[med-svn] [vsearch] 02/04: Merge tag 'upstream/2.4.3'

[Andreas Tille]

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tille pushed a commit to branch master
in repository vsearch.

commit a62b050dcb1984a18001a43e1dc705bddc0f4d8b
Merge: 6aa93f1 38304cc
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jun 19 11:55:24 2017 +0200

    Merge tag 'upstream/2.4.3'
    
    Upstream version 2.4.3

 .gitignore           |   2 +
 LICENSE.txt          |   2 +-
 README.md            |  62 ++--
 configure.ac         |  12 +-
 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 ++++
 88 files changed, 2688 insertions(+), 1800 deletions(-)

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