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SeqAn 3.3.0

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@eseiler eseiler released this 17 Aug 11:13
3.3.0
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eseiler Enrico Seiler
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Learn about vigilant mode.
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Learn about vigilant mode.

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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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