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Fixing SelectVariants documentation 

getting rid of messages telling users to go for the YAML file. The idea is to not support these anymore.
This commit is contained in:
Mauricio Carneiro 2011-09-09 16:25:31 -04:00
parent 7f9000382e
commit 9e650dfc17
1 changed files with 6 additions and 7 deletions
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13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -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<Integer, Integer> {
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<Integer, Integer> {
@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 */