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2024-08-17mvlmm: Dump the initial data.Artyom Bologov
2024-08-16gemma,lmm,mvlmm: Add data debug printing everywhere.Artyom Bologov
2021-08-25Disable debugging outputPjotr Prins
2021-08-16README.md...README Pjotr Prins
2018-09-28Fixes regression #179Pjotr Prins
2018-09-06Sometimes a value gets negative zero causing a NaN on the sqrt....Closes #61 Pjotr Prins
2018-09-06More debugging and a performance checkPjotr Prins
2018-09-06More debugging info and raise SIGINT instead of exitPjotr Prins
2018-08-31Improving readabilityPjotr Prins
2018-08-31Continue debugging calcpabPjotr Prins
2018-02-28renamed import io.h to gemma_io.hDannyArends
2017-12-07Travis: fixesPjotr Prins
2017-12-06Some cleanup on matrix checkingPjotr Prins
2017-11-22Remove compiler warningsPjotr 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
2017-10-13Refactored debug settings...Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA Pjotr Prins
2017-10-13Consolidate into ProgressBar into one function and related updatesPjotr Prins
2017-10-05Removed Oxford format as per https://github.com/genetics-statistics/GEMMA/iss...Pjotr Prins
2017-10-05Adding debug statements on entering functions and added test for issue 58Pjotr Prins
2017-08-22Fixes matrix checks - looking saner now...- Matrix checks as described in https://github.com/genetics-statistics/GEMMA/issues/72 - introduces -strict switch which will exit on certain conditions - zero small eigenvalues in EigenDecomp_Zeroed which also checks for negative values - commented out float versions of functions in lapack.cpp (pre-removal) - reverted on disabled regression tests (GEMMA shows its previous behaviour now) Pjotr Prins
2017-08-20Added checks for KPjotr Prins
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
2017-08-02Massive patch using LLVM coding style. It was generated with:... clang-format -style=LLVM -i *.cpp *.h Please set your editor to replace tabs with spaces and use indentation of 2 spaces. Pjotr Prins
2017-07-21Removed some more commented-out code from mvlmm.cpp.Peter Carbonetto
2017-07-19Removed some commented out code from mvlmm.cpp.Peter Carbonetto
2017-07-07Removed FORCE_FLOAT from mvlmm.cpp.Peter Carbonetto
2017-05-09fixed #36xiangzhou
2016-07-24version 0.95alphaxiangzhou
2016-05-23version 0.95alphaxiangzhou
2015-07-11add GXE testxiangzhou
2014-09-22version 0.95alphaxiangzhou
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