genetics-statistics/GEMMA v0.97

GEMMA version 0.97

on GitHub

Second stable release. This is a bug fix release with many improvements.

Binary executable gemma.macosx was built on a MacBook Pro (3.5 Ghz Intel Core i7) with Mac OS X 10.12.6, gcc Apple LLVM version 8.1.0, Eigen 3.3.4 and statically linked against gsl 2.4 and zlib 1.2.11 (both installed using Homebrew).

For Linux, we recommend using the provided Guix installers gemma-git-gn2-0.97-*. See here for the installation instructions. Use the optimized haswell installer on Intel Haswell computers, otherwise use the generic installer.

We also provide a Linux binary executable gemma.linux.gz for those that prefer not to use the Guix installer. However, we recommend that all Linux users first try the Guix installer. It was built on a machine with CentOS 6.6, gcc 4.9.2 and Eigen 3.3.4 and statically linked against gsl 2.3, zlib 1.2.8 and OpenBLAS 0.2.18.

Speedup of GEMMA by using optimized OpenBlas

• Providing a binary release with OpenBlas optimization for Intel Haswell.
• Dropped using standard LAPACK and gslcblas libraries.
• Fixed NaN bug caused by GSL 2.x and made recent GSL libraries the default.
• Minimized use of Eigen libraries (which can slow compilation and matrix computation).
• -legacy switch provides v0.96 behaviour (including Eigen)

Added Leave One Chromosome Out (LOCO) support for Bimbam (K and LMM)

• See commit 449d882
• -snps [filename] option allows selecting a subset of SNPs for analysis.
• -loco [chr] option for K and LMM computations.
• Added gemma-wrapper to make using LOCO easy.
• LOCO examples

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 support.
• Improved debug information and testing of input files.

Other

• #81 printing out beta, se(beta) and logl_H1 under -lmm 2.
• Improved README and INSTALL docs.
• Added support info and code of conduct.
• Updated copyright banner, info and license information for included software.
• Reformatted the full source tree with commit 3935ba3
• Merged LMM computation for PLINK and BIMBAM formats.
• Fixed progress bar issues.
• #46 removed support for Oxford format.
• Got rid of all compiler warnings.
• Started a discussion list.