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2025-12-09Allow skipping out of loop with LOCO HEAD masterPjotr Prins
2025-12-07Support loco for mdb kinship computePjotr Prins
2025-12-06LOCO support works for mdbPjotr Prins
2025-12-06Adding loco support for mdbPjotr Prins
2025-12-06For LOCO we wont use gwassnpsPjotr Prins
2025-12-05Output is on par with earlier gemma - only allele values are missingPjotr Prins
2025-12-05Rename to MarkerInfoPjotr Prins
2025-12-05Replace tuple with aggregatePjotr Prins
2025-12-05Compute maf againPjotr Prins
2025-12-04Output has same values as original!Pjotr Prins
2025-12-04Pass in markerinfoPjotr Prins
2025-12-04Unpack markerPjotr Prins
2025-12-03Pass in snp infoPjotr Prins
2025-12-02All SNPs computedPjotr Prins
2025-12-01Code loads markers - getting ready to computePjotr Prins
2025-12-01Copy function so I can modifyPjotr Prins
2025-12-01Wiring in mdb GWAPjotr Prins
2025-11-27Update copyrightsPjotr Prins
2025-11-27Minor tweaksPjotr Prins
2020-12-15No need to pass lambda by addressPjotr Prins
2018-02-28renamed import io.h to gemma_io.hDannyArends
2017-12-12Updated copyright infoPjotr Prins
2017-10-13Refactored debug settingsPjotr Prins
Replaced eigenlib_dgemm with fast_dgemm - 10-30% speed gain for GEMMA
2017-10-13Fixed mean and iterations in Plink - now this worksPjotr 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
2017-10-05Removed Oxford format as per ↵Pjotr Prins
https://github.com/genetics-statistics/GEMMA/issues/46
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
2017-06-07Removed FORCE_FLOAT from a few more files.Peter Carbonetto
2015-07-11add GXE testxiangzhou
2014-09-22version 0.95alphaxiangzhou
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