fix firth regression

zhanxw · Apr 2, 2015 · 622bf3d · 622bf3d
1 parent d2f8a38
commit 622bf3d
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Showing 4 changed files with 11 additions and 5 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,7 @@
+2015-04-02  Xiaowei Zhan  <zhanxw@dumbo.csgstat.sph.umich.edu>
+
+	* Fix output formats for Firth regression
+
 2015-04-01  Xiaowei Zhan  <zhanxw@fantasia.csgstat.sph.umich.edu>
 
 	* Fix bug when dealing binary phenotypes

diff --git a/README.md b/README.md
@@ -47,7 +47,7 @@ Rvtests, which stands for Rare Variant tests, is a flexible software package for
 # Download
 
 Source files can be downloaded from [github](https://github.com/zhanxw/rvtests/archive/master.zip) or [github page](https://github.com/zhanxw/rvtests).
-Executable binary files (for Linux 64bit) can be downloaded from [here](https://github.com/zhanxw/rvtests/releases/download/v1.9.0/rvtests-20150401.tar.gz).
+Executable binary files (for Linux 64bit) can be downloaded from [here](https://github.com/zhanxw/rvtests/releases/download/v1.9.1/rvtests-20150402.tar.gz).
 
 
 # Quick tutorial

diff --git a/src/Main.cpp b/src/Main.cpp
@@ -28,7 +28,7 @@
 
 Logger* logger = NULL;
 
-const char* VERSION = "20150401";
+const char* VERSION = "20150402";
 
 void banner(FILE* fp) {
   const char* string =

diff --git a/src/Model.h b/src/Model.h
@@ -211,19 +211,18 @@ class SingleVariantFirthTest : public ModelFitter {
   }
   // write model output
   void writeOutput(FileWriter* fp, const Result& siteInfo) {
-    siteInfo.writeValueTab(fp);
-
     // skip interecept (column 0)
     for (int i = 1; i < this->X.cols; ++i) {
+      siteInfo.writeValueTab(fp);
       result.clearValue();
       result.updateValue("Test", this->X.GetColumnLabel(i));
       if (fitOK) {
         result.updateValue("Beta", firth.GetCovEst()[i]);
         result.updateValue("SE", sqrt(firth.GetCovB()[i][i]));
         result.updateValue("Pvalue", firth.GetAsyPvalue()[i]);
       }
+      result.writeValueLine(fp);      
     }
-    result.writeValueLine(fp);
   }
 
  private:
@@ -3652,9 +3651,12 @@ class MetaCovTest : public ModelFitter {
         }
       }
     } else {
+#if 0
+      //// allow binary traits
       /// for binary, no need to center. and not support family.
       fprintf(stderr, "Not supported mode!\n");
       abort();
+#endif
     }
     fitOK = true;
     return (fitOK ? 0 : -1);