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Adding checks for hasBasePileup() before calling getBasePileup() as per GS thread

This commit is contained in:
Eric Banks 2011-11-09 22:37:26 -05:00
parent 82bf09edf3
commit 6313aae2c4
3 changed files with 5 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -69,7 +69,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
if ( context == null ) if ( context == null )
continue; continue;
if ( vc.isSNP() ) { if ( vc.isSNP() && context.hasBasePileup() ) {
final String bases = new String(context.getBasePileup().getBases()); final String bases = new String(context.getBasePileup().getBases());
if ( bases.length() == 0 ) if ( bases.length() == 0 )
return null; return null;

3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
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@ -51,6 +51,9 @@ public class AlleleBalanceBySample extends GenotypeAnnotation implements Experim
if ( altAlleles.size() == 0 ) if ( altAlleles.size() == 0 )
return null; return null;
if ( !stratifiedContext.hasBasePileup() )
return null;
final String bases = new String(stratifiedContext.getBasePileup().getBases()); final String bases = new String(stratifiedContext.getBasePileup().getBases());
if ( bases.length() == 0 ) if ( bases.length() == 0 )
return null; return null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidateWalker.java
View File

@ -365,7 +365,7 @@ public class GenotypeAndValidateWalker extends RodWalker<GenotypeAndValidateWalk
return counter; return counter;
// Do not operate on variants that are not covered to the optional minimum depth // Do not operate on variants that are not covered to the optional minimum depth
if (!context.hasReads() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) { if (!context.hasReads() || !context.hasBasePileup() || (minDepth > 0 && context.getBasePileup().getBases().length < minDepth)) {
counter.nUncovered = 1L; counter.nUncovered = 1L;
if (vcComp.getAttribute("GV").equals("T")) if (vcComp.getAttribute("GV").equals("T"))
counter.nAltNotCalled = 1L; counter.nAltNotCalled = 1L;