[med-svn] [mothur] 04/06: Merge tag 'upstream/1.39.3'

[Tomasz Buchert]

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tomasz pushed a commit to branch master
in repository mothur.

commit fce009d633f646266e5d3b4b6ed99574b059410d
Merge: 49675ba b7377f0
Author: Tomasz Buchert <tomasz at debian.org>
Date:   Sun Feb 26 15:33:35 2017 +0100

    Merge tag 'upstream/1.39.3'
    
    Upstream version 1.39.3

 Makefile                                  |  9 +--
 Mothur.xcodeproj/project.pbxproj          | 16 +++---
 makefile-internal                         | 18 +++---
 source/classifier/classify.cpp            | 16 +-----
 source/classifier/phylosummary.cpp        |  2 +-
 source/classifier/phylotree.cpp           | 35 ++++++------
 source/commands/chimeravsearchcommand.cpp |  6 +-
 source/commands/classifyotucommand.cpp    | 14 +++--
 source/commands/clustersplitcommand.cpp   | 11 +++-
 source/commands/clustersplitcommand.h     |  2 +-
 source/commands/getcurrentcommand.cpp     |  2 +
 source/commands/makecontigscommand.cpp    | 81 +++++++++++++++------------
 source/commands/makecontigscommand.h      | 64 ++++++++++++----------
 source/commands/makefilecommand.cpp       | 30 +++++++++-
 source/commands/pcrseqscommand.cpp        |  6 +-
 source/commands/preclustercommand.cpp     |  6 +-
 source/commands/renamefilecommand.cpp     | 10 ++--
 source/commands/sensspeccommand.cpp       | 50 ++++++-----------
 source/commands/sensspeccommand.h         |  2 +-
 source/commands/seqsummarycommand.cpp     | 16 +++++-
 source/commands/setcurrentcommand.cpp     | 20 ++++++-
 source/commands/setcurrentcommand.h       |  2 +-
 source/commands/sffinfocommand.cpp        |  2 +-
 source/commands/sracommand.cpp            |  3 +-
 source/datastructures/optimatrix.cpp      | 62 ++++++++++-----------
 source/engine.cpp                         | 10 ++--
 source/mothurout.cpp                      | 91 +++++++++++++++++++++++--------
 source/mothurout.h                        | 10 +++-
 source/optionparser.cpp                   |  2 +
 29 files changed, 353 insertions(+), 245 deletions(-)

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