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2020-05-22Fixes for gcc (GCC) 10.1.0Pjotr Prins
Started to remove eigenlib (again)
2018-12-10Fixes regression introduced by sharing plink algorithm with BIMBAM.Pjotr Prins
closes #188
2018-09-15Remove noisy batch_compute messagePjotr Prins
2018-09-06Sometimes a value gets negative zero causing a NaN on the sqrt.Pjotr Prins
Closes #61
2018-09-06More debugging and a performance checkPjotr Prins
2018-09-06More debugging info and raise SIGINT instead of exitPjotr Prins
2018-09-06Further debuggingPjotr Prins
2018-09-01CalcPab notesPjotr Prins
2018-08-31More testingPjotr Prins
2018-08-31Improving readabilityPjotr Prins
2018-08-31Continue debugging calcpabPjotr Prins
2018-08-30Debugging calcPabPjotr Prins
2018-08-26More value checking and bounds checkingPjotr Prins
2018-08-25Number format checking in strict mode. Also fixes #149Pjotr Prins
2018-08-25segfpe handlingPjotr Prins
2018-06-29Merge branch 'master' of github.com:genetics-statistics/GEMMAPjotr Prins
2018-02-28renamed import io.h to gemma_io.hDannyArends
2018-01-27Extra error info on strtok parsing failure - should help supportPjotr Prins
2017-12-12Updated copyright infoPjotr Prins
2017-12-08Legacy mode does not show logl_H1 column in outputPjotr 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
2017-11-15Nans: introducing checking on mem freePjotr Prins
2017-11-11Fix compiler warningsPjotr Prins
2017-10-26Get rid of compiler warningPjotr 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
2017-10-13Replacing first dgemm - tests failPjotr Prins
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
2017-10-13Fix header for not showing sePjotr Prins
2017-10-13Disable se for lmm=2, see https://github.com/genetics-statistics/GEMMA/issues/81Pjotr Prins
2017-10-13Fixed mean and iterations in Plink - now this worksPjotr Prins
2017-10-13Fix embarrassing bug that broke BIMBAM for larger datasets - found it when ↵Pjotr Prins
porting Plink to the new Analyze function
2017-10-06LMM: small cleanup and default to NaN initializationPjotr Prins
2017-10-06LMM: BIMBAM and PLINK share same LMM code - test passPjotr Prins
2017-10-06LMM: lifter genotype parsing for BIMBAM. All tests pass.Pjotr Prins
2017-10-06LMM: lifter line noPjotr Prins
2017-10-06LMM: lifted out file accessPjotr Prins
2017-10-06Oops: fixed logic problem after removing Oxford dataPjotr Prins
2017-10-05Removed Oxford format as per ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/46
2017-10-05LMM: skip beta (again) with LRTPjotr Prins
2017-10-05AddressesPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/81
2017-10-05Adding debug statements on entering functions and added test for issue 58Pjotr 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
2017-08-02Massive 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.
2017-07-07Fix spacingPjotr Prins
2017-06-08Removed commented-out code from gemma.cpp.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.
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