org.broadinstitute.hellbender.utils.collections

Class IntervalsSkipListOneContig<T extends htsjdk.samtools.util.Locatable>

java.lang.Object

org.broadinstitute.hellbender.utils.collections.IntervalsSkipListOneContig<T>

All Implemented Interfaces:

java.io.Serializable

public final class IntervalsSkipListOneContig<T extends htsjdk.samtools.util.Locatable>
extends java.lang.Object
implements java.io.Serializable

Holds many intervals in memory, with an efficient operation to get intervals that overlap a given query interval. This version assumes that all the intervals lie on the same contig.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
IntervalsSkipListOneContig(java.lang.Iterable<T> loc) Creates an IntervalsSkipList that holds a copy of the given intervals, sorted and indexed.

Method Summary

Modifier and Type	Method and Description
java.util.List<T>	getOverlapping(SimpleInterval query) Returns all the intervals that overlap with the query.

Methods inherited from class java.lang.Object

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

Constructor Detail

IntervalsSkipListOneContig

public IntervalsSkipListOneContig(java.lang.Iterable<T> loc)

Creates an IntervalsSkipList that holds a copy of the given intervals, sorted and indexed.

Parameters:

loc - Locatables, not necessarily sorted. Will be iterated over exactly once.

Method Detail

getOverlapping

public java.util.List<T> getOverlapping(SimpleInterval query)

Returns all the intervals that overlap with the query. The query doesn't *have* to be in the same contig as the intervals we hold, but of course if it isn't you'll get an empty result. You may modify the returned list.