[med-svn] [Git][med-team/adapterremoval][upstream] New upstream version 2.3.4

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / adapterremoval


Commits:
1c01e67f by Étienne Mollier at 2025-03-01T13:06:52+01:00
New upstream version 2.3.4
- - - - -


98 changed files:

- .gitignore
- − .travis.yml
- AdapterRemoval.1
- CHANGES.md
- LICENSE
- Makefile
- README.md
- docs/conf.py
- docs/examples.rst
- docs/getting_started.rst
- − docs/input_and_output.rst
- docs/installation.rst
- docs/manpage.rst
- examples/Makefile
- src/fastq.cpp
- src/fastq.hpp
- src/fastq_enc.cpp
- src/fastq_enc.hpp
- src/main.hpp
- src/main_demultiplex.cpp
- src/scheduler.hpp
- src/timer.cpp
- src/timer.hpp
- src/userconfig.cpp
- + tests/regression/misc/convert_bases/pe/basic/info.json
- + tests/regression/misc/convert_bases/pe/basic/input_1.fastq
- + tests/regression/misc/convert_bases/pe/basic/input_2.fastq
- + tests/regression/misc/convert_bases/pe/basic/your_output.discarded
- + tests/regression/misc/convert_bases/pe/basic/your_output.pair1.truncated
- + tests/regression/misc/convert_bases/pe/basic/your_output.pair2.truncated
- + tests/regression/misc/convert_bases/pe/basic/your_output.settings
- + tests/regression/misc/convert_bases/pe/basic/your_output.singleton.truncated
- + tests/regression/misc/convert_bases/pe/both/info.json
- + tests/regression/misc/convert_bases/pe/both/input_1.fastq
- + tests/regression/misc/convert_bases/pe/both/input_2.fastq
- + tests/regression/misc/convert_bases/pe/both/your_output.discarded
- + tests/regression/misc/convert_bases/pe/both/your_output.pair1.truncated
- + tests/regression/misc/convert_bases/pe/both/your_output.pair2.truncated
- + tests/regression/misc/convert_bases/pe/both/your_output.settings
- + tests/regression/misc/convert_bases/pe/both/your_output.singleton.truncated
- + tests/regression/misc/convert_bases/pe/both_fail_1/info.json
- + tests/regression/misc/convert_bases/pe/both_fail_1/input_1.fastq
- + tests/regression/misc/convert_bases/pe/both_fail_1/input_2.fastq
- + tests/regression/misc/convert_bases/pe/both_fail_2/info.json
- + tests/regression/misc/convert_bases/pe/both_fail_2/input_1.fastq
- + tests/regression/misc/convert_bases/pe/both_fail_2/input_2.fastq
- + tests/regression/misc/convert_bases/pe/both_fail_3/info.json
- + tests/regression/misc/convert_bases/pe/both_fail_3/input_1.fastq
- + tests/regression/misc/convert_bases/pe/both_fail_3/input_2.fastq
- + tests/regression/misc/convert_bases/pe/degenerate/input_1.fastq
- + tests/regression/misc/convert_bases/pe/degenerate/input_2.fastq
- + tests/regression/misc/convert_bases/pe/degenerate/your_output.discarded
- + tests/regression/misc/convert_bases/pe/degenerate/your_output.pair1.truncated
- + tests/regression/misc/convert_bases/pe/degenerate/your_output.pair2.truncated
- + tests/regression/misc/convert_bases/pe/degenerate/your_output.settings
- + tests/regression/misc/convert_bases/pe/degenerate/your_output.singleton.truncated
- + tests/regression/misc/convert_bases/pe/degenerate_fail/info.json
- + tests/regression/misc/convert_bases/pe/degenerate_fail/input_1.fastq
- + tests/regression/misc/convert_bases/pe/degenerate_fail/input_2.fastq
- + tests/regression/misc/convert_bases/pe/uracil/input_1.fastq
- + tests/regression/misc/convert_bases/pe/uracil/input_2.fastq
- + tests/regression/misc/convert_bases/pe/uracil/your_output.discarded
- + tests/regression/misc/convert_bases/pe/uracil/your_output.pair1.truncated
- + tests/regression/misc/convert_bases/pe/uracil/your_output.pair2.truncated
- + tests/regression/misc/convert_bases/pe/uracil/your_output.settings
- + tests/regression/misc/convert_bases/pe/uracil/your_output.singleton.truncated
- + tests/regression/misc/convert_bases/pe/uracil_fail/info.json
- + tests/regression/misc/convert_bases/pe/uracil_fail/input_1.fastq
- + tests/regression/misc/convert_bases/pe/uracil_fail/input_2.fastq
- + tests/regression/misc/convert_bases/se/basic/info.json
- + tests/regression/misc/convert_bases/se/basic/input_1.fastq
- + tests/regression/misc/convert_bases/se/basic/your_output.discarded
- + tests/regression/misc/convert_bases/se/basic/your_output.settings
- + tests/regression/misc/convert_bases/se/basic/your_output.truncated
- + tests/regression/misc/convert_bases/se/both/info.json
- + tests/regression/misc/convert_bases/se/both/input_1.fastq
- + tests/regression/misc/convert_bases/se/both/your_output.discarded
- + tests/regression/misc/convert_bases/se/both/your_output.settings
- + tests/regression/misc/convert_bases/se/both/your_output.truncated
- + tests/regression/misc/convert_bases/se/both_fail_1/info.json
- + tests/regression/misc/convert_bases/se/both_fail_1/input_1.fastq
- + tests/regression/misc/convert_bases/se/both_fail_2/info.json
- + tests/regression/misc/convert_bases/se/both_fail_2/input_1.fastq
- + tests/regression/misc/convert_bases/se/both_fail_3/info.json
- + tests/regression/misc/convert_bases/se/both_fail_3/input_1.fastq
- + tests/regression/misc/convert_bases/se/degenerate/input_1.fastq
- + tests/regression/misc/convert_bases/se/degenerate/your_output.discarded
- + tests/regression/misc/convert_bases/se/degenerate/your_output.settings
- + tests/regression/misc/convert_bases/se/degenerate/your_output.truncated
- + tests/regression/misc/convert_bases/se/degenerate_fail/info.json
- + tests/regression/misc/convert_bases/se/degenerate_fail/input_1.fastq
- + tests/regression/misc/convert_bases/se/uracil/input_1.fastq
- + tests/regression/misc/convert_bases/se/uracil/your_output.discarded
- + tests/regression/misc/convert_bases/se/uracil/your_output.settings
- + tests/regression/misc/convert_bases/se/uracil/your_output.truncated
- + tests/regression/misc/convert_bases/se/uracil_fail/info.json
- + tests/regression/misc/convert_bases/se/uracil_fail/input_1.fastq
- tests/unit/argparse_test.cpp


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/adapterremoval/-/commit/1c01e67f511274c29316b2cba8aa9e251f44371c

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View it on GitLab: https://salsa.debian.org/med-team/adapterremoval/-/commit/1c01e67f511274c29316b2cba8aa9e251f44371c
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