[med-svn] [garli] 09/10: Update upstream source from tag 'upstream/2.1'
Andreas Tille
tille at debian.org
Tue Nov 14 09:53:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository garli.
commit 062ddf0e617fb3fbda4d2d9a387027fa8386b2e4
Merge: 2311c4c 6dce4f7
Author: Andreas Tille <tille at debian.org>
Date: Tue Nov 14 10:52:24 2017 +0100
Update upstream source from tag 'upstream/2.1'
Update to upstream version '2.1'
with Debian dir bd8d0cfadb133505731f6a362c96ca102dc93a35
COPYING | 622 ++
INSTALL | 156 +
Makefile.am | 19 +
QuickStart.txt | 55 +
README.txt | 156 +
bootstrap.sh | 13 +
build_garli.sh | 96 +
config.h.in | 125 +
config/acx_mpi.m4 | 181 +
config/compile | 347 +
config/config.guess | 1501 +++
config/config.sub | 1566 ++++
config/depcomp | 423 +
config/install-sh | 251 +
config/libtool.m4 | 7831 ++++++++++++++++
config/ltmain.sh | 9636 ++++++++++++++++++++
config/missing | 336 +
configure.ac | 389 +
doc/Garli0.96Manual.pdf | Bin 0 -> 228229 bytes
doc/NOTE.txt | 4 +
example/basic/EXAMPLES.txt | 46 +
example/basic/LGmodel.mod | 92 +
example/basic/garli.conf | 65 +
example/basic/garli.conf.AA.LGmodel | 66 +
example/basic/garli.conf.AA.defaultSettings | 65 +
example/basic/garli.conf.AA.test | 66 +
example/basic/garli.conf.codon.defaultSettings | 66 +
example/basic/garli.conf.codon.test | 66 +
example/basic/garli.conf.nuc.defaultSettings | 65 +
example/basic/garli.conf.nuc.test | 65 +
example/basic/rana.nex | 76 +
example/basic/rana.phy | 65 +
example/basic/ranaconstraint.format1 | 2 +
example/basic/ranaconstraint.format2 | 2 +
example/basic/ranastart.nexus.tre | 75 +
example/basic/ranastart.oldformat.tre | 1 +
example/basic/zakonEtAl2006.11tax.nex | 25 +
example/partition/EXAMPLES.txt | 18 +
.../3diffModels.byCodonPos.best.all.tre | 45 +
.../3diffModels.byCodonPos.best.tre | 20 +
.../3diffModels.byCodonPos.log00.log | 3980 ++++++++
.../3diffModels.byCodonPos.screen.log | 1450 +++
.../exampleRuns/3parts.diffModelTypes/garli.conf | 83 +
.../3parts.diffModelTypes/zakonEtAl2006.11tax.nex | 32 +
.../GTRG.byCodonPos.best.all.tre | 45 +
.../3parts.sameModelType/GTRG.byCodonPos.best.tre | 20 +
.../3parts.sameModelType/GTRG.byCodonPos.log00.log | 3980 ++++++++
.../GTRG.byCodonPos.screen.log | 1376 +++
.../exampleRuns/3parts.sameModelType/garli.conf | 67 +
.../3parts.sameModelType/zakonEtAl2006.11tax.nex | 32 +
.../exampleRuns/dna+Mkv/dnaPlusGapCoding.nex | 2873 ++++++
example/partition/exampleRuns/dna+Mkv/garli.conf | 75 +
.../exampleRuns/dna+Mkv/mixedDnaMkv.best.all.tre | 79 +
.../exampleRuns/dna+Mkv/mixedDnaMkv.best.tre | 73 +
.../exampleRuns/dna+Mkv/mixedDnaMkv.log00.log | 3292 +++++++
.../exampleRuns/dna+Mkv/mixedDnaMkv.screen.log | 780 ++
example/partition/exampleRuns/mkv/Lewis2001.nex | 239 +
example/partition/exampleRuns/mkv/garli.conf | 67 +
example/partition/exampleRuns/mkv/mkv.best.all.tre | 40 +
example/partition/exampleRuns/mkv/mkv.best.tre | 36 +
example/partition/exampleRuns/mkv/mkv.log00.log | 8940 ++++++++++++++++++
example/partition/exampleRuns/mkv/mkv.screen.log | 1651 ++++
