diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java index fc946c9a1..8c432f371 100755 --- a/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java @@ -191,7 +191,7 @@ public class LocusIteratorByState extends LocusIterator { // past the insertion right after that if ( eventDelayedFlag > 1 ) throw new StingException("Adjacent I/D events in read "+read.getReadName()); insertedBases = Arrays.copyOfRange(read.getReadBases(),readOffset+1,readOffset+1+curElement.getLength()); - eventLength = cigarElementCounter ; + eventLength = curElement.getLength() ; eventStart = readOffset; eventDelayedFlag = 2; // insertion causes re-entry into stepForwardOnGenome, so we set the delay to 2 // System.out.println("Inserted "+(new String (insertedBases)) +" after "+readOffset);