[med-svn] [mothur] branch upstream updated (b7377f0 -> e59bb6f)

[Tomasz Buchert]

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tomasz pushed a change to branch upstream
in repository mothur.

      from  b7377f0   New upstream version 1.39.3
       new  e59bb6f   New upstream version 1.39.4

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 Makefile                                       |   4 +-
 Mothur.xcodeproj/project.pbxproj               |  59 +++++------
 makefile-internal                              |   4 +-
 source/chimera/chimeracheckrdp.cpp             |   2 +-
 source/chimera/slayer.cpp                      |   4 +-
 source/classifier/bayesian.cpp                 |   2 +-
 source/clusterclassic.cpp                      |   2 +-
 source/commands/aligncommand.cpp               |   2 +-
 source/commands/amovacommand.cpp               |   2 +-
 source/commands/anosimcommand.cpp              |   2 +-
 source/commands/chimeraslayercommand.cpp       |   4 +-
 source/commands/classifyseqscommand.cpp        |   6 +-
 source/commands/cooccurrencecommand.cpp        |   8 +-
 source/commands/homovacommand.cpp              |   2 +-
 source/commands/lefsecommand.cpp               |   6 +-
 source/commands/makecontigscommand.cpp         |   6 +-
 source/commands/makecontigscommand.h           |   4 +
 source/commands/makefilecommand.cpp            | 130 +++++++++++++----------
 source/commands/makefilecommand.h              |   2 +-
 source/commands/mantelcommand.cpp              |   2 +-
 source/commands/nmdscommand.cpp                |   4 +-
 source/commands/phylodiversitycommand.cpp      |   2 +-
 source/commands/phylodiversitycommand.h        |   2 +-
 source/commands/sparcccommand.cpp              |   2 +-
 source/commands/sparcccommand.h                |   2 +-
 source/commands/subsamplecommand.cpp           |  28 +++--
 source/commands/summarytaxcommand.cpp          |   4 +-
 source/communitytype/communitytype.cpp         |   2 +-
 source/datastructures/blastalign.cpp           |   2 +-
 source/datastructures/blastdb.cpp              |   8 +-
 source/datastructures/oligos.cpp               |   2 +
 source/datastructures/sparsedistancematrix.cpp |   2 +-
 source/datastructures/sparsedistancematrix.h   |  15 ---
 source/datastructures/sparsematrix.cpp         |   2 +-
 source/datastructures/sparsematrix.hpp         |  12 ---
 source/datastructures/tree.cpp                 |   6 +-
 source/libshuff.cpp                            |   2 +-
 source/linearalgebra.cpp                       |   4 +-
 source/metastats/mothurmetastats.cpp           |   2 +-
 source/mothur.h                                |  33 ++++++
 source/mothurout.cpp                           | 139 ++++++++++++++++++++++++-
 source/mothurout.h                             |   8 ++
 source/opticluster.cpp                         |   4 +-
 source/randomforest/abstractdecisiontree.cpp   |   4 +-
 source/randomforest/decisiontree.cpp           |   5 +-
 source/sharedutilities.cpp                     |   2 +-
 source/subsample.cpp                           |  17 +--
 source/subsample.h                             |   8 --
 48 files changed, 369 insertions(+), 207 deletions(-)

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