[med-svn] [Git][med-team/vsearch][master] 7 commits: New upstream version 2.30.1

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / vsearch


Commits:
3a5cba11 by Étienne Mollier at 2025-12-03T22:40:10+01:00
New upstream version 2.30.1
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012cc2bf by Étienne Mollier at 2025-12-03T22:40:15+01:00
Update upstream source from tag 'upstream/2.30.1'

Update to upstream version '2.30.1'
with Debian dir f436ca4441a556b6e1d252c75ec21e3349edf9f2
- - - - -
d6ef135b by Étienne Mollier at 2025-12-03T22:44:50+01:00
d/copyright: bump upstream copyright year.

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48809a81 by Étienne Mollier at 2025-12-03T22:46:29+01:00
occurrences.patch: delete: applied upstream.

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1e0f7d40 by Étienne Mollier at 2025-12-03T22:46:51+01:00
d/control: drop redundant Rules-Requires-Root: no.

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003b18cc by Étienne Mollier at 2025-12-03T22:48:32+01:00
d/watch: convert to v5 Github template.

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86045ec5 by Étienne Mollier at 2025-12-03T22:56:57+01:00
d/changelog: ready for upload to unstable.

- - - - -


223 changed files:

- .github/workflows/jekyll-gh-pages.yml
- .gitignore
- LICENSE.txt
- README.md
- + _config.yml
- configure.ac
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/occurrences.patch
- − debian/patches/series
- debian/watch
- + man/commands/fragments/date.md
- + man/commands/fragments/footer.md
- + man/commands/fragments/option_abskew_1.md
- + man/commands/fragments/option_abskew_16.md
- + man/commands/fragments/option_abskew_2.md
- + man/commands/fragments/option_alignwidth.md
- + man/commands/fragments/option_bzip2_decompress.md
- + man/commands/fragments/option_chimeras.md
- + man/commands/fragments/option_chimeras_diff_pct.md
- + man/commands/fragments/option_chimeras_length_min.md
- + man/commands/fragments/option_chimeras_parents_max.md
- + man/commands/fragments/option_chimeras_parts.md
- + man/commands/fragments/option_dbmask.md
- + man/commands/fragments/option_fasta_width.md
- + man/commands/fragments/option_fastq_ascii.md
- + man/commands/fragments/option_fastq_asciiout.md
- + man/commands/fragments/option_fastq_qmax.md
- + man/commands/fragments/option_fastq_qmax_ignored.md
- + man/commands/fragments/option_fastq_qmin.md
- + man/commands/fragments/option_fastq_qmin_ignored.md
- + man/commands/fragments/option_gapext.md
- + man/commands/fragments/option_gapopen.md
- + man/commands/fragments/option_gzip_decompress.md
- + man/commands/fragments/option_hardmask.md
- + man/commands/fragments/option_label_suffix.md
- + man/commands/fragments/option_lengthout.md
- + man/commands/fragments/option_log.md
- + man/commands/fragments/option_match.md
- + man/commands/fragments/option_maxseqlength.md
- + man/commands/fragments/option_minseqlength_1.md
- + man/commands/fragments/option_minseqlength_32.md
- + man/commands/fragments/option_mismatch.md
- + man/commands/fragments/option_no_progress.md
- + man/commands/fragments/option_nonchimeras.md
- + man/commands/fragments/option_notrunclabels.md
- + man/commands/fragments/option_output.md
- + man/commands/fragments/option_qmask.md
- + man/commands/fragments/option_quiet.md
- + man/commands/fragments/option_randseed.md
- + man/commands/fragments/option_relabel.md
- + man/commands/fragments/option_relabel_keep.md
- + man/commands/fragments/option_relabel_md5.md
- + man/commands/fragments/option_relabel_self.md
- + man/commands/fragments/option_relabel_sha1.md
- + man/commands/fragments/option_sample.md
- + man/commands/fragments/option_sizein.md
- + man/commands/fragments/option_sizein_implied.md
- + man/commands/fragments/option_sizeout.md
- + man/commands/fragments/option_threads_not_multithreaded.md
- + man/commands/fragments/option_topn.md
- + man/commands/fragments/option_wordlength.md
- + man/commands/fragments/option_xee.md
- + man/commands/fragments/option_xlength.md
