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2018-02-28io.h is a std lib function for MinGW64, renamed it to gemma_io.hDannyArends
2017-12-17Reverted on using eigenlib_dgemm because of hanging K compute with datasetPjotr Prins
2017-12-17BimbamKin: show error when genotypes do not matchPjotr Prins
2017-12-12Updated copyright infoPjotr Prins
2017-12-06Some cleanup on matrix checkingPjotr Prins
2017-11-30Fixed never-ending run when analyzing only a single SNP, refPjotr Prins
https://groups.google.com/forum/#!topic/gemma-discussion/a-ommTiucC8
2017-11-22Remove compiler warnings and add check is_nanPjotr Prins
2017-11-09Adding tests for bslmmPjotr Prins
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
2017-10-18Tests still pass with safe_alloc (which sets the buffers to NaNs on allocation)Pjotr Prins
2017-10-14More disabling of eigenlib (faster compilation) and avoid OPENBLAS_CONST ↵Pjotr Prins
which does not work on older cblas.h
2017-10-13Refactored debug settingsPjotr Prins
Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
2017-10-13Fixed mean and iterations in Plink - now this worksPjotr Prins
2017-10-13Consolidate into ProgressBar into one function and related updatesPjotr Prins
2017-10-13Change ulong type to long.Peter Carbonetto
2017-10-05Removed Oxford format as per ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/46
2017-10-05Adding debug statements on entering functions and added test for issue 58Pjotr Prins
2017-10-05Added a few checks and infoPjotr Prins
2017-08-27-aPjotr Prins
ReadFile_geno: stop warnings after 10x
2017-08-26Debug: only output check on -debugPjotr Prins
2017-08-26Tests and enforces added related to ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/78
2017-08-20Added checks for KPjotr Prins
2017-08-15Fixes output file with kinship has extra columnPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/14
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
2017-08-02Massive patch using LLVM coding style. It was generated with:Pjotr Prins
clang-format -style=LLVM -i *.cpp *.h Please set your editor to replace tabs with spaces and use indentation of 2 spaces.
2017-07-07Some three compile time fixes for the GNU GCC 7.1.0 compiler on Linux.Pjotr Prins
This patch is a mess because we use different line endings. I propose to convert to standard Unix mode (as was the original GEMMA code). To convert with vim one can use set fileformat=unix Do not merge this pull request, we can handle te fixes later.
2017-07-04Removed FORCE_FLOAT from io.cpp.Peter Carbonetto
2017-06-19Removed FORCE_FLOAT from param.cpp.Peter Carbonetto
2017-05-31Removed WITH_LAPACK compile/build option.Peter Carbonetto
2017-05-31Removing FORCE_FLOAT from some more C++ source files.Peter Carbonetto
2017-05-09Putatively fixed -Wc++11-narrowing error in io.cpp (see Issue #24).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.
2017-05-04Local updates made by Xiang---shared via email on May 4, 2017, subject: ↵Peter Carbonetto
gemma on expression data.
2017-05-04Fixed problems with duplicate symbols in io.o, lmm.o, param.o and vc.o; ↵Peter Carbonetto
created a Makefile for Mac OS X (tested on 10.11, i.e., El Capitan).
2016-05-23version 0.95alphaxiangzhou
2015-07-11add GxE testxiangzhou
2015-07-11add GXE testxiangzhou
2014-10-30version 0.95alphaxiangzhou
2014-09-22version 0.95alphaxiangzhou
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 03:32:15 +0000