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2017-08-22EigenDecomp: also show warning on multiple zero valuesPjotr Prins
2017-08-22Fixes matrix checks - looking saner nowPjotr Prins
- 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)
2017-08-21Added explanation of "beta estimates" in log.txt outputs.Peter Carbonetto
2017-08-21Merge branch 'master' of github.com:xiangzhou/GEMMAPeter Carbonetto
2017-08-21Added more detailed description of -widv option following Xiang's ↵Peter Carbonetto
description given in Issue #59.
2017-08-21Bumped up version for Makefile.macosx.Peter Carbonetto
2017-08-21Bumped up version.Peter Carbonetto
2017-08-21Merge pull request #73 from genenetwork/merge-checkKPeter Carbonetto
Check K and added unit test framework.
2017-08-20Move shunit2 into ./contrib and add catch-1.8.7Pjotr Prins
2017-08-20Unit testsPjotr Prins
2017-08-20Support filesPjotr Prins
2017-08-20Added checks for KPjotr Prins
2017-08-15Merge pull request #70 from genenetwork/issue14Peter Carbonetto
Fixes output file with kinship has extra column.
2017-08-15Fixes output file with kinship has extra columnPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/14
2017-08-14Merge pull request #69 from genenetwork/issue58.Peter Carbonetto
Tests for https://github.com/genetics-statistics/GEMMA/issues/58.
2017-08-14Merge pull request #68 from genenetwork/issue26.Peter Carbonetto
Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26.
2017-08-14Issue 58, add tests for GSLv2 NaN's showing up with covariatesPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/58
2017-08-14Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26Pjotr Prins
2017-08-13Merge pull request #67 from genenetwork/travisPeter Carbonetto
Travis.
2017-08-13Merge pull request #66 from genenetwork/issue64.Peter Carbonetto
Fixes https://github.com/genetics-statistics/GEMMA/issues/64.
2017-08-13Adding travis-ci support for g++-4.9 and g++-6 on Linux. Tests pass.Pjotr Prins
2017-08-13Fixes https://github.com/genetics-statistics/GEMMA/issues/64Pjotr Prins
debug.h: replaced assert_fail with enforce_fail
2017-08-07Bumped version in all Makefiles.Peter Carbonetto
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.
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