[med-svn] [mothur] branch upstream updated (99749cf -> 9f88981)
Andreas Tille
tille at debian.org
Sat May 7 21:32:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository mothur.
from 99749cf Imported Upstream version 1.36.1
new 9f88981 Imported Upstream version 1.37.3
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:
.travis.yml | 17 +
INSTALL.md | 15 +-
makefile => Makefile | 64 +-
Mothur.xcodeproj/project.pbxproj | 1731 +-
README.md | 2 +
TestMothur/dataset.cpp | 192840 ++++++++++++++++++
TestMothur/dataset.h | 55 +
TestMothur/fastqdataset.cpp | 16034 ++
TestMothur/fastqdataset.h | 34 +
TestMothur/main.cpp | 21 +
TestMothur/testbiominfocommand.cpp | 73 +
TestMothur/testbiominfocommand.h | 29 +
TestMothur/testcommands/testgetgroupscommand.cpp | 18 +
TestMothur/testcommands/testgetgroupscommand.h | 34 +
TestMothur/testcommands/testmergegroupscommand.cpp | 19 +
TestMothur/testcommands/testmergegroupscommand.h | 26 +
.../testcommands/testremovegroupscommand.cpp | 18 +
TestMothur/testcommands/testremovegroupscommand.h | 34 +
TestMothur/testcommands/testrenameseqscommand.cpp | 39 +
TestMothur/testcommands/testrenameseqscommand.h | 40 +
TestMothur/testcommands/testsetseedcommand.cpp | 2 +-
TestMothur/testcontainers/testfastqread.cpp | 65 +
TestMothur/testcontainers/testfastqread.h | 32 +
.../testsequence.cpp | 5 +-
TestMothur/testcontainers/testsequence.h | 22 +
TestMothur/testvsearchfileparser.cpp | 118 +
TestMothur/testvsearchfileparser.h | 35 +
makefile => makefile-internal | 77 +-
source/chimera/bellerophon.cpp | 194 +-
source/chimera/bellerophon.h | 8 +-
source/chimera/ccode.cpp | 178 +-
source/chimera/ccode.h | 15 +-
source/chimera/chimeracheckrdp.cpp | 163 +-
source/chimera/chimeracheckrdp.h | 8 +-
source/chimera/chimerarealigner.h | 2 +-
source/chimera/chimeraslayer.cpp | 286 +-
source/chimera/chimeraslayer.h | 9 +-
source/chimera/decalc.cpp | 2 +-
source/chimera/maligner.h | 2 +-
source/chimera/{chimera.cpp => mothurchimera.cpp} | 185 +-
source/chimera/{chimera.h => mothurchimera.h} | 17 +-
source/chimera/pintail.cpp | 204 +-
source/chimera/pintail.h | 10 +-
source/chimera/slayer.h | 2 +-
source/classifier/bayesian.cpp | 310 +-
source/classifier/classify.cpp | 137 +-
source/classifier/classify.h | 3 +-
source/classifier/phylosummary.cpp | 210 +-
source/classifier/phylosummary.h | 17 +-
source/classifier/phylotree.cpp | 243 +-
source/clearcut/cmdargs.cpp | 8 +-
source/clearcut/getopt_long.cpp | 20 +-
source/commandfactory.cpp | 98 +-
source/commandfactory.hpp | 1 -
source/commands/aligncommand.cpp | 303 +-
source/commands/aligncommand.h | 7 +-
source/commands/biominfocommand.cpp | 874 +
source/commands/biominfocommand.h | 58 +
source/commands/catchallcommand.cpp | 18 +-
source/commands/chimerabellerophoncommand.cpp | 31 +-
source/commands/chimerabellerophoncommand.h | 4 +-
source/commands/chimeraccodecommand.cpp | 150 -
source/commands/chimeraccodecommand.h | 8 +-
source/commands/chimeracheckcommand.cpp | 135 +-
source/commands/chimeracheckcommand.h | 8 +-
source/commands/chimerapintailcommand.cpp | 136 -
source/commands/chimerapintailcommand.h | 8 +-
source/commands/chimeraslayercommand.cpp | 452 +-
source/commands/chimeraslayercommand.h | 15 +-
source/commands/chimerauchimecommand.cpp | 53 +-
source/commands/chimerauchimecommand.h | 1 -
source/commands/chopseqscommand.cpp | 2 +-
source/commands/classifyotucommand.cpp | 114 +-
source/commands/classifyotucommand.h | 7 +-
source/commands/classifyrfsharedcommand.cpp | 0
source/commands/classifyseqscommand.cpp | 465 +-
source/commands/classifyseqscommand.h | 10 +-
source/commands/clustercommand.cpp | 585 +-
source/commands/clustercommand.h | 5 +-
