Package picard.util

Class QuerySortedReadPairIteratorUtil

java.lang.Object
picard.util.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 Details

    • QuerySortedReadPairIteratorUtil

      public QuerySortedReadPairIteratorUtil()
  • Method Details

    • 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