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2018-09-18Performance metricsPjotr Prins
2018-09-15Using Guix container to build with gcc and clangPjotr Prins
2018-09-07Matrices positive definite issuesPjotr Prins
2018-09-06More debugging and a performance checkPjotr Prins
2018-09-06More debugging info and raise SIGINT instead of exitPjotr Prins
2018-09-06Further debuggingPjotr Prins
2018-08-30Debugging calcPabPjotr Prins
2018-08-25Added a test for LMPjotr Prins
2018-07-27Add floating point hardware checking for Intel on GNU compilersPjotr Prins
When using the -check function (the default) it is enabled for Kinship computation and LM/LMM up to individual SNP computation. This means there can no longer be NaN values for matrices that are reused for every SNP, but it is possible to have NaN for individual SNPs. Fixes #161
2018-07-26Unittest: added test for forcing and catching floating point errors (this works)Pjotr Prins
2018-07-14- Guix Makefile added RPATHPjotr Prins
- Added performance metrics in ./test/performance
2017-11-22Remove compiler warnings and add check is_nanPjotr Prins
2017-11-11Disable some tests for bslmm which fail with different BLAS versions.Pjotr Prins
2017-11-11Cleaning up buffer use thanks to compiler warningsPjotr Prins
2017-11-10Tests: quotesPjotr Prins
2017-11-10Fix testPjotr Prins
2017-11-10Tests: added more bslmm testsPjotr Prins
2017-11-09Adding tests for bslmmPjotr Prins
2017-11-09Tests: add -lm testPjotr Prins
2017-11-09Tests: added bslmm testPjotr Prins
2017-10-23Travis-ci:Pjotr Prins
- Disabled gcc-6 since we develop with later tools anyway - Turned the release test into a simple integration test - Adding MacOSX on Travis-ci Tests: Adding tests for Plink w. LOCO Safety: Introduce strtok_safe to get rid of segfaults
2017-10-13Refactored debug settingsPjotr Prins
Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
2017-10-13Replacing first dgemm - tests failPjotr Prins
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
2017-10-13Fix header for not showing sePjotr Prins
2017-10-13Consolidate into ProgressBar into one function and related updatesPjotr Prins
2017-10-05LMM: skip beta (again) with LRTPjotr Prins
2017-10-05AddressesPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/81
2017-10-05Adding debug statements on entering functions and added test for issue 58Pjotr Prins
2017-08-26Debug: only output check on -debugPjotr Prins
2017-08-26Tests and enforces added related to ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/78
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)
2017-08-20Move shunit2 into ./contrib and add catch-1.8.7Pjotr Prins
2017-08-20Unit testsPjotr Prins
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
2017-08-13Fixes https://github.com/genetics-statistics/GEMMA/issues/64Pjotr Prins
debug.h: replaced assert_fail with enforce_fail
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
2017-07-26test_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
2017-07-18Moved 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%
2017-07-16sunit2: added instructionsPjotr Prins
2017-07-09Makefile: force unit tests to throw a make error on less than 100% successPjotr 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
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