From b4dde6a78c6a3527dd7f80392e10b36ef1b2ca3d Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Thu, 27 Feb 2014 10:07:38 -0500 Subject: [PATCH 1/2] Add WARN to the valid log types error message - order if statements and error message in increasing severity --- .../sting/commandline/CommandLineProgram.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java index 8c7e11f35..8b1a390f4 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java @@ -277,19 +277,19 @@ public abstract class CommandLineProgram { Level par; if (logging_level.toUpperCase().equals("DEBUG")) { par = Level.DEBUG; - } else if (logging_level.toUpperCase().equals("ERROR")) { - par = Level.ERROR; - } else if (logging_level.toUpperCase().equals("FATAL")) { - par = Level.FATAL; } else if (logging_level.toUpperCase().equals("INFO")) { par = Level.INFO; } else if (logging_level.toUpperCase().equals("WARN")) { par = Level.WARN; + } else if (logging_level.toUpperCase().equals("ERROR")) { + par = Level.ERROR; + } else if (logging_level.toUpperCase().equals("FATAL")) { + par = Level.FATAL; } else if (logging_level.toUpperCase().equals("OFF")) { par = Level.OFF; } else { // we don't understand the logging level, let's get out of here - throw new ArgumentException("Unable to match: " + logging_level + " to a logging level, make sure it's a valid level (INFO, DEBUG, ERROR, FATAL, OFF)"); + throw new ArgumentException("Unable to match: " + logging_level + " to a logging level, make sure it's a valid level (DEBUG, INFO, WARN, ERROR, FATAL, OFF)"); } Logger.getRootLogger().setLevel(par); From 57747ad35e3154004ad6f27df5337366ac1942ec Mon Sep 17 00:00:00 2001 From: Joel Thibault Date: Tue, 4 Mar 2014 19:40:08 -0500 Subject: [PATCH 2/2] Logger output should go to STDERR instead of STDOUT --- .../org/broadinstitute/sting/commandline/CommandLineUtils.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java index ddedda054..cb9a781c3 100644 --- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java +++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java @@ -173,7 +173,7 @@ public class CommandLineUtils { } // Extracted from BasicConfigurator.configure(), but only applied to the Sting logger. Logger.getRootLogger().addAppender(new ConsoleAppender( - new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN))); + new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), ConsoleAppender.SYSTEM_ERR)); } /**