diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 337a8758f..dcb87b79a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -171,7 +171,7 @@ public class IndelRealigner extends ReadWalker { 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(); @@ -362,7 +362,6 @@ public class IndelRealigner extends ReadWalker { 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