zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
public/java/src/org/broadinstitute/sting/utils/fragments/FragmentUtils.java
View File

@ -135,7 +135,7 @@ public class FragmentUtils {
GATKSAMRecord firstRead = overlappingPair.get(0); GATKSAMRecord firstRead = overlappingPair.get(0);
GATKSAMRecord secondRead = overlappingPair.get(1); GATKSAMRecord secondRead = overlappingPair.get(1);
if( !(secondRead.getUnclippedStart() <= firstRead.getUnclippedEnd() && secondRead.getUnclippedStart() >= firstRead.getUnclippedStart() && secondRead.getUnclippedEnd() >= firstRead.getUnclippedEnd()) ) { 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); secondRead = overlappingPair.get(0);
} }
if( !(secondRead.getUnclippedStart() <= firstRead.getUnclippedEnd() && secondRead.getUnclippedStart() >= firstRead.getUnclippedStart() && secondRead.getUnclippedEnd() >= firstRead.getUnclippedEnd()) ) { 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]; quals[iii] = secondReadQuals[iii-firstReadStop];
} }
final GATKSAMRecord returnRead = new GATKSAMRecord(firstRead.getHeader()); final GATKSAMRecord returnRead = new GATKSAMRecord( firstRead.getHeader() );
returnRead.setAlignmentStart(firstRead.getUnclippedStart()); returnRead.setAlignmentStart( firstRead.getUnclippedStart() );
returnRead.setReadBases( bases ); returnRead.setReadBases( bases );
returnRead.setBaseQualities( quals ); returnRead.setBaseQualities( quals );
returnRead.setReadGroup( firstRead.getReadGroup() ); returnRead.setReadGroup( firstRead.getReadGroup() );
returnRead.setReferenceName( firstRead.getReferenceName() ); returnRead.setReferenceName( firstRead.getReferenceName() );
returnRead.setReadName( firstRead.getReadName() );
final CigarElement c = new CigarElement(bases.length, CigarOperator.M); final CigarElement c = new CigarElement(bases.length, CigarOperator.M);
final ArrayList<CigarElement> cList = new ArrayList<CigarElement>(); final ArrayList<CigarElement> cList = new ArrayList<CigarElement>();
cList.add(c); cList.add(c);