Joshua Kim comments

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Joshua Kim

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

I think this is to prevent ambiguity as described [here](http://docs.seqan.de/seqan/3-master-dev/group__alphabet.html) under "Assigning and retrieving values". For a one line initialization you could do this: ```cpp using namespace seqan3::literals; seqan3::phred42 quality_value{'A'_phred42};...

Change how seqan3::field::alignment works with SAM/BAM files.

Minimal example: ```cpp seqan3::sam_file_input input_file{input_path}; for (auto & record : input_file) { seqan3::debug_stream

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

Hello, can I ask about an update to this? I'd be happy to work on this myself if nobody else is currently doing so. I'd also like "valid" BAM files...

[TEST,FIX] Several more benchmarks, minor optimisations

@h-2 I'm not sure what all of the seqan2 stuff is for... But I'm sure it makes sense!

Cerealizing a file offset of type `std::streampos`?

Hello @AzothAmmo! Thanks for your suggestion and sorry for the late response. What I'm currently doing is the following: ```cpp class X { private: std::streampos position{}; public: template void serialize(Archive...

Cerealizing a file offset of type `std::streampos`?

Hi @AzothAmmo, I'm still dealing with this issue and was wondering if you could offer any more insight. The workaround I proposed earlier doesn't actually work. It writes fine, by...

Obtaining primary alignment position from secondary alignment?

Hey Daniel! I do mean secondary alignments. Supplementary alignments are also important for variant calling, but as you mention they use the SA tag. Crucially, for supplementary alignments, all positions...