source/commands/clusterdoturcommand.cpp | 2 +-
source/commands/clustersplitcommand.cpp | 806 +-
source/commands/clustersplitcommand.h | 7 +-
source/commands/collectcommand.cpp | 32 +-
source/commands/countseqscommand.cpp | 2 +-
source/commands/deconvolutecommand.cpp | 134 +-
source/commands/deconvolutecommand.h | 2 +-
source/commands/degapseqscommand.cpp | 4 +-
source/commands/distancecommand.cpp | 600 +-
source/commands/distancecommand.h | 17 +-
source/commands/filterseqscommand.cpp | 369 +-
source/commands/filterseqscommand.h | 10 +-
source/commands/filtersharedcommand.cpp | 28 +-
source/commands/getcurrentcommand.cpp | 48 +-
source/commands/getcurrentcommand.h | 4 +-
source/commands/getgroupscommand.cpp | 267 +-
source/commands/getgroupscommand.h | 8 +-
source/commands/getlineagecommand.cpp | 2 +-
source/commands/getmetacommunitycommand.cpp | 4 +-
source/commands/getotulabelscommand.cpp | 14 +-
source/commands/getotulabelscommand.h | 4 +-
source/commands/getoturepcommand.cpp | 42 +-
source/commands/getseqscommand.cpp | 279 +-
source/commands/getseqscommand.h | 2 +-
source/commands/getsharedotucommand.cpp | 93 +-
source/commands/getsharedotucommand.h | 6 +-
source/commands/lefsecommand.cpp | 20 +-
source/commands/listseqscommand.cpp | 48 +-
source/commands/listseqscommand.h | 2 +-
source/commands/loadlogfilecommand.cpp | 289 -
source/commands/loadlogfilecommand.h | 47 -
source/commands/makebiomcommand.cpp | 2 +
source/commands/makecontigscommand.cpp | 606 +-
source/commands/makecontigscommand.h | 1281 +-
source/commands/makefastqcommand.cpp | 30 +-
source/commands/makefilecommand.cpp | 27 +-
source/commands/makefilecommand.h | 1 +
source/commands/matrixoutputcommand.cpp | 2 +-
source/commands/mergegroupscommand.cpp | 537 +-
source/commands/mergegroupscommand.h | 10 +-
source/commands/mgclustercommand.cpp | 6 +-
source/commands/otuhierarchycommand.cpp | 6 +-
source/commands/pairwiseseqscommand.cpp | 450 +-
source/commands/pairwiseseqscommand.h | 6 -
source/commands/parsefastaqcommand.cpp | 278 +-
source/commands/parsefastaqcommand.h | 19 +-
source/commands/parselistscommand.cpp | 52 +-
source/commands/pcrseqscommand.cpp | 2 +-
source/commands/phylotypecommand.cpp | 2 +-
source/commands/pipelinepdscommand.cpp | 23 +-
source/commands/preclustercommand.cpp | 1 +
source/commands/preclustercommand.h | 7 +-
source/commands/rarefactcommand.cpp | 83 +-
source/commands/removedistscommand.cpp | 2 +-
source/commands/removegroupscommand.cpp | 274 +-
source/commands/removegroupscommand.h | 8 +-
source/commands/removelineagecommand.cpp | 3 +-
source/commands/removeotulabelscommand.cpp | 10 +-
source/commands/removeotulabelscommand.h | 4 +-
source/commands/removerarecommand.cpp | 2 +-
source/commands/removeseqscommand.cpp | 207 +-
source/commands/removeseqscommand.h | 2 +-
source/commands/renameseqscommand.cpp | 728 +-
source/commands/renameseqscommand.h | 13 +-
source/commands/screenseqscommand.cpp | 503 +-
source/commands/screenseqscommand.h | 10 +-
source/commands/sensspeccommand.cpp | 751 +-
source/commands/sensspeccommand.h | 36 +-
source/commands/seqsummarycommand.cpp | 28 +-
source/commands/setcurrentcommand.cpp | 143 +-
source/commands/setcurrentcommand.h | 5 +-
source/commands/sffmultiplecommand.cpp | 2 +-
source/commands/sharedcommand.cpp | 2 +-
source/commands/shhhercommand.cpp | 1602 +-
source/commands/shhhercommand.h | 1264 +-
source/commands/splitabundcommand.cpp | 171 +-
source/commands/splitgroupscommand.cpp | 32 +-
source/commands/sracommand.cpp | 354 +-
source/commands/sracommand.h | 2 +-
source/commands/subsamplecommand.cpp | 2 +-
source/commands/summarycommand.cpp | 76 +-
