Age | Commit message (Expand) | Author |
2018-06-29 | Merge branch 'master' of github.com:genetics-statistics/GEMMA | Pjotr Prins |
2018-02-28 | renamed import io.h to gemma_io.h | DannyArends |
2018-01-26 | Change OpenBLAS warning | Pjotr Prins |
2017-12-19 | Documentation and Travis fixes | Pjotr Prins |
2017-12-12 | Updated copyright info | Pjotr Prins |
2017-12-08 | Changed banner and behaviour | Pjotr Prins |
2017-12-08 | Legacy mode does not show logl_H1 column in output | Pjotr Prins |
2017-11-22 | Remove compiler warnings | Pjotr Prins |
2017-11-15 | Nans: introducing checking on mem free | Pjotr Prins |
2017-10-26 | VERSION now contains the GEMMA version number. A script generates a header...file named ./src/version.h. See Makefile for details.
| Pjotr Prins |
2017-10-26 | Changed SNPs into SNPs/var in output, ref https://github.com/genetics-statist... | Pjotr Prins |
2017-10-18 | Tests still pass with safe_alloc (which sets the buffers to NaNs on allocation) | Pjotr Prins |
2017-10-14 | Travis: more fixes | Pjotr Prins |
2017-10-14 | Travis | Pjotr Prins |
2017-10-14 | OpenBlas info | Pjotr Prins |
2017-10-14 | More disabling of eigenlib (faster compilation) and avoid OPENBLAS_CONST whic... | 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 | OpenBlas: preparing for dgemm use | Pjotr Prins |
2017-10-13 | Progressbar update | Pjotr Prins |
2017-10-13 | Bumped up version. | Peter Carbonetto |
2017-10-06 | LMM: BIMBAM and PLINK share same LMM code - test pass | 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 | Added a few checks and info | Pjotr Prins |
2017-09-12 | Show GSL and Eigen versions in .log output | Pjotr Prins |
2017-08-27 | Removed large sections of commented out code | Pjotr Prins |
2017-08-22 | Fixes matrix checks - looking saner now...- Matrix checks as described in https://github.com/genetics-statistics/GEMMA/issues/72
- introduces -strict switch which will exit on certain conditions
- zero small eigenvalues in EigenDecomp_Zeroed which also checks for negative values
- commented out float versions of functions in lapack.cpp (pre-removal)
- reverted on disabled regression tests (GEMMA shows its previous behaviour now)
| Pjotr Prins |
2017-08-21 | Added more detailed description of -widv option following Xiang's description... | Peter Carbonetto |
2017-08-21 | Bumped up version. | Peter Carbonetto |
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 |
2017-08-14 | Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26 | Pjotr Prins |
2017-08-07 | Bumped up development version. | Peter Carbonetto |
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 |
2017-07-27 | Updated version to 0.97. | Peter Carbonetto |
2017-07-07 | Merge pull request #51 from genenetwork/spacing...Spacing fixes. | Peter Carbonetto |
2017-07-07 | Bumped up version; added Pjotr to README. | Peter Carbonetto |
2017-07-07 | Fix spacing | Pjotr Prins |
2017-06-08 | Removed commented-out code from gemma.cpp. | Peter Carbonetto |
2017-05-17 | Bumped up version. | Peter Carbonetto |
2017-05-09 | Bumped version to 0.95.2a. | Peter Carbonetto |
2017-05-09 | Bumped version to 0.95.1. | Peter Carbonetto |
2017-05-04 | Local updates made by Xiang---shared via email on May 4, 2017, subject: gemma... | Peter Carbonetto |
2016-08-17 | version 0.95alpha | xiangzhou |
2016-08-17 | version 0.95alpha | xiangzhou |
2016-07-24 | version 0.95alpha | xiangzhou |
2016-05-23 | version 0.95alpha | xiangzhou |
2016-05-23 | version 0.95alpha | xiangzhou |
2014-09-22 | version 0.95alpha | xiangzhou |