From 21729d9311e675ca0dc1f93f137ad217a9322e64 Mon Sep 17 00:00:00 2001 From: asivache Date: Mon, 16 Nov 2009 20:28:41 +0000 Subject: [PATCH] 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 --- .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index d6ebb81c4..b11131bd2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -143,6 +143,8 @@ public class IndelGenotyperV2Walker extends ReadWalker { @Override public Integer map(char[] ref, SAMRecord read) { + // if ( read.getReadName().equals("428EFAAXX090610:2:36:1384:639#0") ) System.out.println("GOT READ"); + if ( DEBUG ) { // System.out.println("DEBUG>> read at "+ read.getAlignmentStart()+"-"+read.getAlignmentEnd()+ // "("+read.getCigarString()+")"); @@ -287,7 +289,7 @@ public class IndelGenotyperV2Walker extends ReadWalker { if ( DEBUG ) System.out.println("DEBUG>> indel observations present within "+NQS_WIDTH+" bases ahead. Resetting shift to "+request); attempts++; 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; break; }