[med-svn] [mothur] branch upstream updated (e59bb6f -> ab8478c)

[Tomasz Buchert]

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tomasz pushed a change to branch upstream
in repository mothur.

      from  e59bb6f   New upstream version 1.39.4
       new  ab8478c   New upstream version 1.39.5

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
been added to this reference.


Summary of changes:
 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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