[med-svn] [vsearch] branch master updated (6aa93f1 -> b1f1d1f)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository vsearch.

      from  6aa93f1   Drop libssl-dev Build-Depends
       new  38304cc   New upstream version 2.4.3
       new  a62b050   Merge tag 'upstream/2.4.3'
       new  27a5177   New upstream version
       new  b1f1d1f   Refresh patches, upload to unstable

The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore                                 |   2 +
 LICENSE.txt                                |   2 +-
 README.md                                  |  62 +-
 configure.ac                               |  12 +-
 debian/changelog                           |   5 +-
 debian/patches/compilerflags.patch         |   2 +-
 debian/patches/sysconf_memory_sizing.patch |   6 +-
 man/vsearch.1                              |  64 +-
 src/Makefile.am                            |  36 +-
 src/abundance.cc                           |  20 +-
 src/abundance.h                            |   6 +-
 src/align.cc                               | 100 +--
 src/align.h                                |  42 +-
 src/align_simd.cc                          | 963 ++++++++++++++++++++++-------
 src/align_simd.h                           |   2 +-
 src/allpairs.cc                            |  91 +--
 src/allpairs.h                             |   2 +-
 src/arch.cc                                | 158 ++++-
 src/arch.h                                 |  13 +-
 src/bitmap.cc                              |   6 +-
 src/bitmap.h                               |   2 +-
 src/chimera.cc                             | 110 ++--
 src/chimera.h                              |   2 +-
 src/cluster.cc                             |  96 +--
 src/cluster.h                              |   2 +-
 src/cpu.cc                                 |  49 +-
 src/cpu.h                                  |   8 +-
 src/db.cc                                  |  60 +-
 src/db.h                                   |  24 +-
 src/dbhash.cc                              |  42 +-
 src/dbhash.h                               |  24 +-
 src/dbindex.cc                             |  24 +-
 src/dbindex.h                              |   6 +-
 src/derep.cc                               | 136 ++--
 src/derep.h                                |   2 +-
 src/dynlibs.cc                             |  73 ++-
 src/dynlibs.h                              |  10 +-
 src/eestats.cc                             |  82 +--
 src/eestats.h                              |   2 +-
 src/fasta.cc                               |  54 +-
 src/fasta.h                                |  34 +-
 src/fastq.cc                               |  66 +-
 src/fastq.h                                |  20 +-
 src/fastqops.cc                            | 216 +++----
 src/fastqops.h                             |   2 +-
 src/fastx.cc                               |  40 +-
 src/fastx.h                                |  43 +-
 src/linmemalign.cc                         | 156 ++---
 src/linmemalign.h                          | 100 +--
 src/maps.cc                                |   2 +-
 src/maps.h                                 |   2 +-
 src/mask.cc                                |  10 +-
 src/mask.h                                 |   2 +-
 src/mergepairs.cc                          | 177 +++---
 src/mergepairs.h                           |   2 +-
 src/minheap.cc                             |   8 +-
 src/minheap.h                              |   3 +-
 src/msa.cc                                 |  26 +-
 src/msa.h                                  |   4 +-
 src/otutable.cc                            |  48 +-
 src/otutable.h                             |   4 +-
 src/rerep.cc                               |  14 +-
 src/rerep.h                                |   2 +-
 src/results.cc                             |  83 +--
 src/results.h                              |  14 +-
 src/search.cc                              |  71 ++-
 src/search.h                               |   2 +-
 src/searchcore.cc                          |  42 +-
 src/searchcore.h                           |   2 +-
 src/searchexact.cc                         |  79 +--
 src/searchexact.h                          |   2 +-
 src/showalign.cc                           |  64 +-
 src/showalign.h                            |  12 +-
 src/shuffle.cc                             |   6 +-
 src/shuffle.h                              |   2 +-
 src/sortbylength.cc                        |   4 +-
 src/sortbylength.h                         |   2 +-
 src/sortbysize.cc                          |   6 +-
 src/sortbysize.h                           |   2 +-
 src/subsample.cc                           |  26 +-
 src/subsample.h                            |   2 +-
 src/unique.cc                              |  40 +-
 src/unique.h                               |   2 +-
 src/userfields.cc                          |   6 +-
 src/userfields.h                           |   2 +-
 src/util.cc                                | 134 ++--
 src/util.h                                 |  20 +-
 src/vsearch.cc                             | 203 +++---
 src/vsearch.h                              | 218 ++++---
 src/xstring.h                              |   2 +-
 test/unclassified.sh                       |  70 +++
 91 files changed, 2695 insertions(+), 1806 deletions(-)

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