aboutsummaryrefslogtreecommitdiff
path: root/src/param.cpp
AgeCommit message (Collapse)Author
2021-01-11Only free randomizer when initializedPjotr Prins
Fixes: #239
2020-12-16Fix checks for `-lmm 9` modePjotr Prins
2020-12-15Introduced `-lmm 9` switch for gemma to capture additive effect togetherPjotr Prins
without the log likelihood without adding computation time. See also #237 Closes #237
2020-11-28Sane random generator handlingPjotr Prins
2020-11-28Remove unused codePjotr Prins
2020-09-26Comments addedPjotr Prins
2020-05-22Fixes for gcc (GCC) 10.1.0Pjotr Prins
Started to remove eigenlib (again)
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
2018-08-31More testingPjotr Prins
2018-08-30Debugging calcPabPjotr Prins
2018-08-26More value checking and bounds checkingPjotr Prins
2018-06-05Typo: sepcified -> specifiedDylan Aïssi
2018-02-28renamed import io.h to gemma_io.hDannyArends
2017-12-12Updated copyright infoPjotr Prins
2017-11-11Cleaning up buffer use thanks to compiler warningsPjotr Prins
2017-11-10Remove compiler warningsPjotr Prins
2017-11-10Tests: added more bslmm testsPjotr Prins
2017-11-09Adding tests for bslmmPjotr Prins
2017-10-26Changed SNPs into SNPs/var in output, ref ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/107#issuecomment-339475978
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
2017-10-13Refactored debug settingsPjotr Prins
Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
2017-10-13Consolidate into ProgressBar into one function and related updatesPjotr Prins
2017-10-05Removed Oxford format as per ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/46
2017-08-28param.cpp: Set error on errorPjotr Prins
2017-08-26Debug: only output check on -debugPjotr Prins
2017-08-22Fix typo intecept -> interceptPjotr 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.
2017-07-07Fix spacingPjotr Prins
2017-06-19Removed FORCE_FLOAT from param.cpp.Peter Carbonetto
2017-06-08Removed commented-out code from gemma.cpp.Peter Carbonetto
2017-05-31Removed WITH_LAPACK compile/build option.Peter Carbonetto
2017-05-30Removing FORCE_FLOAT from some C++ source files.Peter Carbonetto
2017-05-04Local updates made by Xiang---shared via email on May 4, 2017, subject: ↵Peter Carbonetto
gemma on expression data.
2016-05-23version 0.95alphaxiangzhou
2015-07-11add GxE testxiangzhou
2015-07-11add GXE testxiangzhou
2014-09-22version 0.95alphaxiangzhou
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 05:07:37 +0000