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;