trace summary (ge_hetro_flexible.cpp only)

src/ge_hetro_flexible.cpp

@@ -1889,18 +1889,23 @@ int main(int argc, char const *argv[]){
                 outfile << "\t-v (verbose) " << std::to_string(command_line_opts.verbose) << endl;
         }
         if (trace)
-                outfile << "\t-tr (trace summaries) " << endl;
+                outfile << "\t-tr (trace summaries for G only;; if pheno is not specified, dummy phenotype is used) " << endl;
 
         outfile << endl;
         outfile << endl;
 
         if (trace){
-            string trpath=prefix + ".trace";
+            string trpath=prefix + ".tr";
             string mnpath=prefix + ".MN";
             trace_file.open(trpath.c_str(), std::ios_base::out);
-            trace_file << "TRACE,NSNPS_JACKKNIFE" << endl;
+            stringstream ss;
+            for (int i=0; i<Nbin; i++){
+                ss << "LD_SUM_" << i << ",";
+            }
+            ss << "NSNPS_JACKKNIFE";
+            trace_file << ss.str() << endl;
             meta_file.open(mnpath.c_str(), std::ios_base::out);
-            meta_file << "NSAMPLE,NSNP,NBLK,NBIN" << endl << Nindv << "," << Nsnp << "," << Njack << "," << Nbin;
+            meta_file << "NSAMPLE,NSNPS,NBLKS,NBINS,K" << endl << Nindv << "," << Nsnp << "," << Njack << "," << Nbin << "," << Nz;
             meta_file.close();
         }
 
@@ -1992,16 +1997,22 @@ int main(int argc, char const *argv[]){
                 Y_r<<c_yky,yy;
 
                 if (trace){
-                    trace_file << X_l.block(0, 0, Nbin, Nbin);
                     if (jack_index < Njack){
-                        for (int j=0; j< Nbin; j++) // TODO: is this the right way to count SNPs in the jn block for partitioned heritability?
-                            trace_file << "," <<  Nsnp_annot - jack_bin[jack_index][j];
-                        trace_file << endl;
+                        for (int i=0; i< Nbin; i++){
+                                for (int j=0; j < Nbin; j++){
+                                        trace_file << (X_l(i, j) - Nindv_mask) * (len[i] - jack_bin[jack_index][i])*(len[j] - jack_bin[jack_index][j])/pow(Nindv_mask, 2)
+                                        << ",";
+                                }
+                                trace_file << len[i] - jack_bin[jack_index][i] << endl;
+                        }
                     }
                     else{
-                        for (int j=0; j< Nbin; j++)
-                            trace_file << "," << len[j];
-                        trace_file << endl;
+                        for (int i=0; i< Nbin; i++){
+                                for (int j=0; j < Nbin; j++){
+                                        trace_file << (X_l(i, j) - Nindv_mask) * len[i]*len[j]/pow(Nindv_mask,2) << ",";
+                                }
+                                trace_file << len[i] << endl;
+                        }
 
                     }
                 }