seqan3

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[Alignment] Is there a way to run align_pairwise without traceback?

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## Platform - SeqAn version: - Operating system: - Compiler: ## Question In earlier versions of SeqAn there was a function called localAlignmentScore (https://docs.seqan.de/seqan/master/?p=locallAlignmentScore) which did not run the quadratic...

leannmlindsey

push_back for aa27

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## Platform - SeqAn version: seqan3 - Operating system: Linux nid00039 5.3.18-24.46_6.0.29-cray_ari_c # 1 SMP Mon Mar 14 09:11:41 UTC 2022 (6c38a31) x86_64 x86_64 x86_64 GNU/Linux - Compiler: c++ (GCC)...

leannmlindsey

Reported alignment score is different from score calculated from the alignment

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### Does this problem persist on the current master? - [X] I have verified the issue on the current master ### Is there an existing issue for this? - [X]...

yceh

[FIX] bgzf_thread_count definition

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Resolves https://github.com/seqan/seqan3/issues/3041

eseiler

Hi we noticed [here](https://github.com/sarahet/RLM/issues/2) that if you don't have zlib installed, the variable `bgzf_thread_count` isn't declared/defined. This leads to the situation that setting this variable will fail at compilation time...

SGSSGene

3.2.0 Release

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- [x] Create a release branch, e.g. `release-[VERSION]`, and enable branch protection in the repository settings. - [x] Update copyright year. https://github.com/seqan/seqan3/pull/3011 - [x] Create at least one pre-release s.t....

eseiler

[WIP] What if alphabets were trivial?

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`std::vector` optimizes assignments to `std::copy` (basically memcpy) iff the value_type is trivial. If not, it will use `std::unintialized_copy` which will use placement-new and is around 2-3 times slower. | Method...

eseiler

[INFRA] macro_benchmark flags

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eseiler

[DOC, FEATURE] Improve dna4 complement performance and add documentation.

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(Aims to) Resolves #1970 - [x] Add a benchmark for computing the complement (and reverse complement). See https://github.com/kloetzl/libdna/blob/master/bench2/revcomp.cxx - [x] Replace the look-up table with an xor+subtraction when computing the...

smehringer

[FEATURE] Add sharg-parser submodule and replace the seqan3::argument_parser.

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Blocked by ~#2952~ #2970 This PR does a lot. - [x] it adds the sharg parser as submodule - [x] it fixes a test in `format_parse_validator_test` where enum `foo` needs...

smehringer