pangemma - PanGEMMA: Genome-wide Efficient Mixed Model Association

Age	Commit message (Expand)	Author
2018-03-06	Added link to RCC workshop.	Peter Carbonetto
2017-10-05	Added simulated phenotypes for HLC....-n 1 2 3 13 are independent. The others depend on 3 and 13.	Pjotr Prins
2017-08-26	Tests and enforces added related to https://github.com/genetics-statistics/GE...	Pjotr Prins
2017-08-21	Added more detailed description of -widv option following Xiang's description...	Peter Carbonetto
2017-08-14	Issue 58, add tests for GSLv2 NaN's showing up with covariates...https://github.com/genetics-statistics/GEMMA/issues/58	Pjotr Prins
2017-08-03	LOCO 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
2017-07-09	Spacing in demo.txt	Pjotr Prins
2017-05-27	Removed src/Eigen; instead, Eigen C++ library is downloaded separately. See I...	Peter Carbonetto
2017-05-09	Putatively fixed -Wc++11-narrowing error in io.cpp (see Issue #24).	Peter Carbonetto
2014-10-07	version 0.95alpha	xiangzhou