[med-svn] [probabel] 01/04: Merge tag 'upstream/0.4.2'
Lennart Karssen
lckarssen-guest at moszumanska.debian.org
Wed Jan 15 15:55:57 UTC 2014
This is an automated email from the git hooks/post-receive script.
lckarssen-guest pushed a commit to branch master
in repository probabel.
commit a6319b946f81cf08505bfd850f319b5322dbeeeb
Merge: 8777b9b 7b2d0e3
Author: L.C. Karssen <lennart at karssen.org>
Date: Wed Jan 15 11:30:26 2014 +0100
Merge tag 'upstream/0.4.2'
Upstream version 0.4.2
Makefile.am | 2 +-
Makefile.in | 297 ++---
aclocal.m4 | 564 +++++-----
checks/Makefile.am | 93 +-
checks/Makefile.in | 767 ++++++++-----
checks/R-tests/Makefile.am | 103 ++
checks/R-tests/Makefile.in | 867 +++++++++++++++
checks/R-tests/initial_checks.R | 93 ++
checks/R-tests/run_R_test_pacox.sh | 11 +
checks/R-tests/run_R_test_palinear.sh | 11 +
checks/R-tests/run_R_test_palogist.sh | 11 +
checks/R-tests/run_model_coxph.R | 98 ++
checks/R-tests/run_model_linear.R | 29 +
checks/R-tests/run_model_logist.R | 23 +
checks/R-tests/run_models_in_R_pacox.R | 109 ++
checks/R-tests/run_models_in_R_palinear.R | 129 +++
checks/R-tests/run_models_in_R_palogist.R | 129 +++
checks/check_dose_input.sh | 2 +-
...robabel.pl_chunk.sh => check_probabel_chunk.sh} | 18 +-
checks/inputfiles/test.dose.fvd | Bin 4000 -> 4800 bytes
checks/inputfiles/test.dose.fvi | Bin 6608 -> 6640 bytes
checks/inputfiles/test.map | 1 +
checks/inputfiles/test.mldose | 400 +++----
checks/inputfiles/test.mlinfo | 1 +
checks/inputfiles/test.mlprob | 400 +++----
checks/inputfiles/test.prob.fvd | Bin 8000 -> 9600 bytes
checks/inputfiles/test.prob.fvi | Bin 6768 -> 6832 bytes
checks/test_bt.sh | 23 +-
checks/test_cox.sh | 20 +-
checks/test_mms.sh | 23 +-
checks/test_qt.sh | 139 +--
checks/verified_results/height_base_add.out.txt | 1 +
configure | 321 +++---
configure.ac | 29 +-
doc/ChangeLog | 29 +
doc/INSTALL | 15 +-
doc/Makefile.am | 2 +-
doc/Makefile.in | 132 ++-
doc/ProbABEL_manual.tex | 39 +-
doc/pacoxph.1 | 2 +-
doc/palinear.1 | 4 +-
doc/palogist.1 | 4 +-
doc/probabel.1 | 91 ++
doc/probabel.pl.1 | 91 ++
examples/Makefile.am | 81 ++
examples/Makefile.in | 191 +++-
examples/example_bt.sh | 24 +-
examples/example_cox.sh | 24 +-
examples/example_qt.sh | 72 +-
missing | 461 +++-----
src/Makefile.am | 27 +-
src/Makefile.in | 332 ++++--
src/command_line_settings.cpp | 31 +-
src/command_line_settings.h | 6 +-
src/config.h.in | 7 -
src/coxfit2.c | 1 -
src/coxph_data.cpp | 206 +++-
src/coxph_data.h | 25 +-
src/data.cpp | 33 +-
src/data.h | 34 +-
src/eigen_mematrix.cpp | 43 +-
src/eigen_mematrix.h | 6 +-
src/extract-snp.cpp | 10 +-
src/fvlib/AbstractMatrix.cpp | 12 +-
src/fvlib/AbstractMatrix.h | 113 +-
src/fvlib/CastUtils.cpp | 295 ++---
src/fvlib/CastUtils.h | 141 +--
src/fvlib/FileVector.cpp | 1145 +++++++++++---------
src/fvlib/FileVector.h | 209 ++--
src/fvlib/FilteredMatrix.cpp | 117 +-
src/fvlib/FilteredMatrix.h | 173 +--
src/fvlib/Logger.cpp | 7 +-
src/fvlib/Logger.h | 30 +-
src/fvlib/RealHandlerWrapper.cpp | 21 +-
src/fvlib/RealHandlerWrapper.h | 10 +-
src/fvlib/ReusableFileHandle.cpp | 31 +-
src/fvlib/ReusableFileHandle.h | 28 +-
src/fvlib/Transposer.cpp | 237 ++--
src/fvlib/Transposer.h | 38 +-
src/fvlib/convert_util.cpp | 567 +++++-----
src/fvlib/convert_util.h | 10 +-
src/fvlib/frutil.cpp | 238 ++--
src/fvlib/frutil.h | 86 +-
src/gendata.cpp | 3 +-
src/gendata.h | 4 +-
src/main.cpp | 497 ++-------
src/main_functions_dump.cpp | 428 ++++++++
src/main_functions_dump.h | 38 +
src/maskedmatrix.h | 6 +-
src/mematrix.h | 2 +-
src/phedata.cpp | 30 +-
src/phedata.h | 2 +-
src/{probabel.pl => probabel} | 25 +-
src/reg1.cpp | 87 +-
src/reg1.h | 6 +-
src/regdata.cpp | 88 +-
src/regdata.h | 12 +-
src/usage.cpp | 18 +-
test-driver | 127 +++
99 files changed, 7406 insertions(+), 4212 deletions(-)
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