org.broadinstitute.hellbender.engine

Class ReadsContext

java.lang.Object

org.broadinstitute.hellbender.engine.ReadsContext

All Implemented Interfaces:

java.lang.Iterable<GATKRead>

public final class ReadsContext
extends java.lang.Object
implements java.lang.Iterable<GATKRead>

Wrapper around ReadsDataSource that presents reads overlapping a specific interval to a client, without improperly exposing the entire ReadsDataSource interface. Reads data in the interval is lazily queried, so there's no overhead if the client chooses not to examine contextual information from the reads. A ReadsContext may have no backing data source and/or interval. In these cases, queries on it will always return empty iterators. You can determine whether there is a backing source of reads data via hasBackingDataSource(), and whether there is an interval via getInterval().

Constructor Summary

Constructors

Constructor and Description
ReadsContext() Create an empty ReadsContext with no backing data source or interval.
ReadsContext(GATKDataSource<GATKRead> dataSource, SimpleInterval interval) Create a ReadsContext backed by the supplied source of reads.
ReadsContext(GATKDataSource<GATKRead> dataSource, SimpleInterval interval, ReadFilter readFilter) Create a ReadsContext backed by the supplied source of reads.

Method Summary

Modifier and Type	Method and Description
SimpleInterval	getInterval() Gets the interval spanned by this context (returned reads will overlap this interval).
boolean	hasBackingDataSource() Does this context have a backing source of reads data?
java.util.Iterator<GATKRead>	iterator() Get an iterator over the reads in this context.
java.util.Iterator<GATKRead>	iterator(SimpleInterval interval) Get an iterator over the reads of the backing data source over a given interval.

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

Constructor Detail

ReadsContext

public ReadsContext()

Create an empty ReadsContext with no backing data source or interval. Calls to iterator() on this context will always return an empty iterator.

ReadsContext

public ReadsContext(GATKDataSource<GATKRead> dataSource,
                    SimpleInterval interval)

Create a ReadsContext backed by the supplied source of reads. Calls to iterator() will return reads overlapping the provided interval. The data source and/or interval may be null, in which case all calls to iterator() will return an empty iterator.

Parameters:

dataSource - backing source of reads data (may be null)

interval - interval over which to query (may be null)

ReadsContext

public ReadsContext(GATKDataSource<GATKRead> dataSource,
                    SimpleInterval interval,
                    ReadFilter readFilter)

Create a ReadsContext backed by the supplied source of reads. Calls to iterator() will return reads overlapping the provided interval, and passing the provided read filter (if non-null). The data source and/or interval may be null, in which case all calls to iterator() will return an empty iterator.

Parameters:

dataSource - backing source of reads data (may be null)

interval - interval over which to query (may be null)

readFilter - read filter to be used to filter reads during iteration (may be null)

Method Detail

hasBackingDataSource

public boolean hasBackingDataSource()

Does this context have a backing source of reads data?

Returns:

true if there is a backing ReadsDataSource, otherwise false

getInterval

public SimpleInterval getInterval()

Gets the interval spanned by this context (returned reads will overlap this interval). Null if this context has no interval.

Returns:

the interval spanned by this context, or null if this context has no interval

iterator

public java.util.Iterator<GATKRead> iterator()

Get an iterator over the reads in this context. Will return an empty iterator if this context has no backing source of reads and/or no interval.

Specified by:

iterator in interface java.lang.Iterable<GATKRead>

Returns:

iterator over the reads in this context

iterator

public java.util.Iterator<GATKRead> iterator(SimpleInterval interval)

Get an iterator over the reads of the backing data source over a given interval. Will return an empty iterator if this context has no backing source of reads.

Returns:

iterator over the reads in this context