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Comments for Chris on cleanup

This commit is contained in:
Mark DePristo 2012-08-24 16:04:58 -04:00
parent 649b82ce85
commit 0996bbd548
1 changed files with 5 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
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@ -71,6 +71,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(MVLR_KEY, 1, VCFHeaderLineType.Float, "Mendelian violation likelihood ratio: L[MV] - L[No MV]")); } public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(MVLR_KEY, 1, VCFHeaderLineType.Float, "Mendelian violation likelihood ratio: L[MV] - L[No MV]")); }
// todo - this entire function should be in samples DB
private Set<Trio> checkAndSetSamples(SampleDB db){ private Set<Trio> checkAndSetSamples(SampleDB db){
Set<Trio> trioSet = new HashSet<Trio>(); Set<Trio> trioSet = new HashSet<Trio>();
for ( String familyString : db.getFamilyIDs() ) { for ( String familyString : db.getFamilyIDs() ) {
@ -97,6 +98,10 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment
return true; return true;
} }
// TODO -- this class is too much.
// TODO -- Why iterable?
// TODO -- shuoldn't this be in samplesDB() so you can just called samplesDB().getTrios()
// TODO -- should just have final string IDs, and getters, no setters
private class Trio implements Iterable<String> { private class Trio implements Iterable<String> {
private String maternalID; private String maternalID;
private String paternalID; private String paternalID;