diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java index a2a39da1f..d6cf50522 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java @@ -71,6 +71,7 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment public List 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 checkAndSetSamples(SampleDB db){ Set trioSet = new HashSet(); for ( String familyString : db.getFamilyIDs() ) { @@ -97,6 +98,10 @@ public class MVLikelihoodRatio extends InfoFieldAnnotation implements Experiment 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 { private String maternalID; private String paternalID;