Field Detail

• CRAI_INDEX_SUFFIX

  public static final String CRAI_INDEX_SUFFIX

  See Also:

  Constant Field Values

Constructor Detail

• CRAIIndex

  public CRAIIndex()

Method Detail

• addEntry

  public void addEntry​(CRAIEntry entry)

  Add a single entry to the CRAI index.

  Parameters:

  entry - entry 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 c)

  Create index entries for a single container.

  Parameters:

  c - the container to index

• openCraiFileAsBaiStream

  public static SeekableStream openCraiFileAsBaiStream​(File cramIndexFile,
                                                       SAMSequenceDictionary dictionary)
                                                throws IOException

  Throws:

  IOException

• openCraiFileAsBaiStream

  public static SeekableStream openCraiFileAsBaiStream​(InputStream indexStream,
                                                       SAMSequenceDictionary dictionary)
                                                throws IOException,
                                                       CRAIIndex.CRAIIndexException

  Throws:

  IOException

  CRAIIndex.CRAIIndexException

• find

  public static List<CRAIEntry> find​(List<CRAIEntry> list,
                                     int seqId,
                                     int start,
                                     int span)

• getLeftmost

  public static CRAIEntry getLeftmost​(List<CRAIEntry> list)

• findLastAlignedEntry

  public static int findLastAlignedEntry​(List<CRAIEntry> list)

  Find index of the last aligned entry in the list. Assumes the index is sorted by coordinate and unmapped entries (with sequence id = -1) follow the mapped entries.

  Parameters:

  list - a list of CRAI entries

  Returns:

  integer index of the last entry with sequence id not equal to -1