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Remove duplicate effort in ReadUtils (with apologies to Mauricio) 

Big (but not major) cleanup of code in ILG - mostly excising the old likelihood model
Activated the early-abort check for ILG. I think it should be better this way.
This commit is contained in:
Christopher Hartl 2011-09-22 10:58:26 -04:00
parent dc96f6da79
commit 982c47bfa7
1 changed files with 0 additions and 3 deletions
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3
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)"})
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();
if (readIsEntirelyInsertion(read))