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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
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asivache 2010-11-10 20:28:40 +00:00
parent 68ce55148e
commit a1adfb91ce
1 changed files with 3 additions and 0 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java
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@ -57,6 +57,7 @@ import org.broadinstitute.sting.utils.collections.PrimitivePair;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.CommandLineUtils; import org.broadinstitute.sting.commandline.CommandLineUtils;
import org.broadinstitute.sting.commandline.Hidden;
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;
@ -88,10 +89,12 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
// @Argument(fullName="vcf_format", shortName="vcf", doc="generate output file in VCF format", required=false) // @Argument(fullName="vcf_format", shortName="vcf", doc="generate output file in VCF format", required=false)
// boolean FORMAT_VCF = false; // boolean FORMAT_VCF = false;
@Hidden
@Argument(fullName = "genotype_intervals", shortName = "genotype", @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) 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; public String genotypeIntervalsFile = null;
@Hidden
@Argument(fullName="genotypeIntervalsAreNotSorted", shortName="giNotSorted", required=false, @Argument(fullName="genotypeIntervalsAreNotSorted", shortName="giNotSorted", required=false,
doc="This tool assumes that the genotyping interval list (--genotype_intervals) is sorted; "+ 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. "+ "if the list turns out to be unsorted, it will throw an exception. "+