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2018-09-06Show warning on some unused matricesPjotr 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
2018-08-26More value checking and bounds checkingPjotr Prins
2018-08-25Number format checking in strict mode. Also fixes #149Pjotr 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
2018-01-27Extra error info on strtok parsing failure - should help supportPjotr Prins
2017-12-12Updated copyright infoPjotr Prins
2017-12-08Reduce debug noise levelsPjotr Prins
2017-12-07Improve error messages, closes ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/116
2017-12-07Some more overflow checksPjotr Prins
2017-11-15Nans: introducing checking on mem freePjotr Prins
2017-11-09Adding tests for bslmmPjotr Prins
2017-11-09Disabled debug output when not using -debugPjotr 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
2017-10-18Tests still pass with safe_alloc (which sets the buffers to NaNs on allocation)Pjotr Prins
2017-10-14More travisPjotr Prins
2017-10-13Refactored debug settingsPjotr Prins
Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
2017-10-13Make sure __ASSERT_VOID_CAST worksPjotr 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)
2017-08-20Added checks for KPjotr 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/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
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