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A fix for the integration test I broke on Friday on my way out the door -- 

some workflows using AlignmentContext were working with it in a way I didn't
expect and wound up treating extended pileups as base pileups.  I'll work to
make sure the AlignmentContext interface is crystal clear.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3815 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-07-17 22:22:44 +00:00
parent ea117957b9
commit 9207c58b8f
2 changed files with 7 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
View File

@ -109,7 +109,11 @@ public class AlignmentContext {
* extended event (indel) pileup.
* @return
*/
public ReadBackedPileup getBasePileup() { return basePileup; }
public ReadBackedPileup getBasePileup() {
if(!hasBasePileup())
throw new StingException("No base pileup is available. Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup.");
return basePileup;
}
/** Returns extended event (indel) pileup over the current genomic location. May return null if this context keeps
* only base pileup.

4
java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -128,8 +128,8 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
}
// look at the normal context to get deletions and positions with high entropy
ReadBackedPileup pileup = context.getBasePileup();
if ( pileup != null ) {
if ( context.hasBasePileup() ) {
ReadBackedPileup pileup = context.getBasePileup();
int mismatchQualities = 0, totalQualities = 0;
byte refBase = ref.getBase();