[med-svn] [Git][med-team/diamond-aligner][master] 8 commits: Fix build with CMake 4 Closes: #1112842

[Andreas Tille (@tille)]

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


Commits:
92bb63b7 by Andreas Tille at 2025-10-17T11:34:07+02:00
Fix build with CMake 4 Closes: #1112842

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f62d0ea5 by Andreas Tille at 2025-10-17T11:35:52+02:00
d/watch: version=5

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738c7f0a by Andreas Tille at 2025-10-17T11:36:05+02:00
New upstream version 2.1.14
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1f07ea1a by Andreas Tille at 2025-10-17T11:36:05+02:00
New upstream version

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50b52f31 by Andreas Tille at 2025-10-17T11:36:11+02:00
Update upstream source from tag 'upstream/2.1.14'

Update to upstream version '2.1.14'
with Debian dir e956277166279a3320e40b9a37200b6b163e1cb9
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cbb7921c by Andreas Tille at 2025-10-17T11:38:24+02:00
debputy lint --auto-fix (routine-update)

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360f93b5 by Andreas Tille at 2025-10-17T11:44:15+02:00
Patches applied upstream

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dd909852 by Andreas Tille at 2025-10-17T11:50:24+02:00
Upload to unstable

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439 changed files:

- + .github/FUNDING.yml
- .gitignore
- CITATION.cff
- CMakeLists.txt
- Dockerfile
- README.md
- debian/changelog
- debian/control
- − debian/patches/fix_missing_cstring_riscv64.patch
- − debian/patches/series
- − debian/patches/typo.patch
- debian/rules
- debian/watch
- 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/extend_chunk.h
- src/align/full_db.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/legacy/banded_swipe_pipeline.cpp
- src/align/legacy/query_mapper.cpp
- 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/reduction.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/value.cpp
- src/basic/value.h
- src/chaining/smith_waterman.cpp
- src/cluster/cascaded/cascaded.cpp
- src/cluster/cascaded/cascaded.h
- src/cluster/cascaded/helpers.cpp
- src/cluster/cascaded/wrapper.cpp
- + src/cluster/external/align.cpp
- + src/cluster/external/build_pair_table.h
- + src/cluster/external/cluster.cpp
- + src/cluster/external/external.cpp
- + src/cluster/external/external.h
- − src/cluster/external/make_seed_table.cpp
- + src/cluster/external/output.cpp
- + src/cluster/external/radix_sort.h
- src/cluster/helpers.cpp
- src/cluster/output.cpp
- src/cluster/realign.cpp
- + src/compile-osx.sh
- 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/index.cpp
- src/data/queries.cpp
- src/data/seed_array.cpp
- src/data/seed_histogram.cpp
- src/data/seed_histogram.h
- src/data/seed_set.cpp
- src/data/sequence_file.cpp
- src/data/sequence_file.h
- src/data/sequence_set.cpp
- src/data/sequence_set.h
- src/data/taxonomy.cpp
- src/data/taxonomy_nodes.h
- src/dp/dp.h
- src/dp/score_profile.cpp
- src/dp/score_profile.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_matrix.h
- src/dp/swipe/banded_swipe.h
- src/dp/swipe/config.h
- src/dp/swipe/full_swipe.h
- src/dp/swipe/swipe_wrapper.cpp
- src/dp/swipe/target_iterator.h
- src/legacy/util/task_queue.h
- src/lib/Eigen/src/Core/util/Meta.h
- − src/lib/WFA2-lib.diamond/CMakeLists.txt
- − src/lib/WFA2-lib.diamond/LICENSE
- − src/lib/WFA2-lib.diamond/README.md
- − src/lib/WFA2-lib.diamond/VERSION.txt
- − src/lib/WFA2-lib.diamond/alignment/affine2p_penalties.c
- − src/lib/WFA2-lib.diamond/alignment/affine2p_penalties.h
- − src/lib/WFA2-lib.diamond/alignment/affine_penalties.c
- − src/lib/WFA2-lib.diamond/alignment/affine_penalties.h
- − src/lib/WFA2-lib.diamond/alignment/cigar.c
- − src/lib/WFA2-lib.diamond/alignment/cigar.h
- − src/lib/WFA2-lib.diamond/alignment/linear_penalties.h
- − src/lib/WFA2-lib.diamond/alignment/score_matrix.c
- − src/lib/WFA2-lib.diamond/alignment/score_matrix.h
- − src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp
- − src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp
- − src/lib/WFA2-lib.diamond/bindings/rust/build.rs
- − src/lib/WFA2-lib.diamond/bindings/rust/example.rs
- − src/lib/WFA2-lib.diamond/examples/README.md
- − src/lib/WFA2-lib.diamond/examples/wfa_adapt.c
- − src/lib/WFA2-lib.diamond/examples/wfa_basic.c
- − src/lib/WFA2-lib.diamond/examples/wfa_bindings.cpp
- − src/lib/WFA2-lib.diamond/examples/wfa_lambda.cpp
- − src/lib/WFA2-lib.diamond/examples/wfa_repeated.c
- − src/lib/WFA2-lib.diamond/guix.scm
- − src/lib/WFA2-lib.diamond/img/heuristics.aband.10.10.png
- − src/lib/WFA2-lib.diamond/img/heuristics.aband.50.50.png
- − src/lib/WFA2-lib.diamond/img/heuristics.band.10.10.png
- − src/lib/WFA2-lib.diamond/img/heuristics.band.10.150.png
- − src/lib/WFA2-lib.diamond/img/heuristics.drop.none.png
- − src/lib/WFA2-lib.diamond/img/heuristics.none.png
- − src/lib/WFA2-lib.diamond/img/heuristics.wfadap.10.50.1.png
- − src/lib/WFA2-lib.diamond/img/heuristics.wfadap.10.50.10.png
- − src/lib/WFA2-lib.diamond/img/heuristics.xdrop.200.png
- − src/lib/WFA2-lib.diamond/img/heuristics.zdrop.200.png
- − src/lib/WFA2-lib.diamond/img/wfa.endsfree.png
- − src/lib/WFA2-lib.diamond/img/wfa.vs.swg.png
- − src/lib/WFA2-lib.diamond/scripts/fasta2seq.sh
- − src/lib/WFA2-lib.diamond/scripts/seq2fasta.sh
