[Genabel-commits] r1214 - in pkg/ProbABEL: doc src

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-05-13 18:20:56 +0200 (Mon, 13 May 2013)
New Revision: 1214

Modified:
   pkg/ProbABEL/doc/ChangeLog
   pkg/ProbABEL/src/command_line_settings.cpp
   pkg/ProbABEL/src/command_line_settings.h
Log:
ProbABEL: Fix bug #2529: "ProbABEL doesn't warn when a required file is not
specified on the command line".
Now palinear/palogist/pacoxph print more informative error messages when -d/-i/-p options have not been specified. 

The copyright for this changes lies with the Erasmus MC, Rotterdam. 




Modified: pkg/ProbABEL/doc/ChangeLog
===================================================================
--- pkg/ProbABEL/doc/ChangeLog	2013-05-13 11:21:31 UTC (rev 1213)
+++ pkg/ProbABEL/doc/ChangeLog	2013-05-13 16:20:56 UTC (rev 1214)
@@ -4,6 +4,8 @@
 * Fixed bug #2598: The prepare_data.R script is mentioned in the manual,
   but not distributed in .deb or .tar.gz
 * Fixed bug #2772: palogist with mmscore crashes (memory issue)
+* Fixed bug #2529: ProbABEL doesn't warn when a required file is not
+  specified on the command line
 
 ***** v.0.3.0 (2013.01.01)
 * This is a major rewrite of several important parts of the ProbABEL

Modified: pkg/ProbABEL/src/command_line_settings.cpp
===================================================================
--- pkg/ProbABEL/src/command_line_settings.cpp	2013-05-13 11:21:31 UTC (rev 1213)
+++ pkg/ProbABEL/src/command_line_settings.cpp	2013-05-13 16:20:56 UTC (rev 1214)
@@ -227,7 +227,7 @@
             break;
 
         case '?':
-            print_usage(program_name, 1);
+            print_usage(program_name, 2);
         case -1:
             break;
         default:
@@ -248,13 +248,30 @@
          << "\n(C) Yurii Aulchenko, Lennart C. Karssen, Maksim Struchalin, "
          << "EMCR\n\n";
 #if EIGEN
-    cout << "Using EIGEN version "<<EIGEN_WORLD_VERSION
-         <<"."<<EIGEN_MAJOR_VERSION<<"."<<EIGEN_MINOR_VERSION
+    cout << "Using EIGEN version " << EIGEN_WORLD_VERSION
+         << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION
          << " for matrix operations\n";
 #endif
 
     if (neco[0] != 1 || neco[1] != 1 || neco[2] != 1)
     {
+        cerr << endl;
+        if (neco[0] != 1)
+        {
+            cerr << "Error: Missing required phenotype file (-p/--pheno option)"
+                 << endl;
+        }
+        if (neco[1] != 1)
+        {
+            cerr << "Error: Missing required info file (-i/--info option)"
+                 << endl;
+        }
+        if (neco[2] != 1)
+        {
+            cerr << "Error: Missing required genotype file (-d/--dose option)"
+                 << endl;
+        }
+        cerr << endl;
         print_usage(program_name, 1);
     }
 

Modified: pkg/ProbABEL/src/command_line_settings.h
===================================================================
--- pkg/ProbABEL/src/command_line_settings.h	2013-05-13 11:21:31 UTC (rev 1213)
+++ pkg/ProbABEL/src/command_line_settings.h	2013-05-13 16:20:56 UTC (rev 1214)
@@ -35,7 +35,7 @@
     int robust;
     string chrom;
     string sep;
-    int neco[3];
+    int neco[3];                /* Necessary command line options */
     bool iscox;
     int isFVF;
     int noutcomes;