| Age | Commit message (Expand) | Author |
|---|
| 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...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 |
| 2017-07-27 | Added note about GSL version in installation instructions. | Peter Carbonetto |
| 2017-07-26 | github: fix links to gemma repo | Pjotr Prins |
| 2017-07-16 | sunit2: added instructions | Pjotr Prins |
| 2017-07-09 | Makefile: add OpenBLAS support | Pjotr Prins |
| 2017-07-09 | Tests: added test for univariate and multivariate LMM...Also added 'make check' command in Makefile and documented in INSTALL.md
| Pjotr Prins |
| 2017-07-08 | README: some links to INSTALL.md | Pjotr Prins |
| 2017-07-08 | Added notes on using make | Pjotr Prins |
| 2017-07-08 | Install doc | Pjotr Prins |
