[med-svn] [mothur] 02/08: Merge tag 'upstream/1.38.1.1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository mothur.

commit 925db9a4c1706393fcd807890426b727327b36bf
Merge: 226e3f5 a2de248
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 10 06:32:40 2016 +0100

    Merge tag 'upstream/1.38.1.1'
    
    Upstream version 1.38.1.1

 .gitignore                                   |   1 +
 Makefile                                     |   4 +-
 Mothur.xcodeproj/project.pbxproj             |  94 ++++----
 source/commandfactory.cpp                    |  17 +-
 source/commands/clustercommand.cpp           |  41 ++--
 source/commands/clustercommand.h             |   2 +-
 source/commands/clusterdoturcommand.cpp      |  16 +-
 source/commands/clusterdoturcommand.h        |   2 +-
 source/commands/clustersplitcommand.cpp      |  35 +--
 source/commands/clustersplitcommand.h        |   2 +-
 source/commands/command.hpp                  |   8 +-
 source/commands/getmimarkspackagecommand.cpp |   2 +-
 source/commands/helpcommand.cpp              | 325 ++++++++++++++++++++++++++-
 source/commands/helpcommand.h                |   8 +-
 source/commands/makecontigscommand.cpp       |   5 +-
 source/commands/makefilecommand.cpp          |  42 ++--
 source/commands/makefilecommand.h            |   2 +-
 source/commands/makegroupcommand.cpp         |   2 +-
 source/commands/mergecountcommand.cpp        | 226 +++++++++++++++++++
 source/commands/mergecountcommand.hpp        |  48 ++++
 source/commands/mergegroupscommand.cpp       |   5 +
 source/commands/parselistscommand.cpp        |  23 +-
 source/commands/seqerrorcommand.cpp          |   5 +
 source/commands/sracommand.cpp               |  11 +-
 source/commands/trimflowscommand.cpp         |   2 +
 source/commands/trimseqscommand.cpp          |   1 +
 source/datastructures/counttable.cpp         |  24 +-
 source/datastructures/counttable.h           |   5 +-
 source/mothurout.cpp                         |   4 +-
 29 files changed, 792 insertions(+), 170 deletions(-)

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