Package picard.util

Class QuerySortedReadPairIteratorUtil


  • public class QuerySortedReadPairIteratorUtil
    extends Object
    A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
    • 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