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, 46 insertions, 0 deletions

diff --git a/src/debug.h b/src/debug.h
new file mode 100644
index 0000000..84637e1
--- /dev/null
+++ b/src/debug.h
@@ -0,0 +1,46 @@
+#ifndef __DEBUG_H__
+#define __DEBUG_H__
+
+// enforce works like assert but also when NDEBUG is set (i.e., it
+// always works). enforce_msg prints message instead of expr
+
+#if defined NDEBUG
+#define debug_msg(msg)
+#else
+#define debug_msg(msg) cout << "**** DEBUG: " << msg << endl;
+#endif
+
+/* This prints an "Assertion failed" message and aborts.  */
+extern "C" void __assert_fail(const char *__assertion, const char *__file,
+                              unsigned int __line,
+                              const char *__function) __THROW
+    __attribute__((__noreturn__));
+
+#define __ASSERT_FUNCTION __PRETTY_FUNCTION__
+
+#define enforce(expr)                                                          \
+  ((expr)                                                                      \
+       ? __ASSERT_VOID_CAST(0)                                                 \
+       : __assert_fail(__STRING(expr), __FILE__, __LINE__, __ASSERT_FUNCTION))
+
+#define enforce_msg(expr, msg)                                                 \
+  ((expr) ? __ASSERT_VOID_CAST(0)                                              \
+          : __assert_fail(msg, __FILE__, __LINE__, __ASSERT_FUNCTION))
+
+#define enforce_str(expr, msg)                                                 \
+  ((expr)                                                                      \
+       ? __ASSERT_VOID_CAST(0)                                                 \
+       : __assert_fail((msg).c_str(), __FILE__, __LINE__, __ASSERT_FUNCTION))
+
+// Helpers to create a unique varname per MACRO
+#define COMBINE1(X, Y) X##Y
+#define COMBINE(X, Y) COMBINE1(X, Y)
+
+#define enforce_gsl(expr)                                                      \
+  auto COMBINE(res, __LINE__) = (expr);                                        \
+  (COMBINE(res, __LINE__) == 0                                                 \
+       ? __ASSERT_VOID_CAST(0)                                                 \
+       : __assert_fail(gsl_strerror(COMBINE(res, __LINE__)), __FILE__,         \
+                       __LINE__, __ASSERT_FUNCTION))
+
+#endif