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2017-08-22Fixes matrix checks - looking saner now...- Matrix checks as described in https://github.com/genetics-statistics/GEMMA/issues/72 - introduces -strict switch which will exit on certain conditions - zero small eigenvalues in EigenDecomp_Zeroed which also checks for negative values - commented out float versions of functions in lapack.cpp (pre-removal) - reverted on disabled regression tests (GEMMA shows its previous behaviour now) Pjotr Prins
2017-08-21Added more detailed description of -widv option following Xiang's description...Peter Carbonetto
2017-08-21Bumped up version.Peter Carbonetto
2017-08-20Added checks for KPjotr Prins
2017-08-15Fixes output file with kinship has extra column...https://github.com/genetics-statistics/GEMMA/issues/14 Pjotr Prins
2017-08-14Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26Pjotr Prins
2017-08-13Fixes https://github.com/genetics-statistics/GEMMA/issues/64...debug.h: replaced assert_fail with enforce_fail Pjotr Prins
2017-08-07Bumped up development version.Peter Carbonetto
2017-08-03LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -loco...1 switch for LOCO of chromosome 1. What are the use cases? 1. User runs vanilla GEMMA: all SNPs are considered input for GWA and K 2. User passes in -snps: all these SNPs are considered for GWA and K 3. User passes in -snps and -ksnps: All these SNPs are used for GWA, Ksnps are used for K 4. User passes in -loco: SNPs are split by chromosome (GWA incl., K excl.) 5. User passes in -snps, -gwasnps and -ksnps could mean that also GWA is subset explicitely (nyi) In all cases indicator_snp is honored and we get the most flexible way for studying SNP combinations that can be passed in in different ways. Overall added: - various comments in source code - tests in test framework inlc. fast-check - NDEBUG compilation support in the Makefile - -debug switch for GEMMA debug output - debug.h which includes enforce functions which work like assert. Unlike assert, enforce also works in release compilation - -nind switch limit the number of individuals used (trim_individuals for testing) - enforcing tests of input files - e.g. are number of individuals correct - checks for memory allocation - we should add more of those - more checks for gsl results - we should add more of those - replaced strtoken with regex as a first case. They should all be replaced. strtoken is not thread safe, for one. - introduced C++ iterators - introduced C++ closure in BimBam LMM for cached processing - more localized initialization of variables - makes for demonstratably more correct code - -ksnps adds snps into setKSnps - -gwasnps adds snps into setGWASnps - both sets are computed by -loco - attempted to make the code easier to read Pjotr Prins
2017-08-02Added section on contributing and coding style and fixed compilationPjotr Prins
2017-08-02Massive patch using LLVM coding style. It was generated with:... clang-format -style=LLVM -i *.cpp *.h Please set your editor to replace tabs with spaces and use indentation of 2 spaces. Pjotr Prins
2017-07-27Updated version to 0.97.Peter Carbonetto
2017-07-21Removed some more commented-out code from mvlmm.cpp.Peter Carbonetto
2017-07-19Removed some commented out code from mvlmm.cpp.Peter Carbonetto
2017-07-07Merge pull request #51 from genenetwork/spacing...Spacing fixes.Peter Carbonetto
2017-07-07Bumped up version; added Pjotr to README.Peter Carbonetto
2017-07-07Merge branch 'master' of github.com:xiangzhou/GEMMAPeter Carbonetto
2017-07-07Removed FORCE_FLOAT from mvlmm.cpp.Peter Carbonetto
2017-07-07Fix spacingPjotr Prins
2017-07-07Some three compile time fixes for the GNU GCC 7.1.0 compiler on Linux....This patch is a mess because we use different line endings. I propose to convert to standard Unix mode (as was the original GEMMA code). To convert with vim one can use set fileformat=unix Do not merge this pull request, we can handle te fixes later. Pjotr Prins
2017-07-04Removed FORCE_FLOAT from io.cpp.Peter Carbonetto
2017-06-29Remove FORCE_FLOAT from vc.cpp.Peter Carbonetto
2017-06-19Removed FORCE_FLOAT from param.cpp.Peter Carbonetto
2017-06-08Removed commented-out code from gemma.cpp.Peter Carbonetto
2017-06-08Removed FORCE_FLOAT from vc.h, logistic.h.Peter Carbonetto
2017-06-07Removed FORCE_FLOAT from a few more files.Peter Carbonetto
2017-06-05Removed FORCE_FLOAT from varcov.h,varcov.cpp.Peter Carbonetto
2017-06-04Removed FORCE_FLOAT from prdt.h/prdt.cpp.Peter Carbonetto
2017-06-02Removed FORCE_FLOAT from mathfunc.*Peter Carbonetto
2017-06-02Removed FORCE_FLOAT from lmm.h,cpp.Peter Carbonetto
2017-06-01Removed FORCE_FLOAT from additional C++ source files.Peter Carbonetto
2017-05-31Removed WITH_LAPACK compile/build option.Peter Carbonetto
2017-05-31Removing FORCE_FLOAT from some more C++ source files.Peter Carbonetto
2017-05-30Removing FORCE_FLOAT from some C++ source files.Peter Carbonetto
2017-05-28Removed FORCE_FLOAT option from Makefiles.Peter Carbonetto
2017-05-28Update to d2f.sh; unfortunately I'm getting a lot of errors when I try to bui...Peter Carbonetto
2017-05-28Fixed d2f.sh; created new Makefile for single-precision floats.Peter Carbonetto
2017-05-27Removed src/Eigen; instead, Eigen C++ library is downloaded separately. See I...Peter Carbonetto
2017-05-25A couple small adjustments to README.Peter Carbonetto
2017-05-25Add files via uploadxiangzhou
2017-05-17Bumped up version.Peter Carbonetto
2017-05-09Bumped version to 0.95.2a.Peter Carbonetto
2017-05-09fixed #36xiangzhou
2017-05-09Bumped version to 0.95.1.Peter Carbonetto
2017-05-09Putatively fixed -Wc++11-narrowing error in io.cpp (see Issue #24).Peter Carbonetto
2017-05-04Fixed problems with duplicate symbols; now using static gsl libraries in Make...Peter Carbonetto
2017-05-04Added new files shared by Xiang via email on May 4, 2017.Peter Carbonetto
2017-05-04Local updates made by Xiang---shared via email on May 4, 2017, subject: gemma...Peter Carbonetto
2017-05-04Fixed problems with duplicate symbols in io.o, lmm.o, param.o and vc.o; creat...Peter Carbonetto
2016-08-17version 0.95alphaxiangzhou
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