keys

1 files changed, 18 insertions, 15 deletions

diff --git a/src/lmm.cpp b/src/lmm.cpp
index 9a1d318..324e310 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1879,7 +1879,6 @@ void LMM::Analyze(std::function< SnpNameValues(size_t) >& fetch_snp,
 // Results for LMM.
 class SUMSTAT2 {
 public:
-  string marker;
   double beta;         // REML estimator for beta.
   double se;           // SE for beta.
   double lambda_remle; // REML estimator for lambda.
@@ -2004,8 +2003,7 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
       time_opt += (clock() - time_start) / (double(CLOCKS_PER_SEC) * 60.0);
 
       // Store summary data.
-      SUMSTAT2 st = {marker, beta,   se,    lambda_remle, lambda_mle,
-                      p_wald, p_lrt, p_score, logl_H1};
+      SUMSTAT2 st = {beta, se, lambda_remle, lambda_mle, p_wald, p_lrt, p_score, logl_H1};
       sumstat2.push_back(st);
     }
   };
@@ -2033,8 +2031,8 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     auto success = get<0>(tup);
     if (!success)
       continue;
-    auto marker = get<1>(tup);
-    auto chr = get<2>(tup);
+    // auto marker = get<1>(tup);
+    // auto chr = get<2>(tup);
     auto mpos = get<3>(tup);
     auto gs = get<4>(tup);
     // cout << t << " SNP: " << snp << endl;
@@ -2109,7 +2107,7 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
   auto sumstats = [&] (SUMSTAT2 st) {
     outfile << scientific << setprecision(6);
 
-    outfile << st.marker << "\t";
+    // outfile << st.marker << "\t";
     if (a_mode != M_LMM2) {
       outfile << st.beta << "\t";
       outfile << st.se << "\t";
@@ -2215,7 +2213,8 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval,
 
     string marker;
     uint8_t chr;
-    size_t pos;
+    uint64_t pos;
+    // size_t pos;
     vector<double> gs;
 
     if (success) {
@@ -2224,21 +2223,25 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval,
       const float* gsbuf = reinterpret_cast<const float*>(value.data());
 
       // unpack chr+pos from key
-      if (key.size() != 5) {
+      if (key.size() != 10) {
+        cerr << "key.size=" << key.size() << endl;
         throw std::runtime_error("Invalid key size");
       }
+      // "S>L>L>"
       const uint8_t* data = reinterpret_cast<const uint8_t*>(key.data());
-      chr = static_cast<uint8_t>(data[0]);
-      // Extract big-endian uint32 manually
-      pos = (static_cast<uint32_t>(data[1]) << 24) |
-        (static_cast<uint32_t>(data[2]) << 16) |
-        (static_cast<uint32_t>(data[3]) << 8)  |
-        (static_cast<uint32_t>(data[4]));
+      chr = static_cast<uint8_t>(data[1]);
+      // Extract big-endian uint32 manually abcd -> dcba
+      pos = (static_cast<uint32_t>(data[2]) << 24) |
+        (static_cast<uint32_t>(data[4]) << 8)  |
+        (static_cast<uint32_t>(data[3]) << 16) |
+        (static_cast<uint32_t>(data[5]));
+      auto pos2 = __builtin_bswap32(pos);
 
       string_view value2;
       marker_mdb.get(rtxn,key,value2);
       marker = string(value2);
-      // cout << static_cast<int>(chr) << ":" << pos << " " << marker << endl ;
+      // 1       rs13476251      174792257
+      cout << static_cast<int>(chr) << ":" << pos2 << "|" << pos << " " << marker << endl ;
 
       auto size = num_floats;
       gs.reserve(size);