From a1adfb91ce6fad15c64724e0192e90d43b6b4dee Mon Sep 17 00:00:00 2001 From: asivache Date: Wed, 10 Nov 2010 20:28:40 +0000 Subject: [PATCH] And now @Hidden tags are really in place :-/ git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4644 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index f14f3ff53..b3ebd57fa 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -57,6 +57,7 @@ import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.CommandLineUtils; +import org.broadinstitute.sting.commandline.Hidden; import java.io.*; import java.util.*; @@ -88,10 +89,12 @@ public class IndelGenotyperV2Walker extends ReadWalker { // @Argument(fullName="vcf_format", shortName="vcf", doc="generate output file in VCF format", required=false) // boolean FORMAT_VCF = false; + @Hidden @Argument(fullName = "genotype_intervals", shortName = "genotype", doc = "Calls will be made at each position within the specified interval(s), whether there is an indel or it's the ref", required = false) public String genotypeIntervalsFile = null; + @Hidden @Argument(fullName="genotypeIntervalsAreNotSorted", shortName="giNotSorted", required=false, doc="This tool assumes that the genotyping interval list (--genotype_intervals) is sorted; "+ "if the list turns out to be unsorted, it will throw an exception. "+