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2021-08-02* Changed banner to show Copyright (C) 2012–2021, Xiang Zhou, Pjotr Prins ↵Pjotr Prins
and team
2021-01-11Update debian badgePjotr Prins
2021-01-11Travis move and version bumpPjotr Prins
2020-12-13Note on ARM buildsPjotr Prins
2020-11-29Updating README and manualPjotr Prins
2020-11-29README and RELEASE-NOTESPjotr Prins
2020-09-29Fixes OSX build on Travis-CIPjotr Prins
Fixes #160
2018-10-14README: badgesPjotr Prins
2018-09-28READMEPjotr Prins
2018-09-27Using -no-check by default nowPjotr Prins
2018-09-15README: updatePjotr Prins
2018-06-29Fix conflictPjotr Prins
2018-05-02doc: data-mungingPjotr Prins
2018-03-06Added link to RCC workshop.Peter Carbonetto
2017-12-19Merge branch 'master' of github.com:genetics-statistics/GEMMAPjotr Prins
2017-12-18READMEPjotr Prins
2017-12-12README: License info for gzstreamPjotr Prins
2017-10-27Added Google Groups link to README.Peter Carbonetto
2017-10-26README: Windows notePjotr Prins
2017-10-26README: small editsPjotr Prins
2017-10-26README: added mailing list and updated textPjotr Prins
2017-10-20README: added section on reporting bugs and code of conductPjotr Prins
2017-10-14README: clearer hintPjotr Prins
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
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
2017-08-03LOCO 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
2017-08-02Added section on contributing and coding style and fixed compilationPjotr Prins
2017-07-27Added note about GSL version in installation instructions.Peter Carbonetto
2017-07-26Fixed link in README.Peter Carbonetto
2017-07-26github: fix links to gemma repoPjotr Prins
2017-07-21Added note in README about LGPL license for shuint2.Peter Carbonetto
2017-07-12Update README.mdxiangzhou
2017-07-08README: some links to INSTALL.mdPjotr Prins
2017-07-08Install docPjotr Prins
2017-07-07Merge pull request #51 from genenetwork/spacingPeter Carbonetto
Spacing fixes.
2017-07-07Bumped up version; added Pjotr to README.Peter Carbonetto
2017-07-07Fix spacingPjotr Prins
2017-05-27Removed src/Eigen; instead, Eigen C++ library is downloaded separately. See ↵Peter Carbonetto
Issue #42 for tests performed.
2017-05-26A few improvements to README.Peter Carbonetto
2017-05-26Added What's Included section to README.Peter Carbonetto
2017-05-25A few more small adjustments to installation instructions in README.Peter Carbonetto
2017-05-25A couple small adjustments to README.Peter Carbonetto
2017-05-25Instructions for using precompiled binaries.Peter Carbonetto
2017-05-25Added ref. to latest stable release.Peter Carbonetto
2017-05-25Revised overview of setup.Peter Carbonetto
2017-05-25Added note about Windows support.Peter Carbonetto
2017-05-24Added some notes to README.Peter Carbonetto
2017-05-24Added link to NEWS from READMEPeter Carbonetto
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