[med-svn] [mothur] branch master updated (226e3f5 -> 70ff244)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository mothur.

      from  226e3f5   release
       new  a2de248   New upstream version 1.38.1.1
       new  925db9a   Merge tag 'upstream/1.38.1.1'
       new  2731517   New upstream version
       new  d2ca6b7   debhelper 10
       new  059a59a   d/watch: version=4
       new  a9a6117   --parallel is default for debhelper 10
       new  7078bb2   Close bug
       new  70ff244   Fix spelling + upload

The 8 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
been added to this reference.


Summary of changes:
 .gitignore                                   |   1 +
 Makefile                                     |   4 +-
 Mothur.xcodeproj/project.pbxproj             |  94 ++++----
 debian/changelog                             |  10 +
 debian/compat                                |   2 +-
 debian/control                               |   2 +-
 debian/patches/series                        |   1 +
 debian/patches/spelling.patch                | 300 +++++++++++++++++++++++++
 debian/rules                                 |   2 +-
 debian/uchime.1                              |   2 +-
 debian/watch                                 |   4 +-
 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 +-
 37 files changed, 1109 insertions(+), 176 deletions(-)
 create mode 100644 debian/patches/spelling.patch
 create mode 100644 source/commands/mergecountcommand.cpp
 create mode 100644 source/commands/mergecountcommand.hpp

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