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Changed the SmithWaterman implementation to default to FASTEST_AVAILABLE #8485

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Aug 21, 2023
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Changed the SmithWaterman implementation to default to FASTEST_AVAILABLE #8485

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2 changes: 1 addition & 1 deletion ...itute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
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Expand Up @@ -166,7 +166,7 @@ public ReadThreadingAssembler createReadThreadingAssembler() {

@Advanced
@Argument(fullName = SMITH_WATERMAN_LONG_NAME, doc = "Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice", optional = true)
public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.JAVA;
public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.FASTEST_AVAILABLE;

/**
* 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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