zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -145,10 +145,9 @@ import java.util.*;
* -R ref.fasta \ * -R ref.fasta \
* -T SelectVariants \ * -T SelectVariants \
* --variant input.vcf \ * --variant input.vcf \
* -o output.vcf \
* -SM family.yaml \
* -family NA12891+NA12892=NA12878 \ * -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: * Creating a sample of exactly 1000 variants randomly chosen with equal probability from the variant VCF:
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \
@ -265,17 +264,17 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
private File AF_FILE = new File(""); private File AF_FILE = new File("");
@Hidden @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; private File FAMILY_STRUCTURE_FILE = null;
/** /**
* String formatted as dad+mom=child where these parameters determine which sample names are examined. * 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 = ""; 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) @Argument(fullName="mendelianViolation", shortName="mv", doc="output mendelian violation sites only", required=false)
private Boolean MENDELIAN_VIOLATIONS = false; private Boolean MENDELIAN_VIOLATIONS = false;
@ -306,7 +305,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
@Hidden @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 String outMVFile = null;
/* Private class used to store the intermediate variants in the integer random selection process */ /* Private class used to store the intermediate variants in the integer random selection process */