Output has same values as original!

2 files changed, 24 insertions, 10 deletions

diff --git a/src/lmm.cpp b/src/lmm.cpp
index 1d3b8e0..d13ce3c 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1928,7 +1928,7 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     statistics (beta, standard errors, p-values) and stores results in
     sumStat.
   */
-  auto batch_compute = [&](size_t l) { // using a C++ closure
+  auto batch_compute = [&](size_t l, const Markers &markers) { // using a C++ closure
     // Compute SNPs in batch, note the computations are independent per SNP
     debug_msg("enter batch_compute");
     assert(l>0);
@@ -1986,8 +1986,9 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
 
       time_opt += (clock() - time_start) / (double(CLOCKS_PER_SEC) * 60.0);
 
+      auto markerinfo = markers[i];
       // Store summary data.
-      SUMSTAT2 st = {beta, se, lambda_remle, lambda_mle, p_wald, p_lrt, p_score, logl_H1};
+      SUMSTAT2 st = {markerinfo, beta, se, lambda_remle, lambda_mle, p_wald, p_lrt, p_score, logl_H1};
       sumstat2.push_back(st);
     }
   };
@@ -2001,6 +2002,7 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
   }
   */
   const size_t progress_step = (num_markers/50>d_pace ? num_markers/50 : d_pace);
+  Markers markers;
 
   assert(num_markers > 0);
   for (size_t t = 0; t < num_markers; ++t) {
@@ -2021,6 +2023,8 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     // auto mpos = get<3>(tup);
     auto markerinfo = get<1>(tup);
     auto gs = get<2>(tup);
+
+    markers.push_back(markerinfo);
     // cout << t << " SNP: " << snp << endl;
 
     // check whether SNP is included in gwasnps (used by LOCO)
@@ -2066,13 +2070,16 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     gsl_vector_safe_memcpy(&Xlarge_col.vector, x);
     c++; // count markers going in
 
+
     if (c % msize == 0) {
-      batch_compute(msize);
+      batch_compute(msize,markers);
+      markers.clear();
+      markers.reserve(msize);
     }
   }
 
   if (c % msize)
-    batch_compute(c % msize);
+    batch_compute(c % msize,markers);
   ProgressBar("Reading markers", num_markers - 1, num_markers - 1);
   cout << endl;
   cout << "Counted markers " << c << " sumStat " << sumstat2.size() << endl;
@@ -2092,8 +2099,14 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
 
   auto sumstats = [&] (SUMSTAT2 st) {
     outfile << scientific << setprecision(6);
-
-    // outfile << st.marker << "\t";
+    auto tup = st.markerinfo;
+    auto name = get<0>(tup);
+    auto chr = get<1>(tup);
+    auto pos = get<2>(tup);
+
+    outfile << chr << "\t";
+    outfile << name << "\t";
+    outfile << pos << "\t";
     if (a_mode != M_LMM2) {
       outfile << st.beta << "\t";
       outfile << st.se << "\t";
diff --git a/src/lmm.h b/src/lmm.h
index c24872c..35064c7 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -45,9 +45,14 @@ public:
   size_t e_mode;
 };
 
+typedef tuple< string, uint16_t, uint32_t, uint32_t > MarkerChrPos;
+typedef vector<MarkerChrPos> Markers;
+typedef tuple< string,vector<double> > SnpNameValues;
+typedef tuple< bool,MarkerChrPos,vector<double> > SnpNameValues2;
 // Results for LMM.
 class SUMSTAT2 {
 public:
+  MarkerChrPos markerinfo;
   double beta;         // REML estimator for beta.
   double se;           // SE for beta.
   double lambda_remle; // REML estimator for lambda.
@@ -60,10 +65,6 @@ public:
                        // see https://github.com/genetics-statistics/GEMMA/issues/81
 };
 
-typedef tuple< string, uint16_t, uint32_t, uint32_t > MarkerChrPos;
-
-typedef tuple< string,vector<double> > SnpNameValues;
-typedef tuple< bool,MarkerChrPos,vector<double> > SnpNameValues2;
 
 class LMM {