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Clipping ends inside deletion and before insertion 

fixed.
This commit is contained in:
Mauricio Carneiro 2011-09-30 15:44:30 -04:00
parent e0b771c233
commit 05fba6f23a
1 changed files with 12 additions and 1 deletions
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13
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -879,9 +879,20 @@ public class ReadUtils {
if (endsWithinCigar) if (endsWithinCigar)
fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION; fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
// if we end outside the current cigar element, we need to check if the next element is a deletion. // if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
else { else {
nextCigarElement = cigarElementIterator.next(); nextCigarElement = cigarElementIterator.next();
// if it's an insertion, we need to clip the whole insertion before looking at the next element
if (nextCigarElement.getOperator() == CigarOperator.INSERTION) {
readBases += nextCigarElement.getLength();
if (!cigarElementIterator.hasNext())
throw new ReviewedStingException("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
nextCigarElement = cigarElementIterator.next();
}
// if it's a deletion, we will pass the information on to be handled downstream.
fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION; fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION;
} }