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Fixes: #239
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Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
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https://github.com/genetics-statistics/GEMMA/issues/46
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https://github.com/genetics-statistics/GEMMA/issues/81
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- 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)
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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
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clang-format -style=LLVM -i *.cpp *.h
Please set your editor to replace tabs with spaces and use indentation of 2 spaces.
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Makefile.osx so that others don't have to download it using Homebrew.
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gemma on expression data.
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created a Makefile for Mac OS X (tested on 10.11, i.e., El Capitan).
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