Interface ReferenceSequenceFile

    • Method Detail

      • getSequenceDictionary

        SAMSequenceDictionary getSequenceDictionary()
        Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.
        Returns:
        a list of sequence records representing the sequences in this reference file
      • nextSequence

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

        void reset()
        Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
      • isIndexed

        boolean isIndexed()
        Returns:
        true if getSequence and getSubsequenceAt methods are allowed.
      • getSequence

        ReferenceSequence getSequence​(String contig)
        Retrieves the complete sequence described by this contig.
        Parameters:
        contig - contig whose data should be returned.
        Returns:
        The full sequence associated with this contig.
        Throws:
        UnsupportedOperationException - if !sIndexed.
      • getSubsequenceAt

        ReferenceSequence getSubsequenceAt​(String contig,
                                           long start,
                                           long stop)
        Gets the subsequence of the contig in the range [start,stop]
        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.
        Throws:
        UnsupportedOperationException - if !sIndexed.
      • toString

        String toString()
        Overrides:
        toString in class Object
        Returns:
        Reference name, file name, or something other human-readable representation.