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2024-12-09Update READMEs for new PanGEMMA developmentPjotr Prins
2024-05-03Built a static version of gemmaPjotr Prins
2022-02-15Notes on GuixPjotr Prins
2020-11-29Fix static buildPjotr Prins
2020-11-29Docker hintPjotr Prins
2020-11-29Update INSTALL docPjotr Prins
2020-09-29GEMMA builds with gcc 5.5.0 on Travis-CI (Ubuntu)Pjotr Prins
Added note on FreeBSD port #201
2020-09-29Fixing Travis build, remove gcc warnings and bump versionPjotr Prins
2020-08-10guix-devPjotr Prins
2020-05-28-aPjotr Prins
Fix test suite
2020-05-22Removing more eigenlib referencesPjotr Prins
2018-12-10INSTALLPjotr Prins
2018-10-14INSTALL.md: update make rulesPjotr Prins
2018-10-14README: badgesPjotr Prins
2018-09-28Preparing for releasePjotr Prins
2018-09-28Atlas compilation (still not working)Pjotr Prins
2018-09-27Inlining GSL callsPjotr Prins
2018-09-26GSL 2.x is preferredPjotr Prins
closes #177
2018-09-18ProfilingPjotr Prins
2018-09-18Added profiling and build instructionsPjotr Prins
2018-09-15Using Guix container to build with gcc and clangPjotr Prins
2018-08-25segfpe handlingPjotr Prins
2018-07-26Unittest: added test for forcing and catching floating point errors (this works)Pjotr Prins
2018-07-14Guix: add more build information to the final binaryPjotr Prins
2018-07-14- Guix Makefile added RPATHPjotr Prins
- Added performance metrics in ./test/performance
2018-07-14Guix: added GUIX flag to automate make settings. Added DAG of dependenciesPjotr Prins
2018-07-13GNU Guix build systemPjotr Prins
2018-01-26Always check input data for strtok - unless -no-check is usedPjotr Prins
2017-12-19Optimizing OpenBlasPjotr Prins
2017-12-19Use OpenBlas cblas interface by defaultPjotr Prins
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
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