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2017-12-19Make eigelib -legacyPjotr Prins
2017-12-18lapack is part of OpenBlasPjotr Prins
2017-12-18Getting ready for release. Defaulting to OpenBlasPjotr Prins
2017-12-06Integer overflow checking for matrix dgemm and adding path for OpenBlas ↵Pjotr Prins
include files
2017-11-11Cleaning up compiler warningsPjotr Prins
2017-11-09Tests: added bslmm testPjotr Prins
2017-11-09Makefiles: reorder, and use version support for macosPjotr Prins
2017-10-26VERSION now contains the GEMMA version number. A script generates a headerPjotr Prins
file named ./src/version.h. See Makefile for details.
2017-10-23Travis-ci:Pjotr Prins
- Disabled gcc-6 since we develop with later tools anyway - Turned the release test into a simple integration test - Adding MacOSX on Travis-ci Tests: Adding tests for Plink w. LOCO Safety: Introduce strtok_safe to get rid of segfaults
2017-10-14Travis: more fixesPjotr Prins
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
2017-10-13Bumped up version.Peter Carbonetto
2017-10-06Makefile: Some notes on test commandsPjotr Prins
2017-10-05AddressesPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/81
2017-08-27Makefile: clean up of the main Makefile and changed build instructionsPjotr Prins
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)
2017-08-26Rename unittests binary to unittests-gemmaPjotr Prins
2017-08-21Bumped up version.Peter Carbonetto
2017-08-20Support filesPjotr Prins
2017-08-14Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26Pjotr Prins
2017-08-13Adding travis-ci support for g++-4.9 and g++-6 on Linux. Tests pass.Pjotr Prins
2017-08-07Bumped up development version.Peter Carbonetto
2017-08-03LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -locoPjotr Prins
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
2017-07-11Makefile: add extra slash to support relative eigen pathsPjotr Prins
2017-07-11Makefile: silence compiler warnings for Eigen libsPjotr Prins
2017-07-11Makefile: compiler warnings optionalPjotr Prins
2017-07-11Makefile: compile without -Weffc++ as suggested by ↵Pjotr Prins
https://stackoverflow.com/questions/11496942/understanding-weffc#11529328 reduces warnings
2017-07-09Makefile: fix output on make checkPjotr Prins
2017-07-09Makefile: force unit tests to throw a make error on less than 100% successPjotr Prins
2017-07-09Run test_suite directly from MakefilePjotr Prins
2017-07-09Makefile: add OpenBLAS supportPjotr Prins
2017-07-09Tests: added test for univariate and multivariate LMMPjotr Prins
Also added 'make check' command in Makefile and documented in INSTALL.md
2017-07-07Bumped up version; added Pjotr to README.Peter Carbonetto
2017-07-07Makefile: find include files for Eigen3Pjotr Prins
2017-07-04Add NO_INTEL_COMPAT flag to Makefile.Efraim Flashner
2017-05-31Removed WITH_LAPACK compile/build option.Peter Carbonetto
2017-05-30Removing FORCE_FLOAT from some C++ source files.Peter Carbonetto
2017-05-28Removed FORCE_FLOAT option from Makefiles.Peter Carbonetto
2017-05-17Bumped up version.Peter Carbonetto
2017-05-09Bumped version to 0.95.2a.Peter Carbonetto
2017-05-09Added bin folder; added -Weffc++ flag to Makefile.Peter Carbonetto
2017-05-09Bumped version to 0.95.1.Peter Carbonetto
2017-05-04Fixed problems with duplicate symbols; now using static gsl libraries in ↵Peter Carbonetto
Makefile.osx so that others don't have to download it using Homebrew.
2015-07-11add GxE testxiangzhou
2014-10-30Merge branch 'master' into fix-make-clean-binsJoshua Randall
Conflicts: Makefile
2014-10-30Merge pull request #10 from wtsi-hgi/fix-dynamic-linking-lblasxiangzhou
Fixes dynamic compilation (fixes #9)
2014-10-30Adds $(OUTPUT) files to `make clean` targetJoshua Randall
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`
2014-10-30Fixes dynamic compilationJoshua Randall
Fixes dynamic compilation on systems where -lblas is required for symbols such as `dgemm_`
2014-10-30makes dist tar file not explode into ./Joshua C. Randall
2014-09-22version 0.95alphaxiangzhou
2014-09-20version 0.95alphaxiangzhou
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