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## ChangeLog v0.97 (2017/12/19)
This is a massive bug fix release with many improvements. For contributions
see
[contributors](https://github.com/genetics-statistics/GEMMA/graphs/contributors)
and
[commits](https://github.com/genetics-statistics/GEMMA/commits/master).
### Speedup of GEMMA by using optimized OpenBlas
* Binary release with OpenBlas optimization for generic x86_64 and for Intel Haswell
* Dropped using standard lapack and gslcblas libs
* Fixed NaN bug with GSL2 and made recent libraries the default
* Minimized use of Eigenlib libraries (single threaded and slow compilation)
* -legacy switch provides v0.96 behaviour (incl. eigenlib)
### Added Leave One Chromosome Out (LOCO) support for Bimbam (K and LMM)
* See 449d882a3b33ef81ef4f0127c3932b01fa796dbb
* -snps [filename] option allow selecting a subset of SNPs for analysis
* -loco [chr] option for K and LMM computations
* added [gemma-wrapper](https://github.com/genetics-statistics/gemma-wrapper) to make using LOCO easy
* LOCO examples in https://github.com/genetics-statistics/GEMMA/blob/master/test/dev_test_suite.sh
### Added checks for matrices
* #72 and #45 implements
1. Fail if K has negative eigen values
2. Fail if K is not symmetric
3. Fail if K is not positive definite
4. Warn in eigen values are very small
5. Warn if K is ill conditioned
* Check for NaN values
### Added test framework and unit tests
* Added integration and unit tests, as well as
[Travis-CI](https://travis-ci.org/genenetwork/GEMMA) support
* Improved debug information and testing of input files
### Other
* #81 printing out beta and se(beta) under -lmm 2 as well as logl_H1
* Improved README and INSTALL docs
* Added support info and code of conduct
* Reformatted the full source tree with 3935ba39d30666dd7d4a831155631847c77b70c4
* Merged LMM computation for Plink and Bimbam formats
* Fixed progressbar issues
* #46 removed support for Oxford format
* Got rid of all compiler warnings
* Updated copyright banner, info and license information for included software
* Started a [discussion list](https://groups.google.com/forum/#!forum/gemma-discussion)
See also [commits](https://github.com/genetics-statistics/GEMMA/commits/master).
## GEMMA 0.96.0
+ First stable release.
## GEMMA 0.95.2
+ Resolved Issue #36.
## GEMMA 0.95.1
+ Created first release of GEMMA 0.95a following request in Issue #33.
## GEMMA 0.94.1
+ Fixed a bug (the predict option for multiple phenotype imputation
was not recoginzed with PLINK files).
## GEMMA 0.94.0
+ Implemented the multivariate linear mixed model.
## GEMMA 0.93
+ Implemented the Bayesian sparse linear mixed model.
## GEMMA 0.92
+ Fixed a few typos.
+ Now allows for missing values in the covariates file.
+ Included REMLE estimate for lambda in the output .log file.
+ Added small GWAS example dataset
+ Added detailed user manual.
## GEMMA 0.91
+ Fixed a bug (BIMBAM annotation file not recognized).
## GEMMA 0.90
+ Initial pre-release.
See also https://github.com/genetics-statistics/GEMMA/releases
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