From 449d882a3b33ef81ef4f0127c3932b01fa796dbb Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 3 Aug 2017 10:26:52 +0000 Subject: 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 --- README.md | 10 ---------- 1 file changed, 10 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 14f5968..9a51770 100644 --- a/README.md +++ b/README.md @@ -191,16 +191,6 @@ last tested using Eigen version 3.3.3.) More information on source code, dependencies and installation can be found in [INSTALL.md](INSTALL.md). -## Contributing - -GEMMA uses the [LLVM style](http://llvm.org/docs/CodingStandards.html) -for C++ code. You should set your editor to replace tabs with spaces -and 2 spaces of indentation. Use - - clang-format -style=LLVM -i *.cpp *.h - -to validate the coding style. - ## Credits The *GEMMA* software was developed by: -- cgit v1.2.3