CramSpanContainerIterator (htsjdk 3.0.4 API)

java.lang.Object

htsjdk.samtools.cram.build.CramContainerIterator

htsjdk.samtools.cram.build.CramSpanContainerIterator

All Implemented Interfaces:: Closeable, AutoCloseable, Iterator<Container>

public final class CramSpanContainerIterator extends CramContainerIterator

An iterator of CRAM containers read from locations in a SeekableStream. The locations are specified with pairs of coordinates, and are basically file pointers as returned for example by SamReader.Indexing.getFilePointerSpanningReads()

Method Summary

Modifier and Type

Method

Description

static CramSpanContainerIterator

fromFileSpan(SeekableStream seekableStream, long[] coordinates)

boolean

hasNext()

Container

next()

void

remove()

Methods inherited from class htsjdk.samtools.cram.build.CramContainerIterator
close, containerFromStream, getCramHeader, getSamFileHeader

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Iterator
forEachRemaining

Method Details
- fromFileSpan
  
  public static CramSpanContainerIterator fromFileSpan(SeekableStream seekableStream, long[] coordinates)
- hasNext
  
  public boolean hasNext()
  
  Specified by:
  
  hasNext in interface Iterator<Container>
  
  Overrides:
  
  hasNext in class CramContainerIterator
- next
  
  public Container next()
  
  Specified by:
  
  next in interface Iterator<Container>
  
  Overrides:
  
  next in class CramContainerIterator
- remove
  
  public void remove()
  
  Specified by:
  
  remove in interface Iterator<Container>
  
  Overrides:
  
  remove in class CramContainerIterator