| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2017-10-13 | OpenBlas: preparing for dgemm use | Pjotr Prins | |
| 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 | |
| 2017-08-03 | 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 | |||
| 2017-08-02 | Added section on contributing and coding style and fixed compilation | Pjotr Prins | |
| 2017-07-27 | Added note about GSL version in installation instructions. | Peter Carbonetto | |
| 2017-07-26 | Fixed link in README. | Peter Carbonetto | |
| 2017-07-26 | github: fix links to gemma repo | Pjotr Prins | |
| 2017-07-21 | Added note in README about LGPL license for shuint2. | Peter Carbonetto | |
| 2017-07-12 | Update README.md | xiangzhou | |
| 2017-07-08 | README: some links to INSTALL.md | Pjotr Prins | |
| 2017-07-08 | Install doc | Pjotr Prins | |
| 2017-07-07 | Merge pull request #51 from genenetwork/spacing | Peter Carbonetto | |
| Spacing fixes. | |||
| 2017-07-07 | Bumped up version; added Pjotr to README. | Peter Carbonetto | |
| 2017-07-07 | Fix spacing | Pjotr Prins | |
| 2017-05-27 | Removed src/Eigen; instead, Eigen C++ library is downloaded separately. See ↵ | Peter Carbonetto | |
| Issue #42 for tests performed. | |||
| 2017-05-26 | A few improvements to README. | Peter Carbonetto | |
| 2017-05-26 | Added What's Included section to README. | Peter Carbonetto | |
| 2017-05-25 | A few more small adjustments to installation instructions in README. | Peter Carbonetto | |
| 2017-05-25 | A couple small adjustments to README. | Peter Carbonetto | |
| 2017-05-25 | Instructions for using precompiled binaries. | Peter Carbonetto | |
| 2017-05-25 | Added ref. to latest stable release. | Peter Carbonetto | |
| 2017-05-25 | Revised overview of setup. | Peter Carbonetto | |
| 2017-05-25 | Added note about Windows support. | Peter Carbonetto | |
| 2017-05-24 | Added some notes to README. | Peter Carbonetto | |
| 2017-05-24 | Added link to NEWS from README | Peter Carbonetto | |
| 2017-05-24 | Moved text from README.txt to README.md. | Peter Carbonetto | |
| 2017-05-24 | Added instructions to build manual; fixed Zhou-2016 ref. | Peter Carbonetto | |
| 2017-05-23 | Minor adjustments to README. | Peter Carbonetto | |
| 2017-05-23 | Fixed date. | Peter Carbonetto | |
| 2017-05-23 | A few adjustments to README. | Peter Carbonetto | |
| 2017-05-23 | Added NEWS.md. | Peter Carbonetto | |
| 2017-05-23 | Added LICENSE. | Peter Carbonetto | |
| 2017-05-23 | Added note about issues to README. | Peter Carbonetto | |
| 2017-05-23 | Adjusted formatting in README. | Peter Carbonetto | |
| 2017-05-23 | Added citation info to README. | Peter Carbonetto | |
| 2017-05-22 | Adjusted note in README. | Peter Carbonetto | |
| 2017-05-22 | A few more small adjustements to README. | Peter Carbonetto | |
| 2017-05-22 | A few adjustments to the README. | Peter Carbonetto | |
| 2017-05-22 | Added note about image to README. | Peter Carbonetto | |
| 2017-05-22 | Revised summary in README.md. | Peter Carbonetto | |
| 2017-05-22 | Created README.md; added image; working on summary in README. | Peter Carbonetto | |
 |
index : pangemma | |
| PanGEMMA: Genome-wide Efficient Mixed Model Association |
| aboutsummaryrefslogtreecommitdiff |