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Releases: seqan/seqan3

3.4.0

27 Aug 14:56
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3.4.0
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3.4.0 Latest
Latest

GitHub commits since latest release

New features

I/O

  • seqan3::sam_file_input now accepts user-defined tags (#3256).

Notable Bug-fixes

Alphabet

  • Resolved an issue that prevented proper conversion, most notably in conjunction with seqan3::bitpacked_sequence (#3268).

Alignment

  • Fixed an issue that caused incorrect begin and end positions for banded alignments (#3269).

I/O

  • seqan3::sam_file_output now takes ownership of the given reference information (#3300).

API changes

Deprecations

Compiler

  • Supported compiler:
    • GCC 12, 13, 14, 15
    • Clang 17, 18, 19, 20
    • IntelOneAPI/IntelLLVM 2024, 2025

Dependencies

  • We now use Doxygen version 1.9.8 to build our documentation (#3197).
  • We bumped the minimal CMake version to 3.20 (#3314).
  • Dependencies are now managed via CPM instead of submodules (#3328).
  • The build_system directory was renamed to cmake (#3292).

Notes for package maintainers

Click to expand

For reference, you can have a look at the Debian package.

Alternative zlib implementation

If your distribution ships an alternative zlib library, for example, zlib-ng, some tests will fail:

The following tests FAILED:
        164 - contrib/stream/gz_ostream_test (Failed)
        166 - contrib/stream/bgzf_ostream_test (Failed)
        203 - io/sam_file/sam_file_output_test (Failed)
        210 - io/sequence_file/sequence_file_output_test (Failed)
        224 - io/structure_file/structure_file_output_test (Failed)

This is because we are testing compression separately for some file formats and the expected output refers to (vanilla) zlib's output.
zlib-ng should be automatically detected and causes those checks to be skipped.
If this is not the case, or you are using another zlib alternative, you can manually skip those checks:

cmake <...> -DCMAKE_CXX_FLAGS="-DSEQAN3_TEST_SKIP_ZLIB_DEFLATE=1"

Dependencies

Dependencies are listed in cmake/package-lock.cmake.
We now use CPM for dependency management.

To use locally installed packages, pass -DCPM_USE_LOCAL_PACKAGES=ON to cmake, or set the environment variable CPM_USE_LOCAL_PACKAGES to ON. CPM documentation

If your locally installed packages has an older version, you may need to additionally pass the version to cmake.
The version variables can be found in cmake/package-lock.cmake.
For example, let's assume your googletest version is 1.14.0 instead of 1.15.2 listed in the package-lock.cmake.
CPM (or rather CMake's find_package) would not use your local version because 1.14.0 < 1.15.2.
Passing -DSEQAN3_GOOGLETEST_VERSION=1.14.0 to CMake will result in your local package being used.
If your local package version is newer, it should be used without any additional CMake arguments.

Post install tests

To configure tests with an installed seqan3 version, CPM needs to be available.
However, CPM isn't installed when seqan3 is installed.
To still configure the tests, you have to pass -DSEQAN3_TEST_CPM_DIR=<path> to your CMake command.
For example, -DSEQAN3_TEST_CPM_DIR=${SEQAN3_PACKAGE_SOURCE_DIRECTORY}/cmake ${SEQAN3_PACKAGE_SOURCE_DIRECTORY}/test/unit.
Where SEQAN3_PACKAGE_SOURCE_DIRECTORY is the downloaded source package.
SEQAN3_TEST_CPM_DIR points to the directory containing CPM.cmake.

What's Changed

Click to expand
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Contributors

SGSSGene, rrahn, and 2 other contributors
Assets 6
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SeqAn 3.4.0-rc.4

21 Jul 13:36
@eseiler eseiler
3.4.0-rc.4
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eseiler Enrico Seiler
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SeqAn 3.4.0-rc.4 Pre-release
Pre-release

GitHub commits since tagged version (branch) GitHub commits since tagged version (branch)

This is the fourth release candidate for SeqAn 3.4.0

What's Changed (Selection)

