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remove printouts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1100 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-25 18:54:14 +00:00
parent 0a16519aa2
commit 0d9041380d
2 changed files with 2 additions and 3 deletions
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3
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
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@ -93,8 +93,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
LocusContext locus = getLocusContext(wrappedIter, interval); LocusContext locus = getLocusContext(wrappedIter, interval);
readIter.close(); readIter.close();
//sum = carryWalkerOverInterval(walker, sum, locus); sum = carryWalkerOverInterval(walker, sum, locus);
System.out.println(locus.getLocation());
} }
return sum; return sum;
} }

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
View File

@ -104,7 +104,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
!read.getDuplicateReadFlag() && !read.getDuplicateReadFlag() &&
read.getMappingQuality() != 0 && read.getMappingQuality() != 0 &&
read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START && read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START &&
(allow454 || !Utils.is454Read(read, getToolkit().getEngine().getSAMHeader())) ) (allow454 || !Utils.is454Read(read, getToolkit().getEngine().getSAMHeader())) )
goodReads.add(read); goodReads.add(read);
else if ( writer != null && !cleanedReadsOnly ) else if ( writer != null && !cleanedReadsOnly )
readsToWrite.add(new ComparableSAMRecord(read)); readsToWrite.add(new ComparableSAMRecord(read));