Class SamLocusAndReferenceIterator

java.lang.Object
htsjdk.samtools.util.IterableOnceIterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
htsjdk.samtools.reference.SamLocusAndReferenceIterator
All Implemented Interfaces:
Closeable, AutoCloseable, Iterable<SamLocusAndReferenceIterator.SAMLocusAndReference>, Iterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
public class SamLocusAndReferenceIterator extends IterableOnceIterator<SamLocusAndReferenceIterator.SAMLocusAndReference>
Iterator that traverses a SAM File and a ReferenceFile, accumulating information on a per-locus basis. Only loci that are covered by the input reads are returned. Duplicate reads and non-primary alignments are filtered out. Iterator element holds both pileup (in the form of a LocusInfo object) and the reference base