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

1 files changed, 15 insertions, 2 deletions

diff --git a/Makefile b/Makefile
index 268174f..33c1f2d 100644
--- a/Makefile
+++ b/Makefile
@@ -30,7 +30,13 @@ SRC_DIR  = ./src
 
 CPP = g++
 
-CPPFLAGS = -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
+ifdef DEBUG
+  # development mode
+  CPPFLAGS = -g -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
+else
+  # release
+  CPPFLAGS = -DNDEBUG -O3 -std=gnu++11 -isystem/$(EIGEN_INCLUDE_PATH)
+endif
 
 ifdef SHOW_COMPILER_WARNINGS
   CPPFLAGS += -Wall
@@ -106,12 +112,19 @@ $(OBJS) : $(HDR)
 	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
-check: all
+fast-check: all
+	cd test && ./dev_test_suite.sh | tee ../dev_test.log
+	grep -q 'success rate: 100%' dev_test.log
+
+slow-check: all
 	cd test && ./test_suite.sh | tee ../test.log
 	grep -q 'success rate: 100%' test.log
 
+check: fast-check slow-check
+
 clean:
 	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT)
+	rm test/output/*
 
 DIST_COMMON = COPYING.txt README.txt Makefile
 DIST_SUBDIRS = src doc example bin