Class SamPairUtil.SetMateInfoIterator

    • Constructor Detail

      • SetMateInfoIterator

        public SetMateInfoIterator​(Iterator<SAMRecord> iterator)
        By default, the mate cigar tag is set
        Parameters:
        iterator - the iterator to wrap
      • SetMateInfoIterator

        public SetMateInfoIterator​(Iterator<SAMRecord> iterator,
                                   boolean setMateCigar)
        Parameters:
        iterator - the iterator to wrap
        setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
      • SetMateInfoIterator

        public SetMateInfoIterator​(Iterator<SAMRecord> iterator,
                                   boolean setMateCigar,
                                   boolean ignoreMissingMates)
        Parameters:
        iterator - the iterator to wrap
        setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.
        ignoreMissingMates - set this to true if we are to ignore missing mates, otherwise an exception will be thrown when a missing mate is encountered