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This upgrades htsjdk to v3.0.0 which was attempted in #7867 and then reverted in #7960 in order to unblock the jukebox merge.
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3 changes: 2 additions & 1 deletion
3
src/main/java/org/broadinstitute/hellbender/tools/funcotator/StrandCorrectedAllele.java
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6 changes: 4 additions & 2 deletions
6
...in/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AlleleAndContext.java
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Original file line number | Diff line number | Diff line change |
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@@ -1,6 +1,7 @@ | ||
package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs; | ||
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import htsjdk.variant.variantcontext.Allele; | ||
import htsjdk.variant.variantcontext.SimpleAllele; | ||
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/** | ||
* Utility class for defining a "not" allele concept that is used to score haplotypes that are not supporting the allele. | ||
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@@ -10,13 +11,13 @@ | |
* @author Ilya Soifer <[email protected] | ||
*/ | ||
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public class InverseAllele extends Allele { | ||
public class InverseAllele extends SimpleAllele { | ||
final static public long serialVersionUID = 1L; | ||
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private final Allele internalAllele; | ||
private final boolean referenceStatus; | ||
private InverseAllele(final Allele allele, boolean isReference) { | ||
super(allele, false); | ||
super(allele.getBases(), false); | ||
this.internalAllele = allele; | ||
referenceStatus = isReference; | ||
} | ||
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