Merge pull request #63 from genenetwork/loco-formatted

LOCO is implemented in GEMMA for the BIMBAM format.

1 files changed, 5 insertions, 1 deletions

diff --git a/src/lmm.h b/src/lmm.h
index c393daf..4d57ab1 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -26,6 +26,8 @@
 
 using namespace std;
 
+#define LMM_BATCH_SIZE 10000 // used for batch processing
+
 class FUNC_PARAM {
 
 public:
@@ -78,6 +80,7 @@ public:
   vector<int> indicator_snp;
 
   vector<SNPINFO> snpInfo; // Record SNP information.
+  set<string> setGWASnps;  // Record SNP information.
 
   // Not included in PARAM.
   vector<SUMSTAT> sumStat; // Output SNPSummary Data.
@@ -97,7 +100,8 @@ public:
                    const gsl_matrix *W, const gsl_vector *y);
   void AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval,
                      const gsl_matrix *UtW, const gsl_vector *Uty,
-                     const gsl_matrix *W, const gsl_vector *y);
+                     const gsl_matrix *W, const gsl_vector *y,
+                     const set<string> gwasnps);
   void AnalyzePlinkGXE(const gsl_matrix *U, const gsl_vector *eval,
                        const gsl_matrix *UtW, const gsl_vector *Uty,
                        const gsl_matrix *W, const gsl_vector *y,