8000 Add records to existing fastq file · Issue #3364 · seqan/seqan3 · GitHub
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PawelWojciechowski opened this issue May 19, 2025 · 4 comments
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Add records to existing fastq file #3364

PawelWojciechowski opened this issue May 19, 2025 · 4 comments
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question a user question how to do certain things

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@PawelWojciechowski
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Platform

  • SeqAn version: 3.4
  • Operating system: n/a
  • Compiler: n/a

Question

Is it possible to open a .fastq file for writing in append mode? I want to split one large file into smaller ones without having to load the entire large file at once.
Thank you!
@PawelWojciechowski PawelWojciechowski added the question a user question how to do certain things label May 19, 2025
@SGSSGene
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Hi @PawelWojciechowski
Yes, appending to a file is possible.

Checkout the example https://docs.seqan.de/seqan3/main_user/cookbook.html#autotoc_md74
In that example an already "opened" file is being used:

    seqan3::sequence_file_output fout{std::cout, seqan3::format_fasta{}};

For your case, you have to use a std::fstream that is opened in write and append mode. So something like this:

    std::fstream fs{"my_file.fastq", std::ios_base::binary | std::ios_base::out};
    seqan3::sequence_file_output fout{fs, seqan3::format_fastq{}};

Writing should work just as in the linked example above.

@PawelWojciechowski
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Hi @SGSSGene
Thank you. It works after adding append mode:

std::fstream fs{"my_file.fastq.gz", std::ios_base::binary | std::ios_base::out | std::fstream::app};

But the final file is not gziped. How to do it?

@SGSSGene
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Hi @PawelWojciechowski
Yes of course std::ios_base::app not std::ios_base::binary....

To achieve compression, you need an extra stream layer that does the compression. Notice that the compression layer must exists longer than the seqan3::sequence_file_output.

    std::fstream fs{"my_file.fastq", std::ios_base::app | std::ios_base::out};
    seqan3::contrib::gz_ostream cfs{fs};
    seqan3::sequence_file_output fout{cfs, seqan3::format_fastq{}};

(I believe seqan3::contrib::gz_ostream is technical not public API, so API might change in the future, but currently I do not see that happening ;-) )

@PawelWojciechowski
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Hi @SGSSGene,
It works perfectly. Thank you again!

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