[med-svn] [mothur] 02/06: Merge tag 'upstream/1.39.0'
Tomasz Buchert
tomasz at moszumanska.debian.org
Sun Feb 26 15:29:32 UTC 2017
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tomasz pushed a commit to branch master
in repository mothur.
commit 49675ba79bc8d30633917dcad6043cc0ad104e3b
Merge: eca5873 4608f7e
Author: Tomasz Buchert <tomasz at debian.org>
Date: Fri Jan 27 07:05:20 2017 +0100
Merge tag 'upstream/1.39.0'
Upstream version 1.39.0
.gitignore | 1 +
Makefile | 7 +-
Mothur.xcodeproj/project.pbxproj | 133 +-
README.md | 2 +-
TestMothur/catch.hpp | 4392 ++-
TestMothur/dataset.h | 10 +-
TestMothur/distcdataset.cpp | 46955 ++++++++++++++++++++++++
TestMothur/distcdataset.h | 32 +
TestMothur/distpdataset.cpp | 2578 ++
TestMothur/distpdataset.h | 30 +
TestMothur/main.cpp | 7 +-
TestMothur/testclassifier/testphylotree.cpp | 129 +
TestMothur/testclassifier/testphylotree.hpp | 32 +
TestMothur/testcontainers/testfastqread.cpp | 5 +-
TestMothur/testcontainers/testoptimatrix.cpp | 101 +
TestMothur/testcontainers/testoptimatrix.h | 31 +
TestMothur/testopticluster.cpp | 132 +
TestMothur/testopticluster.h | 35 +
TestMothur/testtrimoligos.hpp | 4 +-
TestMothur/testvsearchfileparser.cpp | 6 +-
TestMothur/testvsearchfileparser.h | 1 -
makefile-internal | 6 +-
source/calculators/filters.h | 12 +
source/chimera/chimeracheckrdp.cpp | 2 +-
source/classifier/classify.cpp | 1 -
source/classifier/phylosummary.cpp | 38 +-
source/classifier/phylotree.cpp | 13 +-
source/classifier/phylotree.h | 5 +
source/classifier/taxonomyequalizer.cpp | 41 +-
source/cluster.cpp | 4 +-
source/cluster.hpp | 10 +-
source/commandfactory.cpp | 6 +-
source/commands/aligncommand.cpp | 2 +-
source/commands/aligncommand.h | 2 +-
source/commands/biominfocommand.cpp | 6 +
source/commands/catchallcommand.cpp | 4 +-
source/commands/chimeraperseuscommand.cpp | 6 +-
source/commands/chimeraperseuscommand.h | 9 +-
source/commands/chimeraslayercommand.cpp | 6 +-
source/commands/chimerauchimecommand.cpp | 34 +-
source/commands/chimerauchimecommand.h | 18 +-
source/commands/chimeravsearchcommand.cpp | 350 +-
source/commands/chimeravsearchcommand.h | 3 -
source/commands/classifyotucommand.cpp | 13 +-
source/commands/classifyseqscommand.cpp | 7 +-
source/commands/clustercommand.cpp | 247 +-
source/commands/clustercommand.h | 15 +-
source/commands/clustersplitcommand.cpp | 307 +-
source/commands/clustersplitcommand.h | 17 +-
source/commands/createdatabasecommand.cpp | 99 +-
source/commands/distancecommand.cpp | 2 +-
source/commands/getcommandinfocommand.cpp | 2 +-
source/commands/getcurrentcommand.cpp | 2 +
source/commands/getgroupscommand.cpp | 6 +-
source/commands/getlineagecommand.cpp | 16 +-
source/commands/getotulabelscommand.cpp | 9 +-
source/commands/getotuscommand.cpp | 432 -
source/commands/getotuscommand.h | 55 -
source/commands/getseqscommand.cpp | 8 +-
source/commands/listseqscommand.cpp | 7 +-
source/commands/makebiomcommand.cpp | 8 +-
source/commands/makecontigscommand.cpp | 150 +-
source/commands/makecontigscommand.h | 792 +-
source/commands/makefilecommand.cpp | 129 +-
source/commands/makefilecommand.h | 3 +
source/commands/mergetaxsummarycommand.cpp | 35 +-
source/commands/mgclustercommand.cpp | 20 +-
source/commands/mgclustercommand.h | 2 +-
source/commands/pcrseqscommand.cpp | 7 +-
source/commands/phylotypecommand.cpp | 30 +-
source/commands/phylotypecommand.h | 2 -
source/commands/preclustercommand.cpp | 170 +-
source/commands/preclustercommand.h | 84 +-
source/commands/removegroupscommand.cpp | 6 +-
source/commands/removelineagecommand.cpp | 15 +-
source/commands/removeotulabelscommand.cpp | 9 +-
source/commands/removeotuscommand.cpp | 439 -
source/commands/removeotuscommand.h | 52 -
source/commands/removeseqscommand.cpp | 8 +-
source/commands/renamefilecommand.cpp | 19 +-
source/commands/screenseqscommand.cpp | 45 +-
source/commands/screenseqscommand.h | 2 +-
source/commands/sensspeccommand.cpp | 58 +-
source/commands/sensspeccommand.h | 3 +-
source/commands/setcurrentcommand.cpp | 18 +-
source/commands/setcurrentcommand.h | 2 +-
source/commands/setdircommand.cpp | 39 +-
source/commands/setdircommand.h | 2 +-
source/commands/sffinfocommand.cpp | 12 +-
source/commands/sffmultiplecommand.cpp | 16 +-
source/commands/sharedcommand.cpp | 8 +-
source/commands/shhhercommand.cpp | 32 +-
source/commands/shhhseqscommand.cpp | 3 +-
source/commands/shhhseqscommand.h | 3 +-
source/commands/sortseqscommand.cpp | 8 +-
source/commands/sparcccommand.cpp | 8 +-
source/commands/splitgroupscommand.cpp | 7 +-
source/commands/sracommand.cpp | 6 +-
source/commands/sracommand.h | 2 +-
source/commands/subsamplecommand.cpp | 4 +-
source/commands/summarytaxcommand.cpp | 113 +-
source/commands/summarytaxcommand.h | 1 +
source/datastructures/alignmentdb.cpp | 6 +-
source/datastructures/alignmentdb.h | 2 +-
source/datastructures/blastalign.cpp | 3 +-
source/datastructures/blastdb.cpp | 18 +-
source/datastructures/counttable.h | 2 +-
source/datastructures/kmerdb.cpp | 2 +-
source/datastructures/optimatrix.cpp | 445 +
source/datastructures/optimatrix.h | 60 +
source/datastructures/sequencecountparser.cpp | 169 +-
source/datastructures/sequencecountparser.h | 12 +-
source/datastructures/sequencedb.cpp | 54 -
source/datastructures/sequencedb.h | 2 -
source/datastructures/sequenceparser.cpp | 275 +-
source/datastructures/sequenceparser.h | 6 +-
source/engine.cpp | 18 +-
source/linearalgebra.cpp | 2 +-
source/makefile | 171 -
source/mothur.cpp | 7 +-
source/mothurout.cpp | 203 +-
source/mothurout.h | 19 +-
source/opticluster.cpp | 632 +
source/opticluster.h | 66 +
source/optionparser.cpp | 26 +-
source/read/splitmatrix.cpp | 13 +-
source/read/splitmatrix.h | 4 +-
source/singlelinkage.cpp | 1 -
source/trimoligos.h | 6 +
source/validparameter.cpp | 10 +-
source/vsearchfileparser.cpp | 5 +-
131 files changed, 56870 insertions(+), 4186 deletions(-)
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