Constructor Detail

• BlockCompressedIndexedFastaSequenceFile

  public BlockCompressedIndexedFastaSequenceFile​(Path path)
                                          throws FileNotFoundException

  Throws:

  FileNotFoundException

• BlockCompressedIndexedFastaSequenceFile

  public BlockCompressedIndexedFastaSequenceFile​(Path path,
                                                 FastaSequenceIndex index)

• BlockCompressedIndexedFastaSequenceFile

  public BlockCompressedIndexedFastaSequenceFile​(Path path,
                                                 FastaSequenceIndex index,
                                                 GZIIndex gziIndex)

• BlockCompressedIndexedFastaSequenceFile

  public BlockCompressedIndexedFastaSequenceFile​(String source,
                                                 SeekableStream in,
                                                 FastaSequenceIndex index,
                                                 SAMSequenceDictionary dictionary,
                                                 GZIIndex gziIndex)

  Initialize the given indexed fasta sequence file stream.

  Parameters:

  source - The named source of the reference file (used in error messages).

  in - The input stream to read the fasta file from; should not be decompressed already.

  index - The fasta index.

  dictionary - The sequence dictionary, or null if there isn't one.

  gziIndex - The GZI index; may not be null.

Method Detail

• readFromPosition

  protected int readFromPosition​(ByteBuffer buffer,
                                 long position)
                          throws IOException

  Reads a sequence of bytes from this sequence file into the given buffer, starting at the given file position.

  Parameters:

  buffer - the buffer into which bytes are to be transferred

  position - the position to start reading at

  Returns:

  the number of bytes read

  Throws:

  IOException - if an I/O error occurs while reading

• close

  public void close()
             throws IOException

  Throws:

  IOException

• findRequiredFastaIndexFile

  protected static Path findRequiredFastaIndexFile​(Path fastaFile)
                                            throws FileNotFoundException

  Throws:

  FileNotFoundException

• findFastaIndex

  protected static Path findFastaIndex​(Path fastaFile)

• sanityCheckDictionaryAgainstIndex

  protected static void sanityCheckDictionaryAgainstIndex​(String fastaFile,
                                                          SAMSequenceDictionary sequenceDictionary,
                                                          FastaSequenceIndex index)

  Do some basic checking to make sure the dictionary and the index match.

  Parameters:

  fastaFile - Used for error reporting only.

  sequenceDictionary - sequence dictionary to check against the index.

  index - index file to check against the dictionary.

• getIndex

  public FastaSequenceIndex getIndex()

• nextSequence

  public ReferenceSequence nextSequence()

  Gets the next sequence if available, or null if not present.

  Returns:

  next sequence if available, or null if not present.

• reset

  public void reset()

  Reset the iterator over the index.

• isIndexed

  public final boolean isIndexed()

  default implementation -- override if index is supported

  Specified by:

  isIndexed in interface ReferenceSequenceFile

  Returns:

  true if getSequence and getSubsequenceAt methods are allowed.

• getSequence

  public ReferenceSequence getSequence​(String contig)

  Retrieves the complete sequence described by this contig.

  Specified by:

  getSequence in interface ReferenceSequenceFile

  Parameters:

  contig - contig whose data should be returned.

  Returns:

  The full sequence associated with this contig.

• getSubsequenceAt

  public ReferenceSequence getSubsequenceAt​(String contig,
                                            long start,
                                            long stop)

  Gets the subsequence of the contig in the range [start,stop]

  Specified by:

  getSubsequenceAt in interface ReferenceSequenceFile

  Parameters:

  contig - Contig whose subsequence to retrieve.

  start - inclusive, 1-based start of region.

  stop - inclusive, 1-based stop of region.

  Returns:

  The partial reference sequence associated with this range.

• findAndLoadSequenceDictionary

  protected SAMSequenceDictionary findAndLoadSequenceDictionary​(Path fasta)

  Attempts to find and load the sequence dictionary if present.

• findSequenceDictionary

  @Deprecated
  protected static File findSequenceDictionary​(File file)

  Deprecated.

  use findSequenceDictionary(Path) instead.

• findSequenceDictionary

  protected static Path findSequenceDictionary​(Path fastaPath)

  Attempts to locate the sequence dictionary file adjacent to the reference fasta file.

• getPath

  protected Path getPath()

  Returns the path to the reference file.

• getSource

  protected String getSource()

  Returns the named source of the reference file.

• getSequenceDictionary

  public SAMSequenceDictionary getSequenceDictionary()

  Returns the list of sequence records associated with the reference sequence if found otherwise null.

  Specified by:

  getSequenceDictionary in interface ReferenceSequenceFile

  Returns:

  a list of sequence records representing the sequences in this reference file

• getAbsolutePath

  protected String getAbsolutePath()

  Returns the full path to the reference file.

• toString

  public String toString()

  Returns the full path to the reference file, or the source if no path was specified.

  Specified by:

  toString in interface ReferenceSequenceFile

  Overrides:

  toString in class Object

  Returns:

  Reference name, file name, or something other human-readable representation.