Changed the SmithWaterman implementation to default to FASTEST_AVAILA…

…BLE (#8485)
broadinstitute · Aug 21, 2023 · 98b3b4f · 98b3b4f
1 parent 7f6ee62
commit 98b3b4f
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/...itute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java b/...itute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
@@ -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.