[med-svn] [mothur] branch master updated (db3ce27 -> e1f2f20)

[Tomasz Buchert]

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tomasz pushed a change to branch master
in repository mothur.

      from  db3ce27   release
       new  e59bb6f   New upstream version 1.39.4
       new  5ff7805   Merge tag 'upstream/1.39.4'
       new  ec37447   d/patches: refresh
       new  e1f2f20   release

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Summary of changes:
 Makefile                                           |   4 +-
 Mothur.xcodeproj/project.pbxproj                   |  59 ++++-----
 debian/changelog                                   |   7 ++
 ...mmand.patch => 0002-Fix-catchall-command.patch} |   0
 .../0002-Update-version-numbers-everywhere.patch   |  77 ------------
 .../0003-Update-version-numbers-everywhere.patch   |  49 ++++++++
 debian/patches/series                              |   4 +-
 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 --
 53 files changed, 427 insertions(+), 286 deletions(-)
 rename debian/patches/{0003-Fix-catchall-command.patch => 0002-Fix-catchall-command.patch} (100%)
 delete mode 100644 debian/patches/0002-Update-version-numbers-everywhere.patch
 create mode 100644 debian/patches/0003-Update-version-numbers-everywhere.patch

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