- + man/commands/fragments/option_xn.md
- + man/commands/fragments/option_xsize.md
- + man/commands/vsearch-chimeras_denovo.1.md
- + man/commands/vsearch-cut.1.md
- + man/commands/vsearch-fasta2fastq.1.md
- + man/commands/vsearch-fastq_chars.1.md
- + man/commands/vsearch-fastq_stats.1.md
- + man/commands/vsearch-orient.1.md
- + man/commands/vsearch-shuffle.1.md
- + man/formats/fragments/format_sequence.md
- + man/formats/vsearch-fasta.5.md
- + man/formats/vsearch-fastq.5.md
- + man/formats/vsearch-sff.5.md
- + man/formats/vsearch-udb.5.md
- + man/index.1.md
- + man/misc/vsearch-expected_error.7.md
- + man/misc/vsearch-pairwise_alignment_parameters.7.md
- + man/scripts/generate_manpages.sh
- + man/scripts/generate_online_documentation.sh
- + man/scripts/include_markdown_files.sh
- + man/scripts/visualize_manpage.sh
- man/vsearch.1
- src/Makefile.am
- src/align_simd.cc
- src/align_simd.h
- src/allpairs.cc
- src/allpairs.h
- src/arch.cc
- src/arch.h
- src/attributes.cc
- src/attributes.h
- src/bitmap.cc
- src/bitmap.h
- src/chimera.cc
- src/chimera.h
- src/city.cc
- src/city.h
- − src/citycrc.h
- src/cluster.cc
- src/cluster.h
- src/cpu.cc
- src/cpu.h
- src/cut.cc
- src/cut.h
- src/db.cc
- src/db.h
- src/dbhash.cc
- src/dbhash.h
- src/dbindex.cc
- src/dbindex.h
- src/derep.cc
- src/derep.h
- src/derep_prefix.cc
- src/derep_prefix.h
- src/derep_smallmem.cc
- src/derep_smallmem.h
- src/dynlibs.cc
- src/dynlibs.h
- src/eestats.cc
- src/eestats.h
- src/fasta.cc
- src/fasta.h
- src/fasta2fastq.cc
- src/fasta2fastq.h
- src/fastq.cc
- src/fastq.h
- src/fastq_chars.cc
- src/fastq_chars.h
- src/fastq_join.cc
- src/fastq_join.h
- src/mergepairs.cc → src/fastq_mergepairs.cc
- src/mergepairs.h → src/fastq_mergepairs.h
- + src/fastq_stats.cc
- src/utils/seqcmp.h → src/fastq_stats.h
- src/fastqops.cc
- src/fastqops.h
- src/fastx.cc
- src/fastx.h
- src/filter.cc
- src/filter.h
- src/getseq.cc
- src/getseq.h
- src/kmerhash.cc
- src/kmerhash.h
- src/linmemalign.cc
- src/linmemalign.h
- − src/maps.cc
- src/mask.cc
- src/mask.h
- src/md5.c
- src/minheap.cc
- src/minheap.h
- src/msa.cc
- src/msa.h
- src/orient.cc
- src/orient.h
- src/otutable.cc
- src/otutable.h
- src/rereplicate.cc
- src/rereplicate.h
- src/results.cc
- src/results.h
- src/search.cc
- src/search.h
- src/search_exact.cc
- src/search_exact.h
- src/searchcore.cc
- src/searchcore.h
- src/sff_convert.cc
- src/sff_convert.h
- src/showalign.cc
- src/showalign.h
- src/shuffle.cc
- src/shuffle.h
- src/sintax.cc
- src/sintax.h
- src/sortbylength.cc
- src/sortbylength.h
- src/sortbysize.cc
- src/sortbysize.h
- src/subsample.cc
- src/subsample.h
- src/tax.cc
- src/tax.h
- src/udb.cc
- src/udb.h
- src/unique.cc
- src/unique.h
- src/userfields.cc
- src/userfields.h
- src/util.cc
- src/util.h
- src/maps.h → src/utils/check_output_filehandle.cpp
- + src/utils/check_output_filehandle.hpp
- + src/utils/cigar.cpp
- src/utils/seqcmp.cc → src/utils/cigar.hpp
- + src/utils/cigar_operations.hpp
- + src/utils/compare_strings_nocase.cpp
- + src/utils/compare_strings_nocase.hpp
- + src/utils/fatal.cpp
- + src/utils/fatal.hpp
- + src/utils/kmer_hash_struct.hpp
- src/utils/maps.cpp
- src/utils/maps.hpp
- + src/utils/open_file.cpp
- + src/utils/open_file.hpp
- + src/utils/os_byteswap.cpp
- + src/utils/os_byteswap.hpp
- + src/utils/progress.hpp
- + src/utils/seqcmp.cpp
- + src/utils/seqcmp.hpp
- + src/utils/span.hpp
- + src/utils/taxonomic_fields.h
- + src/utils/xpthread.cpp
- + src/utils/xpthread.hpp
- src/vsearch.cc
- src/vsearch.h
- src/xstring.h


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View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/compare/c84c1d418ed97347225fbcb4d572a4e6e7454ed6...86045ec502e620bb8db422516ef4957c2c0ec61a

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View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/compare/c84c1d418ed97347225fbcb4d572a4e6e7454ed6...86045ec502e620bb8db422516ef4957c2c0ec61a
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