Class SamLocusIterator

    • Constructor Detail

      • SamLocusIterator

        public SamLocusIterator​(SamReader samReader)
        Prepare to iterate through the given SAM records, skipping non-primary alignments. Do not use BAM index even if available.
        Parameters:
        samReader - must be coordinate sorted
      • SamLocusIterator

        public SamLocusIterator​(SamReader samReader,
                                IntervalList intervalList)
        Prepare to iterate through the given SAM records, skipping non-primary alignments. Do not use BAM index even if available.
        Parameters:
        samReader - must be coordinate sorted
        intervalList - Either the list of desired intervals, or null. Note that if an intervalList is passed in that is not coordinate sorted, it will eventually be coordinated sorted by this class.
      • SamLocusIterator

        public SamLocusIterator​(SamReader samReader,
                                IntervalList intervalList,
                                boolean useIndex)
        Prepare to iterate through the given SAM records, skipping non-primary alignments
        Parameters:
        samReader - must be coordinate sorted
        intervalList - Either the list of desired intervals, or null. Note that if an intervalList is passed in that is not coordinate sorted, it will eventually be coordinated sorted by this class.
        useIndex - If true, do indexed lookup to improve performance. Not relevant if intervalList == null. It is no longer the case the useIndex==true can make performance worse. It should always perform at least as well as useIndex==false, and generally will be much faster.