  • [INFRA] The SDSL dependency is now included as amalgamated header (#3334)
  • [FIX,INFRA] SeqAn3 does no longer try to find_package itself (#3345)
  • [INFRA] Renamed SEQAN3_WITH_CEREAL to SEQAN3_HAS_CEREAL (#3337)
  • [INFRA] gcc-15, clang-20, C++26 support (#3350, #3360, #3367, #3368)

Full Changelog: 3.4.0-rc.3...3.4.0-rc.4

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SeqAn 3.4.0-rc.3

22 Jan 11:59
@eseiler eseiler
3.4.0-rc.3
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SeqAn 3.4.0-rc.3 Pre-release
Pre-release

GitHub commits since tagged version (branch) GitHub commits since tagged version (branch)

This is the third release candidate for SeqAn 3.4.0

What's Changed

Full Changelog: 3.4.0-rc.2...3.4.0-rc.3

Notes for package maintainers

For reference, you can have a look at the Debian package.

Alternative zlib implementation

If your distribution ships an alternative zlib library, for example, zlib-ng, some tests will fail:

The following tests FAILED:
        164 - contrib/stream/gz_ostream_test (Failed)
        166 - contrib/stream/bgzf_ostream_test (Failed)
        203 - io/sam_file/sam_file_output_test (Failed)
        210 - io/sequence_file/sequence_file_output_test (Failed)
        224 - io/structure_file/structure_file_output_test (Failed)

This is because we are testing compression separately for some file formats and the expected output refers to (vanilla) zlib's output.
zlib-ng should be automatically detected and causes those checks to be skipped.
If this is not the case, or you are using another zlib alternative, you can manually skip those checks:

cmake <...> -DCMAKE_CXX_FLAGS="-DSEQAN3_TEST_SKIP_ZLIB_DEFLATE=1"

Dependencies

Dependencies are listed in cmake/package-lock.cmake.
We now use CPM for dependency management.

To use locally installed packages, pass -DCPM_USE_LOCAL_PACKAGES=ON to cmake, or set the environment variable CPM_USE_LOCAL_PACKAGES to ON. CPM documentation

If your locally installed packages has an older version, you may need to additionally pass the version to cmake.
The version variables can be found in cmake/package-lock.cmake.
For example, let's assume your googletest version is 1.14.0 instead of 1.15.2 listed in the package-lock.cmake.
CPM (or rather CMake's find_package) would not use your local version because 1.14.0 < 1.15.2.
Passing -DSEQAN3_GOOGLETEST_VERSION=1.14.0 to CMake will result in your local package being used.
If your local package version is newer, it should be used without any additional CMake arguments.

Post install tests

To configure tests with an installed seqan3 version, CPM needs to be available.
However, CPM isn't installed when seqan3 is installed.
To still configure the tests, you have to pass -DSEQAN3_TEST_CPM_DIR=<path> to your CMake command.
For example, -DSEQAN3_TEST_CPM_DIR=${SEQAN3_PACKAGE_SOURCE_DIRECTORY}/cmake ${SEQAN3_PACKAGE_SOURCE_DIRECTORY}/test/unit.
Where SEQAN3_PACKAGE_SOURCE_DIRECTORY is the downloaded source package.
SEQAN3_TEST_CPM_DIR points to the directory containing CPM.cmake.

Contributors

eseiler and seqan-actions
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SeqAn 3.4.0-rc.2

13 Dec 17:48
@eseiler eseiler
3.4.0-rc.2
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eseiler Enrico Seiler
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SeqAn 3.4.0-rc.2 Pre-release
Pre-release

GitHub commits since tagged version (branch) GitHub commits since tagged version (branch)

This is the second release candidate for SeqAn 3.4.0

What's Changed

Click to expand

Full Changelog: 3.4.0-rc.1...3.4.0-rc.2

Contributors

SGSSGene, rrahn, and 4 other contributors
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SeqAn 3.4.0-rc.1

22 Jan 16:44
@eseiler eseiler
3.4.0-rc.1
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eseiler Enrico Seiler
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SeqAn 3.4.0-rc.1 Pre-release
Pre-release

GitHub commits since tagged version (branch)

This is the first release candidate for SeqAn 3.4.0

SeqAn 3.4.0 offers support for GCC 11/12/13, and new clang 17

Changelog

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SeqAn 3.3.0

17 Aug 11:13
@eseiler eseiler
3.3.0
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SeqAn 3.3.0

GitHub commits since tagged version (branch)

We are glad to announce the SeqAn 3.3.0 release that has a major compiler update:

We dropped GCC 10 and we added GCC 13 support.

