Pass in snp info

2 files changed, 18 insertions, 16 deletions

diff --git a/src/lmm.cpp b/src/lmm.cpp
index da3e100..0a5d8e6 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -2014,8 +2014,10 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     auto success = get<0>(tup);
     if (!success)
       continue;
-    auto snp = get<1>(tup);
-    auto gs = 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;
 
     // check whether SNP is included in gwasnps (used by LOCO)
@@ -2025,7 +2027,7 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
     */
     // drop missing idv and plug mean values for missing geno
     double x_total = 0.0; // sum genotype values to compute x_mean
-    uint pos = 0;         // position in target vector
+    uint vpos = 0;         // position in target vector
     uint n_miss = 0;
     gsl_vector_set_zero(x_miss);
     for (size_t i = 0; i < ni_total; ++i) {
@@ -2035,15 +2037,15 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
 
       double geno = gs[i];
       if (isnan(geno)) {
-        gsl_vector_set(x_miss, pos, 1.0);
+        gsl_vector_set(x_miss, vpos, 1.0);
         n_miss++;
       } else {
-        gsl_vector_set(x, pos, geno);
+        gsl_vector_set(x, vpos, geno);
         x_total += geno;
       }
-      pos++;
+      vpos++;
     }
-    enforce(pos == ni_test);
+    enforce(vpos == ni_test);
 
     const double x_mean = x_total/(double)(ni_test - n_miss);
 
@@ -2068,9 +2070,9 @@ void LMM::mdb_analyze(std::function< SnpNameValues2(size_t) >& fetch_snp,
 
   if (c % msize)
     batch_compute(c % msize);
-  ProgressBar("Reading SNPS", num_markers - 1, num_markers - 1);
+  ProgressBar("Reading markers", num_markers - 1, num_markers - 1);
   cout << endl;
-  cout << "Counted SNPs " << c << " sumStat " << sumStat.size() << endl;
+  cout << "Counted markers " << c << " sumStat " << sumStat.size() << endl;
   checkpoint_nofile("end-lmm-mdb-analyze");
 
   gsl_vector_safe_free(x);
@@ -2142,6 +2144,8 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval,
     mdb_fetch = MDB_NEXT;
 
     string marker;
+    uint8_t chr;
+    size_t pos;
     vector<double> gs;
 
     if (success) {
@@ -2154,12 +2158,9 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval,
         throw std::runtime_error("Invalid key size");
       }
       const uint8_t* data = reinterpret_cast<const uint8_t*>(key.data());
-
-      // Extract signed char
-      auto chr = static_cast<uint8_t>(data[0]);
-
+      chr = static_cast<uint8_t>(data[0]);
       // Extract big-endian uint32 manually
-      auto pos = (static_cast<uint32_t>(data[1]) << 24) |
+      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]));
@@ -2176,7 +2177,7 @@ void LMM::mdb_calc_gwa(const gsl_matrix *U, const gsl_vector *eval,
       }
       // cout << "!!!!" << size << snp << ": " << gs[0] << "," << gs[1] << "," << gs[2] << "," << gs[3] << endl;
     }
-    return make_tuple(success, marker, gs);
+    return make_tuple(success, chr, pos, marker, gs);
   };
   LMM::mdb_analyze(fetch_snp,U,eval,UtW,Uty,W,y,gwasnps,num_markers);
 }
diff --git a/src/lmm.h b/src/lmm.h
index 75ed6de..65d37b2 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -27,6 +27,7 @@
 #include "param.h"
 #include <functional>
 #include <tuple>
+#include <cstdint>
 
 using namespace std;
 
@@ -45,7 +46,7 @@ public:
 };
 
 typedef tuple< string,vector<double> > SnpNameValues;
-typedef tuple< bool,string,vector<double> > SnpNameValues2;
+typedef tuple< bool,uint8_t,size_t,string,vector<double> > SnpNameValues2;
 
 class LMM {