpp
- src/dp/swipe/config.h → src/dp/anchored_swipe/config.h
- src/dp/dp.h
- src/dp/score_profile.cpp → src/dp/long_profile/score_profile.cpp
- src/dp/score_profile.h → src/dp/long_profile/score_profile.h
- src/dp/scan_diags.cpp
- src/dp/scan_diags.h
- src/dp/score_vector_int16.h
- src/dp/score_vector_int8.h
- − src/dp/swipe/anchored_wrapper.cpp
- src/output/blast_pairwise_format.cpp
- src/output/blast_tab_format.cpp
- src/output/output_sink.cpp
- src/search/hit_buffer.cpp
- src/search/lin_index/lin_index.cpp
- src/search/lin_index/lin_index.h
- src/search/lin_index/scan.cpp
- + src/search/lin_index/web_graph.cpp
- + src/search/lin_index/web_graph.h
- src/search/setup.cpp
- src/stats/cbs.cpp
- + src/test/anchored-swipe.out
- src/test/linclust.out
- + src/test/new-ext.out
- src/test/realign.out
- src/test/test.cmake
- src/tools/benchmark.cpp
- src/tools/greedy_vertex_cover.cpp
- src/tools/tools.h
- src/util/options/option.h
- src/util/simd/transpose.h
- src/util/simd/transpose16x16.h


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/38da2abb52c975642a39b74156406c8abfea9246

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View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/commit/38da2abb52c975642a39b74156406c8abfea9246
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