From 42fccfc658a20f10859f0da92cebb3605050f131 Mon Sep 17 00:00:00 2001
From: jamesemery
Date: Wed, 29 Mar 2023 18:16:04 -0400
Subject: [PATCH] Remove spurious flags from beloved argument (#8271)
* removing Advanced and Hidden from --dont-use-softclipped-bases
---
.../AssemblyBasedCallerArgumentCollection.java | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
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 b9dc7357424..ef329eb9c4b 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
@@ -145,9 +145,7 @@ public ReadThreadingAssembler createReadThreadingAssembler() {
@Hidden
@Argument(fullName = ALLELE_LIKELIHOOD_MATRIX_INTERVAL, doc="Interval for which to write the alleleLikelihoodMatrix", optional=true)
public String alleleLikelihoodMatrixInterval=null;
-
- @Advanced
- @Hidden
+
@Argument(fullName = DONT_USE_SOFT_CLIPPED_BASES_LONG_NAME, doc = "Do not analyze soft clipped bases in the reads", optional = true)
public boolean dontUseSoftClippedBases = false;