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2017-12-18Getting ready for release. Defaulting to OpenBlasPjotr Prins
2017-12-07More notes and removed unused LULndetPjotr Prins
2017-12-07Some more overflow checksPjotr Prins
2017-12-06Some cleanup on matrix checkingPjotr Prins
2017-11-10Docs: add flag for include filesPjotr Prins
2017-10-14More travisPjotr Prins
2017-10-14Note on OpenBlas buildPjotr Prins
2017-10-14More disabling of eigenlib (faster compilation) and avoid OPENBLAS_CONST ↵Pjotr Prins
which does not work on older cblas.h
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
2017-08-27Makefile: clean up of the main Makefile and changed build instructionsPjotr Prins
to align with normal build systems * Debug mode is now the default (use DEBUG= to disable) * Dynamic linking is now the default (use FORCE_STATIC=1 for static) * Removed references to 32-bit compilation (default is $arch)
2017-08-26Tests and enforces added related to ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/78
2017-08-20Support filesPjotr Prins
2017-08-14Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26Pjotr Prins
2017-08-13Adding travis-ci support for g++-4.9 and g++-6 on Linux. Tests pass.Pjotr Prins
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
2017-07-27Added note about GSL version in installation instructions.Peter Carbonetto
2017-07-26github: fix links to gemma repoPjotr Prins
2017-07-16sunit2: added instructionsPjotr Prins
2017-07-09Makefile: add OpenBLAS supportPjotr Prins
2017-07-09Tests: added test for univariate and multivariate LMMPjotr Prins
Also added 'make check' command in Makefile and documented in INSTALL.md
2017-07-08README: some links to INSTALL.mdPjotr Prins
2017-07-08Added notes on using makePjotr Prins
2017-07-08Install docPjotr Prins
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