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

First step towards indel qualities in RR 

Let the BI's and BD's pass through the reduce reads machinery
This commit is contained in:
Mauricio Carneiro 2012-06-14 15:24:35 -04:00
parent e68038c5d8
commit 7d12429917
1 changed files with 6 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

15
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -337,17 +337,14 @@ public class GATKSAMRecord extends BAMRecord {
*/
public GATKSAMRecord simplify () {
GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information
byte [] insertionQuals = getBaseInsertionQualities(); // save the insertion quality score
byte [] deletionQualities = getBaseDeletionQualities(); // save the deletion quality score
byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities();
byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES) == null) ? null : getBaseDeletionQualities();
this.clearAttributes(); // clear all attributes from the read
this.setReadGroup(rg); // restore read group
if (insertionQuals != null)
this.setBaseQualities(insertionQuals, EventType.BASE_INSERTION); // restore base insertion if we had any
if (deletionQualities != null)
this.setBaseQualities(deletionQualities, EventType.BASE_DELETION); // restore base deletion if we had any
if (insQuals != null)
this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any
if (delQuals != null)
this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any
return this;
}