Provide a default logger, some config settings, and some doc updates.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@557 348d0f76-0448-11de-a6fe-93d51630548a

doc/GATK_User_Manual.tex

@@ -102,4 +102,20 @@ Users can write to these streams just as they write to System.out and
 System.err.  This output can be redirected to a file using the out,
 err, and outerr command-line arguments.
 
+\subsection{Logging}
+The walkers provide a protected logger instance.  Users can adjust the
+debug level of the walkers using the -l command line option.
+
+Turning on verbose logging can produce more output than the user
+really needs.  To selectively turn on logging for a class or package,
+the user can specify a log4j.properties property file from the command
+line as follows:
+
+\begin{verbatim}
+-Dlog4j.configuration=file:///humgen/gsa-scr1/hanna/src/Sting/java/config/log4j.properties
+\end{verbatim}
+
+An example log4j.properties file is available in the java/config
+directory of the subversion repository.
+
 \end{document}

java/config/log4j.properties

@@ -0,0 +1,10 @@
+log4j.logger.org.broadinstitute.sting.gatk.walkers.Walker=INFO, walker
+
+# use this to append walker data to the console only
+log4j.appender.walker=org.apache.log4j.ConsoleAppender
+
+# uncomment the following instead for writing debug info to a file called walker.log
+#log4j.appender.walker=org.apache.log4j.FileAppender
+#log4j.appender.walker.File=walker.log
+#log4j.appender.walker.layout=org.apache.log4j.PatternLayout
+#log4j.appender.walker.layout.ConversionPattern=%r [%t] %-5p %c - %m%n

java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -8,6 +8,7 @@ import java.util.List;
 import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Pair;
+import org.apache.log4j.Logger;
 
 /**
  * Created by IntelliJ IDEA.
@@ -19,6 +20,8 @@ import org.broadinstitute.sting.utils.Pair;
 public abstract class Walker<MapType, ReduceType> {
     // TODO: Can a walker be templatized so that map and reduce live here?
 
+    protected static Logger logger = Logger.getLogger(Walker.class);
+
     /**
      * A stream for writing normal (non-error) output.  System.out by default.
      */