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Removing unclipSoftClipBases from ReadUtils 

* it was buggy and dangerous.
 * Updated Chris' code to use the ReadClipper.
This commit is contained in:
Mauricio Carneiro 2011-12-20 00:11:26 -05:00
parent 78d9bf7196
commit 37e0044c48
1 changed files with 0 additions and 44 deletions
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44
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -851,50 +851,6 @@ public class ReadUtils {
return new Pair<Integer, Boolean>(readBases, fallsInsideDeletion);
}
public static GATKSAMRecord unclipSoftClippedBases(GATKSAMRecord read) {
int newReadStart = read.getAlignmentStart();
int newReadEnd = read.getAlignmentEnd();
List<CigarElement> newCigarElements = new ArrayList<CigarElement>(read.getCigar().getCigarElements().size());
int heldOver = -1;
boolean sSeen = false;
for ( CigarElement e : read.getCigar().getCigarElements() ) {
if ( e.getOperator().equals(CigarOperator.S) ) {
newCigarElements.add(new CigarElement(e.getLength(),CigarOperator.M));
if ( sSeen ) {
newReadEnd += e.getLength();
sSeen = true;
} else {
newReadStart -= e.getLength();
}
} else {
newCigarElements.add(e);
}
}
// merge duplicate operators together
int idx = 0;
List<CigarElement> finalCigarElements = new ArrayList<CigarElement>(read.getCigar().getCigarElements().size());
while ( idx < newCigarElements.size() -1 ) {
if ( newCigarElements.get(idx).getOperator().equals(newCigarElements.get(idx+1).getOperator()) ) {
int combSize = newCigarElements.get(idx).getLength();
int offset = 0;
while ( idx + offset < newCigarElements.size()-1 && newCigarElements.get(idx+offset).getOperator().equals(newCigarElements.get(idx+1+offset).getOperator()) ) {
combSize += newCigarElements.get(idx+offset+1).getLength();
offset++;
}
finalCigarElements.add(new CigarElement(combSize,newCigarElements.get(idx).getOperator()));
idx = idx + offset -1;
} else {
finalCigarElements.add(newCigarElements.get(idx));
}
idx++;
}
read.setCigar(new Cigar(finalCigarElements));
read.setAlignmentStart(newReadStart);
return read;
}
/**
* Compares two SAMRecords only the basis on alignment start. Note that
* comparisons are performed ONLY on the basis of alignment start; any