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Upgrade htsjdk to v3.0.1 and picard to 2.27.5 #8025
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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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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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@@ -10,15 +11,14 @@ | |
* @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; | ||
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private InverseAllele(final Allele allele, boolean isReference) { | ||
super(allele, false); | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. i shudder to imagine where else we have made this mistake... There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. 🤷 |
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super(allele.getBases(), isReference); | ||
this.internalAllele = allele; | ||
referenceStatus = isReference; | ||
} | ||
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// InverseAllele of inverseAllele. By definition it is the allele. In Allele filtering code we normally genotype | ||
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@@ -35,10 +35,6 @@ public static Allele of(final Allele allele, boolean refFlag){ | |
public byte [] getBases(){ | ||
return getDisplayString().getBytes(); | ||
} | ||
@Override | ||
public boolean isReference() { | ||
return referenceStatus; | ||
} | ||
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@Override | ||
public boolean isSymbolic() { | ||
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can we just get rid of all the old calls to this copy constructor.
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There are no other calls to it in our codebase, we can deprecate it and replace it with a more appropriately named method.
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can you also maybe depricate it because its confusing as hell and a trap?