Class MultiRefSliceAlignmentSpanReader


  • public class MultiRefSliceAlignmentSpanReader
    extends CramRecordReader
    A reader that only keeps track of alignment spans. The intended use is for CRAI indexing.
    • Constructor Detail

      • MultiRefSliceAlignmentSpanReader

        public MultiRefSliceAlignmentSpanReader​(BitInputStream coreInputStream,
                                                Map<Integer,​ByteArrayInputStream> externalInputMap,
                                                CompressionHeader header,
                                                ValidationStringency validationStringency,
                                                int initialAlignmentStart,
                                                int recordCount)
        Initializes a Multiple Reference Sequence ID Reader. The intended use is for CRAI indexing.
        Parameters:
        coreInputStream - Core data block bit stream, to be read by non-external Encodings
        externalInputMap - External data block byte stream map, to be read by external Encodings
        header - the associated Cram Compression Header
        validationStringency - how strict to be when reading this CRAM record
        initialAlignmentStart - the alignmentStart used for initial calculation of spans
        recordCount - the number of CRAM records to read