[med-svn] [mothur] 02/04: Merge tag 'upstream/1.39.5'

[Tomasz Buchert]

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tomasz pushed a commit to branch master
in repository mothur.

commit 01cbb29fb416e6f8cce93b7d56d7a13460910514
Merge: e1f2f20 ab8478c
Author: Tomasz Buchert <tomasz at debian.org>
Date:   Sat Mar 25 11:59:42 2017 +0100

    Merge tag 'upstream/1.39.5'
    
    Upstream version 1.39.5

 Makefile                                           |     14 +-
 Mothur.xcodeproj/project.pbxproj                   |     17 +-
 TestMothur/dataset.cpp                             | 192780 +-----------------
 TestMothur/distcdataset.cpp                        |  46876 +----
 TestMothur/distcdataset.h                          |      7 +-
 TestMothur/distpdataset.cpp                        |   2564 +-
 TestMothur/distpdataset.h                          |      4 +-
 TestMothur/fastqdataset.cpp                        |  16037 +-
 TestMothur/fastqdataset.h                          |      4 +-
 TestMothur/main.cpp                                |     42 +-
 TestMothur/testbiominfocommand.cpp                 |      5 +-
 TestMothur/testcommands/testgetgroupscommand.cpp   |      3 +-
 TestMothur/testcommands/testmergegroupscommand.cpp |      3 +-
 .../testcommands/testremovegroupscommand.cpp       |      6 +-
 TestMothur/testcommands/testrenamefilecommand.cpp  |      6 +-
 TestMothur/testcommands/testrenameseqscommand.cpp  |      6 +-
 TestMothur/testcommands/testsetseedcommand.cpp     |      5 +-
 TestMothur/testcontainers/testfastqread.cpp        |      9 +-
 TestMothur/testcontainers/testoptimatrix.cpp       |      7 +-
 TestMothur/testcontainers/testsequence.cpp         |      5 +-
 TestMothur/testopticluster.cpp                     |    129 +-
 TestMothur/testopticluster.h                       |      8 +-
 TestMothur/testtrimoligos.cpp                      |      2 +-
 TestMothur/testvsearchfileparser.cpp               |      6 +-
 makefile-internal                                  |      8 +-
 source/commandfactory.cpp                          |      2 +-
 source/commands/clustercommand.cpp                 |      4 +-
 source/commands/clustersplitcommand.cpp            |      3 +-
 source/commands/makebiomcommand.cpp                |      7 +-
 source/commands/makefilecommand.cpp                |     12 +-
 source/commands/makelefsecommand.cpp               |      6 +-
 source/commands/nmdscommand.cpp                    |      2 +-
 source/commands/parsefastaqcommand.cpp             |      4 +-
 source/commands/rarefactcommand.cpp                |      6 +-
 source/commands/summarytaxcommand.cpp              |      2 +-
 source/datastructures/listvector.cpp               |      2 +-
 source/datastructures/rabundvector.cpp             |      2 +-
 source/datastructures/sabundvector.cpp             |      4 +-
 source/datastructures/sabundvector.hpp             |      2 +-
 source/datastructures/sharedlistvector.cpp         |      4 +-
 source/datastructures/sharedordervector.cpp        |      4 +-
 source/datastructures/sharedrabundfloatvector.cpp  |      4 +-
 source/datastructures/sharedrabundvector.cpp       |      4 +-
 source/datastructures/sharedsabundvector.cpp       |      2 +-
 source/mothurout.cpp                               |    100 +-
 source/mothurout.h                                 |     16 +-
 source/opticluster.h                               |      3 +-
 source/rarefact.cpp                                |     10 +-
 source/rarefact.h                                  |      6 +-
 source/subsample.cpp                               |     41 +-
 50 files changed, 368 insertions(+), 258437 deletions(-)

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