source/commands/summaryqualcommand.cpp | 2 +-
source/commands/summarytaxcommand.cpp | 118 +-
source/commands/summarytaxcommand.h | 5 +-
source/commands/treegroupscommand.cpp | 2 +-
source/commands/trimseqscommand.cpp | 4 +-
source/datastructures/alignmentdb.cpp | 85 +-
source/datastructures/counttable.cpp | 73 +-
source/datastructures/counttable.h | 6 +-
source/datastructures/datavector.hpp | 1 +
source/datastructures/designmap.cpp | 82 +-
source/datastructures/distancedb.cpp | 4 +-
source/datastructures/distancedb.hpp | 5 -
source/datastructures/fastqread.cpp | 103 +
source/datastructures/fastqread.h | 19 +-
source/datastructures/groupmap.cpp | 25 +
source/datastructures/groupmap.h | 2 +-
source/datastructures/listvector.cpp | 25 +
source/datastructures/listvector.hpp | 1 +
source/datastructures/sequence.hpp | 5 +
source/datastructures/sharedrabundfloatvector.cpp | 36 +-
source/datastructures/sharedrabundfloatvector.h | 6 +-
source/datastructures/sharedrabundvector.cpp | 26 +-
source/datastructures/sharedrabundvector.h | 5 +-
source/datastructures/sparsedistancematrix.cpp | 2 +-
source/datastructures/tree.cpp | 4 +-
source/engine.cpp | 147 +-
source/linearalgebra.cpp | 2 +
source/mothur.cpp | 25 +-
source/mothur.h | 11 +-
source/mothurout.cpp | 917 +-
source/mothurout.h | 31 +-
source/optionparser.cpp | 8 +
source/read/splitmatrix.cpp | 401 +-
source/read/splitmatrix.h | 8 +-
source/svm/svm.cpp | 7 +-
source/trimoligos.cpp | 5 +-
source/uchime_src/mk | 16 +-
source/validparameter.cpp | 38 +-
source/venn.cpp | 2 +-
source/vsearchfileparser.cpp | 274 +
source/vsearchfileparser.h | 50 +
201 files changed, 219045 insertions(+), 13682 deletions(-)
create mode 100644 .travis.yml
copy makefile => Makefile (62%)
mode change 100644 => 100755
mode change 100644 => 100755 Mothur.xcodeproj/project.pbxproj
create mode 100755 TestMothur/dataset.cpp
create mode 100644 TestMothur/dataset.h
create mode 100644 TestMothur/fastqdataset.cpp
create mode 100644 TestMothur/fastqdataset.h
create mode 100644 TestMothur/testbiominfocommand.cpp
create mode 100644 TestMothur/testbiominfocommand.h
create mode 100644 TestMothur/testcommands/testgetgroupscommand.cpp
create mode 100644 TestMothur/testcommands/testgetgroupscommand.h
create mode 100644 TestMothur/testcommands/testmergegroupscommand.cpp
create mode 100644 TestMothur/testcommands/testmergegroupscommand.h
create mode 100644 TestMothur/testcommands/testremovegroupscommand.cpp
create mode 100644 TestMothur/testcommands/testremovegroupscommand.h
create mode 100644 TestMothur/testcommands/testrenameseqscommand.cpp
create mode 100644 TestMothur/testcommands/testrenameseqscommand.h
create mode 100644 TestMothur/testcontainers/testfastqread.cpp
create mode 100644 TestMothur/testcontainers/testfastqread.h
rename TestMothur/{testdatastructures => testcontainers}/testsequence.cpp (95%)
create mode 100644 TestMothur/testcontainers/testsequence.h
create mode 100644 TestMothur/testvsearchfileparser.cpp
create mode 100644 TestMothur/testvsearchfileparser.h
rename makefile => makefile-internal (57%)
mode change 100644 => 100755
rename source/chimera/{chimera.cpp => mothurchimera.cpp} (71%)
rename source/chimera/{chimera.h => mothurchimera.h} (89%)
create mode 100644 source/commands/biominfocommand.cpp
create mode 100644 source/commands/biominfocommand.h
mode change 100755 => 100644 source/commands/classifyrfsharedcommand.cpp
delete mode 100644 source/commands/loadlogfilecommand.cpp
delete mode 100644 source/commands/loadlogfilecommand.h
create mode 100644 source/vsearchfileparser.cpp
create mode 100644 source/vsearchfileparser.h
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