- − src/lib/WFA2-lib.diamond/scripts/wfa.alg.cmp.py
- − src/lib/WFA2-lib.diamond/scripts/wfa.alg.cmp.score.sh
- − src/lib/WFA2-lib.diamond/scripts/wfa.alg.rescore.py
- − src/lib/WFA2-lib.diamond/scripts/wfa.plot.py
- − src/lib/WFA2-lib.diamond/system/mm_allocator.c
- − src/lib/WFA2-lib.diamond/system/mm_allocator.h
- − src/lib/WFA2-lib.diamond/system/mm_stack.c
- − src/lib/WFA2-lib.diamond/system/mm_stack.h
- − src/lib/WFA2-lib.diamond/system/profiler_counter.c
- − src/lib/WFA2-lib.diamond/system/profiler_counter.h
- − src/lib/WFA2-lib.diamond/system/profiler_timer.c
- − src/lib/WFA2-lib.diamond/system/profiler_timer.h
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.p0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.p1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.p2.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.p3.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.p4.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.p5.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.wfapt0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine.wfapt1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.affine2p.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.p0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.p1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.p2.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.p3.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.p4.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.p5.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.wfapt0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine.wfapt1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.affine2p.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.edit.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.indel.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.p0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.p1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.p2.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.p3.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.p4.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.p5.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.wfapt0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine.wfapt1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.affine2p.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.edit.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.biwfa.score.indel.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.edit.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.indel.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.p0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.p1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.p2.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.p3.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.p4.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.p5.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.wfapt0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine.wfapt1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.affine2p.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.edit.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.pb.indel.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.p0.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.p1.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.p2.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.p3.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.p4.alg
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- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine.wfapt0.alg
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- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.affine2p.alg
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/test.score.edit.alg
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- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/wfa.utest.log
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/wfa.utest.log.mem
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.check/wfa.utest.log.time
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.clean.sh
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.cmp.sh
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.performance.sh
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.seq
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.sh
- − src/lib/WFA2-lib.diamond/tests/wfa.utest.valgrind.sh
- − src/lib/WFA2-lib.diamond/tools/README.md
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_check.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_check.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_edit.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_edit.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_affine.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_affine.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_affine2p.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_affine2p.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_linear.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_linear.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_indel.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_indel.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_utils.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_utils.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_dp.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_dp.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/affine_matrix.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/affine_matrix.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_dp.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_dp.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_matrix.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_matrix.h
