fastest available

broadinstitute · Oct 26, 2021 · 2b3fa96 · 2b3fa96
1 parent 2d2a47b
commit 2b3fa96
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/...g/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java b/...g/broadinstitute/hellbender/tools/walkers/realignmentfilter/FilterAlignmentArtifacts.java
@@ -137,7 +137,7 @@ public class FilterAlignmentArtifacts extends MultiVariantWalkerGroupedOnStart {
 
     @Advanced
     @Argument(fullName = AssemblyBasedCallerArgumentCollection.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;
 
 
     @ArgumentCollection