picard.util

Class QuerySortedReadPairIteratorUtil

java.lang.Object

picard.util.QuerySortedReadPairIteratorUtil

public class QuerySortedReadPairIteratorUtil
extends java.lang.Object

A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	QuerySortedReadPairIteratorUtil.ReadPair

Constructor Summary

Constructors

Constructor and Description
QuerySortedReadPairIteratorUtil()

Method Summary

Modifier and Type	Method and Description
static QuerySortedReadPairIteratorUtil.ReadPair	getNextReadPair(htsjdk.samtools.util.PeekableIterator<htsjdk.samtools.SAMRecord> iterator) Get the next read pair (where both have the same read name).

Methods inherited from class java.lang.Object

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

Constructor Detail

QuerySortedReadPairIteratorUtil

public QuerySortedReadPairIteratorUtil()

Method Detail

getNextReadPair

public static QuerySortedReadPairIteratorUtil.ReadPair getNextReadPair(htsjdk.samtools.util.PeekableIterator<htsjdk.samtools.SAMRecord> iterator)

Get the next read pair (where both have the same read name). If we encounter an unpaired read, the second read in the pair will be set to null.

Parameters:

iterator - iterator of reads

Returns:

ReadPair object holding the reads, or null if there are no more reads in the iterator