Package htsjdk.samtools

Class CRAMCRAIIndexer

java.lang.Object
htsjdk.samtools.CRAMCRAIIndexer
All Implemented Interfaces:
CRAMIndexer
public class CRAMCRAIIndexer extends Object implements CRAMIndexer
Indexer for creating/reading/writing a CRAIIndex for a CRAM file/stream. There are three ways to obtain an index:

  • create an index for an entire CRAM stream and write it to an output stream
  • create an index on-the-fly by processing one container at a time
  • read an existing index from an input stream

  • Constructor Details

    • CRAMCRAIIndexer

      public CRAMCRAIIndexer(OutputStream os, SAMFileHeader samHeader)
      Create a CRAMCRAIIndexer that writes to the given output stream.
      Parameters:
      os - output stream to which the index will be written
      samHeader - SAMFileHeader - user to verify sort order

    • CRAMCRAIIndexer

      public CRAMCRAIIndexer(OutputStream os, SAMFileHeader samHeader, Collection<CRAIEntry> entries)
      Create a CRAMCRAIIndexer that writes to the given output stream, initialized with a Collection of CRAIEntry objects.
      Parameters:
      os - output stream to which the index will be written
      samHeader - SAMFileHeader - user to verify sort order
      entries - the CRAI entries to index

  • Method Details

    • processContainer

      public void processContainer(Container container)
      Create index entries for a single container.
      Parameters:
      container - the container to index

    • processContainer

      public void processContainer(Container container, ValidationStringency validationStringency)
      Description copied from interface: CRAMIndexer
      Create index entries for a single container.
      Specified by:
      processContainer in interface CRAMIndexer
      Parameters:
      container - the container to index
      validationStringency - stringency for validating records (used when processing multi-reference slices, since creating an index on a multi-ref slices requires actually decoding the records in order to resove the constituent reference spans}

    • finish

      public void finish()
      Finish creating the index by writing the accumulated entries out to the stream.
      Specified by:
      finish in interface CRAMIndexer

    • writeIndex

      public static void writeIndex(SeekableStream cramStream, OutputStream craiStream)
      Generate and write a CRAI index to an output stream from a CRAM input stream
      Parameters:
      cramStream - CRAM stream to index; must be coordinate sorted
      craiStream - stream for output index

    • readIndex

      public static CRAIIndex readIndex(InputStream is)
      Read an input stream containing a .crai index and return a CRAIIndex object.
      Parameters:
      is - Input stream to read
      Returns:
      A CRAIIndex object representing the index.