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2017-08-07Bumped up development version.Peter Carbonetto
2017-08-07Merge branch 'master' of github.com:genetics-statistics/GEMMAPeter Carbonetto
2017-08-07Merge pull request #63 from genenetwork/loco-formattedPeter Carbonetto
LOCO is implemented in GEMMA for the BIMBAM format.
2017-08-03LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -locoPjotr Prins
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
2017-08-02Reformatted gemma calls in test_suite.sh.Peter Carbonetto
2017-08-02Merge pull request #62 from genenetwork/spacingPeter Carbonetto
Spacing and coding style.
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:Pjotr Prins
clang-format -style=LLVM -i *.cpp *.h Please set your editor to replace tabs with spaces and use indentation of 2 spaces.
2017-07-27Added note about GSL version in installation instructions.Peter Carbonetto
2017-07-27Merge branch 'master' of github.com:genetics-statistics/GEMMA.Peter Carbonetto
2017-07-27Linking to gemma 2.21 instead of gsl 2.2.1 in Makefile.linux.Peter Carbonetto
2017-07-27Made a couple small adjustments to Makefile.macosx.Peter Carbonetto
2017-07-27Updated version to 0.97.Peter Carbonetto
2017-07-26Fixed link in README.Peter Carbonetto
2017-07-26Merge pull request #60 from genenetwork/tests.Peter Carbonetto
2017-07-26test_suite: run shunit2 from system when availablePjotr Prins
2017-07-26test_suite: replace awk with perl to compute file contents and default to ↵Pjotr Prins
shunit2 in repo fixes https://github.com/genetics-statistics/GEMMA/issues/55
2017-07-26Added a line count test for KPjotr Prins
2017-07-26github: fix links to gemma repoPjotr Prins
2017-07-21Added note in README about LGPL license for shuint2.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
2017-07-18Moved shunit2 files to test directory.Peter Carbonetto
2017-07-18Fixed failing test. New test report summary:Peter Carbonetto
tests passed: 13 tests failed: 0 tests total: 13 success rate: 100%
2017-07-18Added shunint2 v2.0.3 files.Peter Carbonetto
2017-07-18Merge pull request #56 from genenetwork/compiler-warningsPeter Carbonetto
Compiler warnings are optional.
2017-07-18Merge pull request #54 from genenetwork/testsPeter Carbonetto
Added test suite, make check and openblas support. Need to fix one test that is still failing.
2017-07-16sunit2: added instructionsPjotr Prins
2017-07-12Update README.mdxiangzhou
2017-07-11Makefile: add extra slash to support relative eigen pathsPjotr Prins
2017-07-11Makefile: silence compiler warnings for Eigen libsPjotr Prins
2017-07-11Makefile: compiler warnings optionalPjotr Prins
2017-07-11Makefile: compile without -Weffc++ as suggested by ↵Pjotr Prins
https://stackoverflow.com/questions/11496942/understanding-weffc#11529328 reduces warnings
2017-07-09Makefile: fix output on make checkPjotr Prins
2017-07-09Makefile: force unit tests to throw a make error on less than 100% successPjotr Prins
2017-07-09Run test_suite directly from MakefilePjotr Prins
2017-07-09Spacing in demo.txtPjotr Prins
2017-07-09Makefile: add OpenBLAS supportPjotr Prins
2017-07-09Tests: more testsPjotr Prins
2017-07-09Tests: added test for univariate and multivariate LMMPjotr Prins
Also added 'make check' command in Makefile and documented in INSTALL.md
2017-07-09Test: check resultPjotr Prins
2017-07-09Add test framework based on shunit2Pjotr Prins
2017-07-08Merge pull request #53 from genenetwork/docPeter Carbonetto
Updated README and created INSTALL.
2017-07-08INSTALL.md: fixed conflictPjotr Prins
2017-07-08README: some links to INSTALL.mdPjotr Prins
2017-07-08Added notes on using makePjotr Prins
2017-07-08Install docPjotr Prins
2017-07-07Merge pull request #51 from genenetwork/spacingPeter Carbonetto
Spacing fixes.
2017-07-07Bumped up version; added Pjotr to README.Peter Carbonetto
2017-07-07Merge branch 'master' of github.com:xiangzhou/GEMMAPeter Carbonetto
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