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Removed walker argument FamilyStructure as this is now supported by the engine (ped file)

This commit is contained in:
Laurent Francioli 2011-11-28 17:18:11 +01:00
parent 795c99d693
commit a09c01fcec
1 changed files with 1 additions and 9 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -161,13 +161,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
@Argument(fullName="minPhaseQuality", shortName="mpq", doc="Minimum phasing quality", required=false)
protected double MIN_PHASE_QUALITY = 10.0;
/**
* This argument is a string formatted as dad+mom=child where these parameters determine which sample names are examined.
*/
@Argument(shortName="family", doc="If provided, genotypes in will be examined for mendelian violations", required=false)
protected String FAMILY_STRUCTURE;
@Argument(shortName="mvq", fullName="mendelianViolationQualThreshold", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation", required=false)
@Argument(shortName="mvq", fullName="mendelianViolationQualThreshold", doc="Minimum genotype QUAL score for each trio member required to accept a site as a violation. Default is 50.", required=false)
protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50;
@Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false)
@ -529,8 +523,6 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
public double getMinPhaseQuality() { return MIN_PHASE_QUALITY; }
public String getFamilyStructure() { return FAMILY_STRUCTURE; }
public double getMendelianViolationQualThreshold() { return MENDELIAN_VIOLATION_QUAL_THRESHOLD; }
public TreeSet<VariantStratifier> getStratificationObjects() { return stratificationObjects; }