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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
This commit is contained in:
aaron 2009-06-25 19:47:29 +00:00
parent 11d83ac7d0
commit 0c3aabd1c5
2 changed files with 10 additions and 4 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadValidationWalker.java
View File

@ -108,10 +108,10 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
if (output == null) if (output == null)
return read; return read;
if ((read.getReferenceIndex() == output.getReferenceIndex()) && (read.getAlignmentStart() < output.getAlignmentStart())) { 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()){ else if (read.getReferenceIndex() != output.getReferenceIndex()){
System.err.println("Switching Chromo"); logger.warn("Switching Chromo");
} }
return read; return read;
} }

10
java/src/org/broadinstitute/sting/utils/cmdLine/CommandLineProgram.java
View File

@ -8,6 +8,7 @@ import java.io.IOException;
import java.text.DateFormat; import java.text.DateFormat;
import java.text.SimpleDateFormat; import java.text.SimpleDateFormat;
import java.util.EnumSet; import java.util.EnumSet;
import java.util.Enumeration;
/** /**
* User: aaron * User: aaron
@ -84,7 +85,7 @@ public abstract class CommandLineProgram {
/** /**
* our logging output patterns * 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"; 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"); //logger.info("not Setting debug");
layout.setConversionPattern(patternString); 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 they set the mode to quiet
if (clp.quietMode) { if (clp.quietMode) {