VSEARCH 2.29.0

vsearch 2.29.0 fixes seven bugs (see changelog below), adds initial support for RISC-V architectures, and improves code quality and code testing (1,210 new tests).

Changelog:

• add: experimental support for RISCV64 and other 64-bit little-endian architectures, thanks to Michael R. Crusoe and his fellow Debian developers (PR #566),
• add: official support for clang-19 and gcc 14,
• add: beta support for clang-20,
• remove: unused --output option for command --fastq_stats (issue #572),
• fix: bug in --sintax when selecting the best lineage (only low confidence values below 0.5 were affected) (issue #573),
• fix: out-of-bounds error in --fastq_stats when processing empty reads (issue #571),
• fix: bug in --cut, patterns with multiple cutting sites were not detected (commit 4c4f9fa),
• fix: memory error (segmentation fault) when using --derep_id and --strand (issue #565),
• fix: --fastq_join now obeys to --quiet and --log options (commit 87f968b),
• fix: --fastq_join quality padding is now also set to Q40 when quality offset is 64 (commit be0bf9b),
• fix: (partial) --fastq_join's handling of abundance annotations (commit f2bbcb4),
• improve: additional safeguards to validate input values and to make sure that they are within acceptable limits. Changes concern options --abskew (commit a530dd8) and --fastq_maxdiffs (commit 4b254db),
• improve: code quality (1.3k+ commits, 6k+ clang-tidy warnings eliminated),
• improve: documentation and help messages (issue #568),
• improve: complete refactoring and modernization of a subset of commands (--sortbylength, --sortbysize, --shuffle, --rereplicate, --cut, --fastq_join, --fasta2fastq, --fastq_chars),
• improve: code-coverage of our test-suite for the above-mentioned commands (1,210 new tests, 4,753 in total).