[med-svn] [Git][med-team/spades][master] 4 commits: routine-update: New upstream version

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / spades


Commits:
b5ad813f by Steffen Moeller at 2020-05-03T20:31:01+02:00
routine-update: New upstream version

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a1d38af1 by Steffen Moeller at 2020-05-03T20:31:02+02:00
New upstream version 3.14.1+dfsg
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cb10850a by Steffen Moeller at 2020-05-03T20:31:15+02:00
Update upstream source from tag 'upstream/3.14.1+dfsg'

Update to upstream version '3.14.1+dfsg'
with Debian dir 6a4eb29a16306de4fd17c1f1e211a24a393dc1fe
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b5f1a7e7 by Steffen Moeller at 2020-05-03T21:25:01+02:00
Adjusting patches

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30 changed files:

- README.md
- assembler/LICENSE
- assembler/VERSION
- assembler/changelog.html
- assembler/manual.html
- assembler/rnaspades_manual.html
- assembler/spades.py
- assembler/src/cmake/pack.cmake
- assembler/src/common/io/CMakeLists.txt
- + assembler/src/common/io/binary/genomic_info.cpp
- assembler/src/common/io/graph/gfa_writer.hpp
- assembler/src/common/modules/chromosome_remover.cpp
- assembler/src/common/modules/mismatch_shall_not_pass.hpp
- assembler/src/common/pipeline/CMakeLists.txt
- assembler/src/common/pipeline/config_struct.cpp
- assembler/src/common/pipeline/genomic_info.hpp
- assembler/src/common/stages/CMakeLists.txt
- assembler/src/common/pipeline/genomic_info_filler.cpp → assembler/src/common/stages/genomic_info_filler.cpp
- assembler/src/common/pipeline/genomic_info_filler.hpp → assembler/src/common/stages/genomic_info_filler.hpp
- assembler/src/common/utils/logger/logger.hpp
- assembler/src/projects/corrector/main.cpp
- assembler/src/projects/kmercount/read_filter.cpp
- assembler/src/projects/spades/CMakeLists.txt
- assembler/src/projects/spades/contig_output_stage.cpp
- assembler/src/projects/spades/contig_output_stage.hpp
- assembler/src/projects/spades/domain_graph.hpp
- assembler/src/projects/spades/main.cpp
- assembler/src/projects/spades/launch.hpp → assembler/src/projects/spades/pipeline.cpp
- assembler/src/projects/spades/second_phase_setup.cpp
- assembler/src/spades_pipeline/common/SeqIO.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/b7b8a5cefcaefe8543a6f7805d864d660f8a2157...b5f1a7e7d90da3c131da47bdbaaa48c3283d1c8b

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View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/b7b8a5cefcaefe8543a6f7805d864d660f8a2157...b5f1a7e7d90da3c131da47bdbaaa48c3283d1c8b
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