| Age | Commit message (Expand) | Author |
|---|---|---|
| 2017-12-12 | Updated copyright info | Pjotr Prins |
| 2017-12-08 | Reduce debug noise levels | Pjotr Prins |
| 2017-12-07 | Improve error messages, closes https://github.com/genetics-statistics/GEMMA/i... | Pjotr Prins |
| 2017-12-07 | Some more overflow checks | Pjotr Prins |
| 2017-11-15 | Nans: introducing checking on mem free | Pjotr Prins |
| 2017-11-09 | Adding tests for bslmm | Pjotr Prins |
| 2017-11-09 | Disabled debug output when not using -debug | Pjotr Prins |
| 2017-10-23 | Travis-ci:...- 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 | Pjotr Prins |
| 2017-10-18 | Tests still pass with safe_alloc (which sets the buffers to NaNs on allocation) | Pjotr Prins |
| 2017-10-14 | More travis | Pjotr Prins |
| 2017-10-13 | Refactored debug settings...Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA | Pjotr Prins |
| 2017-10-13 | OpenBlas: preparing for dgemm use | Pjotr Prins |
| 2017-10-13 | Make sure __ASSERT_VOID_CAST works | Pjotr Prins |
| 2017-08-26 | Tests and enforces added related to https://github.com/genetics-statistics/GE... | Pjotr Prins |
| 2017-08-22 | Fixes matrix checks - looking saner now...- 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) | Pjotr Prins |
| 2017-08-20 | Added checks for K | Pjotr Prins |
| 2017-08-14 | Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26 | Pjotr Prins |
| 2017-08-13 | Fixes https://github.com/genetics-statistics/GEMMA/issues/64...debug.h: replaced assert_fail with enforce_fail | Pjotr Prins |
| 2017-08-03 | LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -loco...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 | Pjotr Prins |
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index : pangemma | |
| PanGEMMA: Genome-wide Efficient Mixed Model Association |
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