Age | Commit message (Expand) | Author |
2017-08-14 | Issue 58, add tests for GSLv2 NaN's showing up with covariates...https://github.com/genetics-statistics/GEMMA/issues/58
| Pjotr Prins |
2017-08-03 | LOCO is implemented in GEMMA for the BIMBAM format. Pass in the -loco...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
| Pjotr Prins |
2017-08-02 | Reformatted gemma calls in test_suite.sh. | Peter Carbonetto |
2017-07-26 | test_suite: run shunit2 from system when available | Pjotr Prins |
2017-07-26 | test_suite: replace awk with perl to compute file contents and default to shu...... fixes https://github.com/genetics-statistics/GEMMA/issues/55
| Pjotr Prins |
2017-07-26 | Added a line count test for K | Pjotr Prins |
2017-07-26 | github: fix links to gemma repo | Pjotr Prins |
2017-07-18 | Moved shunit2 files to test directory. | Peter Carbonetto |
2017-07-18 | Fixed failing test. New test report summary:...tests passed: 13
tests failed: 0
tests total: 13
success rate: 100%
| Peter Carbonetto |
2017-07-16 | sunit2: added instructions | Pjotr Prins |
2017-07-09 | Makefile: force unit tests to throw a make error on less than 100% success | Pjotr Prins |
2017-07-09 | Tests: more tests | Pjotr Prins |
2017-07-09 | Tests: added test for univariate and multivariate LMM...Also added 'make check' command in Makefile and documented in INSTALL.md
| Pjotr Prins |
2017-07-09 | Test: check result | Pjotr Prins |
2017-07-09 | Add test framework based on shunit2 | Pjotr Prins |