Class BAMSBIIndexer

java.lang.Object
htsjdk.samtools.BAMSBIIndexer

public final class BAMSBIIndexer extends Object
Writes SBI files for BAM files, as understood by SBIIndex.
  • Constructor Details

    • BAMSBIIndexer

      public BAMSBIIndexer()
  • Method Details

    • createIndex

      public static void createIndex(Path bamFile, long granularity) throws IOException
      Perform indexing on the given BAM file, at the granularity level specified.
      Parameters:
      bamFile - the path to the BAM file
      granularity - write the offset of every n-th alignment to the index
      Throws:
      IOException - as per java IO contract
    • createIndex

      public static void createIndex(SeekableStream in, OutputStream out, long granularity) throws IOException
      Perform indexing on the given BAM file, at the granularity level specified.
      Parameters:
      in - a seekable stream for reading the BAM file from
      out - the stream to write the index to
      granularity - write the offset of every n-th alignment to the index
      Throws:
      IOException - as per java IO contract