Class SamRecordIntervalIteratorFactory


  • public class SamRecordIntervalIteratorFactory
    extends Object
    Create an iterator over a SamReader that only returns reads that overlap one of the intervals in an interval list.
    • Constructor Detail

      • SamRecordIntervalIteratorFactory

        public SamRecordIntervalIteratorFactory()
    • Method Detail

      • makeSamRecordIntervalIterator

        public CloseableIterator<SAMRecord> makeSamRecordIntervalIterator​(SamReader samReader,
                                                                          List<Interval> uniqueIntervals,
                                                                          boolean useIndex)
        Parameters:
        samReader -
        uniqueIntervals - list of intervals of interest, with overlaps merged, in coordinate order
        useIndex - if false, do not use a BAM index even if it is present.
        Returns:
        an iterator that will be filtered so that only SAMRecords overlapping the intervals in uniqueIntervals will be returned. If a BAM index is available, it will be used to improve performance. Note however that if there are many intervals that cover a great deal of the genome, using the BAM index may actually make performance worse.