SamLocusAndReferenceIterator (htsjdk 2.18.2 API)

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

Nested Class Summary

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

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method 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 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:
    
    IllegalArgumentException - if arguments have non-equal SAMSequenceDictionarys
- Method Detail
  - hasNext
```
public boolean hasNext()
```
  - next
```
public SamLocusAndReferenceIterator.SAMLocusAndReference next()
```