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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 Fail if K has negative eigen values Fail if K is not symmetric Fail if K is not positive definite Warn in eigen values are very small 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. |
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