Class BAMStreamWriter


  • public class BAMStreamWriter
    extends Object
    Class for writing SAMRecords in BAM format to an output stream.
    • Constructor Detail

      • BAMStreamWriter

        public BAMStreamWriter​(OutputStream outputStream,
                               OutputStream indexStream,
                               OutputStream sbiStream,
                               long sbiGranularity,
                               SAMFileHeader header)
        Create a BAMStreamWriter for writing. All output streams should be uncompressed streams, since this class performs the necessary compression. All output streams are closed by this class after finish(boolean) returns.
        Parameters:
        outputStream - an output stream for the main BAM output
        indexStream - an output stream for the BAI index, or null if no index is required
        sbiStream - an output stream for the SBI index, or null if no index is required
        sbiGranularity - the granularity of the SBI index (reads per entry)
        header - the SAM header
    • Method Detail

      • writeHeader

        public void writeHeader​(SAMFileHeader header)
      • writeAlignment

        public void writeAlignment​(SAMRecord alignment)
      • finish

        public void finish​(boolean writeTerminatorBlock)
        Finish writing and close all the streams.
        Parameters:
        writeTerminatorBlock - whether to write a BAM terminator block to the main output stream