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path: root/src/gemma.cpp
AgeCommit message (Collapse)Author
2017-12-12Updated copyright infoPjotr Prins
2017-12-08Changed banner and behaviourPjotr Prins
2017-12-08Legacy mode does not show logl_H1 column in outputPjotr Prins
2017-11-22Remove compiler warningsPjotr Prins
2017-11-15Nans: introducing checking on mem freePjotr Prins
2017-10-26VERSION now contains the GEMMA version number. A script generates a headerPjotr Prins
file named ./src/version.h. See Makefile for details.
2017-10-26Changed SNPs into SNPs/var in output, ref ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/107#issuecomment-339475978
2017-10-18Tests still pass with safe_alloc (which sets the buffers to NaNs on allocation)Pjotr Prins
2017-10-14Travis: more fixesPjotr Prins
2017-10-14TravisPjotr Prins
2017-10-14OpenBlas infoPjotr 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
2017-10-13OpenBlas: preparing for dgemm usePjotr Prins
2017-10-13Progressbar updatePjotr Prins
2017-10-13Bumped up version.Peter Carbonetto
2017-10-06LMM: BIMBAM and PLINK share same LMM code - test passPjotr 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
2017-10-05Added a few checks and infoPjotr Prins
2017-09-12Show GSL and Eigen versions in .log outputPjotr Prins
2017-08-27Removed large sections of commented out codePjotr Prins
2017-08-22Fixes matrix checks - looking saner nowPjotr Prins
- 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)
2017-08-21Added more detailed description of -widv option following Xiang's ↵Peter Carbonetto
description given in Issue #59.
2017-08-21Bumped up version.Peter Carbonetto
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
2017-08-14Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26Pjotr Prins
2017-08-07Bumped up development version.Peter Carbonetto
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.
2017-07-27Updated version to 0.97.Peter Carbonetto
2017-07-07Merge pull request #51 from genenetwork/spacingPeter Carbonetto
Spacing fixes.
2017-07-07Bumped up version; added Pjotr to README.Peter Carbonetto
2017-07-07Fix spacingPjotr Prins
2017-06-08Removed commented-out code from gemma.cpp.Peter Carbonetto
2017-05-17Bumped up version.Peter Carbonetto
2017-05-09Bumped version to 0.95.2a.Peter Carbonetto
2017-05-09Bumped version to 0.95.1.Peter Carbonetto
2017-05-04Local updates made by Xiang---shared via email on May 4, 2017, subject: ↵Peter Carbonetto
gemma on expression data.
2016-08-17version 0.95alphaxiangzhou
2016-08-17version 0.95alphaxiangzhou
2016-07-24version 0.95alphaxiangzhou
2016-05-23version 0.95alphaxiangzhou
2016-05-23version 0.95alphaxiangzhou
2014-09-22version 0.95alphaxiangzhou
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 09:14:58 +0000