[med-svn] [Git][med-team/swarm-cluster][upstream] New upstream version 3.1.6+dfsg

[Lance Lin (@linqigang)]

Lance Lin pushed to branch upstream at Debian Med / swarm-cluster


Commits:
0ae3c29e by Lance Lin at 2025-11-21T19:23:34+07:00
New upstream version 3.1.6+dfsg
- - - - -


87 changed files:

- CITATION.cff
- Makefile
- README.md
- man/Makefile
- man/swarm.1
- src/Makefile
- src/algo.cc
- src/algo.h
- src/algod1.cc
- src/algod1.h
- src/arch.cc
- src/arch.h
- src/bloomflex.cc
- src/bloomflex.h
- src/bloompat.cc
- src/bloompat.h
- src/db.cc
- src/db.h
- src/derep.cc
- src/derep.h
- src/hashtable.cc
- src/hashtable.h
- src/nw.cc
- src/nw.h
- src/popcnt.cc
- src/popcnt.h
- src/qgram.cc
- src/qgram.h
- src/scan.cc
- src/scan.h
- src/search16.cc
- src/search16.h
- src/search8.cc
- src/search8.h
- src/sse41.cc
- src/sse41.h
- src/ssse3.cc
- src/ssse3.h
- src/swarm.cc
- src/swarm.h
- src/util.cc
- src/util.h
- src/utils/alignment_parameters.h
- src/utils/backtrack.h
- src/utils/cigar.cc
- src/utils/cigar.h
- src/utils/fatal.cc
- src/utils/fatal.h
- src/utils/gcd.h
- src/utils/hashtable_size.cc
- src/utils/hashtable_size.h
- src/utils/input_output.cc
- src/utils/input_output.h
- src/utils/intrinsics_to_functions_aarch64.cc
- src/utils/intrinsics_to_functions_aarch64.h
- src/utils/intrinsics_to_functions_ppc.cc
- src/utils/intrinsics_to_functions_ppc.h
- src/utils/intrinsics_to_functions_x86_64.cc
- src/utils/intrinsics_to_functions_x86_64.h
- src/utils/nt_codec.cc
- src/utils/nt_codec.h
- src/utils/open_and_close_files.cc
- src/utils/open_and_close_files.h
- src/utils/opt_boundary.h
- src/utils/opt_log.h
- src/utils/opt_logfile.h
- src/utils/opt_no_cluster_breaking.h
- src/utils/opt_threads.h
- src/utils/progress.cc
- src/utils/progress.h
- src/utils/pseudo_rng.h
- src/utils/qgram_array.h
- src/utils/qgram_threadinfo.h
- src/utils/queryinfo.h
- src/utils/score_matrix.h
- src/utils/search_data.h
- src/utils/seqinfo.h
- src/utils/threads.h
- src/utils/x86_cpu_feature_popcnt.h
- src/utils/x86_cpu_feature_sse41.h
- src/utils/x86_cpu_feature_ssse3.h
- src/utils/x86_cpu_features.cc
- src/utils/x86_cpu_features.h
- src/variants.cc
- src/variants.h
- src/zobrist.cc
- src/zobrist.h


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/swarm-cluster/-/commit/0ae3c29eefb4fc2b703f4403d889ebe045ae672d

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