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Bug fix in fragment utils: the read name wasn't being set in the merged read. Misc minor updates to the HaplotypeCaller.

This commit is contained in:
Ryan Poplin 2012-06-11 10:38:35 -04:00
parent 0ac4ba9ad3
commit 683d4b508e
1 changed files with 4 additions and 3 deletions
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7
public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
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@ -135,7 +135,7 @@ public class FragmentUtils {
GATKSAMRecord firstRead = overlappingPair.get(0);
GATKSAMRecord secondRead = overlappingPair.get(1);
if( !(secondRead.getUnclippedStart() <= firstRead.getUnclippedEnd() && secondRead.getUnclippedStart() >= firstRead.getUnclippedStart() && secondRead.getUnclippedEnd() >= firstRead.getUnclippedEnd()) ) {
firstRead = overlappingPair.get(1);
firstRead = overlappingPair.get(1); // swap them
secondRead = overlappingPair.get(0);
}
if( !(secondRead.getUnclippedStart() <= firstRead.getUnclippedEnd() && secondRead.getUnclippedStart() >= firstRead.getUnclippedStart() && secondRead.getUnclippedEnd() >= firstRead.getUnclippedEnd()) ) {
@ -177,12 +177,13 @@ public class FragmentUtils {
quals[iii] = secondReadQuals[iii-firstReadStop];
}
final GATKSAMRecord returnRead = new GATKSAMRecord(firstRead.getHeader());
returnRead.setAlignmentStart(firstRead.getUnclippedStart());
final GATKSAMRecord returnRead = new GATKSAMRecord( firstRead.getHeader() );
returnRead.setAlignmentStart( firstRead.getUnclippedStart() );
returnRead.setReadBases( bases );
returnRead.setBaseQualities( quals );
returnRead.setReadGroup( firstRead.getReadGroup() );
returnRead.setReferenceName( firstRead.getReferenceName() );
returnRead.setReadName( firstRead.getReadName() );
final CigarElement c = new CigarElement(bases.length, CigarOperator.M);
final ArrayList<CigarElement> cList = new ArrayList<CigarElement>();
cList.add(c);