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ooops, debug print now removed 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-06-14 18:07:12 +00:00
parent abdc8521ea
commit 9666d47d17
1 changed files with 1 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -171,7 +171,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
intervals = locs.iterator();
}
currentInterval = intervals.hasNext() ? intervals.next() : null;
System.out.println("Interval: "+currentInterval);
// set up the output writer(s)
if ( baseWriterFilename != null ) {
writers = new HashMap<String, SAMFileWriter>();
@ -362,7 +362,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
do {
currentInterval = intervals.hasNext() ? intervals.next() : null;
System.out.println("Interval: "+currentInterval);
} while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
// call back into map now that the state has been updated