org.broadinstitute.hellbender.utils.iterators

Class ReadCachingIterator

java.lang.Object

org.broadinstitute.hellbender.utils.iterators.ReadCachingIterator

All Implemented Interfaces:

java.util.Iterator<GATKRead>

public class ReadCachingIterator
extends java.lang.Object
implements java.util.Iterator<GATKRead>

Trivial wrapper around a GATKRead iterator that saves all reads returned in a cache, which can be periodically returned and emptied by the client. Note: if consumeCachedReads() is not called periodically by the client, memory use will grow arbitrarily until the heap is exhausted!

Constructor Summary

Constructors

Constructor and Description
ReadCachingIterator(java.util.Iterator<GATKRead> wrappedIter)

Method Summary

Modifier and Type	Method and Description
java.util.List<GATKRead>	consumeCachedReads()
boolean	hasNext()
GATKRead	next()
void	remove()

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

Constructor Detail

ReadCachingIterator

public ReadCachingIterator(java.util.Iterator<GATKRead> wrappedIter)

Parameters:

wrappedIter - GATKRead iterator to wrap

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<GATKRead>

next

public GATKRead next()

Specified by:

next in interface java.util.Iterator<GATKRead>

consumeCachedReads

public java.util.List<GATKRead> consumeCachedReads()

Returns:

All reads currently saved in the cache. The cache is emptied as a side effect of calling this.

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<GATKRead>