[med-svn] [mothur] branch upstream updated (30c91fe -> 4767758)
Tomasz Buchert
tomasz at moszumanska.debian.org
Sat Jul 30 00:22:29 UTC 2016
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tomasz pushed a change to branch upstream
in repository mothur.
from 30c91fe Imported Upstream version 1.37.6
new 4767758 Imported Upstream version 1.38.0
The 1 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:
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(-)
mode change 100755 => 100644 Makefile
mode change 100755 => 100644 Mothur.xcodeproj/project.pbxproj
create mode 100644 TestMothur/testcommands/testrenamefilecommand.cpp
create mode 100644 TestMothur/testcommands/testrenamefilecommand.h
create mode 100644 TestMothur/testtrimoligos.cpp
create mode 100644 TestMothur/testtrimoligos.hpp
mode change 100755 => 100644 makefile-internal
create mode 100644 source/commands/chimeravsearchcommand.cpp
create mode 100644 source/commands/chimeravsearchcommand.h
delete mode 100644 source/commands/clearmemorycommand.cpp
delete mode 100644 source/commands/clearmemorycommand.h
delete mode 100644 source/commands/hclustercommand.cpp
delete mode 100644 source/commands/hclustercommand.h
delete mode 100644 source/commands/pipelinepdscommand.cpp
delete mode 100644 source/commands/pipelinepdscommand.h
create mode 100644 source/commands/renamefilecommand.cpp
create mode 100644 source/commands/renamefilecommand.h
delete mode 100644 source/datastructures/referencedb.cpp
delete mode 100644 source/datastructures/referencedb.h
delete mode 100644 source/hcluster.cpp
delete mode 100644 source/hcluster.h
delete mode 100644 source/randomforest/abstractrandomforest.cpp
delete mode 100644 source/randomforest/abstractrandomforest.hpp
delete mode 100644 source/randomforest/regularizedrandomforest.cpp
delete mode 100644 source/randomforest/regularizedrandomforest.h
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