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Bug fixed: now the length of an insertion is determined correctly. Thought I committed this... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2599 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-15 20:58:48 +00:00
parent d2f752dbc1
commit a12933a26d
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -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);