.../partitionedDna+Mkv/dnaPlusGapCoding.nex | 2882 ++++++
.../exampleRuns/partitionedDna+Mkv/garli.conf | 91 +
.../partitionedDna+Mkv/mixedDnaMkv.best.all.tre | 79 +
.../partitionedDna+Mkv/mixedDnaMkv.best.tre | 73 +
.../partitionedDna+Mkv/mixedDnaMkv.log00.log | 3292 +++++++
.../partitionedDna+Mkv/mixedDnaMkv.screen.log | 205 +
.../templateConfigs/garli.3diffModels.bigData.conf | 83 +
.../garli.3diffModels.smallData.conf | 83 +
.../templateConfigs/garli.mixedDnaMkv.conf | 75 +
example/partition/templateConfigs/garli.mkv.conf | 67 +
.../garli.oneModelType.bigData.conf | 67 +
.../garli.oneModelType.smallData.conf | 67 +
project/standardGarliVC/BOINCGarli.sln | 91 +
project/standardGarliVC/BOINCGarli.vcproj | 1027 +++
project/standardGarliVC/standardGarli.sln | 39 +
project/standardGarliVC/standardGarli.vcproj | 651 ++
src/Makefile.am | 70 +
src/Makefile.ser | 118 +
src/adaptation.cpp | 520 ++
src/adaptation.h | 133 +
src/bipartition.cpp | 377 +
src/bipartition.h | 680 ++
src/clamanager.h | 381 +
src/condlike.cpp | 154 +
src/condlike.h | 122 +
src/configoptions.cpp | 789 ++
src/configoptions.h | 241 +
src/configreader.cpp | 640 ++
src/configreader.h | 87 +
src/datamatr.cpp | 1946 ++++
src/datamatr.h | 517 ++
src/defs.h | 161 +
src/errorexception.h | 125 +
src/funcs.cpp | 1038 +++
src/funcs.h | 224 +
src/garli.br | 87 +
src/garlimain.cpp | 904 ++
src/garlireader.cpp | 1435 +++
src/garlireader.h | 236 +
src/individual.cpp | 1054 +++
src/individual.h | 173 +
src/linalg.cpp | 1363 +++
src/linalg.h | 22 +
src/memchk.h | 325 +
src/model.cpp | 4966 ++++++++++
src/model.h | 2199 +++++
src/mpifuncs.cpp | 1290 +++
src/mpifuncs.h | 82 +
src/mpitrick.cpp | 287 +
src/optimization.cpp | 3718 ++++++++
src/optimizationinfo.h | 88 +
src/outputman.h | 343 +
src/population.cpp | 7970 ++++++++++++++++
src/population.h | 590 ++
src/reconnode.h | 544 ++
src/rng.cpp | 659 ++
src/rng.h | 127 +
src/sequencedata.cpp | 1579 ++++
src/sequencedata.h | 959 ++
src/set.cpp | 90 +
src/set.h | 145 +
src/stopwatch.h | 93 +
src/threaddcls.h | 43 +
src/threadfunc.cpp | 499 +
src/translatetable.cpp | 89 +
src/translatetable.h | 58 +
src/tree.cpp | 8597 +++++++++++++++++
src/tree.h | 843 ++
src/treenode.cpp | 890 ++
src/treenode.h | 153 +
src/utility.h | 323 +
tests/Makefile.am | 3 +
tests/check/a.G3.conf | 68 +
tests/check/a.G4.conf | 67 +
tests/check/a.conf | 66 +
tests/check/c.M3x2.conf | 67 +
tests/check/c.conf | 68 +
tests/check/g.dnaBnoZ.conf | 76 +
tests/check/g.dnaMix.conf | 76 +
tests/check/n.G3.conf | 66 +
tests/check/n.G4.conf | 66 +
tests/check/n.conf | 66 +
tests/check/n.const.conf | 66 +
tests/check/p.3diff.conf | 83 +
tests/check/p.mk.ssr.conf | 68 +
tests/check/p.mkO.ssr.conf | 68 +
tests/check/p.mkv.ssr.conf | 68 +
tests/check/p.mkvO.ssr.conf | 68 +
tests/const/n.neg.const.conf | 64 +
tests/const/n.negBack.const.conf | 64 +
tests/const/n.pos.const.conf | 65 +
tests/const/n.posBack.const.conf | 65 +
tests/data/L.start | 44 +
tests/data/L2001.30x52.nex | 240 +
