From 449d882a3b33ef81ef4f0127c3932b01fa796dbb Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 3 Aug 2017 10:26:52 +0000
Subject: 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
---
 src/vc.h | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'src/vc.h')

diff --git a/src/vc.h b/src/vc.h
index c6f66b4..49397bb 100644
--- a/src/vc.h
+++ b/src/vc.h
@@ -40,6 +40,8 @@ public:
   bool noconstrain;
 };
 
+// Methods for variant component (VC) estimation
+
 class VC {
 
 public:
-- 
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