Interface ReadsQuery<R extends HtsRecord>

All Known Subinterfaces:
ReadsDecoder
All Known Implementing Classes:
BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, CRAMDecoderV3_1, HtsgetBAMDecoder, HtsgetBAMDecoderV1_2, SAMDecoder, SAMDecoderV1_0
public interface ReadsQuery<R extends HtsRecord>
Query methods specific to ReadsDecoders.

  • Method Details

    • queryUnmapped

      CloseableIterator<R> queryUnmapped()
      Get an iterator of unmapped reads.

    • queryMate

      Optional<R> queryMate(R record)
      Fetch the mate for the given read.
      Parameters:
      record - the source record
      Returns:
      the source record's mate, or Optional.empty() if the source record has no mate