[med-svn] [vsearch] branch upstream updated (fbd885d -> 34bca89)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository vsearch.

      from  fbd885d   Imported Upstream version 2.0.5
       new  cc668cc   New upstream version 2.3.0
       new  34bca89   Imported Upstream version 2.3.2

The 2 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:
 README.md                      |  110 +---
 configure.ac                   |    2 +-
 man/vsearch.1                  | 1241 ++++++++++++++++++++++++++--------------
 src/Makefile.am                |    2 +
 src/align_simd.cc              |   30 +-
 src/allpairs.cc                |    6 +-
 src/chimera.cc                 |    4 +-
 src/cluster.cc                 |  129 ++++-
 src/derep.cc                   |   26 +-
 src/fasta.cc                   |    2 +
 src/fastq.cc                   |    4 +
 src/fastqops.cc                |  113 ++--
 src/fastqops.h                 |    3 +-
 src/linmemalign.cc             |   17 +-
 src/linmemalign.h              |    2 +
 src/mergepairs.cc              |    4 +-
 src/otutable.cc                |  405 +++++++++++++
 src/{allpairs.h => otutable.h} |    9 +-
 src/results.cc                 |   15 +-
 src/results.h                  |    3 +-
 src/search.cc                  |   67 ++-
 src/searchcore.cc              |   66 ++-
 src/searchcore.h               |    4 +-
 src/searchexact.cc             |   73 ++-
 src/vsearch.cc                 |  358 +++++++-----
 src/vsearch.h                  |    8 +
 test/unclassified.sh           |  356 ++++++++++++
 27 files changed, 2289 insertions(+), 770 deletions(-)
 create mode 100644 src/otutable.cc
 copy src/{allpairs.h => otutable.h} (88%)
 create mode 100644 test/unclassified.sh

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