| Age | Commit message (Expand) | Author |
|---|
| 2017-08-27 | Makefile: clean up of the main Makefile and changed build instructions••• to align with normal build systems
* Debug mode is now the default (use DEBUG= to disable)
* Dynamic linking is now the default (use FORCE_STATIC=1 for static)
* Removed references to 32-bit compilation (default is $arch)
| Pjotr Prins |
| 2017-08-26 | Rename unittests binary to unittests-gemma | Pjotr Prins |
| 2017-08-21 | Bumped up version. | Peter Carbonetto |
| 2017-08-20 | Support files | Pjotr Prins |
| 2017-08-14 | Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26 | Pjotr Prins |
| 2017-08-13 | Adding travis-ci support for g++-4.9 and g++-6 on Linux. Tests pass. | 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 |
| 2017-07-11 | Makefile: add extra slash to support relative eigen paths | Pjotr Prins |
| 2017-07-11 | Makefile: silence compiler warnings for Eigen libs | Pjotr Prins |
| 2017-07-11 | Makefile: compiler warnings optional | Pjotr Prins |
| 2017-07-11 | Makefile: compile without -Weffc++ as suggested by https://stackoverflow.com/... | Pjotr Prins |
| 2017-07-09 | Makefile: fix output on make check | Pjotr Prins |
| 2017-07-09 | Makefile: force unit tests to throw a make error on less than 100% success | Pjotr Prins |
| 2017-07-09 | Run test_suite directly from Makefile | Pjotr Prins |
| 2017-07-09 | Makefile: add OpenBLAS support | Pjotr Prins |
| 2017-07-09 | Tests: added test for univariate and multivariate LMM•••Also added 'make check' command in Makefile and documented in INSTALL.md
| Pjotr Prins |
| 2017-07-07 | Bumped up version; added Pjotr to README. | Peter Carbonetto |
| 2017-07-07 | Makefile: find include files for Eigen3 | Pjotr Prins |
| 2017-07-04 | Add NO_INTEL_COMPAT flag to Makefile. | Efraim Flashner |
| 2017-05-31 | Removed WITH_LAPACK compile/build option. | Peter Carbonetto |
| 2017-05-30 | Removing FORCE_FLOAT from some C++ source files. | Peter Carbonetto |
| 2017-05-28 | Removed FORCE_FLOAT option from Makefiles. | Peter Carbonetto |
| 2017-05-17 | Bumped up version. | Peter Carbonetto |
| 2017-05-09 | Bumped version to 0.95.2a. | Peter Carbonetto |
| 2017-05-09 | Added bin folder; added -Weffc++ flag to Makefile. | Peter Carbonetto |
| 2017-05-09 | Bumped version to 0.95.1. | Peter Carbonetto |
| 2017-05-04 | Fixed problems with duplicate symbols; now using static gsl libraries in Make... | Peter Carbonetto |
| 2015-07-11 | add GxE test | xiangzhou |
| 2014-10-30 | Merge branch 'master' into fix-make-clean-bins•••Conflicts:
Makefile
| Joshua Randall |
| 2014-10-30 | Merge pull request #10 from wtsi-hgi/fix-dynamic-linking-lblas•••Fixes dynamic compilation (fixes #9) | xiangzhou |
| 2014-10-30 | Adds $(OUTPUT) files to `make clean` target•••Modifies the `make clean` target so that output binaries
bin/gemma and/or bin/gemmaf will be removed so that they
will definitely be rebuilt after `make clean`
| Joshua Randall |
| 2014-10-30 | Fixes dynamic compilation•••Fixes dynamic compilation on systems where -lblas is required
for symbols such as `dgemm_`
| Joshua Randall |
| 2014-10-30 | makes dist tar file not explode into ./ | Joshua C. Randall |
| 2014-09-22 | version 0.95alpha | xiangzhou |
| 2014-09-20 | version 0.95alpha | xiangzhou |
