[med-svn] [mothur] branch master updated (eca5873 -> db3ce27)
Tomasz Buchert
tomasz at moszumanska.debian.org
Sun Feb 26 15:29:30 UTC 2017
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tomasz pushed a change to branch master
in repository mothur.
from eca5873 Corrected EDAM annotation file
new 4608f7e New upstream version 1.39.0
new 49675ba Merge tag 'upstream/1.39.0'
new b7377f0 New upstream version 1.39.3
new fce009d Merge tag 'upstream/1.39.3'
new 982fe22 Refresh patches
new db3ce27 release
The 6 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 -
debian/changelog | 13 +-
...-flags.patch => 0001-Add-hardening-flags.patch} | 0
.../0002-Update-version-numbers-everywhere.patch | 77 +
...0003-Fix-VERSION-variable-in-the-makefile.patch | 21 -
...mmand.patch => 0003-Fix-catchall-command.patch} | 25 +-
debian/patches/series | 7 +-
debian/patches/spelling.patch | 300 -
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 +-
139 files changed, 57202 insertions(+), 4645 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
rename debian/patches/{0002-Add-hardening-flags.patch => 0001-Add-hardening-flags.patch} (100%)
create mode 100644 debian/patches/0002-Update-version-numbers-everywhere.patch
delete mode 100644 debian/patches/0003-Fix-VERSION-variable-in-the-makefile.patch
rename debian/patches/{0001-Fix-catchall-command.patch => 0003-Fix-catchall-command.patch} (67%)
delete mode 100644 debian/patches/spelling.patch
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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