seqan3

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Possibility of having a single header to include

3

We are using Seqan3 in a couple of projects, and it is generally working nicely. However, one issue we have is that over time our builds start failing when they...

johnlees

[Search] Query the text size

1

For calculating e-values or other purposes it is often necessary to query the text size of a (bi) FM index. I have experimented with the `size()` function of `seqan3::bi_fm_index` in...

joergi-w

[IO] Access list of file extensions of seqan3 I/O input classes

1

While solving https://github.com/seqan/sharg-parser/issues/42 we would like to to access the file extensions via: ```cpp #include #include sharg::input_file_validator validator1{seqan3::sequence_file_input::file_extensions}; std::cerr

Irallia

[MISC] Use tmp_directory instead of tmp_filename

2

Moves forward https://github.com/seqan/product_backlog/issues/281 This replaces occurrences of `tmp_filename` and replaces them with `tmp_directory`. This PR doesn't remove `tmp_filename`, because it is unclear how the *.patch files must be updated to...

SGSSGene

What is the size of a dnaX_vector?

1

## Question I am wondering about the size of a `dna5_vector`. I've found that it is an alias for `std::vector` and `dna5` itself occupies one byte (`uint8_t`). **Does `dnaX_vector` allocate...

JanSiebert

[IO] Parsing for genome alignment formats (MAF and HAL)

6

Big fan of the Seqan3 library, thanks for all of your hard work! I have been using the MSA parser recently and it has worked quite well, however, the majority...

bkille

What is the desired behavior when writing an empty BAM file?

4

## Platform - SeqAn version: latest - Operating system: Ubuntu - Compiler: gcc ## Question Just a quick question: I am using SeqAn3's BAM output. I need to create a...

tloka

[Alphabet] Alphabet types can no longer be constructed using their rank

12

I am just working on an SeqAn3 upgrade to have the newest version running. I recognized with the quality alphabets (in my case mostly phred42), that it is no longer...

tloka

How to add seqan3 as external project in cmake?

26

## Platform - SeqAn version: 3.0.0 - Operating system: Ubuntu LTS 18.04 - Compiler: GCC-7.4.0 ## Question I would like to add Seqan3 as an external project to the cmake...

JensUweUlrich

Change the sampling rate of the suffix array for the fm_index

2

## Platform - SeqAn version: 3.0.2 - Operating system: Linux 3.10.0-693.5.2.el7.x86_64 \# 1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 GNU/Linux - Compiler: gcc (GCC) 9.2.0 ## Question...

Sawwave