Class CramRecordWriter


  • public class CramRecordWriter
    extends Object
    • Constructor Detail

      • CramRecordWriter

        public CramRecordWriter​(BitOutputStream coreOutputStream,
                                Map<Integer,​ByteArrayOutputStream> externalOutputMap,
                                CompressionHeader header,
                                int refId)
        Initializes a Cram Record Writer
        Parameters:
        coreOutputStream - Core data block bit stream, to be written by non-external Encodings
        externalOutputMap - External data block byte stream map, to be written by external Encodings
        header - the associated Cram Compression Header
        refId - the reference sequence ID to assign to these records
    • Method Detail

      • writeCramCompressionRecords

        public void writeCramCompressionRecords​(List<CramCompressionRecord> records,
                                                int prevAlignmentStart)
        Writes a series of Cram Compression Records, using this class's Encodings
        Parameters:
        records - the Cram Compression Records to write
        prevAlignmentStart - the alignmentStart of the previous record, for delta calculation