| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2017-08-02 | Massive patch using LLVM coding style. It was generated with:... clang-format -style=LLVM -i *.cpp *.h
Please set your editor to replace tabs with spaces and use indentation of 2 spaces.
| Pjotr Prins |
| 2017-07-07 | Fix spacing | Pjotr Prins |
| 2017-06-08 | Removed commented-out code from gemma.cpp. | Peter Carbonetto |
| 2017-05-04 | Fixed problems with duplicate symbols; now using static gsl libraries in Make... | Peter Carbonetto |
| 2017-05-04 | Local updates made by Xiang---shared via email on May 4, 2017, subject: gemma... | Peter Carbonetto |
| 2017-05-04 | Fixed problems with duplicate symbols in io.o, lmm.o, param.o and vc.o; creat... | Peter Carbonetto |
| 2016-07-24 | version 0.95alpha | xiangzhou |
| 2016-05-23 | version 0.95alpha | xiangzhou |
| 2015-07-11 | add GXE test | xiangzhou |
| 2014-09-22 | version 0.95alpha | xiangzhou |
