[med-svn] [mothur] branch upstream updated (4767758 -> a2de248)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository mothur.

      from  4767758   Imported Upstream version 1.38.0
       new  a2de248   New upstream version 1.38.1.1

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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Summary of changes:
 .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(-)
 create mode 100644 source/commands/mergecountcommand.cpp
 create mode 100644 source/commands/mergecountcommand.hpp

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