[med-svn] [mothur] branch upstream updated (a2de248 -> b7377f0)
Tomasz Buchert
tomasz at moszumanska.debian.org
Sun Feb 26 15:29:34 UTC 2017
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tomasz pushed a change to branch upstream
in repository mothur.
from a2de248 New upstream version 1.38.1.1
new 4608f7e New upstream version 1.39.0
new b7377f0 New upstream version 1.39.3
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 1 +
Makefile | 6 +-
Mothur.xcodeproj/project.pbxproj | 137 +-
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 | 16 +-
source/calculators/filters.h | 12 +
source/chimera/chimeracheckrdp.cpp | 2 +-
source/classifier/classify.cpp | 17 +-
source/classifier/phylosummary.cpp | 40 +-
source/classifier/phylotree.cpp | 48 +-
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 | 356 +-
source/commands/chimeravsearchcommand.h | 3 -
source/commands/classifyotucommand.cpp | 27 +-
source/commands/classifyseqscommand.cpp | 7 +-
source/commands/clustercommand.cpp | 247 +-
source/commands/clustercommand.h | 15 +-
source/commands/clustersplitcommand.cpp | 312 +-
source/commands/clustersplitcommand.h | 17 +-
source/commands/createdatabasecommand.cpp | 99 +-
source/commands/distancecommand.cpp | 2 +-
source/commands/getcommandinfocommand.cpp | 2 +-
source/commands/getcurrentcommand.cpp | 4 +
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 | 169 +-
source/commands/makecontigscommand.h | 798 +-
source/commands/makefilecommand.cpp | 155 +-
source/commands/makefilecommand.h | 3 +
source/commands/mergetaxsummarycommand.cpp | 35 +-
source/commands/mgclustercommand.cpp | 20 +-
source/commands/mgclustercommand.h | 2 +-
source/commands/pcrseqscommand.cpp | 13 +-
source/commands/phylotypecommand.cpp | 30 +-
source/commands/phylotypecommand.h | 2 -
source/commands/preclustercommand.cpp | 174 +-
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 | 25 +-
source/commands/screenseqscommand.cpp | 45 +-
source/commands/screenseqscommand.h | 2 +-
source/commands/sensspeccommand.cpp | 106 +-
source/commands/sensspeccommand.h | 5 +-
source/commands/seqsummarycommand.cpp | 16 +-
source/commands/setcurrentcommand.cpp | 36 +-
source/commands/setcurrentcommand.h | 2 +-
source/commands/setdircommand.cpp | 39 +-
source/commands/setdircommand.h | 2 +-
source/commands/sffinfocommand.cpp | 14 +-
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 | 9 +-
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 | 28 +-
source/linearalgebra.cpp | 2 +-
source/makefile | 171 -
source/mothur.cpp | 7 +-
source/mothurout.cpp | 282 +-
source/mothurout.h | 27 +-
source/opticluster.cpp | 632 +
source/opticluster.h | 66 +
source/optionparser.cpp | 28 +-
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 +-
132 files changed, 57098 insertions(+), 4306 deletions(-)
mode change 100755 => 100644 TestMothur/catch.hpp
create mode 100644 TestMothur/distcdataset.cpp
create mode 100644 TestMothur/distcdataset.h
create mode 100644 TestMothur/distpdataset.cpp
create mode 100644 TestMothur/distpdataset.h
create mode 100644 TestMothur/testclassifier/testphylotree.cpp
create mode 100644 TestMothur/testclassifier/testphylotree.hpp
create mode 100644 TestMothur/testcontainers/testoptimatrix.cpp
create mode 100644 TestMothur/testcontainers/testoptimatrix.h
create mode 100644 TestMothur/testopticluster.cpp
create mode 100644 TestMothur/testopticluster.h
delete mode 100644 source/commands/getotuscommand.cpp
delete mode 100644 source/commands/getotuscommand.h
delete mode 100644 source/commands/removeotuscommand.cpp
delete mode 100644 source/commands/removeotuscommand.h
create mode 100644 source/datastructures/optimatrix.cpp
create mode 100644 source/datastructures/optimatrix.h
delete mode 100644 source/makefile
create mode 100644 source/opticluster.cpp
create mode 100644 source/opticluster.h
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