From 0c3aabd1c5f7d07a923ee6034c82bc26de026d58 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 25 Jun 2009 19:47:29 +0000
Subject: [PATCH] logger output should be less verbose by default.  Also fixed
 a printout in my read validation walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1102 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/ReadValidationWalker.java  |  4 ++--
 .../sting/utils/cmdLine/CommandLineProgram.java        | 10 ++++++++--
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadValidationWalker.java
index 0de487922..424d7166c 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadValidationWalker.java
@@ -108,10 +108,10 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
         if (output == null)
             return read;
         if ((read.getReferenceIndex() == output.getReferenceIndex()) && (read.getAlignmentStart() < output.getAlignmentStart())) {
-            System.err.println("saw the read " + read.getReadName() + " duplicated,  old alignment = " + output.getAlignmentStart());
+            logger.error("saw the read " + read.getReadName() + " duplicated,  old alignment = " + output.getAlignmentStart());
         }
         else if (read.getReferenceIndex() != output.getReferenceIndex()){
-            System.err.println("Switching Chromo");   
+            logger.warn("Switching Chromo");   
         }
         return read;
     }
diff --git a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
index e379b61a5..9d7ce1d7e 100644
--- a/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
+++ b/java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
@@ -8,6 +8,7 @@ import java.io.IOException;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
 import java.util.EnumSet;
+import java.util.Enumeration;
 
 /**
  * User: aaron
@@ -84,7 +85,7 @@ public abstract class CommandLineProgram {
     /**
      * our logging output patterns
      */
-    private static String patternString = "%p %m %n";
+    private static String patternString = "%-5p %d{HH:mm:ss,SSS} %C{1} - %m %n";
     private static String debugPatternString = "%n[level] %p%n[date]\t\t %d{dd MMM yyyy HH:mm:ss,SSS} %n[class]\t\t %C %n[location]\t %l %n[line number]\t %L %n[message]\t %m %n";
 
     /**
@@ -203,7 +204,12 @@ public abstract class CommandLineProgram {
                 //logger.info("not Setting debug");
                 layout.setConversionPattern(patternString);
             }
-            
+            // now set the layout of all the loggers to our layout
+            Enumeration<Appender> en = logger.getAllAppenders();
+            for (; en.hasMoreElements();) {
+                Appender app = en.nextElement();
+                app.setLayout(layout);
+            }
 
             // if they set the mode to quiet
             if (clp.quietMode) {