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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mark DePristo 2011-09-22 11:20:10 -04:00
parent a05c959e5a 63758efc17
commit 93dd1faa5f
1 changed files with 0 additions and 3 deletions
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public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -681,9 +681,6 @@ public class ReadUtils {
@Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"}) @Ensures({"result >= read.getUnclippedStart()", "result <= read.getUnclippedEnd() || readIsEntirelyInsertion(read)"})
public static int getRefCoordSoftUnclippedEnd(SAMRecord read) { public static int getRefCoordSoftUnclippedEnd(SAMRecord read) {
if ( read.getCigar().numCigarElements() == 1 && read.getCigar().getCigarElement(0).getOperator().equals(CigarOperator.INSERTION)) {
return read.getUnclippedEnd();
}
int stop = read.getUnclippedStart(); int stop = read.getUnclippedStart();
if (readIsEntirelyInsertion(read)) if (readIsEntirelyInsertion(read))