Package htsjdk.samtools

Class SBIIndexWriter

java.lang.Object
htsjdk.samtools.SBIIndexWriter
public final class SBIIndexWriter extends Object
Writes SBI files as understood by SBIIndex.

To use this class, first construct an instance from an output stream, and a desired granularity. Then for each record in the file being indexed, pass the virtual file offset of the record to the processRecord(long) method. The indexer will keep a count of the records passed in an index every nth record. When there are no records left call finish(long, long) to complete writing the index.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final long
    DEFAULT_GRANULARITY
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    SBIIndexWriter(OutputStream out)
    Prepare to write an SBI index with the default granularity.
    SBIIndexWriter(OutputStream out, long granularity)
    Prepare to write an SBI index.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    finish(long finalVirtualOffset, long dataFileLength)
    Complete the index, and close the output stream.
    void
    finish(long finalVirtualOffset, long dataFileLength, byte[] md5, byte[] uuid)
    Complete the index, and close the output stream.
    void
    processRecord(long virtualOffset)
    Process a record for the index: the offset of every nth record will be written to the index.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

  • Constructor Details

    • SBIIndexWriter

      public SBIIndexWriter(OutputStream out)
      Prepare to write an SBI index with the default granularity.
      Parameters:
      out - the stream to write the index to

    • SBIIndexWriter

      public SBIIndexWriter(OutputStream out, long granularity)
      Prepare to write an SBI index.
      Parameters:
      out - the stream to write the index to
      granularity - write the offset of every nth record to the index

  • Method Details

    • processRecord

      public void processRecord(long virtualOffset)
      Process a record for the index: the offset of every nth record will be written to the index.
      Parameters:
      virtualOffset - virtual file pointer of the record

    • finish

      public void finish(long finalVirtualOffset, long dataFileLength)
      Complete the index, and close the output stream.
      Parameters:
      finalVirtualOffset - the virtual offset at which the next record would start if it were added to the file
      dataFileLength - the length of the data file in bytes

    • finish

      public void finish(long finalVirtualOffset, long dataFileLength, byte[] md5, byte[] uuid)
      Complete the index, and close the output stream.
      Parameters:
      finalVirtualOffset - the virtual offset at which the next record would start if it were added to the file
      dataFileLength - the length of the data file in bytes
      md5 - the MD5 hash of the data file, or null if not specified
      uuid - the UUID for the data file, or null if not specified