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Merge pull request #545 from broadinstitute/jt_logging 

Log to STDERR instead of STDOUT
This commit is contained in:
droazen 2014-03-05 11:40:35 -05:00
parent c5751870ca 57747ad35e
commit 1a1fb8cf6f
2 changed files with 6 additions and 6 deletions
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10
public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineProgram.java
View File

@ -277,19 +277,19 @@ public abstract class CommandLineProgram {
Level par; Level par;
if (logging_level.toUpperCase().equals("DEBUG")) { if (logging_level.toUpperCase().equals("DEBUG")) {
par = Level.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")) { } else if (logging_level.toUpperCase().equals("INFO")) {
par = Level.INFO; par = Level.INFO;
} else if (logging_level.toUpperCase().equals("WARN")) { } else if (logging_level.toUpperCase().equals("WARN")) {
par = Level.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")) { } else if (logging_level.toUpperCase().equals("OFF")) {
par = Level.OFF; par = Level.OFF;
} else { } else {
// we don't understand the logging level, let's get out of here // 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); Logger.getRootLogger().setLevel(par);

2
public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/CommandLineUtils.java
View File

@ -173,7 +173,7 @@ public class CommandLineUtils {
} }
// Extracted from BasicConfigurator.configure(), but only applied to the Sting logger. // Extracted from BasicConfigurator.configure(), but only applied to the Sting logger.
Logger.getRootLogger().addAppender(new ConsoleAppender( Logger.getRootLogger().addAppender(new ConsoleAppender(
new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN))); new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), ConsoleAppender.SYSTEM_ERR));
} }
/** /**