While we will present essential changes of the 3.3.0 release in this message, you can also find a comprehensive list of the changes in our changelog.

🎉 New Features

Alignment

  • The function seqan3::alignment_from_cigar creates an alignment from a CIGAR vector (#3057) or a CIGAR string (#3077).
  • The function seqan3::cigar_from_alignment creates a CIGAR vector from an alignment (#3057).

Alphabet

  • Improved performance of vector assignment for alphabets by a factor 2.5 (#3038).
  • Improved performance of seqan3::dna4::complement() (#3026).
  • Char literals returning std::vector are now constexpr if supported by the compiler (#3073).

I/O

  • Made seqan3::sam_file_header::program_info_t easier to copy (#3145).
  • Reading SAM/BAM files is 2x faster than before (#3106).

Search

  • The uncompressed seqan3::interleaved_bloom_filter (IBF) can now be constructed from a compressed IBF (#3082).

🐛 Notable bug fixes

Alignment

  • Resolved an issue resulting in a wrong alignment score (#3098).

I/O

  • Fixed writing an empty SAM-BAM file resulting in an invalid file (#3081).
  • seqan3::sequence_file_input_traits now allows char as a sequence alphabet (#3128).

Utility

  • Fixed spin delay having no effect on the PowerPC platform (#3129).

🛠️ Notable API changes

Alignment

  • The fields seqan3::field::offset and seqan3::field::alignment have been removed from seqan3::sam_record (#3058, #3089).
    For seqan3::field::offset, please check the soft clipping of the CIGAR string (seqan3::sam_record::cigar()).
    For seqan3::field::alignment, please use seqan3::alignment_from_cigar.

🔌 External dependencies

  • Dropped support for GCC 10 (#3148).
  • Added support for GCC 13 (#3148).
  • We require at least CMake 3.16 for our test suite. Note that the minimum requirement for using SeqAn3 is unchanged (#3050).
  • We now use Doxygen version 1.9.6 to build our documentation (#3116).
  • Updated sdsl-lite to 3.0.3 (#3170, #3174).
  • Compatibility with SeqAn2: SeqAn2's namespace was changed from seqan to seqan2. For interoperability, an up-to-date checkout of SeqAn2's main branch is required (#3156).
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SeqAn 3.3.0-rc.2

09 Aug 16:59
@eseiler eseiler
3.3.0-rc.2
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SeqAn 3.3.0-rc.2 Pre-release
Pre-release

This is the second release candidate for SeqAn 3.3.0

Changelog

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SeqAn 3.3.0-rc.1

17 Jul 10:36
@eseiler eseiler
3.3.0-rc.1
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eseiler Enrico Seiler
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SeqAn 3.3.0-rc.1 Pre-release
Pre-release

This is the first release candidate for SeqAn 3.3.0

Changelog

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SeqAn 3.2.0

20 Jun 14:03
@eseiler eseiler
3.2.0
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eseiler Enrico Seiler
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SeqAn 3.2.0

GitHub commits since tagged version (branch)

We are excited to announce the SeqAn 3.2.0 release that has a major compiler update:

We dropped GCC 7, GCC 8, and GCC 9 and we added GCC 12 support.

As a consequence, we also dropped C++17 support and are fully C++20 compatible.

Furthermore, we could drop the range-v3 dependency completely, so be sure to delete the submodule after updating to SeqAn 3.2.0!

While we will present essential changes of the 3.2.0 release in this message, you can also find a comprehensive list of the changes in our changelog.

Get to know SeqAn3 with our tutorials.

🎉 New Features

We added GCC 12 support!

Alphabet

  • seqan3::cigar can now be assigned from std::string_view which is much faster (no allocations) than the former assignment from seqan3::small_string.
  • The new view seqan3::views::char_strictly_to behaves like seqan3::views::char_to, but throws on invalid input.

