Étienne Mollier pushed to branch upstream at Debian Med / vsearch
Commits: 3a5cba11 by Étienne Mollier at 2025-12-03T22:40:10+01:00 New upstream version 2.30.1 - - - - - 217 changed files: - .github/workflows/jekyll-gh-pages.yml - .gitignore - LICENSE.txt - README.md - + _config.yml - configure.ac - + 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 The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/commit/3a5cba1135498d8e665b521e05f206809e3fd9c0 -- View it on GitLab: https://salsa.debian.org/med-team/vsearch/-/commit/3a5cba1135498d8e665b521e05f206809e3fd9c0 You're receiving this email because of your account on salsa.debian.org.
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