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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
2017-10-05Added simulated phenotypes for HLC.Pjotr Prins
-n 1 2 3 13 are independent. The others depend on 3 and 13.
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
2017-09-12Merge pull request #83 from genenetwork/masterPjotr Prins
Show GSL and Eigen versions in .log output
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
2017-08-27Makefile: clean up of the main Makefile and changed build instructionsPjotr Prins
to align with normal build systems * Debug mode is now the default (use DEBUG= to disable) * Dynamic linking is now the default (use FORCE_STATIC=1 for static) * Removed references to 32-bit compilation (default is $arch)
2017-08-27Removed large sections of commented out codePjotr Prins
2017-08-27Merge pull request #79 from genenetwork/issue78Pjotr Prins
Issue78
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
2017-08-26Rename unittests binary to unittests-gemmaPjotr Prins
2017-08-22Merge pull request #76 from genenetwork/merge-checkKPeter Carbonetto
Fixes matrix checks---looking saner now.
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 explanation of "beta estimates" in log.txt outputs.Peter Carbonetto
2017-08-21Merge branch 'master' of github.com:xiangzhou/GEMMAPeter Carbonetto
2017-08-21Added more detailed description of -widv option following Xiang's ↵Peter Carbonetto
description given in Issue #59.
2017-08-21Bumped up version for Makefile.macosx.Peter Carbonetto
2017-08-21Bumped up version.Peter Carbonetto
2017-08-21Merge pull request #73 from genenetwork/merge-checkKPeter Carbonetto
Check K and added unit test framework.
2017-08-20Move shunit2 into ./contrib and add catch-1.8.7Pjotr Prins
2017-08-20Unit testsPjotr Prins
2017-08-20Support filesPjotr Prins
2017-08-20Added checks for KPjotr Prins
2017-08-15Merge pull request #70 from genenetwork/issue14Peter Carbonetto
Fixes output file with kinship has extra column.
2017-08-15Fixes output file with kinship has extra columnPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/14
2017-08-14Merge pull request #69 from genenetwork/issue58.Peter Carbonetto
Tests for https://github.com/genetics-statistics/GEMMA/issues/58.
2017-08-14Merge pull request #68 from genenetwork/issue26.Peter Carbonetto
Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26.
2017-08-14Issue 58, add tests for GSLv2 NaN's showing up with covariatesPjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/58
2017-08-14Tests and fixes https://github.com/genetics-statistics/GEMMA/issues/26Pjotr Prins
2017-08-13Merge pull request #67 from genenetwork/travisPeter Carbonetto
Travis.
2017-08-13Merge pull request #66 from genenetwork/issue64.Peter Carbonetto
Fixes https://github.com/genetics-statistics/GEMMA/issues/64.
2017-08-13Adding travis-ci support for g++-4.9 and g++-6 on Linux. Tests pass.Pjotr Prins
2017-08-13Fixes https://github.com/genetics-statistics/GEMMA/issues/64Pjotr Prins
debug.h: replaced assert_fail with enforce_fail
2017-08-07Bumped version in all Makefiles.Peter Carbonetto
2017-08-07Bumped up development version.Peter Carbonetto
2017-08-07Merge branch 'master' of github.com:genetics-statistics/GEMMAPeter Carbonetto
2017-08-07Merge pull request #63 from genenetwork/loco-formattedPeter Carbonetto
LOCO is implemented in GEMMA for the BIMBAM format.
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
2017-08-02Reformatted gemma calls in test_suite.sh.Peter Carbonetto
2017-08-02Merge pull request #62 from genenetwork/spacingPeter Carbonetto
Spacing and coding style.
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