I/O

  • The new option seqan3::sequence_file_option::fasta_ignore_blanks_before_id lets you keep blanks before IDs when reading FASTA files.
    This ensures a "perfekt roundtrip" when reading and writing FASTA files.
    E.g., fasta_ignore_blanks_before_id = true (default): >    some_id will only store "some_id" as ID.
    E.g., fasta_ignore_blanks_before_id = false: >    some_id will store "    some_id" as ID.

Search

  • Improved performance of seqan3::counting_vector::operator+= by 25%.

Utility

  • Added seqan3::list_traits::repeat.

🛠️ Notable API changes

seqan3::views::to is no view anymore but C++23 conform

We replaced seqan3::views::to (implemented via range-v3) with seqan3::ranges::to (implemented in SeqAn3). seqan3::ranges::to provides a subset of C++23's std::ranges::to and will be replaced with the STL-equivalent in a future version.
Since it is not a view anymore, it cannot be properly deprecated. Please keep this in mind if you encounter errors with seqan3::views::to.

Example:

auto vec = std::views::iota(0, 10) | seqan3::views::to<std::vector>; // Before
auto vec = std::views::iota(0, 10) | seqan3::ranges::to<std::vector>(); // After

Removed several headers in seqan3/std/

All headers in seqan3/std/ except charconv and new have been deprecated, since their STL-equivalents are available in GCC >= 10. Please use the equivalent std includes.

Example:

// Before
#include <seqan3/std/bit>
#include <seqan3/std/charconv>
// After
#include <bit>
#include <seqan3/std/charconv>

Removed namespace std::cpp20

The namespace std::cpp20 has been deprecated, since, e.g., the implementation of the std::back_inserter among others are now C++20-conform with GCC >= 10. Please use the std:: namespace.

Example:

std::ranges::copy(range, std::cpp20::back_inserter(other_range)); // Before
std::ranges::copy(range, std::back_inserter(other_range)); // After

🐛 Notable bug fixes

Core

  • Added missing implementations for AVX512 .

IO

  • FASTA files containing IDs starting with >, e.g., > >MyID, are now parsed correctly.

Search

  • Relaxed kmer_hash_view::iterator difference requirement .
  • Relaxed seqan3::views::minimiser requirements to be C++20-compatible.
  • Relaxed seqan3::views::kmer_hash requirements to be C++20-compatible.

Utility

  • seqan3::views::single_pass_input cannot propagate the std::ranges::output_range property because it cannot satisfy the following requirement: 
    *it++ = value;
// must be the same as
*it = value; ++it;
// but it actually would be the same as
++it; *it = value;
  • Fixed signature of seqan3::detail::store_sse4. This might have affected some public API.
  • Relaxed seqan3::views::to_simd requirements to be C++20-compatible.

🔌 External dependencies

  • GCC 7, 8, and 9 have been removed.
  • SeqAn 3.2.0 is known to compile with GCC 10.3, 11.3, and 12.1. Future versions might work, but were not yet available at the time of this release.
  • Other compilers, e.g., clang, and MSVC, are known to not be compatible with SeqAn 3.2.0.
  • We removed range-v3, and now require cereal 1.3.2 as well as sdsl-lite 3.0.1.
  • We use doxygen 1.9.4 to build our documentation.
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SeqAn 3.2.0-rc.1

15 Jun 18:11
@eseiler eseiler
3.2.0-rc.1
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SeqAn 3.2.0-rc.1 Pre-release
Pre-release

This is the first release candidate for SeqAn 3.2.0

You can find a list of changes in our changelog.

Notable API-changes (not final)

  • We removed the std::cpp20 namespace. We use std instead, since all supported compilers provide the C++20 versions of the entities we used with std::cpp20.
  • We replaced seqan3::views::to with seqan3::range::to. As planned for C++23, it is no longer a view, but a function object. seqan3::views::to<std::vector> changes to seqan3::range::to<std::vector>().

Dependencies

  • cereal bumped to 1.3.2
  • sdsl-lite bumped to 3.0.1
  • range-v3 removed
  • For documentation: doxygen bumped to 1.9.4
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