Interface SamReader.Indexing

    • Method Detail

      • getIndex

        BAMIndex getIndex()
        Retrieves the index for the given file type. Ensure that the index is of the specified type.
        Returns:
        An index of the given type.
      • hasBrowseableIndex

        boolean hasBrowseableIndex()
        Returns true if the supported index is browseable, meaning the bins in it can be traversed and chunk data inspected and retrieved.
        Returns:
        True if the index supports the BrowseableBAMIndex interface. False otherwise.
      • getBrowseableIndex

        BrowseableBAMIndex getBrowseableIndex()
        Gets an index tagged with the BrowseableBAMIndex interface. Throws an exception if no such index is available.
        Returns:
        An index with a browseable interface, if possible.
        Throws:
        SAMException - if no such index is available.
      • iterator

        SAMRecordIterator iterator​(SAMFileSpan chunks)
        Iterate through the given chunks in the file.
        Parameters:
        chunks - List of chunks for which to retrieve data.
        Returns:
        An iterator over the given chunks.
      • getFilePointerSpanningReads

        SAMFileSpan getFilePointerSpanningReads()
        Gets a pointer spanning all reads in the BAM file.
        Returns:
        Unbounded pointer to the first record, in chunk format.