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Deprecating AlignmentContext.getExtendedEventPileup(). At this point the only walkers left with any relaiance on extended events are Guillermo's pooled code (he'll update soon) and the Pileup walker. David, I'll leave that last one for you (it should be easy). We can now officially rip the extended event code from the engine.

This commit is contained in:
Eric Banks 2012-03-30 10:37:14 -04:00
parent 6b49af253b
commit 533c283783
1 changed files with 2 additions and 0 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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@ -98,6 +98,7 @@ public class AlignmentContext implements HasGenomeLocation {
* only base pileup.
* @return
*/
@Deprecated
public ReadBackedExtendedEventPileup getExtendedEventPileup() {
if(!hasExtendedEventPileup())
throw new ReviewedStingException("No extended event pileup is present.");
@ -115,6 +116,7 @@ public class AlignmentContext implements HasGenomeLocation {
*
* @return
*/
@Deprecated
public boolean hasExtendedEventPileup() { return basePileup instanceof ReadBackedExtendedEventPileup; }
/**