SeqAn 3.3.0 released

Dear SeqAn users, supporters, and subscribers,

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.

• Get to know SeqAn3 with our tutorials.
• Visit our API documentation.
• Check out our SeqAn3 Cookbook with all the copy & paste snippets you need.

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).