Age | Commit message (Expand) | Author |
2018-09-06 | More debugging and a performance check | Pjotr Prins |
2018-09-06 | More debugging info and raise SIGINT instead of exit | Pjotr Prins |
2018-09-06 | Further debugging | Pjotr Prins |
2018-08-31 | More testing | Pjotr Prins |
2018-08-30 | Debugging calcPab | Pjotr Prins |
2018-08-26 | More value checking and bounds checking | Pjotr Prins |
2018-06-05 | Typo: sepcified -> specified | Dylan Aïssi |
2018-02-28 | renamed import io.h to gemma_io.h | DannyArends |
2017-12-12 | Updated copyright info | Pjotr Prins |
2017-11-11 | Cleaning up buffer use thanks to compiler warnings | Pjotr Prins |
2017-11-10 | Remove compiler warnings | Pjotr Prins |
2017-11-10 | Tests: added more bslmm tests | Pjotr Prins |
2017-11-09 | Adding tests for bslmm | Pjotr Prins |
2017-10-26 | Changed SNPs into SNPs/var in output, ref https://github.com/genetics-statist... | 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 |
2017-10-13 | Refactored debug settings...Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
| Pjotr Prins |
2017-10-13 | Consolidate into ProgressBar into one function and related updates | Pjotr Prins |
2017-10-05 | Removed Oxford format as per https://github.com/genetics-statistics/GEMMA/iss... | Pjotr Prins |
2017-08-28 | param.cpp: Set error on error | Pjotr Prins |
2017-08-26 | Debug: only output check on -debug | Pjotr Prins |
2017-08-22 | Fix typo intecept -> intercept | Pjotr Prins |
2017-08-15 | Fixes output file with kinship has extra column...https://github.com/genetics-statistics/GEMMA/issues/14
| 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 |
2017-06-19 | Removed FORCE_FLOAT from param.cpp. | Peter Carbonetto |
2017-06-08 | Removed commented-out code from gemma.cpp. | Peter Carbonetto |
2017-05-31 | Removed WITH_LAPACK compile/build option. | Peter Carbonetto |
2017-05-30 | Removing FORCE_FLOAT from some C++ source files. | Peter Carbonetto |
2017-05-04 | Local updates made by Xiang---shared via email on May 4, 2017, subject: gemma... | Peter Carbonetto |
2016-05-23 | version 0.95alpha | xiangzhou |
2015-07-11 | add GxE test | xiangzhou |
2015-07-11 | add GXE test | xiangzhou |
2014-09-22 | version 0.95alpha | xiangzhou |