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2018-09-18Added profiling and build instructionsPjotr Prins
2018-09-15Using Guix container to build with gcc and clangPjotr Prins
2018-09-15README: updatePjotr Prins
2018-09-07Matrices positive definite issuesPjotr Prins
2018-08-31Continue debugging calcpabPjotr Prins
2018-08-26More value checking and bounds checkingPjotr Prins
2018-07-14Guix: add more build information to the final binaryPjotr Prins
2018-07-14- Guix Makefile added RPATH...- Added performance metrics in ./test/performance Pjotr Prins
2018-07-14Guix: added GUIX flag to automate make settings. Added DAG of dependenciesPjotr Prins
2018-06-29Fix conflictPjotr Prins
2018-03-01Early morning extra fwd slash failure, fixed in this commitDannyArends
2018-03-01Trying to fix the -isystem/ failure of travisDannyArends
2018-02-28Makefile changes, to compile under windowsDannyArends
2018-02-28Windows compilation paths, and restructuring the -isystemDannyArends
2018-02-28OS detection, and version script generator selection via VGENDannyArends
2018-02-22Changed handling of version number so it does not modify every compilePjotr Prins
2017-12-19Documentation and Travis fixesPjotr Prins
2017-12-19Optimizing OpenBlasPjotr Prins
2017-12-19Use OpenBlas cblas interface by defaultPjotr Prins
2017-12-19Openblas not linkingPjotr Prins
2017-12-19MakefilePjotr Prins
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 inclu...Pjotr Prins
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 header...file named ./src/version.h. See Makefile for details. Pjotr Prins
2017-10-23Travis-ci:...- 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 Pjotr Prins
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
2017-10-05Addresses... https://github.com/genetics-statistics/GEMMA/issues/81 Pjotr Prins
2017-08-27Makefile: 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
2017-08-26Rename 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 -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
2017-07-11Makefile: 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 https://stackoverflow.com/...Pjotr Prins
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
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