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Fix two instances of immutable collections being used to initialize List arguments #4703

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Apr 25, 2018
Merged

Fix two instances of immutable collections being used to initialize List arguments #4703

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2 changes: 1 addition & 1 deletion ...adinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java
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Expand Up @@ -158,7 +158,7 @@ public GenotypeCalculationArgumentCollection( final GenotypeCalculationArgumentC
*/
@Advanced
@Argument(fullName = "input-prior", doc = "Input prior for calls", optional = true)
public List<Double> inputPrior = Collections.emptyList();
public List<Double> inputPrior = new ArrayList<>();

/**
* Sample ploidy - equivalent to number of chromosomes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy
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2 changes: 1 addition & 1 deletion ...institute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java
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Expand Up @@ -62,7 +62,7 @@ public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgume
*/
@Advanced
@Argument(fullName = "comp", shortName = "comp", doc = "Comparison VCF file(s)", optional = true)
public List<FeatureInput<VariantContext>> comps = Collections.emptyList();
public List<FeatureInput<VariantContext>> comps = new ArrayList<>();

/**
* The reference confidence mode makes it possible to emit a per-bp or summarized confidence estimate for a site being strictly homozygous-reference.
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