Class FastaSequenceFile

    • Constructor Detail

      • FastaSequenceFile

        public FastaSequenceFile​(File file,
                                 boolean truncateNamesAtWhitespace)
        Constructs a FastaSequenceFile that reads from the specified file.
      • FastaSequenceFile

        public FastaSequenceFile​(Path path,
                                 boolean truncateNamesAtWhitespace)
        Constructs a FastaSequenceFile that reads from the specified file.
      • FastaSequenceFile

        public FastaSequenceFile​(String source,
                                 SeekableStream seekableStream,
                                 SAMSequenceDictionary dictionary,
                                 boolean truncateNamesAtWhitespace)
        Constructs a FastaSequenceFile that reads from the specified stream (which must not be compressed, i.e. the caller is responsible for decompressing the stream).
    • Method Detail

      • close

        public void close()
        It's good to call this to free up memory.
      • nextSequence

        public ReferenceSequence nextSequence()
        Description copied from interface: ReferenceSequenceFile
        Retrieves the next whole sequences from the file.
        Returns:
        a ReferenceSequence or null if at the end of the file
      • reset

        public void reset()
        Description copied from interface: ReferenceSequenceFile
        Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
      • 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.
      • isIndexed

        public 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)
        default implementation -- override if index is supported
        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)
        default implementation -- override if index is supported
        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.