htsjdk.samtools.reference

Class SamLocusAndReferenceIterator

java.lang.Object

htsjdk.samtools.util.IterableOnceIterator<SamLocusAndReferenceIterator.SAMLocusAndReference>

htsjdk.samtools.reference.SamLocusAndReferenceIterator

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, java.lang.Iterable<SamLocusAndReferenceIterator.SAMLocusAndReference>, java.util.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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SamLocusAndReferenceIterator.SAMLocusAndReference Small class to hold together a SamLocusIterator.LocusInfo and the reference base over that locus.

Constructor Summary

Constructors

Constructor and Description
SamLocusAndReferenceIterator(ReferenceSequenceFileWalker referenceFile, SamLocusIterator locusIterator) Constructor that takes a ReferenceSequenceFile and a SamLocusIterator.

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
SamLocusAndReferenceIterator.SAMLocusAndReference	next()

Methods inherited from class htsjdk.samtools.util.IterableOnceIterator

close, iterator, remove

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Methods inherited from interface java.util.Iterator

forEachRemaining

Constructor Detail

SamLocusAndReferenceIterator

public SamLocusAndReferenceIterator(ReferenceSequenceFileWalker referenceFile,
                                    SamLocusIterator locusIterator)
                             throws java.lang.IllegalArgumentException

Constructor that takes a ReferenceSequenceFile and a SamLocusIterator. The inputs must have equal SAMSequenceDictionarys and an IllegalArgumentException will be thrown otherwise.

Parameters:

referenceFile -

locusIterator -

Throws:

java.lang.IllegalArgumentException - if arguments have non-equal SAMSequenceDictionarys

Method Detail

hasNext

public boolean hasNext()

next

public SamLocusAndReferenceIterator.SAMLocusAndReference next()