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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
2017-07-09Add test framework based on shunit2Pjotr Prins
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