[med-svn] [Git][med-team/kallisto][master] 8 commits: Packaging update (routine-update)

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / kallisto


Commits:
0eec4804 by Andreas Tille at 2026-10-20T16:45:13+02:00
Packaging update (routine-update)

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a657cdbc by Andreas Tille at 2026-10-20T16:45:36+02:00
New upstream version

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8c3e0764 by Andreas Tille at 2026-10-20T16:45:37+02:00
New upstream version 0.52.0+dfsg
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19f14634 by Andreas Tille at 2026-10-20T16:45:49+02:00
Update upstream source from tag 'upstream/0.52.0+dfsg'

Update to upstream version '0.52.0+dfsg'
with Debian dir 14e11adb94daf8acd2ac91cd07c50a24d4dd202b
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26b2ce25 by Andreas Tille at 2026-10-20T16:45:58+02:00
Changes made by cme

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69ee4313 by Andreas Tille at 2026-10-20T16:46:06+02:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)

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dd6ecf9e by Andreas Tille at 2026-10-20T15:46:14+01:00
Reformat the Last-Update date as ISO YYYY-MM-DD.

Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/use_debian_packaged_htslib.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html

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ff9a764b by Andreas Tille at 2026-10-20T16:49:50+02:00
Cleanup changelog

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70 changed files:

- + .clang-format
- .gitignore
- + .make_binaries.linux.txt
- + .make_binaries.sh
- + .make_binaries.windows.txt
- CMakeLists.txt
- debian/changelog
- debian/control
- debian/patches/use_debian_packaged_htslib.patch
- ext/bifrost/src/BitContainer.cpp
- ext/bifrost/src/BitContainer.hpp
- ext/bifrost/src/BooPHF.h
- ext/bifrost/src/ColorSet.cpp
- ext/bifrost/src/ColorSet.hpp
- ext/bifrost/src/ColoredCDBG.hpp
- ext/bifrost/src/ColoredCDBG.tcc
- ext/bifrost/src/Common.hpp
- ext/bifrost/src/CompactedDBG.hpp
- ext/bifrost/src/CompactedDBG.tcc
- ext/bifrost/src/CompressedCoverage.hpp
- ext/bifrost/src/CompressedSequence.cpp
- ext/bifrost/src/CompressedSequence.hpp
- ext/bifrost/src/DataAccessor.hpp
- ext/bifrost/src/DataAccessor.tcc
- ext/bifrost/src/DataStorage.hpp
- ext/bifrost/src/DataStorage.tcc
- ext/bifrost/src/FASTX_Parser.cpp
- ext/bifrost/src/FASTX_Parser.hpp
- ext/bifrost/src/File_Parser.hpp
- ext/bifrost/src/GFA_Parser.cpp
- ext/bifrost/src/GFA_Parser.hpp
- ext/bifrost/src/IO.tcc
- ext/bifrost/src/KmerCovIndex.hpp
- ext/bifrost/src/KmerCovIndex.tcc
- ext/bifrost/src/KmerHashTable.hpp
- ext/bifrost/src/KmerIterator.hpp
- ext/bifrost/src/KmerStream.hpp
- ext/bifrost/src/MinimizerIndex.cpp
- ext/bifrost/src/MinimizerIndex.hpp
- ext/bifrost/src/RepHash.hpp
- ext/bifrost/src/Search.tcc
- ext/bifrost/src/StreamCounter.hpp
- ext/bifrost/src/TinyBitmap.cpp
- ext/bifrost/src/TinyBitmap.hpp
- ext/bifrost/src/Unitig.hpp
- ext/bifrost/src/UnitigMap.hpp
- ext/bifrost/src/UnitigMap.tcc
- ext/bifrost/src/minHashIterator.hpp
- ext/bifrost/src/rw_spin_lock.h
- src/BUSTools.cpp
- src/BlockArray.hpp
- src/CMakeLists.txt
- src/Fusion.hpp → src/Fusion.cpp
- + src/Fusion.h
- src/GeneModel.cpp
- src/Inspect.h
- src/KmerIndex.cpp
- src/KmerIndex.h
- src/MinCollector.cpp
- src/Multinomial.hpp
- src/Node.hpp
- src/PlaintextWriter.cpp
- src/ProcessReads.cpp
- src/ProcessReads.h
- src/PseudoBam.cpp
- src/SparseVector.hpp
- src/common.h
- src/main.cpp
- src/weights.cpp
- unit_tests/test_weights.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/bb259eafd9a2ffeb84d0f657b35cbfaf6e824b59...ff9a764bd70c316b5f0c46167186b63e56c611b5

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View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/bb259eafd9a2ffeb84d0f657b35cbfaf6e824b59...ff9a764bd70c316b5f0c46167186b63e56c611b5
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