[Genabel-commits] r966 - in pkg/ProbABEL: doc src

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

Author: lckarssen
Date: 2012-10-03 23:40:10 +0200 (Wed, 03 Oct 2012)
New Revision: 966

Modified:
   pkg/ProbABEL/doc/CHANGES.LOG
   pkg/ProbABEL/src/data.h
Log:
Fixed bug #1186: Wrong error message in ProbABEL when .map file missing. Thanks to Nicola Pirastu for reporting this.

Also updated CHANGES.LOG to reflect this as well as the previous bugfix.


Modified: pkg/ProbABEL/doc/CHANGES.LOG
===================================================================
--- pkg/ProbABEL/doc/CHANGES.LOG	2012-10-03 21:18:26 UTC (rev 965)
+++ pkg/ProbABEL/doc/CHANGES.LOG	2012-10-03 21:40:10 UTC (rev 966)
@@ -1,10 +1,21 @@
 *****
+* Fix bug #1186: When .map file is missing (but --map option was
+  given), the wrong error message was displayed. Thanks to Nicola
+  Pirastu for reporting this bug.
+
+* Fix bug #2295: the inverse variance-covariance matrix (used with the
+  --mmscore option) was incorrectly subsetted when NAs are present for
+  one or more SNP dosages. As a result the invvarmatrix that was
+  actually used in the regression contained rows and columns of
+  zeroes. Thanks to Maarten Kooyman for reporting this bug.
+
 * Update of the probabel.pl script and probabel_config.cfg.
   The .cfg file now accepts the chr separator in multiple locations in the path
   (thanks to Marijn Verkerk).
   probabel.pl can now also run Y chromosome analysis and the help
   message has been updated.
 
+
 ***** v.0.2.0 (2012.06.10)
 * The v.0.1-9e fix for working with prob files in pacoxph has been
   forward-ported to this branch as well (Lennart and Yurii).

Modified: pkg/ProbABEL/src/data.h
===================================================================
--- pkg/ProbABEL/src/data.h	2012-10-03 21:18:26 UTC (rev 965)
+++ pkg/ProbABEL/src/data.h	2012-10-03 21:40:10 UTC (rev 966)
@@ -882,7 +882,7 @@
 	}
 	else
 	{
-	    std::cerr << "mlinfo: cannot open file " << filename << endl;
+	    std::cerr << "mlinfo: cannot open info file " << filename << endl;
 	    exit(1);
 	}
 	infile.close();
@@ -905,7 +905,7 @@
 
 	infile.open(filename);
 	if(!infile) { // file couldn't be opened
-	    std::cerr << "mlinfo: cannot open file " << filename << endl;
+	    std::cerr << "mlinfo: cannot open info file " << filename << endl;
 	    exit(1);
 	}
 	/* Read the header and discard it */
@@ -938,7 +938,7 @@
 	    char line [BFS], tmp[BFS];
 	    if (!instr.is_open())
 	    {
-		std::cerr << "mlinfo: cannot open file " << mapname << endl;
+		std::cerr << "mlinfo: cannot open map file " << mapname << endl;
 		exit(1);
 	    }
 	    instr.getline(line, BFS);