From 0960bb76084b3ff1120bc002886325d10be83692 Mon Sep 17 00:00:00 2001
From: Jonn Smith <jonn@broadinstitute.org>
Date: Fri, 18 Aug 2023 11:54:11 -0400
Subject: [PATCH] Changed the SmithWaterman implementation to default to
 FASTEST_AVAILABLE

---
 .../haplotypecaller/AssemblyBasedCallerArgumentCollection.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
index ef329eb9c4b..de7fb0d4e57 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerArgumentCollection.java
+++ b/src/main/java/org/broadinstitute/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.