| Age | Commit message (Expand) | Author |
|---|
| 2017-10-26 | Get rid of compiler warning | Pjotr Prins |
| 2017-10-23 | Travis-ci:...- Disabled gcc-6 since we develop with later tools anyway
- Turned the release test into a simple integration test
- Adding MacOSX on Travis-ci
Tests: Adding tests for Plink w. LOCO
Safety: Introduce strtok_safe to get rid of segfaults
| Pjotr Prins |
| 2017-10-18 | Tests still pass with safe_alloc (which sets the buffers to NaNs on allocation) | Pjotr Prins |
| 2017-10-13 | Replacing first dgemm - tests fail | Pjotr Prins |
| 2017-10-13 | OpenBlas: preparing for dgemm use | Pjotr Prins |
| 2017-10-13 | Fix header for not showing se | Pjotr Prins |
| 2017-10-13 | Disable se for lmm=2, see https://github.com/genetics-statistics/GEMMA/issues/81 | Pjotr Prins |
| 2017-10-13 | Fixed mean and iterations in Plink - now this works | Pjotr Prins |
| 2017-10-13 | Fix embarrassing bug that broke BIMBAM for larger datasets - found it when po... | Pjotr Prins |
| 2017-10-06 | LMM: small cleanup and default to NaN initialization | Pjotr Prins |
| 2017-10-06 | LMM: BIMBAM and PLINK share same LMM code - test pass | Pjotr Prins |
| 2017-10-06 | LMM: lifter genotype parsing for BIMBAM. All tests pass. | Pjotr Prins |
| 2017-10-06 | LMM: lifter line no | Pjotr Prins |
| 2017-10-06 | LMM: lifted out file access | Pjotr Prins |
| 2017-10-06 | Oops: fixed logic problem after removing Oxford data | Pjotr Prins |
| 2017-10-05 | Removed Oxford format as per https://github.com/genetics-statistics/GEMMA/iss... | Pjotr Prins |
| 2017-10-05 | LMM: skip beta (again) with LRT | Pjotr Prins |
| 2017-10-05 | Addresses... https://github.com/genetics-statistics/GEMMA/issues/81
| Pjotr Prins |
| 2017-10-05 | Adding debug statements on entering functions and added test for issue 58 | 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 |
| 2017-08-02 | 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 |
