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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
2017-10-13Progressbar updatePjotr Prins
2017-10-13Consolidate into ProgressBar into one function and related updatesPjotr Prins
2017-10-13Fix embarrassing bug that broke BIMBAM for larger datasets - found it when ↵Pjotr Prins
porting Plink to the new Analyze function
2017-10-13debug message: minor changePjotr Prins
2017-10-13Bumped up version.Peter Carbonetto
2017-10-13Change ulong type to long.Peter Carbonetto
2017-10-13Fixed warning with assignment in if statement.Peter Carbonetto
2017-10-13Make sure __ASSERT_VOID_CAST worksPjotr Prins
2017-10-13Removing warnings on debug.h assignmentPjotr Prins
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
2017-10-05Added a few checks and infoPjotr Prins
2017-09-14Merge pull request #85 from prasunanand/gsl_version_patchPjotr Prins
check GSL_MINOR_VERSION while compiling
2017-09-14check GSL_MINOR_VERSION while compilingprasun
2017-09-12Show GSL and Eigen versions in .log outputPjotr Prins
2017-08-28param.cpp: Set error on errorPjotr Prins
2017-08-27-aPjotr Prins
ReadFile_geno: stop warnings after 10x
2017-08-27Removed large sections of commented out codePjotr Prins
2017-08-26LULndet: remove bad enforcePjotr Prins
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
2017-08-22Fix typo intecept -> interceptPjotr Prins
2017-08-22EigenDecomp: also show warning on multiple zero valuesPjotr 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
2017-08-13Fixes https://github.com/genetics-statistics/GEMMA/issues/64Pjotr Prins
debug.h: replaced assert_fail with enforce_fail
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
2017-08-02Added section on contributing and coding style and fixed compilationPjotr Prins
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
2017-07-21Removed some more commented-out code from mvlmm.cpp.Peter Carbonetto
2017-07-19Removed some commented out code from mvlmm.cpp.Peter Carbonetto
2017-07-07Merge pull request #51 from genenetwork/spacingPeter Carbonetto
Spacing fixes.
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