[med-svn] [mothur] 02/04: Merge tag 'upstream/1.38.0'

[Tomasz Buchert]

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tomasz pushed a commit to branch master
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commit 15a4bf12e1f7c824c6f79fb2c7b6affc4904c357
Merge: d00b4e5 4767758
Author: Tomasz Buchert <tomasz at debian.org>
Date:   Sat Jul 30 01:16:32 2016 +0200

    Merge tag 'upstream/1.38.0'
    
    Upstream version 1.38.0

 Makefile                                          |    4 +-
 Mothur.xcodeproj/project.pbxproj                  |  104 +-
 TestMothur/dataset.h                              |    2 +-
 TestMothur/testcommands/testrenamefilecommand.cpp |   97 ++
 TestMothur/testcommands/testrenamefilecommand.h   |   40 +
 TestMothur/testtrimoligos.cpp                     |   43 +
 TestMothur/testtrimoligos.hpp                     |   38 +
 makefile-internal                                 |    4 +-
 source/averagelinkage.cpp                         |    3 -
 source/chimera/mothurchimera.cpp                  |   70 +-
 source/classifier/bayesian.cpp                    |   77 +-
 source/classifier/classify.cpp                    |  210 +--
 source/classifier/phylosummary.cpp                |    3 -
 source/classifier/phylotree.cpp                   |    2 +-
 source/cluster.hpp                                |    6 +-
 source/commandfactory.cpp                         |   25 +-
 source/commands/aligncommand.cpp                  |   26 +-
 source/commands/chimeraccodecommand.cpp           |   26 +-
 source/commands/chimeracheckcommand.cpp           |   27 +-
 source/commands/chimerapintailcommand.cpp         |   23 +-
 source/commands/chimerapintailcommand.h           |    2 -
 source/commands/chimeraslayercommand.cpp          |   31 +-
 source/commands/chimerauchimecommand.cpp          |   41 +-
 source/commands/chimerauchimecommand.h            |   24 +-
 source/commands/chimeravsearchcommand.cpp         | 1661 +++++++++++++++++++++
 source/commands/chimeravsearchcommand.h           |   66 +
 source/commands/classifyotucommand.cpp            |  147 +-
 source/commands/classifyotucommand.h              |    4 +-
 source/commands/classifyrfsharedcommand.cpp       |   51 +-
 source/commands/classifyrfsharedcommand.h         |    4 +-
 source/commands/classifyseqscommand.cpp           |   42 +-
 source/commands/classifyseqscommand.h             |    2 -
 source/commands/clearmemorycommand.cpp            |   70 -
 source/commands/clearmemorycommand.h              |   41 -
 source/commands/clustercommand.cpp                |    2 +
 source/commands/clustersplitcommand.cpp           |   14 +-
 source/commands/countseqscommand.cpp              |  131 +-
 source/commands/countseqscommand.h                |    5 +-
 source/commands/getmimarkspackagecommand.cpp      |    1 +
 source/commands/hclustercommand.cpp               |  499 -------
 source/commands/hclustercommand.h                 |   73 -
 source/commands/lefsecommand.cpp                  |   23 +-
 source/commands/lefsecommand.h                    |    4 +-
 source/commands/makebiomcommand.cpp               |   20 +-
 source/commands/makecontigscommand.cpp            |   81 +-
 source/commands/mgclustercommand.cpp              |  354 ++---
 source/commands/mgclustercommand.h                |    2 -
 source/commands/parsefastaqcommand.cpp            |    1 +
 source/commands/pcrseqscommand.cpp                |   22 +-
 source/commands/pcrseqscommand.h                  |   15 +-
 source/commands/pipelinepdscommand.cpp            |  790 ----------
 source/commands/pipelinepdscommand.h              |   57 -
 source/commands/renamefilecommand.cpp             |  706 +++++++++
 source/commands/renamefilecommand.h               |   50 +
 source/commands/renameseqscommand.cpp             |    1 +
 source/commands/sensspeccommand.cpp               |   60 +-
 source/commands/sensspeccommand.h                 |    2 +-
 source/commands/seqerrorcommand.cpp               |    1 +
 source/commands/splitgroupscommand.cpp            |    2 +-
 source/commands/sracommand.cpp                    |    1 +
 source/commands/summarytaxcommand.cpp             |   32 +-
 source/commands/summarytaxcommand.h               |    2 +-
 source/datastructures/alignmentdb.cpp             |   98 +-
 source/datastructures/designmap.cpp               |    7 +-
 source/datastructures/groupmap.cpp                |   26 +-
 source/datastructures/oligos.cpp                  |   70 +-
 source/datastructures/referencedb.cpp             |   34 -
 source/datastructures/referencedb.h               |   49 -
 source/datastructures/sequence.cpp                |    6 +
 source/datastructures/sequence.hpp                |    1 +
 source/datastructures/sequencecountparser.cpp     |    6 +-
 source/datastructures/sequencecountparser.h       |    2 +-
 source/datastructures/sequenceparser.cpp          |    6 +-
 source/datastructures/sequenceparser.h            |    2 +-
 source/hcluster.cpp                               |  807 ----------
 source/hcluster.h                                 |   86 --
 source/heatmapsim.cpp                             |   38 +-
 source/heatmapsim.h                               |    2 +-
 source/mothur.cpp                                 |    9 +-
 source/mothurout.cpp                              |  205 ++-
 source/mothurout.h                                |    5 +-
 source/randomforest/abstractrandomforest.cpp      |   59 -
 source/randomforest/abstractrandomforest.hpp      |   67 -
 source/randomforest/regularizedrandomforest.cpp   |   63 -
 source/randomforest/regularizedrandomforest.h     |   30 -
 source/read/readblast.cpp                         |  117 +-
 source/read/readblast.h                           |    3 +-
 source/trimoligos.cpp                             | 1061 +++++++------
 source/trimoligos.h                               |    4 +-
 source/validparameter.cpp                         |   38 +-
 source/vsearchfileparser.cpp                      |   12 +-
 source/vsearchfileparser.h                        |    5 +-
 source/weightedlinkage.cpp                        |    3 -
 93 files changed, 4318 insertions(+), 4570 deletions(-)

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