[med-svn] [mothur] branch master updated (e1f2f20 -> 21913bf)

[Tomasz Buchert]

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tomasz pushed a change to branch master
in repository mothur.

      from  e1f2f20   release
       new  ab8478c   New upstream version 1.39.5
       new  01cbb29   Merge tag 'upstream/1.39.5'
       new  9fbaafe   d/patches: refresh
       new  21913bf   release

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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 +-
 debian/changelog                                   |      7 +
 .../0003-Update-version-numbers-everywhere.patch   |     20 +-
 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 +-
 52 files changed, 385 insertions(+), 258447 deletions(-)

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