diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java index f77819426..3ff6e34fb 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java @@ -214,7 +214,13 @@ public abstract class LocusView extends LocusIterator implements View { return locus.containsP(location); } - // TODO -- remove me + /** + * {@inheritDoc} + * + * Since this class has an actual LIBS, so this function will never throw an exception + * + * @return the LocusIteratorByState used by this view to get pileups + */ @Override public LocusIteratorByState getLIBS() { return loci.getLIBS(); diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java index fc114b4f0..1243b2893 100644 --- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java +++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/LocusIterator.java @@ -34,11 +34,6 @@ import java.util.Iterator; * Iterator that traverses a SAM File, accumulating information on a per-locus basis */ public abstract class LocusIterator implements Iterable, CloseableIterator { - // ----------------------------------------------------------------------------------------------------------------- - // - // constructors and other basic operations - // - // ----------------------------------------------------------------------------------------------------------------- public Iterator iterator() { return this; } @@ -50,9 +45,15 @@ public abstract class LocusIterator implements Iterable, Close public abstract boolean hasNext(); public abstract AlignmentContext next(); - // TODO -- remove me when ART testing is done + /** + * Get, if possible, the underlying LocusIteratorByState from this LocusIterator. + * + * @throws UnsupportedOperationException if we don't support this operation + * + * @return a non-null locus iterator by state + */ public LocusIteratorByState getLIBS() { - return null; + throw new UnsupportedOperationException("This locus iterator does not support getting the underlying LocusIteratorByState"); } public void remove() {