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_linear/nw.c
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- − src/lib/WFA2-lib.diamond/tools/align_benchmark/indel/indel_dp.c
- − src/lib/WFA2-lib.diamond/tools/align_benchmark/indel/indel_dp.h
- − src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c
- − src/lib/WFA2-lib.diamond/utils/bitmap.c
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- − src/lib/WFA2-lib.diamond/utils/commons.c
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- − src/lib/WFA2-lib.diamond/utils/dna_text.c
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- − src/lib/WFA2-lib.diamond/utils/heatmap.c
- − src/lib/WFA2-lib.diamond/utils/heatmap.h
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- − src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_offset.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_sequences.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_sequences.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_slab.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_slab.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_termination.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_termination.h
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c
- − src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.h
- − src/lib/WFA2-lib.diamond/wavefront/wfa.h
- − src/lib/WFA2-lib.diamond/wavefront/wfa.hpp
- src/lib/alp/njn_dynprogproblim.hpp
- src/lib/alp/sls_alp_data.cpp
- src/lib/atomic_wait/atomic_wait
- src/lib/atomic_wait/semaphore
- src/lib/blast/blastn_score.cpp
- − src/lib/cgranges/IITree.h
- src/lib/mio/mmap.hpp
- src/lib/mio/page.hpp
- src/masking/tantan.cpp
- src/output/blast_pairwise_format.cpp
- src/output/blast_tab_format.cpp
- src/output/daa/daa_record.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/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.h
- src/search/finger_print.h
- src/search/hit.h
- + src/search/hit_buffer.cpp
- src/util/async_buffer.h → src/search/hit_buffer.h
- src/search/search.h
- src/search/seed_complexity.cpp
- src/search/setup.cpp
- src/search/sse_dist.h
- src/search/stage0.cpp
- src/search/stage2.h
- + src/stats/blast/linear_algebra.h
- + src/stats/blast/linear_algebra_ncbi.h
- + src/stats/blast/math.h
- + src/stats/blast/matrix_adjust.cpp
- + src/stats/blast/matrix_adjust.h
- + src/stats/blast/ncbi.cpp
- src/stats/cbs.cpp
- src/stats/cbs.h
- src/stats/comp_based_stats.cpp
- src/stats/matrices/blosum45.cpp → src/stats/matrices/blosum45.h
- src/stats/matrices/blosum50.cpp → src/stats/matrices/blosum50.h
- src/stats/matrices/blosum62.cpp → src/stats/matrices/blosum62.h
- src/stats/matrices/blosum80.cpp → src/stats/matrices/blosum80.h
- src/stats/matrices/blosum90.cpp → src/stats/matrices/blosum90.h
- src/stats/matrices/pam250.cpp → src/stats/matrices/pam250.h
- src/stats/matrices/pam30.cpp → src/stats/matrices/pam30.h
- src/stats/matrices/pam70.cpp → src/stats/matrices/pam70.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/test_cases.cpp
- src/tools/benchmark.cpp
- src/tools/greedy_vertex_cover.cpp
- src/tools/tools.cpp
- src/util/algo/algo.h
- src/util/algo/greedy_vertex_cover.cpp
- + src/util/algo/hyperloglog.h
- + src/util/algo/mcl.cpp
- src/util/algo/merge_files.h
- + src/util/algo/pagerank.cpp
- src/util/algo/sort_helper.h
- src/util/algo/transform_iterator.h
- src/util/binary_buffer.h
- src/util/data_structures/deque.h
- src/util/data_structures/flat_array.h
- + src/util/data_structures/queue.h
- − src/util/data_structures/writer.h
- − src/util/io/async_file.h
- + src/util/io/compressed_buffer.h
- src/util/io/compressed_stream.h
- src/util/io/file_sink.cpp
- src/util/io/file_sink.h
- + src/util/io/mmap.h
- src/util/io/output_file.cpp
- src/util/io/output_file.h
- − src/util/io/serialize.h
- src/util/io/serializer.h
- src/util/io/stream_entity.h
- src/util/io/temp_file.cpp
- src/util/io/text_input_file.cpp
- src/util/io/text_input_file.h
- src/util/io/zstd_stream.h
- + src/util/memory_resource.h
- src/util/options/option.h
- + src/util/parallel/atomic.h
- src/util/parallel/filestack.cpp
- src/util/parallel/filestack.h
- src/util/parallel/parallelizer.cpp
- src/util/parallel/thread_pool.h
- src/util/sequence/sequence.cpp
- src/util/sequence/sequence.h
- src/util/string/string.cpp
- src/util/string/string.h
- src/util/string/tokenizer_dyn.h
- src/util/system/getRSS.cpp
- src/util/system/system.cpp
- src/util/system/system.h
- src/util/tsv/file.cpp
- src/util/tsv/file.h
- src/util/tsv/read_tsv.cpp
- src/util/util.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/08a9db9c54c90622b1210036d486472b01a50a69...dd9098526076532bb5a4198965bb339f6d6eb471

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View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/08a9db9c54c90622b1210036d486472b01a50a69...dd9098526076532bb5a4198965bb339f6d6eb471
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