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Refactor post-processing downsampling using David's generic downsampler interface

This commit is contained in:
Mauricio Carneiro 2012-06-14 15:24:15 -04:00
parent 0398ae9695
commit e68038c5d8
1 changed files with 12 additions and 3 deletions
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15
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -336,9 +336,18 @@ public class GATKSAMRecord extends BAMRecord {
* Clears all attributes except ReadGroup of the read.
*/
public GATKSAMRecord simplify () {
GATKSAMReadGroupRecord rg = getReadGroup();
this.clearAttributes();
setReadGroup(rg);
GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information
byte [] insertionQuals = getBaseInsertionQualities(); // save the insertion quality score
byte [] deletionQualities = getBaseDeletionQualities(); // save the deletion quality score
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
return this;
}