Package htsjdk.samtools

Class BAMStreamWriter

java.lang.Object
htsjdk.samtools.BAMStreamWriter
public class BAMStreamWriter extends Object
Class for writing SAMRecords in BAM format to an output stream.

  • Constructor Details

    • 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 Details

    • 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