| Age | Commit message (Expand) | Author |
|---|
| 2017-08-27 | -a...ReadFile_geno: stop warnings after 10x
| Pjotr Prins |
| 2017-08-26 | Debug: only output check on -debug | Pjotr Prins |
| 2017-08-26 | Tests and enforces added related to https://github.com/genetics-statistics/GE... | Pjotr Prins |
| 2017-08-20 | Added checks for K | 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 | Some three compile time fixes for the GNU GCC 7.1.0 compiler on Linux....This patch is a mess because we use different line endings. I propose
to convert to standard Unix mode (as was the original GEMMA code).
To convert with vim one can use
set fileformat=unix
Do not merge this pull request, we can handle te fixes later.
| Pjotr Prins |
| 2017-07-04 | Removed FORCE_FLOAT from io.cpp. | Peter Carbonetto |
| 2017-06-19 | Removed FORCE_FLOAT from param.cpp. | Peter Carbonetto |
| 2017-05-31 | Removed WITH_LAPACK compile/build option. | Peter Carbonetto |
| 2017-05-31 | Removing FORCE_FLOAT from some more C++ source files. | Peter Carbonetto |
| 2017-05-09 | Putatively fixed -Wc++11-narrowing error in io.cpp (see Issue #24). | 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 |
| 2016-05-23 | version 0.95alpha | xiangzhou |
| 2015-07-11 | add GxE test | xiangzhou |
| 2015-07-11 | add GXE test | xiangzhou |
| 2014-10-30 | version 0.95alpha | xiangzhou |
| 2014-09-22 | version 0.95alpha | xiangzhou |
