Package htsjdk.samtools.cram

Class CRAIIndex

java.lang.Object
htsjdk.samtools.cram.CRAIIndex
public class CRAIIndex extends Object
CRAI index used for CRAM files.

  • Field Details

  • Constructor Details

    • CRAIIndex

      public CRAIIndex()

  • Method Details

    • addEntry

      public void addEntry(CRAIEntry entry)
      Add a single entry to the CRAI index.
      Parameters:
      entry - entry to be added

    • addEntries

      public void addEntries(Collection<CRAIEntry> toAdd)
      Add multiple entries to the CRAI index.
      Parameters:
      toAdd - entries to be added

    • getCRAIEntries

      public List<CRAIEntry> getCRAIEntries()

    • writeIndex

      public void writeIndex(OutputStream os)
      Write out the index to an output stream;
      Parameters:
      os - Stream to write index to

    • processContainer

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

    • openCraiFileAsBaiStream

      public static SeekableStream openCraiFileAsBaiStream(File cramIndexFile, SAMSequenceDictionary dictionary)

    • openCraiFileAsBaiStream

      public static SeekableStream openCraiFileAsBaiStream(InputStream indexStream, SAMSequenceDictionary dictionary)

    • find

      public static List<CRAIEntry> find(List<CRAIEntry> list, int seqId, int start, int span)
      Currently unused, but retained for the native rai query implementation

    • getLeftmost

      public static CRAIEntry getLeftmost(List<CRAIEntry> list)
      Currently unused, but retained for the native rai query implementation

    • findLastAlignedEntry

      public static int findLastAlignedEntry(List<CRAIEntry> list)
      Currently unused, but retained for the native rai query implementation