| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2017-10-10 | Bumped up version. | Peter Carbonetto | |
| 2017-10-05 | Addresses | Pjotr Prins | |
| https://github.com/genetics-statistics/GEMMA/issues/81 | |||
| 2017-08-27 | Makefile: clean up of the main Makefile and changed build instructions | Pjotr 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) | |||
| 2017-08-26 | Rename unittests binary to unittests-gemma | Pjotr Prins | |
| 2017-08-21 | Bumped up version. | Peter Carbonetto | |
| 2017-08-20 | Support files | Pjotr Prins | |
| 2017-08-14 | Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26 | Pjotr Prins | |
| 2017-08-13 | Adding travis-ci support for g++-4.9 and g++-6 on Linux. Tests pass. | Pjotr Prins | |
| 2017-08-07 | Bumped up development version. | Peter Carbonetto | |
| 2017-08-03 | LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -loco | Pjotr 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 | |||
| 2017-07-11 | Makefile: add extra slash to support relative eigen paths | Pjotr Prins | |
| 2017-07-11 | Makefile: silence compiler warnings for Eigen libs | Pjotr Prins | |
| 2017-07-11 | Makefile: compiler warnings optional | Pjotr Prins | |
| 2017-07-11 | Makefile: compile without -Weffc++ as suggested by ↵ | Pjotr Prins | |
| https://stackoverflow.com/questions/11496942/understanding-weffc#11529328 reduces warnings | |||
| 2017-07-09 | Makefile: fix output on make check | Pjotr Prins | |
| 2017-07-09 | Makefile: force unit tests to throw a make error on less than 100% success | Pjotr Prins | |
| 2017-07-09 | Run test_suite directly from Makefile | Pjotr Prins | |
| 2017-07-09 | Makefile: add OpenBLAS support | Pjotr Prins | |
| 2017-07-09 | Tests: added test for univariate and multivariate LMM | Pjotr Prins | |
| Also added 'make check' command in Makefile and documented in INSTALL.md | |||
| 2017-07-07 | Bumped up version; added Pjotr to README. | Peter Carbonetto | |
| 2017-07-07 | Makefile: find include files for Eigen3 | Pjotr Prins | |
| 2017-07-04 | Add NO_INTEL_COMPAT flag to Makefile. | Efraim Flashner | |
| 2017-05-31 | Removed WITH_LAPACK compile/build option. | Peter Carbonetto | |
| 2017-05-30 | Removing FORCE_FLOAT from some C++ source files. | Peter Carbonetto | |
| 2017-05-28 | Removed FORCE_FLOAT option from Makefiles. | Peter Carbonetto | |
| 2017-05-17 | Bumped up version. | Peter Carbonetto | |
| 2017-05-09 | Bumped version to 0.95.2a. | Peter Carbonetto | |
| 2017-05-09 | Added bin folder; added -Weffc++ flag to Makefile. | Peter Carbonetto | |
| 2017-05-09 | Bumped version to 0.95.1. | Peter Carbonetto | |
| 2017-05-04 | Fixed problems with duplicate symbols; now using static gsl libraries in ↵ | Peter Carbonetto | |
| Makefile.osx so that others don't have to download it using Homebrew. | |||
| 2015-07-11 | add GxE test | xiangzhou | |
| 2014-10-30 | Merge branch 'master' into fix-make-clean-bins | Joshua Randall | |
| Conflicts: Makefile | |||
| 2014-10-30 | Merge pull request #10 from wtsi-hgi/fix-dynamic-linking-lblas | xiangzhou | |
| Fixes dynamic compilation (fixes #9) | |||
| 2014-10-30 | Adds $(OUTPUT) files to `make clean` target | Joshua Randall | |
| Modifies the `make clean` target so that output binaries bin/gemma and/or bin/gemmaf will be removed so that they will definitely be rebuilt after `make clean` | |||
| 2014-10-30 | Fixes dynamic compilation | Joshua Randall | |
| Fixes dynamic compilation on systems where -lblas is required for symbols such as `dgemm_` | |||
| 2014-10-30 | makes dist tar file not explode into ./ | Joshua C. Randall | |
| 2014-09-22 | version 0.95alpha | xiangzhou | |
| 2014-09-20 | version 0.95alpha | xiangzhou | |
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index : pangemma | |
| PanGEMMA: Genome-wide Efficient Mixed Model Association |
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