[med-svn] [vsearch] 02/04: Merge tag 'upstream/2.0.0'

[Andreas Tille]

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tille pushed a commit to branch master
in repository vsearch.

commit 516b274dd3896d8fae999b2e5b8b56cfd515e1b6
Merge: 05b78bd ecb9cf5
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 30 10:06:31 2016 +0200

    Merge tag 'upstream/2.0.0'
    
    Upstream version 2.0.0
    
    Conflicts:
    	configure.ac
    	man/vsearch.1
    	src/fasta.cc
    	src/fastq.cc

 configure.ac       |   2 +-
 man/vsearch.1      |  87 +++++++---
 src/chimera.cc     |   2 +-
 src/dynlibs.cc     |  17 +-
 src/dynlibs.h      |   4 +
 src/eestats.cc     |   2 +-
 src/fasta.cc       | 316 +++-------------------------------
 src/fasta.h        |  63 ++-----
 src/fastq.cc       | 368 ++++-----------------------------------
 src/fastq.h        |  71 ++------
 src/fastqops.cc    |   8 +-
 src/fastx.cc       | 491 ++++++++++++++++++++++++++++++++++++++---------------
 src/fastx.h        |  53 +++++-
 src/maps.cc        |  53 ++++++
 src/maps.h         |   1 +
 src/mergepairs.cc  |   4 +-
 src/msa.cc         |  82 +++------
 src/rerep.cc       |   2 +-
 src/search.cc      |   2 +-
 src/searchcore.cc  |   4 +-
 src/searchexact.cc |   2 +-
 src/util.cc        |   2 +-
 src/vsearch.cc     | 113 +++++++++++-
 src/vsearch.h      |   4 +-
 24 files changed, 783 insertions(+), 970 deletions(-)

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