tests/data/a.G3.start | 22 +
tests/data/a.G4.start | 22 +
tests/data/a.start | 17 +
tests/data/c.M3x2.start | 21 +
tests/data/c.start | 21 +
tests/data/dnaGap.8x1K.nex | 1055 +++
tests/data/expected.scr | 19 +
tests/data/moore.matK90-120.nex | 94 +
tests/data/moore.start | 122 +
tests/data/n.G4.start | 25 +
tests/data/n.G5.start | 25 +
tests/data/n.start | 6 +
tests/data/p.3diff.start | 33 +
tests/data/z.11x2178.AA.nex | 59 +
tests/data/z.11x2178.nex | 25 +
tests/data/z.11x2178.wtset.nex | 41 +
tests/data/z.11x30.AA.fas | 22 +
tests/data/z.11x30.phy | 12 +
tests/data/z.11x30.stop.nex | 19 +
tests/data/z.11x30.wackyNames.nex | 19 +
tests/data/z.byPos.11x2178.nex | 36 +
tests/data/z.neg.const.tre | 1 +
tests/data/z.negBack.const.tre | 1 +
tests/data/z.pos.const.tre | 1 +
tests/data/z.posBack.const.tre | 1 +
tests/internal/a.G3.conf | 65 +
tests/internal/a.G4.conf | 65 +
tests/internal/a.conf | 65 +
tests/internal/c.M3x2.conf | 67 +
tests/internal/c.conf | 65 +
tests/internal/n.G3.conf | 65 +
tests/internal/n.G4.conf | 64 +
tests/internal/n.conf | 65 +
tests/internal/p.3diff.conf | 82 +
tests/internal/p.mk.conf | 68 +
tests/internal/p.mk.ssr.conf | 68 +
tests/internal/p.mkO.conf | 68 +
tests/internal/p.mkO.ssr.conf | 68 +
tests/internal/p.mkv.conf | 68 +
tests/internal/p.mkv.ssr.conf | 68 +
tests/internal/p.mkvO.conf | 67 +
tests/internal/p.mkvO.ssr.conf | 68 +
tests/output/a.G3.conf | 67 +
tests/output/a.G4.conf | 67 +
tests/output/a.conf | 67 +
tests/output/c.M3x2.conf | 67 +
tests/output/c.conf | 67 +
tests/output/n.G3.conf | 66 +
tests/output/n.G4.conf | 66 +
tests/output/n.conf | 66 +
tests/output/n.wackyNames.conf | 66 +
tests/output/p.3diff.conf | 86 +
tests/output/p.mkvO.ssr.conf | 69 +
tests/restart/a.G3.conf | 68 +
tests/restart/a.G4.conf | 67 +
tests/restart/a.conf | 67 +
tests/restart/c.M3x2.conf | 68 +
tests/restart/c.conf | 68 +
tests/restart/g.dnaBnoZ.conf | 76 +
tests/restart/g.dnaMix.conf | 76 +
tests/restart/n.G3.conf | 66 +
tests/restart/n.G4.conf | 66 +
tests/restart/n.conf | 66 +
tests/restart/n.const.conf | 66 +
tests/restart/p.3diff.conf | 84 +
tests/restart/p.mk.ssr.conf | 68 +
tests/restart/p.mkO.ssr.conf | 68 +
tests/restart/p.mkv.ssr.conf | 68 +
tests/restart/p.mkvO.ssr.conf | 68 +
tests/runtests.sh | 237 +
tests/scoring/a.G3.conf | 69 +
tests/scoring/a.G4.conf | 67 +
tests/scoring/a.conf | 67 +
tests/scoring/c.M3x2.conf | 68 +
tests/scoring/c.conf | 68 +
tests/scoring/g.dnaBnoZ.conf | 76 +
tests/scoring/g.dnaMix.conf | 76 +
tests/scoring/n.G4.conf | 66 +
tests/scoring/n.G5.conf | 66 +
tests/scoring/n.conf | 66 +
tests/scoring/p.3diff.conf | 83 +
tests/scoring/p.mk.conf | 68 +
tests/scoring/p.mk.ssr.conf | 68 +
tests/scoring/p.mkO.conf | 68 +
tests/scoring/p.mkO.ssr.conf | 68 +
tests/scoring/p.mkv.conf | 68 +
tests/scoring/p.mkv.ssr.conf | 68 +
tests/scoring/p.mkvO.conf | 68 +
tests/scoring/p.mkvO.ssr.conf | 68 +
tests/scoring/runScoring.sh | 32 +
246 files changed, 121892 insertions(+)
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