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cmd line args changed - again; internally uses VariantType enum 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-26 21:03:58 +00:00
parent 9ef1a21112
commit 8f1cabd33d
1 changed files with 8 additions and 9 deletions
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17
java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
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@ -42,10 +42,11 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
shortName="VT", shortName="VT",
doc="Assess concordance for the variants of the specified type, INDEL or POINT. If genotype track(s) provide both types, the requested one will be selected", doc="Assess concordance for the variants of the specified type, INDEL or POINT. If genotype track(s) provide both types, the requested one will be selected",
required=true) required=true)
public GenotypeUtils.VariantType VARIANT_TYPE; public String VTYPE_STR;
private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class); private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);
private final static String star = new String("*"); private final static String star = new String("*");
private GenotypeUtils.VariantType VARIANT_TYPE;
@Override @Override
public TrioConcordanceRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) { public TrioConcordanceRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) {
@ -63,18 +64,16 @@ public class MendelianInheritanceWalker extends RefWalker<TrioConcordanceRecord
return assessGenotypesInTrio(mom, dad, kid); return assessGenotypesInTrio(mom, dad, kid);
} }
/*
* @Override(non-Javadoc) /**
* @Override
* @see org.broadinstitute.sting.gatk.walkers.Walker#initialize() * @see org.broadinstitute.sting.gatk.walkers.Walker#initialize()
*/
public void initialize() { public void initialize() {
super.initialize(); super.initialize();
if ( defCalls == null ) return; VARIANT_TYPE = GenotypeUtils.VariantType.valueOf(VTYPE_STR.toUpperCase());
defCalls = defCalls.toUpperCase();
if ( defCalls.equals("INDEL")) default_calls = 1;
else throw new StingException("POINT or BOTH default calls are not implemented yet");
}; };
*/
/** Takes a single genotype object and returns properly filled new assessment object (covered/assessed/ref/variant set to 0/1 /** Takes a single genotype object and returns properly filled new assessment object (covered/assessed/ref/variant set to 0/1
* according to what the genotype says) * according to what the genotype says)