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Do not print debug message when debug mode is not requested!! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2056 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-11-16 20:28:41 +00:00
parent 967215066d
commit 21729d9311
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -143,6 +143,8 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
@Override @Override
public Integer map(char[] ref, SAMRecord read) { public Integer map(char[] ref, SAMRecord read) {
// if ( read.getReadName().equals("428EFAAXX090610:2:36:1384:639#0") ) System.out.println("GOT READ");
if ( DEBUG ) { if ( DEBUG ) {
// System.out.println("DEBUG>> read at "+ read.getAlignmentStart()+"-"+read.getAlignmentEnd()+ // System.out.println("DEBUG>> read at "+ read.getAlignmentStart()+"-"+read.getAlignmentEnd()+
// "("+read.getCigarString()+")"); // "("+read.getCigarString()+")");
@ -287,7 +289,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request); if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request);
attempts++; attempts++;
if ( attempts == 4 ) { if ( attempts == 4 ) {
System.out.println("DEBUG>> attempts to preserve full NQS window failed; now trying to find any suitable position.") ; if ( DEBUG ) System.out.println("DEBUG>> attempts to preserve full NQS window failed; now trying to find any suitable position.") ;
failure = true; failure = true;
break; break;
} }