[med-svn] [mothur] branch master updated (9daebbf -> 20b288c)
Andreas Tille
tille at debian.org
Sat May 7 21:40:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository mothur.
from 9daebbf Introduced EDAM annotation.
new a121ab8 Imported Upstream version 1.37.3
new b4bb2d4 cme fix dpkg-control
new f48392c better description for mothur-mpi
new 0f316cd Upstream applied most of the patches
new f5848ec propagate hardening options to uchime build
new 7bcd58a better hardening
new 20b288c Try to cope with messed up repository
The 7 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 +
debian/changelog | 11 +-
debian/control | 11 +-
...link-uchime-statically-and-don-t-strip-it.patch | 33 -
.../patches/0002-Some-spelling-corrections.patch | 174 -
...link-against-lncurses-no-symbols-are-used.patch | 22 -
...FS-cc1plus-error-unrecognized-command-lin.patch | 25 -
.../0005-Don-t-redirect-anything-to-dev-tty.patch | 22 -
...-off-unportable-optimizations-in-makefile.patch | 42 -
debian/patches/0008-Fix-catchall-command.patch | 4 +-
.../patches/0009-Fix-boost_iostreams-flags.patch | 30 -
...0010-Pass-hardening-flags-to-uchime-build.patch | 55 -
.../0011-Don-t-hardcode-mpic-as-the-compiler.patch | 24 -
debian/patches/hardening.patch | 15 +
debian/patches/series | 10 +-
debian/rules | 2 +
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 +
216 files changed, 219080 insertions(+), 14127 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
delete mode 100644 debian/patches/0001-Don-t-link-uchime-statically-and-don-t-strip-it.patch
delete mode 100644 debian/patches/0002-Some-spelling-corrections.patch
delete mode 100644 debian/patches/0003-Don-t-link-against-lncurses-no-symbols-are-used.patch
delete mode 100644 debian/patches/0004-Fix-for-FTBFS-cc1plus-error-unrecognized-command-lin.patch
delete mode 100644 debian/patches/0005-Don-t-redirect-anything-to-dev-tty.patch
delete mode 100644 debian/patches/0006-Turn-off-unportable-optimizations-in-makefile.patch
delete mode 100644 debian/patches/0009-Fix-boost_iostreams-flags.patch
delete mode 100644 debian/patches/0010-Pass-hardening-flags-to-uchime-build.patch
delete mode 100644 debian/patches/0011-Don-t-hardcode-mpic-as-the-compiler.patch
create mode 100644 debian/patches/hardening.patch
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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