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@eseiler eseiler released this 28 May 09:58
3.0.3
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eseiler Enrico Seiler
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Learn about vigilant mode.
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Learn about vigilant mode.

GitHub commits since tagged version (branch)

We are proud to announce the last 3.0.x Release of the SeqAn Library.

This is a rather big release for us, encompassing 923 commits and changing 1750 files. This sums up to over 75,000 insertions and more than 50,000 deletions.
Despite this huge diff, we have good reasons to believe that upgrading from 3.0.2 will be extremely smooth and easy.

You can find a comprehensive list of the changes in our changelog.

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

Our final push to 3.1.0

For 3.0.3, we heavily focused on making the final push towards 3.1.0 and took our time to really define the scope of our Sequence Analysis Library.

That means the next Release (3.1.0) will be the first stable one, exciting right? 🥳

📖 Module structure

We now utilise the following module structure.

Sequence Analysis Modules

  • #include <seqan3/alphabet/*.hpp>:
    Contains alphabet related entities, like seqan3::dna4.
  • #include <seqan3/alignment/*.hpp>:
    Contains sequence alignment related entities, like seqan3::align_pairwise.
  • #include <seqan3/io/*.hpp>:
    Contains I/O related entities, like seqan3::sequence_file_input.
  • #include <seqan3/search/*.hpp>:
    Contains search related entities, like seqan3::search.

We also moved containers and views from the former range module into related Sequence Analysis Module (e.g., seqan3::bitpacked_sequence and seqan3::translate are now part of the alphabet module).

All Sequence Analysis Modules will have strong API Stability guarantees. So far we finished declaring the stability in our documentation for alphabets, containers, and ranges. Sequence Alignment and I/O will follow in the next release.

General Purpose Modules

  • #include <seqan3/argument_parser/*.hpp>:
    Our argument parser library that helps to write apps.
  • #include <seqan3/range/*.hpp> (split since 3.0.3):
    We moved most entities within this module into the other modules: alphabet, alignment, io, search or utility. But, we also deprecated some of them that did not fit our scope anymore.
  • #include <seqan3/core/*.hpp>:
    Our internal module for entities that are shared across our sequence analysis modules and are needed to implement our own algorithms and data structures.
  • #include <seqan3/utility/*.hpp>:
    utility contains entities that are completely unrelated to biology-problems. We think of these as something that could be made separate libraries.

All General Purpose Modules will have no API Stability guarantees.

🔒 API Stability

We are especially thrilled to announce 3.0.3, because this release should be the first one that just compiles™️ your app when upgrading from 3.0.2 to 3.0.3. Arguably, you will encounter scattered "deprecation" notices, but all of those messages should point you to an upgrade path. Unless you treat warnings as errors, your app will still compile even when encountering deprecation notices.

Furthermore, we see this release as a test run of our way to handle API Stability in the upcoming era of stable releases. We are happy to hear your feedback, so please let us know whether it worked for you and if something could be improved. We believe we found a good system for hinting changes between releases to our users.

But how do we know that we did not miss anything? Our idea is simple: compile our current SeqAn version (3.0.3 in this case) against the tests of our previous Release (3.0.2). If everything compiles and the previous tests pass, we most likely did not break our API.

🎉 Notable new features

  • A new Phred Quality Score alphabet seqan3::phred94 that represents the full Phred Score range (Sanger format) and is used for PacBio Phred scores of HiFi reads.

  • A new seqan3::literals namespace, which can be used in lieu of importing individual literal operators.

    Click for an example 
    #include <seqan3/alphabet/nucleotide/dna4.hpp>

int main()
{
    using namespace seqan3::literals; // Still works: using seqan3::operator''_dna4;

    seqan3::dna4 adenine = 'A'_dna4;
}

  • Records of I/O files have member functions.

    Click for an example 
    #include <seqan3/core/debug_stream.hpp>
#include <seqan3/io/sequence_file/input.hpp>

int main()
{
    seqan3::sequence_file_input fin{"my.fastq"};

    for (auto && record: fin)
    {
        seqan3::debug_stream << "id: " << record.id() << '\n';
        seqan3::debug_stream << "sequence: " << record.sequence() << '\n';
        seqan3::debug_stream << "base_qualities: " << record.base_qualities() << '\n';
    }
}

:trollface: Notable breaking changes (API)

  • Starting with 3.0.3, seqan3::seqan3_version is a number and equivalent to the SEQAN3_VERSION macro. Consequently, seqan3::seqan3_version_cstring is the C-String (char const *) which was named seqan3::seqan3_version in the previous release (and was a std::string).
  • The meanings of seqan3::alphabet_variant::{is_alternative, holds_alternative} have been swapped.

🛠️ Notable API changes

  • Entities have been renamed, a short but incomplete excerpt
    • seqan3::phred68legacy to seqan3::phred68solexa
    • seqan3::sam_dna16 to seqan3::dna16sam
    • seqan3::bitcompressed_vector to seqan3::bitpacked_sequence
    • seqan3::alignment_file_* to seqan3::sam_file_*
    • multiple UPPER_CASE to lower_case names, mostly in enums
  • Accessing an I/O file record by seqan3::get, e.g., seqan3::get<seqan3::field::id>(record), has been deprecated in favour of the new member accessors, e.g., record.id().

🐛 Notable bug fixes

  • A couple of fixes in the argument parser.
  • Fixed a nasty issue when combining seqan3::views::kmer_hash and std::views::reverse.
  • Fixed an issue with compressing .gz files with the BGZF compression algorithm.
  • Various fixes to our SAM/BAM file implementation.

🔌 External dependencies

  • SeqAn 3.0.3 is known to compile with GCC 7.5, 8.4, 9.3, 10.3, and 11.1. Future versions (such as GCC 11.2 and 12) might work, but were not yet available at the time of this release.
  • We support ranges-v3 versions ≥ 0.11.0 and < 0.12.0.
  • We use doxygen 1.9.1 to build our documentation.
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