From 9e650dfc17621a76e421184ae33b03c2515f193c Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 9 Sep 2011 16:25:31 -0400 Subject: [PATCH] Fixing SelectVariants documentation getting rid of messages telling users to go for the YAML file. The idea is to not support these anymore. --- .../gatk/walkers/variantutils/SelectVariants.java | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 35ff66243..018c4dcc2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -145,10 +145,9 @@ import java.util.*; * -R ref.fasta \ * -T SelectVariants \ * --variant input.vcf \ - * -o output.vcf \ - * -SM family.yaml \ * -family NA12891+NA12892=NA12878 \ - * -mvq 50 + * -mvq 50 \ + * -o violations.vcf * * Creating a sample of exactly 1000 variants randomly chosen with equal probability from the variant VCF: * java -Xmx2g -jar GenomeAnalysisTK.jar \ @@ -265,17 +264,17 @@ public class SelectVariants extends RodWalker { private File AF_FILE = new File(""); @Hidden - @Argument(fullName="family_structure_file", shortName="familyFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false) + @Argument(fullName="family_structure_file", shortName="familyFile", doc="use -family unless you know what you're doing", required=false) private File FAMILY_STRUCTURE_FILE = null; /** * String formatted as dad+mom=child where these parameters determine which sample names are examined. */ - @Argument(fullName="family_structure", shortName="family", doc="Deprecated; use the -SM argument instead", required=false) + @Argument(fullName="family_structure", shortName="family", doc="string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false) private String FAMILY_STRUCTURE = ""; /** - * Sample metadata information will be taken from a YAML file (see the -SM argument). + * This activates the mendelian violation module that will select all variants that correspond to a mendelian violation following the rules given by the family structure. */ @Argument(fullName="mendelianViolation", shortName="mv", doc="output mendelian violation sites only", required=false) private Boolean MENDELIAN_VIOLATIONS = false; @@ -306,7 +305,7 @@ public class SelectVariants extends RodWalker { @Hidden - @Argument(fullName="outMVFile", shortName="outMVFile", doc="USE YAML FILE INSTEAD (-SM) !!! string formatted as dad+mom=child where these parameters determine which sample names are examined", required=false) + @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false) private String outMVFile = null; /* Private class used to store the intermediate variants in the integer random selection process */