From 4d69af189e69d084991f84442ff9adb3301561a2 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 27 Feb 2014 13:29:10 -0500 Subject: [PATCH] Minor change: make the --dontUseSoftClippedBases @Advanced instead of @Hidden --- .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 13403c0ac..91e763a0d 100644 --- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -459,7 +459,7 @@ public class HaplotypeCaller extends ActiveRegionWalker, In @Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="If specified, we will write DOT formatted graph files out of the assembler for only this graph size", required = false) protected boolean debugGraphTransformations = false; - @Hidden + @Advanced @Argument(fullName="dontUseSoftClippedBases", shortName="dontUseSoftClippedBases", doc="If specified, we will not analyze soft clipped bases in the reads", required = false) protected boolean dontUseSoftClippedBases = false;