From 44f160f29fcec834507ae67b7afbfb4aa77c8b3e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 6 Aug 2012 11:42:36 -0400 Subject: [PATCH] indelGOP and indelGCP are now advanced, not hidden arguments --- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 69f1176cc..a885d8a58 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -146,12 +146,12 @@ public class UnifiedArgumentCollection { @Argument(fullName = "indel_heterozygosity", shortName = "indelHeterozygosity", doc = "Heterozygosity for indel calling", required = false) public double INDEL_HETEROZYGOSITY = 1.0/8000; - @Hidden - @Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty", required = false) + @Advanced + @Argument(fullName = "indelGapContinuationPenalty", shortName = "indelGCP", doc = "Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10", required = false) public byte INDEL_GAP_CONTINUATION_PENALTY = 10; - @Hidden - @Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty", required = false) + @Advanced + @Argument(fullName = "indelGapOpenPenalty", shortName = "indelGOP", doc = "Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10", required = false) public byte INDEL_GAP_OPEN_PENALTY = 45; @Hidden