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Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-04-20 17:40:30 +00:00
parent 01e6492ba9
commit 5d2fab93f4
2 changed files with 2 additions and 2 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
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@ -102,7 +102,7 @@ public abstract class GenotypeCalculationModel implements Cloneable {
* @return call
*/
public abstract VariantCallContext callExtendedLocus(RefMetaDataTracker tracker,
char ref,
char[] ref,
GenomeLoc loc,
Map<String, StratifiedAlignmentContext> stratifiedContexts);

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
View File

@ -40,7 +40,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
protected JointEstimateGenotypeCalculationModel() {}
public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> stratifiedContexts) {
public VariantCallContext callExtendedLocus(RefMetaDataTracker tracker, char[] ref, GenomeLoc loc, Map<String, StratifiedAlignmentContext> stratifiedContexts) {
return null;
}